Post on 02-May-2015
Struttura primaria
Struttura secondaria(alfa-elica filamento beta turn)
Struttura supersecondaria (motivi strutturali)
fold
dominio
classe
subunitagrave
Struttura terziaria
Struttura quaternaria
All alphaAll betaAlpha and betaAlpha + beta
All- topologies
The lone helixThere are a number of examples of small proteins (or peptides) which consist of little more than a single helix A striking example is alamethicin a transmembrane voltage gated ion channel acting as a peptide antibiotic
The helix-turn-helix motifThe simplest packing arrangement of a domain of two helices is for them to lie antiparallel connected by a short loop This constitutes the structure of the small (63 residue) RNA-binding protein Rop which is found in certain plasmids (small circular molecules of double-stranded DNA occurring in bacteria and yeast) and involved in their replication There is a slight twist in the arrangement as shown
Catene laterali idrofobe
Catene laterali idrofileFASCIO DI QUATTRO ELICHE
Cytochrome c1
ferritin
cytokines
Fascio di 4 eliche antiparallele 2 coppie di eliche parallele unite in modo antiparallelo
domains which bind DNA
A three-helix bundle forms the basis of a DNA-binding domain which occurs in a number of proteins
globins
Strutture ldquoall alphardquo
elica solitaria
elica-turn-elica
Fascio di 4 eliche
Globine (fascio di 8 eliche)
Domini ad alfa elica di grandi dimensioni
All- topologies
The Greek Key topology
The Greek Key topology named after a pattern that was common on Greek pottery is shown below Three up-and-down -strands connected by hairpins are followed by a longer connection to the fourth strand which lies adjacent to the first
Ipotetica modalitagrave di ripiegamento di una struttura a
forcina per formare la struttura a chiave greca I filamenti 2 e 3
si ripiegano sugli altri due in modo che il filamento 2 viene ad essere allineato e antiparallelo al
filamento 1
Gamma-crystallin has two domains each of which is an eight- stranded -barrel-type structure composed of two Greek keys In fact the structure is more accurately described as consisting of two -sheets one consisting of strands 2147 (white) and the other of strands 6583 (red) as indicated in the diagram
Gamma-crystallin
Aligned and orthogonal sandwiches
Diagram of this -sheet arrangement in the Lipocalin family which binds small molecules between the sheets of the sandwich
barrels
Strutture alfabeta
topologies The most regular and common domain structures consist of repeating -- supersecondary units such that the outer layer of the structure is composed of helices packing against a central core of parallel -sheets These folds are called or wound Many enzymes including all those involved in glycolysis are structures Most proteins are cytosolicThe -- is always right-handed In structures there is a repetition of this arrangement giving a ---etc sequence The strands are parallel and hydrogen bonded to each other while the helices are all parallel to each other and are antiparallel to the strands Thus the helices form a layer packing against the sheetThe ---- subunit often present in nucleotide-binding proteins is named the Rossman Fold after Michael Rossman (Rao and Rossman1973)
Beta-alfa-beta destrorsa Beta-alfa-beta sinistrorsa
Alfa-eliche sul medesimo piano del foglietto beta
Alfa-eliche su piani opposti del foglietto beta
Elica di collegamento
barrels
Consider a sequence of eight - motifsIf the first strand hydrogen bonds to the last then the structure closes on itself forming a barrel-like structure
Enzima triosofosfato isomerasi
Struttura a ldquoTIM barrelrdquo
Enzima lattato deidrogenasi
Rossman Fold
In tutte le strutture a botte il sito attivo si trova in una tasca formata dalle regioni loop che collegano le estremitagrave carbossiliche dei filamenti beta con le adiacenti alfa eliche
Nei domini con struttura aperta ruotata il sito attivo si trova in una fessura localizzata esternamente allrsquoestremitagrave carbossilica del filamenti Questa fessura egrave formata da due regioni loop adiacenti che collegano i due filamenti con eliche presenti su facce opposte del foglietto
Adenilato chinasiflavodossina
Punti di inversione topologica (topological switch points)
Strutture alfabeta
I) TIM barrel
II) a)Struttura aperta e ruotata (di tipo parallelo o misto) - b) Rossmann fold
III) horseshoe (ferro di cavallo)
Alpha+Beta Topologies
bullRibonuclease-H
Structural Classification of Proteins (SCOP)Authors Alexey G Murzin Loredana Lo Conte Bartlett G Ailey Steven E Brenner Tim J P Hubbard and Cyrus Chothia Reference Murzin A G Brenner S E Hubbard T Chothia C (1995) SCOP a structural classification of proteins database for the investigation of sequences and structures J Mol Biol 247 536-540Classes
1All alpha proteins (151) 2All beta proteins (111) 3Alpha and beta proteins (ab) (117) Mainly parallel beta sheets (beta-alpha-beta units) 4Alpha and beta proteins (a+b) (212) Mainly antiparallel beta sheets (segregated alpha and beta regions) 5Multi-domain proteins (alpha and beta) (39) Folds consisting of two or more domains belonging to different classes 6Membrane and cell surface proteins and peptides (12) Does not include proteins in the immune system 7Small proteins (59) Usually dominated by metal ligand heme andor disulfide bridges 8Coiled coil proteins (5) Not a true class 9Low resolution protein structures (17) Not a true class 10Peptides (95) Peptides and fragments Not a true class 11Designed proteins (36) Experimental structures of proteins with essentially non-natural sequences Not a true class
Membrane protein topology
Paradosso di Levinthalbull Proteina di 100 residuibull Due gradi di libertarsquo torsionaliresiduo (phipsi)bull 3 conformazioni accessibili per ogni grado dilibertarsquo torsionalebull 1048774 32x100 possibili conformazionibull 1013 conformazioni esploratesecbull Tempo richiesto per esplorare tutte leconformazioni t = 20 x 109 anni bull Le proteine si devono ripiegare seguendo uncammino definito caratterizzato da conformazionivia via piursquo stabili (diminuizione di G)
All- topologies
The lone helixThere are a number of examples of small proteins (or peptides) which consist of little more than a single helix A striking example is alamethicin a transmembrane voltage gated ion channel acting as a peptide antibiotic
The helix-turn-helix motifThe simplest packing arrangement of a domain of two helices is for them to lie antiparallel connected by a short loop This constitutes the structure of the small (63 residue) RNA-binding protein Rop which is found in certain plasmids (small circular molecules of double-stranded DNA occurring in bacteria and yeast) and involved in their replication There is a slight twist in the arrangement as shown
Catene laterali idrofobe
Catene laterali idrofileFASCIO DI QUATTRO ELICHE
Cytochrome c1
ferritin
cytokines
Fascio di 4 eliche antiparallele 2 coppie di eliche parallele unite in modo antiparallelo
domains which bind DNA
A three-helix bundle forms the basis of a DNA-binding domain which occurs in a number of proteins
globins
Strutture ldquoall alphardquo
elica solitaria
elica-turn-elica
Fascio di 4 eliche
Globine (fascio di 8 eliche)
Domini ad alfa elica di grandi dimensioni
All- topologies
The Greek Key topology
The Greek Key topology named after a pattern that was common on Greek pottery is shown below Three up-and-down -strands connected by hairpins are followed by a longer connection to the fourth strand which lies adjacent to the first
Ipotetica modalitagrave di ripiegamento di una struttura a
forcina per formare la struttura a chiave greca I filamenti 2 e 3
si ripiegano sugli altri due in modo che il filamento 2 viene ad essere allineato e antiparallelo al
filamento 1
Gamma-crystallin has two domains each of which is an eight- stranded -barrel-type structure composed of two Greek keys In fact the structure is more accurately described as consisting of two -sheets one consisting of strands 2147 (white) and the other of strands 6583 (red) as indicated in the diagram
Gamma-crystallin
Aligned and orthogonal sandwiches
Diagram of this -sheet arrangement in the Lipocalin family which binds small molecules between the sheets of the sandwich
barrels
Strutture alfabeta
topologies The most regular and common domain structures consist of repeating -- supersecondary units such that the outer layer of the structure is composed of helices packing against a central core of parallel -sheets These folds are called or wound Many enzymes including all those involved in glycolysis are structures Most proteins are cytosolicThe -- is always right-handed In structures there is a repetition of this arrangement giving a ---etc sequence The strands are parallel and hydrogen bonded to each other while the helices are all parallel to each other and are antiparallel to the strands Thus the helices form a layer packing against the sheetThe ---- subunit often present in nucleotide-binding proteins is named the Rossman Fold after Michael Rossman (Rao and Rossman1973)
Beta-alfa-beta destrorsa Beta-alfa-beta sinistrorsa
Alfa-eliche sul medesimo piano del foglietto beta
Alfa-eliche su piani opposti del foglietto beta
Elica di collegamento
barrels
Consider a sequence of eight - motifsIf the first strand hydrogen bonds to the last then the structure closes on itself forming a barrel-like structure
Enzima triosofosfato isomerasi
Struttura a ldquoTIM barrelrdquo
Enzima lattato deidrogenasi
Rossman Fold
In tutte le strutture a botte il sito attivo si trova in una tasca formata dalle regioni loop che collegano le estremitagrave carbossiliche dei filamenti beta con le adiacenti alfa eliche
Nei domini con struttura aperta ruotata il sito attivo si trova in una fessura localizzata esternamente allrsquoestremitagrave carbossilica del filamenti Questa fessura egrave formata da due regioni loop adiacenti che collegano i due filamenti con eliche presenti su facce opposte del foglietto
Adenilato chinasiflavodossina
Punti di inversione topologica (topological switch points)
Strutture alfabeta
I) TIM barrel
II) a)Struttura aperta e ruotata (di tipo parallelo o misto) - b) Rossmann fold
III) horseshoe (ferro di cavallo)
Alpha+Beta Topologies
bullRibonuclease-H
Structural Classification of Proteins (SCOP)Authors Alexey G Murzin Loredana Lo Conte Bartlett G Ailey Steven E Brenner Tim J P Hubbard and Cyrus Chothia Reference Murzin A G Brenner S E Hubbard T Chothia C (1995) SCOP a structural classification of proteins database for the investigation of sequences and structures J Mol Biol 247 536-540Classes
1All alpha proteins (151) 2All beta proteins (111) 3Alpha and beta proteins (ab) (117) Mainly parallel beta sheets (beta-alpha-beta units) 4Alpha and beta proteins (a+b) (212) Mainly antiparallel beta sheets (segregated alpha and beta regions) 5Multi-domain proteins (alpha and beta) (39) Folds consisting of two or more domains belonging to different classes 6Membrane and cell surface proteins and peptides (12) Does not include proteins in the immune system 7Small proteins (59) Usually dominated by metal ligand heme andor disulfide bridges 8Coiled coil proteins (5) Not a true class 9Low resolution protein structures (17) Not a true class 10Peptides (95) Peptides and fragments Not a true class 11Designed proteins (36) Experimental structures of proteins with essentially non-natural sequences Not a true class
Membrane protein topology
Paradosso di Levinthalbull Proteina di 100 residuibull Due gradi di libertarsquo torsionaliresiduo (phipsi)bull 3 conformazioni accessibili per ogni grado dilibertarsquo torsionalebull 1048774 32x100 possibili conformazionibull 1013 conformazioni esploratesecbull Tempo richiesto per esplorare tutte leconformazioni t = 20 x 109 anni bull Le proteine si devono ripiegare seguendo uncammino definito caratterizzato da conformazionivia via piursquo stabili (diminuizione di G)
The lone helixThere are a number of examples of small proteins (or peptides) which consist of little more than a single helix A striking example is alamethicin a transmembrane voltage gated ion channel acting as a peptide antibiotic
The helix-turn-helix motifThe simplest packing arrangement of a domain of two helices is for them to lie antiparallel connected by a short loop This constitutes the structure of the small (63 residue) RNA-binding protein Rop which is found in certain plasmids (small circular molecules of double-stranded DNA occurring in bacteria and yeast) and involved in their replication There is a slight twist in the arrangement as shown
Catene laterali idrofobe
Catene laterali idrofileFASCIO DI QUATTRO ELICHE
Cytochrome c1
ferritin
cytokines
Fascio di 4 eliche antiparallele 2 coppie di eliche parallele unite in modo antiparallelo
domains which bind DNA
A three-helix bundle forms the basis of a DNA-binding domain which occurs in a number of proteins
globins
Strutture ldquoall alphardquo
elica solitaria
elica-turn-elica
Fascio di 4 eliche
Globine (fascio di 8 eliche)
Domini ad alfa elica di grandi dimensioni
All- topologies
The Greek Key topology
The Greek Key topology named after a pattern that was common on Greek pottery is shown below Three up-and-down -strands connected by hairpins are followed by a longer connection to the fourth strand which lies adjacent to the first
Ipotetica modalitagrave di ripiegamento di una struttura a
forcina per formare la struttura a chiave greca I filamenti 2 e 3
si ripiegano sugli altri due in modo che il filamento 2 viene ad essere allineato e antiparallelo al
filamento 1
Gamma-crystallin has two domains each of which is an eight- stranded -barrel-type structure composed of two Greek keys In fact the structure is more accurately described as consisting of two -sheets one consisting of strands 2147 (white) and the other of strands 6583 (red) as indicated in the diagram
Gamma-crystallin
Aligned and orthogonal sandwiches
Diagram of this -sheet arrangement in the Lipocalin family which binds small molecules between the sheets of the sandwich
barrels
Strutture alfabeta
topologies The most regular and common domain structures consist of repeating -- supersecondary units such that the outer layer of the structure is composed of helices packing against a central core of parallel -sheets These folds are called or wound Many enzymes including all those involved in glycolysis are structures Most proteins are cytosolicThe -- is always right-handed In structures there is a repetition of this arrangement giving a ---etc sequence The strands are parallel and hydrogen bonded to each other while the helices are all parallel to each other and are antiparallel to the strands Thus the helices form a layer packing against the sheetThe ---- subunit often present in nucleotide-binding proteins is named the Rossman Fold after Michael Rossman (Rao and Rossman1973)
Beta-alfa-beta destrorsa Beta-alfa-beta sinistrorsa
Alfa-eliche sul medesimo piano del foglietto beta
Alfa-eliche su piani opposti del foglietto beta
Elica di collegamento
barrels
Consider a sequence of eight - motifsIf the first strand hydrogen bonds to the last then the structure closes on itself forming a barrel-like structure
Enzima triosofosfato isomerasi
Struttura a ldquoTIM barrelrdquo
Enzima lattato deidrogenasi
Rossman Fold
In tutte le strutture a botte il sito attivo si trova in una tasca formata dalle regioni loop che collegano le estremitagrave carbossiliche dei filamenti beta con le adiacenti alfa eliche
Nei domini con struttura aperta ruotata il sito attivo si trova in una fessura localizzata esternamente allrsquoestremitagrave carbossilica del filamenti Questa fessura egrave formata da due regioni loop adiacenti che collegano i due filamenti con eliche presenti su facce opposte del foglietto
Adenilato chinasiflavodossina
Punti di inversione topologica (topological switch points)
Strutture alfabeta
I) TIM barrel
II) a)Struttura aperta e ruotata (di tipo parallelo o misto) - b) Rossmann fold
III) horseshoe (ferro di cavallo)
Alpha+Beta Topologies
bullRibonuclease-H
Structural Classification of Proteins (SCOP)Authors Alexey G Murzin Loredana Lo Conte Bartlett G Ailey Steven E Brenner Tim J P Hubbard and Cyrus Chothia Reference Murzin A G Brenner S E Hubbard T Chothia C (1995) SCOP a structural classification of proteins database for the investigation of sequences and structures J Mol Biol 247 536-540Classes
1All alpha proteins (151) 2All beta proteins (111) 3Alpha and beta proteins (ab) (117) Mainly parallel beta sheets (beta-alpha-beta units) 4Alpha and beta proteins (a+b) (212) Mainly antiparallel beta sheets (segregated alpha and beta regions) 5Multi-domain proteins (alpha and beta) (39) Folds consisting of two or more domains belonging to different classes 6Membrane and cell surface proteins and peptides (12) Does not include proteins in the immune system 7Small proteins (59) Usually dominated by metal ligand heme andor disulfide bridges 8Coiled coil proteins (5) Not a true class 9Low resolution protein structures (17) Not a true class 10Peptides (95) Peptides and fragments Not a true class 11Designed proteins (36) Experimental structures of proteins with essentially non-natural sequences Not a true class
Membrane protein topology
Paradosso di Levinthalbull Proteina di 100 residuibull Due gradi di libertarsquo torsionaliresiduo (phipsi)bull 3 conformazioni accessibili per ogni grado dilibertarsquo torsionalebull 1048774 32x100 possibili conformazionibull 1013 conformazioni esploratesecbull Tempo richiesto per esplorare tutte leconformazioni t = 20 x 109 anni bull Le proteine si devono ripiegare seguendo uncammino definito caratterizzato da conformazionivia via piursquo stabili (diminuizione di G)
The helix-turn-helix motifThe simplest packing arrangement of a domain of two helices is for them to lie antiparallel connected by a short loop This constitutes the structure of the small (63 residue) RNA-binding protein Rop which is found in certain plasmids (small circular molecules of double-stranded DNA occurring in bacteria and yeast) and involved in their replication There is a slight twist in the arrangement as shown
Catene laterali idrofobe
Catene laterali idrofileFASCIO DI QUATTRO ELICHE
Cytochrome c1
ferritin
cytokines
Fascio di 4 eliche antiparallele 2 coppie di eliche parallele unite in modo antiparallelo
domains which bind DNA
A three-helix bundle forms the basis of a DNA-binding domain which occurs in a number of proteins
globins
Strutture ldquoall alphardquo
elica solitaria
elica-turn-elica
Fascio di 4 eliche
Globine (fascio di 8 eliche)
Domini ad alfa elica di grandi dimensioni
All- topologies
The Greek Key topology
The Greek Key topology named after a pattern that was common on Greek pottery is shown below Three up-and-down -strands connected by hairpins are followed by a longer connection to the fourth strand which lies adjacent to the first
Ipotetica modalitagrave di ripiegamento di una struttura a
forcina per formare la struttura a chiave greca I filamenti 2 e 3
si ripiegano sugli altri due in modo che il filamento 2 viene ad essere allineato e antiparallelo al
filamento 1
Gamma-crystallin has two domains each of which is an eight- stranded -barrel-type structure composed of two Greek keys In fact the structure is more accurately described as consisting of two -sheets one consisting of strands 2147 (white) and the other of strands 6583 (red) as indicated in the diagram
Gamma-crystallin
Aligned and orthogonal sandwiches
Diagram of this -sheet arrangement in the Lipocalin family which binds small molecules between the sheets of the sandwich
barrels
Strutture alfabeta
topologies The most regular and common domain structures consist of repeating -- supersecondary units such that the outer layer of the structure is composed of helices packing against a central core of parallel -sheets These folds are called or wound Many enzymes including all those involved in glycolysis are structures Most proteins are cytosolicThe -- is always right-handed In structures there is a repetition of this arrangement giving a ---etc sequence The strands are parallel and hydrogen bonded to each other while the helices are all parallel to each other and are antiparallel to the strands Thus the helices form a layer packing against the sheetThe ---- subunit often present in nucleotide-binding proteins is named the Rossman Fold after Michael Rossman (Rao and Rossman1973)
Beta-alfa-beta destrorsa Beta-alfa-beta sinistrorsa
Alfa-eliche sul medesimo piano del foglietto beta
Alfa-eliche su piani opposti del foglietto beta
Elica di collegamento
barrels
Consider a sequence of eight - motifsIf the first strand hydrogen bonds to the last then the structure closes on itself forming a barrel-like structure
Enzima triosofosfato isomerasi
Struttura a ldquoTIM barrelrdquo
Enzima lattato deidrogenasi
Rossman Fold
In tutte le strutture a botte il sito attivo si trova in una tasca formata dalle regioni loop che collegano le estremitagrave carbossiliche dei filamenti beta con le adiacenti alfa eliche
Nei domini con struttura aperta ruotata il sito attivo si trova in una fessura localizzata esternamente allrsquoestremitagrave carbossilica del filamenti Questa fessura egrave formata da due regioni loop adiacenti che collegano i due filamenti con eliche presenti su facce opposte del foglietto
Adenilato chinasiflavodossina
Punti di inversione topologica (topological switch points)
Strutture alfabeta
I) TIM barrel
II) a)Struttura aperta e ruotata (di tipo parallelo o misto) - b) Rossmann fold
III) horseshoe (ferro di cavallo)
Alpha+Beta Topologies
bullRibonuclease-H
Structural Classification of Proteins (SCOP)Authors Alexey G Murzin Loredana Lo Conte Bartlett G Ailey Steven E Brenner Tim J P Hubbard and Cyrus Chothia Reference Murzin A G Brenner S E Hubbard T Chothia C (1995) SCOP a structural classification of proteins database for the investigation of sequences and structures J Mol Biol 247 536-540Classes
1All alpha proteins (151) 2All beta proteins (111) 3Alpha and beta proteins (ab) (117) Mainly parallel beta sheets (beta-alpha-beta units) 4Alpha and beta proteins (a+b) (212) Mainly antiparallel beta sheets (segregated alpha and beta regions) 5Multi-domain proteins (alpha and beta) (39) Folds consisting of two or more domains belonging to different classes 6Membrane and cell surface proteins and peptides (12) Does not include proteins in the immune system 7Small proteins (59) Usually dominated by metal ligand heme andor disulfide bridges 8Coiled coil proteins (5) Not a true class 9Low resolution protein structures (17) Not a true class 10Peptides (95) Peptides and fragments Not a true class 11Designed proteins (36) Experimental structures of proteins with essentially non-natural sequences Not a true class
Membrane protein topology
Paradosso di Levinthalbull Proteina di 100 residuibull Due gradi di libertarsquo torsionaliresiduo (phipsi)bull 3 conformazioni accessibili per ogni grado dilibertarsquo torsionalebull 1048774 32x100 possibili conformazionibull 1013 conformazioni esploratesecbull Tempo richiesto per esplorare tutte leconformazioni t = 20 x 109 anni bull Le proteine si devono ripiegare seguendo uncammino definito caratterizzato da conformazionivia via piursquo stabili (diminuizione di G)
Catene laterali idrofobe
Catene laterali idrofileFASCIO DI QUATTRO ELICHE
Cytochrome c1
ferritin
cytokines
Fascio di 4 eliche antiparallele 2 coppie di eliche parallele unite in modo antiparallelo
domains which bind DNA
A three-helix bundle forms the basis of a DNA-binding domain which occurs in a number of proteins
globins
Strutture ldquoall alphardquo
elica solitaria
elica-turn-elica
Fascio di 4 eliche
Globine (fascio di 8 eliche)
Domini ad alfa elica di grandi dimensioni
All- topologies
The Greek Key topology
The Greek Key topology named after a pattern that was common on Greek pottery is shown below Three up-and-down -strands connected by hairpins are followed by a longer connection to the fourth strand which lies adjacent to the first
Ipotetica modalitagrave di ripiegamento di una struttura a
forcina per formare la struttura a chiave greca I filamenti 2 e 3
si ripiegano sugli altri due in modo che il filamento 2 viene ad essere allineato e antiparallelo al
filamento 1
Gamma-crystallin has two domains each of which is an eight- stranded -barrel-type structure composed of two Greek keys In fact the structure is more accurately described as consisting of two -sheets one consisting of strands 2147 (white) and the other of strands 6583 (red) as indicated in the diagram
Gamma-crystallin
Aligned and orthogonal sandwiches
Diagram of this -sheet arrangement in the Lipocalin family which binds small molecules between the sheets of the sandwich
barrels
Strutture alfabeta
topologies The most regular and common domain structures consist of repeating -- supersecondary units such that the outer layer of the structure is composed of helices packing against a central core of parallel -sheets These folds are called or wound Many enzymes including all those involved in glycolysis are structures Most proteins are cytosolicThe -- is always right-handed In structures there is a repetition of this arrangement giving a ---etc sequence The strands are parallel and hydrogen bonded to each other while the helices are all parallel to each other and are antiparallel to the strands Thus the helices form a layer packing against the sheetThe ---- subunit often present in nucleotide-binding proteins is named the Rossman Fold after Michael Rossman (Rao and Rossman1973)
Beta-alfa-beta destrorsa Beta-alfa-beta sinistrorsa
Alfa-eliche sul medesimo piano del foglietto beta
Alfa-eliche su piani opposti del foglietto beta
Elica di collegamento
barrels
Consider a sequence of eight - motifsIf the first strand hydrogen bonds to the last then the structure closes on itself forming a barrel-like structure
Enzima triosofosfato isomerasi
Struttura a ldquoTIM barrelrdquo
Enzima lattato deidrogenasi
Rossman Fold
In tutte le strutture a botte il sito attivo si trova in una tasca formata dalle regioni loop che collegano le estremitagrave carbossiliche dei filamenti beta con le adiacenti alfa eliche
Nei domini con struttura aperta ruotata il sito attivo si trova in una fessura localizzata esternamente allrsquoestremitagrave carbossilica del filamenti Questa fessura egrave formata da due regioni loop adiacenti che collegano i due filamenti con eliche presenti su facce opposte del foglietto
Adenilato chinasiflavodossina
Punti di inversione topologica (topological switch points)
Strutture alfabeta
I) TIM barrel
II) a)Struttura aperta e ruotata (di tipo parallelo o misto) - b) Rossmann fold
III) horseshoe (ferro di cavallo)
Alpha+Beta Topologies
bullRibonuclease-H
Structural Classification of Proteins (SCOP)Authors Alexey G Murzin Loredana Lo Conte Bartlett G Ailey Steven E Brenner Tim J P Hubbard and Cyrus Chothia Reference Murzin A G Brenner S E Hubbard T Chothia C (1995) SCOP a structural classification of proteins database for the investigation of sequences and structures J Mol Biol 247 536-540Classes
1All alpha proteins (151) 2All beta proteins (111) 3Alpha and beta proteins (ab) (117) Mainly parallel beta sheets (beta-alpha-beta units) 4Alpha and beta proteins (a+b) (212) Mainly antiparallel beta sheets (segregated alpha and beta regions) 5Multi-domain proteins (alpha and beta) (39) Folds consisting of two or more domains belonging to different classes 6Membrane and cell surface proteins and peptides (12) Does not include proteins in the immune system 7Small proteins (59) Usually dominated by metal ligand heme andor disulfide bridges 8Coiled coil proteins (5) Not a true class 9Low resolution protein structures (17) Not a true class 10Peptides (95) Peptides and fragments Not a true class 11Designed proteins (36) Experimental structures of proteins with essentially non-natural sequences Not a true class
Membrane protein topology
Paradosso di Levinthalbull Proteina di 100 residuibull Due gradi di libertarsquo torsionaliresiduo (phipsi)bull 3 conformazioni accessibili per ogni grado dilibertarsquo torsionalebull 1048774 32x100 possibili conformazionibull 1013 conformazioni esploratesecbull Tempo richiesto per esplorare tutte leconformazioni t = 20 x 109 anni bull Le proteine si devono ripiegare seguendo uncammino definito caratterizzato da conformazionivia via piursquo stabili (diminuizione di G)
Cytochrome c1
ferritin
cytokines
Fascio di 4 eliche antiparallele 2 coppie di eliche parallele unite in modo antiparallelo
domains which bind DNA
A three-helix bundle forms the basis of a DNA-binding domain which occurs in a number of proteins
globins
Strutture ldquoall alphardquo
elica solitaria
elica-turn-elica
Fascio di 4 eliche
Globine (fascio di 8 eliche)
Domini ad alfa elica di grandi dimensioni
All- topologies
The Greek Key topology
The Greek Key topology named after a pattern that was common on Greek pottery is shown below Three up-and-down -strands connected by hairpins are followed by a longer connection to the fourth strand which lies adjacent to the first
Ipotetica modalitagrave di ripiegamento di una struttura a
forcina per formare la struttura a chiave greca I filamenti 2 e 3
si ripiegano sugli altri due in modo che il filamento 2 viene ad essere allineato e antiparallelo al
filamento 1
Gamma-crystallin has two domains each of which is an eight- stranded -barrel-type structure composed of two Greek keys In fact the structure is more accurately described as consisting of two -sheets one consisting of strands 2147 (white) and the other of strands 6583 (red) as indicated in the diagram
Gamma-crystallin
Aligned and orthogonal sandwiches
Diagram of this -sheet arrangement in the Lipocalin family which binds small molecules between the sheets of the sandwich
barrels
Strutture alfabeta
topologies The most regular and common domain structures consist of repeating -- supersecondary units such that the outer layer of the structure is composed of helices packing against a central core of parallel -sheets These folds are called or wound Many enzymes including all those involved in glycolysis are structures Most proteins are cytosolicThe -- is always right-handed In structures there is a repetition of this arrangement giving a ---etc sequence The strands are parallel and hydrogen bonded to each other while the helices are all parallel to each other and are antiparallel to the strands Thus the helices form a layer packing against the sheetThe ---- subunit often present in nucleotide-binding proteins is named the Rossman Fold after Michael Rossman (Rao and Rossman1973)
Beta-alfa-beta destrorsa Beta-alfa-beta sinistrorsa
Alfa-eliche sul medesimo piano del foglietto beta
Alfa-eliche su piani opposti del foglietto beta
Elica di collegamento
barrels
Consider a sequence of eight - motifsIf the first strand hydrogen bonds to the last then the structure closes on itself forming a barrel-like structure
Enzima triosofosfato isomerasi
Struttura a ldquoTIM barrelrdquo
Enzima lattato deidrogenasi
Rossman Fold
In tutte le strutture a botte il sito attivo si trova in una tasca formata dalle regioni loop che collegano le estremitagrave carbossiliche dei filamenti beta con le adiacenti alfa eliche
Nei domini con struttura aperta ruotata il sito attivo si trova in una fessura localizzata esternamente allrsquoestremitagrave carbossilica del filamenti Questa fessura egrave formata da due regioni loop adiacenti che collegano i due filamenti con eliche presenti su facce opposte del foglietto
Adenilato chinasiflavodossina
Punti di inversione topologica (topological switch points)
Strutture alfabeta
I) TIM barrel
II) a)Struttura aperta e ruotata (di tipo parallelo o misto) - b) Rossmann fold
III) horseshoe (ferro di cavallo)
Alpha+Beta Topologies
bullRibonuclease-H
Structural Classification of Proteins (SCOP)Authors Alexey G Murzin Loredana Lo Conte Bartlett G Ailey Steven E Brenner Tim J P Hubbard and Cyrus Chothia Reference Murzin A G Brenner S E Hubbard T Chothia C (1995) SCOP a structural classification of proteins database for the investigation of sequences and structures J Mol Biol 247 536-540Classes
1All alpha proteins (151) 2All beta proteins (111) 3Alpha and beta proteins (ab) (117) Mainly parallel beta sheets (beta-alpha-beta units) 4Alpha and beta proteins (a+b) (212) Mainly antiparallel beta sheets (segregated alpha and beta regions) 5Multi-domain proteins (alpha and beta) (39) Folds consisting of two or more domains belonging to different classes 6Membrane and cell surface proteins and peptides (12) Does not include proteins in the immune system 7Small proteins (59) Usually dominated by metal ligand heme andor disulfide bridges 8Coiled coil proteins (5) Not a true class 9Low resolution protein structures (17) Not a true class 10Peptides (95) Peptides and fragments Not a true class 11Designed proteins (36) Experimental structures of proteins with essentially non-natural sequences Not a true class
Membrane protein topology
Paradosso di Levinthalbull Proteina di 100 residuibull Due gradi di libertarsquo torsionaliresiduo (phipsi)bull 3 conformazioni accessibili per ogni grado dilibertarsquo torsionalebull 1048774 32x100 possibili conformazionibull 1013 conformazioni esploratesecbull Tempo richiesto per esplorare tutte leconformazioni t = 20 x 109 anni bull Le proteine si devono ripiegare seguendo uncammino definito caratterizzato da conformazionivia via piursquo stabili (diminuizione di G)
cytokines
Fascio di 4 eliche antiparallele 2 coppie di eliche parallele unite in modo antiparallelo
domains which bind DNA
A three-helix bundle forms the basis of a DNA-binding domain which occurs in a number of proteins
globins
Strutture ldquoall alphardquo
elica solitaria
elica-turn-elica
Fascio di 4 eliche
Globine (fascio di 8 eliche)
Domini ad alfa elica di grandi dimensioni
All- topologies
The Greek Key topology
The Greek Key topology named after a pattern that was common on Greek pottery is shown below Three up-and-down -strands connected by hairpins are followed by a longer connection to the fourth strand which lies adjacent to the first
Ipotetica modalitagrave di ripiegamento di una struttura a
forcina per formare la struttura a chiave greca I filamenti 2 e 3
si ripiegano sugli altri due in modo che il filamento 2 viene ad essere allineato e antiparallelo al
filamento 1
Gamma-crystallin has two domains each of which is an eight- stranded -barrel-type structure composed of two Greek keys In fact the structure is more accurately described as consisting of two -sheets one consisting of strands 2147 (white) and the other of strands 6583 (red) as indicated in the diagram
Gamma-crystallin
Aligned and orthogonal sandwiches
Diagram of this -sheet arrangement in the Lipocalin family which binds small molecules between the sheets of the sandwich
barrels
Strutture alfabeta
topologies The most regular and common domain structures consist of repeating -- supersecondary units such that the outer layer of the structure is composed of helices packing against a central core of parallel -sheets These folds are called or wound Many enzymes including all those involved in glycolysis are structures Most proteins are cytosolicThe -- is always right-handed In structures there is a repetition of this arrangement giving a ---etc sequence The strands are parallel and hydrogen bonded to each other while the helices are all parallel to each other and are antiparallel to the strands Thus the helices form a layer packing against the sheetThe ---- subunit often present in nucleotide-binding proteins is named the Rossman Fold after Michael Rossman (Rao and Rossman1973)
Beta-alfa-beta destrorsa Beta-alfa-beta sinistrorsa
Alfa-eliche sul medesimo piano del foglietto beta
Alfa-eliche su piani opposti del foglietto beta
Elica di collegamento
barrels
Consider a sequence of eight - motifsIf the first strand hydrogen bonds to the last then the structure closes on itself forming a barrel-like structure
Enzima triosofosfato isomerasi
Struttura a ldquoTIM barrelrdquo
Enzima lattato deidrogenasi
Rossman Fold
In tutte le strutture a botte il sito attivo si trova in una tasca formata dalle regioni loop che collegano le estremitagrave carbossiliche dei filamenti beta con le adiacenti alfa eliche
Nei domini con struttura aperta ruotata il sito attivo si trova in una fessura localizzata esternamente allrsquoestremitagrave carbossilica del filamenti Questa fessura egrave formata da due regioni loop adiacenti che collegano i due filamenti con eliche presenti su facce opposte del foglietto
Adenilato chinasiflavodossina
Punti di inversione topologica (topological switch points)
Strutture alfabeta
I) TIM barrel
II) a)Struttura aperta e ruotata (di tipo parallelo o misto) - b) Rossmann fold
III) horseshoe (ferro di cavallo)
Alpha+Beta Topologies
bullRibonuclease-H
Structural Classification of Proteins (SCOP)Authors Alexey G Murzin Loredana Lo Conte Bartlett G Ailey Steven E Brenner Tim J P Hubbard and Cyrus Chothia Reference Murzin A G Brenner S E Hubbard T Chothia C (1995) SCOP a structural classification of proteins database for the investigation of sequences and structures J Mol Biol 247 536-540Classes
1All alpha proteins (151) 2All beta proteins (111) 3Alpha and beta proteins (ab) (117) Mainly parallel beta sheets (beta-alpha-beta units) 4Alpha and beta proteins (a+b) (212) Mainly antiparallel beta sheets (segregated alpha and beta regions) 5Multi-domain proteins (alpha and beta) (39) Folds consisting of two or more domains belonging to different classes 6Membrane and cell surface proteins and peptides (12) Does not include proteins in the immune system 7Small proteins (59) Usually dominated by metal ligand heme andor disulfide bridges 8Coiled coil proteins (5) Not a true class 9Low resolution protein structures (17) Not a true class 10Peptides (95) Peptides and fragments Not a true class 11Designed proteins (36) Experimental structures of proteins with essentially non-natural sequences Not a true class
Membrane protein topology
Paradosso di Levinthalbull Proteina di 100 residuibull Due gradi di libertarsquo torsionaliresiduo (phipsi)bull 3 conformazioni accessibili per ogni grado dilibertarsquo torsionalebull 1048774 32x100 possibili conformazionibull 1013 conformazioni esploratesecbull Tempo richiesto per esplorare tutte leconformazioni t = 20 x 109 anni bull Le proteine si devono ripiegare seguendo uncammino definito caratterizzato da conformazionivia via piursquo stabili (diminuizione di G)
Fascio di 4 eliche antiparallele 2 coppie di eliche parallele unite in modo antiparallelo
domains which bind DNA
A three-helix bundle forms the basis of a DNA-binding domain which occurs in a number of proteins
globins
Strutture ldquoall alphardquo
elica solitaria
elica-turn-elica
Fascio di 4 eliche
Globine (fascio di 8 eliche)
Domini ad alfa elica di grandi dimensioni
All- topologies
The Greek Key topology
The Greek Key topology named after a pattern that was common on Greek pottery is shown below Three up-and-down -strands connected by hairpins are followed by a longer connection to the fourth strand which lies adjacent to the first
Ipotetica modalitagrave di ripiegamento di una struttura a
forcina per formare la struttura a chiave greca I filamenti 2 e 3
si ripiegano sugli altri due in modo che il filamento 2 viene ad essere allineato e antiparallelo al
filamento 1
Gamma-crystallin has two domains each of which is an eight- stranded -barrel-type structure composed of two Greek keys In fact the structure is more accurately described as consisting of two -sheets one consisting of strands 2147 (white) and the other of strands 6583 (red) as indicated in the diagram
Gamma-crystallin
Aligned and orthogonal sandwiches
Diagram of this -sheet arrangement in the Lipocalin family which binds small molecules between the sheets of the sandwich
barrels
Strutture alfabeta
topologies The most regular and common domain structures consist of repeating -- supersecondary units such that the outer layer of the structure is composed of helices packing against a central core of parallel -sheets These folds are called or wound Many enzymes including all those involved in glycolysis are structures Most proteins are cytosolicThe -- is always right-handed In structures there is a repetition of this arrangement giving a ---etc sequence The strands are parallel and hydrogen bonded to each other while the helices are all parallel to each other and are antiparallel to the strands Thus the helices form a layer packing against the sheetThe ---- subunit often present in nucleotide-binding proteins is named the Rossman Fold after Michael Rossman (Rao and Rossman1973)
Beta-alfa-beta destrorsa Beta-alfa-beta sinistrorsa
Alfa-eliche sul medesimo piano del foglietto beta
Alfa-eliche su piani opposti del foglietto beta
Elica di collegamento
barrels
Consider a sequence of eight - motifsIf the first strand hydrogen bonds to the last then the structure closes on itself forming a barrel-like structure
Enzima triosofosfato isomerasi
Struttura a ldquoTIM barrelrdquo
Enzima lattato deidrogenasi
Rossman Fold
In tutte le strutture a botte il sito attivo si trova in una tasca formata dalle regioni loop che collegano le estremitagrave carbossiliche dei filamenti beta con le adiacenti alfa eliche
Nei domini con struttura aperta ruotata il sito attivo si trova in una fessura localizzata esternamente allrsquoestremitagrave carbossilica del filamenti Questa fessura egrave formata da due regioni loop adiacenti che collegano i due filamenti con eliche presenti su facce opposte del foglietto
Adenilato chinasiflavodossina
Punti di inversione topologica (topological switch points)
Strutture alfabeta
I) TIM barrel
II) a)Struttura aperta e ruotata (di tipo parallelo o misto) - b) Rossmann fold
III) horseshoe (ferro di cavallo)
Alpha+Beta Topologies
bullRibonuclease-H
Structural Classification of Proteins (SCOP)Authors Alexey G Murzin Loredana Lo Conte Bartlett G Ailey Steven E Brenner Tim J P Hubbard and Cyrus Chothia Reference Murzin A G Brenner S E Hubbard T Chothia C (1995) SCOP a structural classification of proteins database for the investigation of sequences and structures J Mol Biol 247 536-540Classes
1All alpha proteins (151) 2All beta proteins (111) 3Alpha and beta proteins (ab) (117) Mainly parallel beta sheets (beta-alpha-beta units) 4Alpha and beta proteins (a+b) (212) Mainly antiparallel beta sheets (segregated alpha and beta regions) 5Multi-domain proteins (alpha and beta) (39) Folds consisting of two or more domains belonging to different classes 6Membrane and cell surface proteins and peptides (12) Does not include proteins in the immune system 7Small proteins (59) Usually dominated by metal ligand heme andor disulfide bridges 8Coiled coil proteins (5) Not a true class 9Low resolution protein structures (17) Not a true class 10Peptides (95) Peptides and fragments Not a true class 11Designed proteins (36) Experimental structures of proteins with essentially non-natural sequences Not a true class
Membrane protein topology
Paradosso di Levinthalbull Proteina di 100 residuibull Due gradi di libertarsquo torsionaliresiduo (phipsi)bull 3 conformazioni accessibili per ogni grado dilibertarsquo torsionalebull 1048774 32x100 possibili conformazionibull 1013 conformazioni esploratesecbull Tempo richiesto per esplorare tutte leconformazioni t = 20 x 109 anni bull Le proteine si devono ripiegare seguendo uncammino definito caratterizzato da conformazionivia via piursquo stabili (diminuizione di G)
domains which bind DNA
A three-helix bundle forms the basis of a DNA-binding domain which occurs in a number of proteins
globins
Strutture ldquoall alphardquo
elica solitaria
elica-turn-elica
Fascio di 4 eliche
Globine (fascio di 8 eliche)
Domini ad alfa elica di grandi dimensioni
All- topologies
The Greek Key topology
The Greek Key topology named after a pattern that was common on Greek pottery is shown below Three up-and-down -strands connected by hairpins are followed by a longer connection to the fourth strand which lies adjacent to the first
Ipotetica modalitagrave di ripiegamento di una struttura a
forcina per formare la struttura a chiave greca I filamenti 2 e 3
si ripiegano sugli altri due in modo che il filamento 2 viene ad essere allineato e antiparallelo al
filamento 1
Gamma-crystallin has two domains each of which is an eight- stranded -barrel-type structure composed of two Greek keys In fact the structure is more accurately described as consisting of two -sheets one consisting of strands 2147 (white) and the other of strands 6583 (red) as indicated in the diagram
Gamma-crystallin
Aligned and orthogonal sandwiches
Diagram of this -sheet arrangement in the Lipocalin family which binds small molecules between the sheets of the sandwich
barrels
Strutture alfabeta
topologies The most regular and common domain structures consist of repeating -- supersecondary units such that the outer layer of the structure is composed of helices packing against a central core of parallel -sheets These folds are called or wound Many enzymes including all those involved in glycolysis are structures Most proteins are cytosolicThe -- is always right-handed In structures there is a repetition of this arrangement giving a ---etc sequence The strands are parallel and hydrogen bonded to each other while the helices are all parallel to each other and are antiparallel to the strands Thus the helices form a layer packing against the sheetThe ---- subunit often present in nucleotide-binding proteins is named the Rossman Fold after Michael Rossman (Rao and Rossman1973)
Beta-alfa-beta destrorsa Beta-alfa-beta sinistrorsa
Alfa-eliche sul medesimo piano del foglietto beta
Alfa-eliche su piani opposti del foglietto beta
Elica di collegamento
barrels
Consider a sequence of eight - motifsIf the first strand hydrogen bonds to the last then the structure closes on itself forming a barrel-like structure
Enzima triosofosfato isomerasi
Struttura a ldquoTIM barrelrdquo
Enzima lattato deidrogenasi
Rossman Fold
In tutte le strutture a botte il sito attivo si trova in una tasca formata dalle regioni loop che collegano le estremitagrave carbossiliche dei filamenti beta con le adiacenti alfa eliche
Nei domini con struttura aperta ruotata il sito attivo si trova in una fessura localizzata esternamente allrsquoestremitagrave carbossilica del filamenti Questa fessura egrave formata da due regioni loop adiacenti che collegano i due filamenti con eliche presenti su facce opposte del foglietto
Adenilato chinasiflavodossina
Punti di inversione topologica (topological switch points)
Strutture alfabeta
I) TIM barrel
II) a)Struttura aperta e ruotata (di tipo parallelo o misto) - b) Rossmann fold
III) horseshoe (ferro di cavallo)
Alpha+Beta Topologies
bullRibonuclease-H
Structural Classification of Proteins (SCOP)Authors Alexey G Murzin Loredana Lo Conte Bartlett G Ailey Steven E Brenner Tim J P Hubbard and Cyrus Chothia Reference Murzin A G Brenner S E Hubbard T Chothia C (1995) SCOP a structural classification of proteins database for the investigation of sequences and structures J Mol Biol 247 536-540Classes
1All alpha proteins (151) 2All beta proteins (111) 3Alpha and beta proteins (ab) (117) Mainly parallel beta sheets (beta-alpha-beta units) 4Alpha and beta proteins (a+b) (212) Mainly antiparallel beta sheets (segregated alpha and beta regions) 5Multi-domain proteins (alpha and beta) (39) Folds consisting of two or more domains belonging to different classes 6Membrane and cell surface proteins and peptides (12) Does not include proteins in the immune system 7Small proteins (59) Usually dominated by metal ligand heme andor disulfide bridges 8Coiled coil proteins (5) Not a true class 9Low resolution protein structures (17) Not a true class 10Peptides (95) Peptides and fragments Not a true class 11Designed proteins (36) Experimental structures of proteins with essentially non-natural sequences Not a true class
Membrane protein topology
Paradosso di Levinthalbull Proteina di 100 residuibull Due gradi di libertarsquo torsionaliresiduo (phipsi)bull 3 conformazioni accessibili per ogni grado dilibertarsquo torsionalebull 1048774 32x100 possibili conformazionibull 1013 conformazioni esploratesecbull Tempo richiesto per esplorare tutte leconformazioni t = 20 x 109 anni bull Le proteine si devono ripiegare seguendo uncammino definito caratterizzato da conformazionivia via piursquo stabili (diminuizione di G)
globins
Strutture ldquoall alphardquo
elica solitaria
elica-turn-elica
Fascio di 4 eliche
Globine (fascio di 8 eliche)
Domini ad alfa elica di grandi dimensioni
All- topologies
The Greek Key topology
The Greek Key topology named after a pattern that was common on Greek pottery is shown below Three up-and-down -strands connected by hairpins are followed by a longer connection to the fourth strand which lies adjacent to the first
Ipotetica modalitagrave di ripiegamento di una struttura a
forcina per formare la struttura a chiave greca I filamenti 2 e 3
si ripiegano sugli altri due in modo che il filamento 2 viene ad essere allineato e antiparallelo al
filamento 1
Gamma-crystallin has two domains each of which is an eight- stranded -barrel-type structure composed of two Greek keys In fact the structure is more accurately described as consisting of two -sheets one consisting of strands 2147 (white) and the other of strands 6583 (red) as indicated in the diagram
Gamma-crystallin
Aligned and orthogonal sandwiches
Diagram of this -sheet arrangement in the Lipocalin family which binds small molecules between the sheets of the sandwich
barrels
Strutture alfabeta
topologies The most regular and common domain structures consist of repeating -- supersecondary units such that the outer layer of the structure is composed of helices packing against a central core of parallel -sheets These folds are called or wound Many enzymes including all those involved in glycolysis are structures Most proteins are cytosolicThe -- is always right-handed In structures there is a repetition of this arrangement giving a ---etc sequence The strands are parallel and hydrogen bonded to each other while the helices are all parallel to each other and are antiparallel to the strands Thus the helices form a layer packing against the sheetThe ---- subunit often present in nucleotide-binding proteins is named the Rossman Fold after Michael Rossman (Rao and Rossman1973)
Beta-alfa-beta destrorsa Beta-alfa-beta sinistrorsa
Alfa-eliche sul medesimo piano del foglietto beta
Alfa-eliche su piani opposti del foglietto beta
Elica di collegamento
barrels
Consider a sequence of eight - motifsIf the first strand hydrogen bonds to the last then the structure closes on itself forming a barrel-like structure
Enzima triosofosfato isomerasi
Struttura a ldquoTIM barrelrdquo
Enzima lattato deidrogenasi
Rossman Fold
In tutte le strutture a botte il sito attivo si trova in una tasca formata dalle regioni loop che collegano le estremitagrave carbossiliche dei filamenti beta con le adiacenti alfa eliche
Nei domini con struttura aperta ruotata il sito attivo si trova in una fessura localizzata esternamente allrsquoestremitagrave carbossilica del filamenti Questa fessura egrave formata da due regioni loop adiacenti che collegano i due filamenti con eliche presenti su facce opposte del foglietto
Adenilato chinasiflavodossina
Punti di inversione topologica (topological switch points)
Strutture alfabeta
I) TIM barrel
II) a)Struttura aperta e ruotata (di tipo parallelo o misto) - b) Rossmann fold
III) horseshoe (ferro di cavallo)
Alpha+Beta Topologies
bullRibonuclease-H
Structural Classification of Proteins (SCOP)Authors Alexey G Murzin Loredana Lo Conte Bartlett G Ailey Steven E Brenner Tim J P Hubbard and Cyrus Chothia Reference Murzin A G Brenner S E Hubbard T Chothia C (1995) SCOP a structural classification of proteins database for the investigation of sequences and structures J Mol Biol 247 536-540Classes
1All alpha proteins (151) 2All beta proteins (111) 3Alpha and beta proteins (ab) (117) Mainly parallel beta sheets (beta-alpha-beta units) 4Alpha and beta proteins (a+b) (212) Mainly antiparallel beta sheets (segregated alpha and beta regions) 5Multi-domain proteins (alpha and beta) (39) Folds consisting of two or more domains belonging to different classes 6Membrane and cell surface proteins and peptides (12) Does not include proteins in the immune system 7Small proteins (59) Usually dominated by metal ligand heme andor disulfide bridges 8Coiled coil proteins (5) Not a true class 9Low resolution protein structures (17) Not a true class 10Peptides (95) Peptides and fragments Not a true class 11Designed proteins (36) Experimental structures of proteins with essentially non-natural sequences Not a true class
Membrane protein topology
Paradosso di Levinthalbull Proteina di 100 residuibull Due gradi di libertarsquo torsionaliresiduo (phipsi)bull 3 conformazioni accessibili per ogni grado dilibertarsquo torsionalebull 1048774 32x100 possibili conformazionibull 1013 conformazioni esploratesecbull Tempo richiesto per esplorare tutte leconformazioni t = 20 x 109 anni bull Le proteine si devono ripiegare seguendo uncammino definito caratterizzato da conformazionivia via piursquo stabili (diminuizione di G)
Strutture ldquoall alphardquo
elica solitaria
elica-turn-elica
Fascio di 4 eliche
Globine (fascio di 8 eliche)
Domini ad alfa elica di grandi dimensioni
All- topologies
The Greek Key topology
The Greek Key topology named after a pattern that was common on Greek pottery is shown below Three up-and-down -strands connected by hairpins are followed by a longer connection to the fourth strand which lies adjacent to the first
Ipotetica modalitagrave di ripiegamento di una struttura a
forcina per formare la struttura a chiave greca I filamenti 2 e 3
si ripiegano sugli altri due in modo che il filamento 2 viene ad essere allineato e antiparallelo al
filamento 1
Gamma-crystallin has two domains each of which is an eight- stranded -barrel-type structure composed of two Greek keys In fact the structure is more accurately described as consisting of two -sheets one consisting of strands 2147 (white) and the other of strands 6583 (red) as indicated in the diagram
Gamma-crystallin
Aligned and orthogonal sandwiches
Diagram of this -sheet arrangement in the Lipocalin family which binds small molecules between the sheets of the sandwich
barrels
Strutture alfabeta
topologies The most regular and common domain structures consist of repeating -- supersecondary units such that the outer layer of the structure is composed of helices packing against a central core of parallel -sheets These folds are called or wound Many enzymes including all those involved in glycolysis are structures Most proteins are cytosolicThe -- is always right-handed In structures there is a repetition of this arrangement giving a ---etc sequence The strands are parallel and hydrogen bonded to each other while the helices are all parallel to each other and are antiparallel to the strands Thus the helices form a layer packing against the sheetThe ---- subunit often present in nucleotide-binding proteins is named the Rossman Fold after Michael Rossman (Rao and Rossman1973)
Beta-alfa-beta destrorsa Beta-alfa-beta sinistrorsa
Alfa-eliche sul medesimo piano del foglietto beta
Alfa-eliche su piani opposti del foglietto beta
Elica di collegamento
barrels
Consider a sequence of eight - motifsIf the first strand hydrogen bonds to the last then the structure closes on itself forming a barrel-like structure
Enzima triosofosfato isomerasi
Struttura a ldquoTIM barrelrdquo
Enzima lattato deidrogenasi
Rossman Fold
In tutte le strutture a botte il sito attivo si trova in una tasca formata dalle regioni loop che collegano le estremitagrave carbossiliche dei filamenti beta con le adiacenti alfa eliche
Nei domini con struttura aperta ruotata il sito attivo si trova in una fessura localizzata esternamente allrsquoestremitagrave carbossilica del filamenti Questa fessura egrave formata da due regioni loop adiacenti che collegano i due filamenti con eliche presenti su facce opposte del foglietto
Adenilato chinasiflavodossina
Punti di inversione topologica (topological switch points)
Strutture alfabeta
I) TIM barrel
II) a)Struttura aperta e ruotata (di tipo parallelo o misto) - b) Rossmann fold
III) horseshoe (ferro di cavallo)
Alpha+Beta Topologies
bullRibonuclease-H
Structural Classification of Proteins (SCOP)Authors Alexey G Murzin Loredana Lo Conte Bartlett G Ailey Steven E Brenner Tim J P Hubbard and Cyrus Chothia Reference Murzin A G Brenner S E Hubbard T Chothia C (1995) SCOP a structural classification of proteins database for the investigation of sequences and structures J Mol Biol 247 536-540Classes
1All alpha proteins (151) 2All beta proteins (111) 3Alpha and beta proteins (ab) (117) Mainly parallel beta sheets (beta-alpha-beta units) 4Alpha and beta proteins (a+b) (212) Mainly antiparallel beta sheets (segregated alpha and beta regions) 5Multi-domain proteins (alpha and beta) (39) Folds consisting of two or more domains belonging to different classes 6Membrane and cell surface proteins and peptides (12) Does not include proteins in the immune system 7Small proteins (59) Usually dominated by metal ligand heme andor disulfide bridges 8Coiled coil proteins (5) Not a true class 9Low resolution protein structures (17) Not a true class 10Peptides (95) Peptides and fragments Not a true class 11Designed proteins (36) Experimental structures of proteins with essentially non-natural sequences Not a true class
Membrane protein topology
Paradosso di Levinthalbull Proteina di 100 residuibull Due gradi di libertarsquo torsionaliresiduo (phipsi)bull 3 conformazioni accessibili per ogni grado dilibertarsquo torsionalebull 1048774 32x100 possibili conformazionibull 1013 conformazioni esploratesecbull Tempo richiesto per esplorare tutte leconformazioni t = 20 x 109 anni bull Le proteine si devono ripiegare seguendo uncammino definito caratterizzato da conformazionivia via piursquo stabili (diminuizione di G)
All- topologies
The Greek Key topology
The Greek Key topology named after a pattern that was common on Greek pottery is shown below Three up-and-down -strands connected by hairpins are followed by a longer connection to the fourth strand which lies adjacent to the first
Ipotetica modalitagrave di ripiegamento di una struttura a
forcina per formare la struttura a chiave greca I filamenti 2 e 3
si ripiegano sugli altri due in modo che il filamento 2 viene ad essere allineato e antiparallelo al
filamento 1
Gamma-crystallin has two domains each of which is an eight- stranded -barrel-type structure composed of two Greek keys In fact the structure is more accurately described as consisting of two -sheets one consisting of strands 2147 (white) and the other of strands 6583 (red) as indicated in the diagram
Gamma-crystallin
Aligned and orthogonal sandwiches
Diagram of this -sheet arrangement in the Lipocalin family which binds small molecules between the sheets of the sandwich
barrels
Strutture alfabeta
topologies The most regular and common domain structures consist of repeating -- supersecondary units such that the outer layer of the structure is composed of helices packing against a central core of parallel -sheets These folds are called or wound Many enzymes including all those involved in glycolysis are structures Most proteins are cytosolicThe -- is always right-handed In structures there is a repetition of this arrangement giving a ---etc sequence The strands are parallel and hydrogen bonded to each other while the helices are all parallel to each other and are antiparallel to the strands Thus the helices form a layer packing against the sheetThe ---- subunit often present in nucleotide-binding proteins is named the Rossman Fold after Michael Rossman (Rao and Rossman1973)
Beta-alfa-beta destrorsa Beta-alfa-beta sinistrorsa
Alfa-eliche sul medesimo piano del foglietto beta
Alfa-eliche su piani opposti del foglietto beta
Elica di collegamento
barrels
Consider a sequence of eight - motifsIf the first strand hydrogen bonds to the last then the structure closes on itself forming a barrel-like structure
Enzima triosofosfato isomerasi
Struttura a ldquoTIM barrelrdquo
Enzima lattato deidrogenasi
Rossman Fold
In tutte le strutture a botte il sito attivo si trova in una tasca formata dalle regioni loop che collegano le estremitagrave carbossiliche dei filamenti beta con le adiacenti alfa eliche
Nei domini con struttura aperta ruotata il sito attivo si trova in una fessura localizzata esternamente allrsquoestremitagrave carbossilica del filamenti Questa fessura egrave formata da due regioni loop adiacenti che collegano i due filamenti con eliche presenti su facce opposte del foglietto
Adenilato chinasiflavodossina
Punti di inversione topologica (topological switch points)
Strutture alfabeta
I) TIM barrel
II) a)Struttura aperta e ruotata (di tipo parallelo o misto) - b) Rossmann fold
III) horseshoe (ferro di cavallo)
Alpha+Beta Topologies
bullRibonuclease-H
Structural Classification of Proteins (SCOP)Authors Alexey G Murzin Loredana Lo Conte Bartlett G Ailey Steven E Brenner Tim J P Hubbard and Cyrus Chothia Reference Murzin A G Brenner S E Hubbard T Chothia C (1995) SCOP a structural classification of proteins database for the investigation of sequences and structures J Mol Biol 247 536-540Classes
1All alpha proteins (151) 2All beta proteins (111) 3Alpha and beta proteins (ab) (117) Mainly parallel beta sheets (beta-alpha-beta units) 4Alpha and beta proteins (a+b) (212) Mainly antiparallel beta sheets (segregated alpha and beta regions) 5Multi-domain proteins (alpha and beta) (39) Folds consisting of two or more domains belonging to different classes 6Membrane and cell surface proteins and peptides (12) Does not include proteins in the immune system 7Small proteins (59) Usually dominated by metal ligand heme andor disulfide bridges 8Coiled coil proteins (5) Not a true class 9Low resolution protein structures (17) Not a true class 10Peptides (95) Peptides and fragments Not a true class 11Designed proteins (36) Experimental structures of proteins with essentially non-natural sequences Not a true class
Membrane protein topology
Paradosso di Levinthalbull Proteina di 100 residuibull Due gradi di libertarsquo torsionaliresiduo (phipsi)bull 3 conformazioni accessibili per ogni grado dilibertarsquo torsionalebull 1048774 32x100 possibili conformazionibull 1013 conformazioni esploratesecbull Tempo richiesto per esplorare tutte leconformazioni t = 20 x 109 anni bull Le proteine si devono ripiegare seguendo uncammino definito caratterizzato da conformazionivia via piursquo stabili (diminuizione di G)
The Greek Key topology
The Greek Key topology named after a pattern that was common on Greek pottery is shown below Three up-and-down -strands connected by hairpins are followed by a longer connection to the fourth strand which lies adjacent to the first
Ipotetica modalitagrave di ripiegamento di una struttura a
forcina per formare la struttura a chiave greca I filamenti 2 e 3
si ripiegano sugli altri due in modo che il filamento 2 viene ad essere allineato e antiparallelo al
filamento 1
Gamma-crystallin has two domains each of which is an eight- stranded -barrel-type structure composed of two Greek keys In fact the structure is more accurately described as consisting of two -sheets one consisting of strands 2147 (white) and the other of strands 6583 (red) as indicated in the diagram
Gamma-crystallin
Aligned and orthogonal sandwiches
Diagram of this -sheet arrangement in the Lipocalin family which binds small molecules between the sheets of the sandwich
barrels
Strutture alfabeta
topologies The most regular and common domain structures consist of repeating -- supersecondary units such that the outer layer of the structure is composed of helices packing against a central core of parallel -sheets These folds are called or wound Many enzymes including all those involved in glycolysis are structures Most proteins are cytosolicThe -- is always right-handed In structures there is a repetition of this arrangement giving a ---etc sequence The strands are parallel and hydrogen bonded to each other while the helices are all parallel to each other and are antiparallel to the strands Thus the helices form a layer packing against the sheetThe ---- subunit often present in nucleotide-binding proteins is named the Rossman Fold after Michael Rossman (Rao and Rossman1973)
Beta-alfa-beta destrorsa Beta-alfa-beta sinistrorsa
Alfa-eliche sul medesimo piano del foglietto beta
Alfa-eliche su piani opposti del foglietto beta
Elica di collegamento
barrels
Consider a sequence of eight - motifsIf the first strand hydrogen bonds to the last then the structure closes on itself forming a barrel-like structure
Enzima triosofosfato isomerasi
Struttura a ldquoTIM barrelrdquo
Enzima lattato deidrogenasi
Rossman Fold
In tutte le strutture a botte il sito attivo si trova in una tasca formata dalle regioni loop che collegano le estremitagrave carbossiliche dei filamenti beta con le adiacenti alfa eliche
Nei domini con struttura aperta ruotata il sito attivo si trova in una fessura localizzata esternamente allrsquoestremitagrave carbossilica del filamenti Questa fessura egrave formata da due regioni loop adiacenti che collegano i due filamenti con eliche presenti su facce opposte del foglietto
Adenilato chinasiflavodossina
Punti di inversione topologica (topological switch points)
Strutture alfabeta
I) TIM barrel
II) a)Struttura aperta e ruotata (di tipo parallelo o misto) - b) Rossmann fold
III) horseshoe (ferro di cavallo)
Alpha+Beta Topologies
bullRibonuclease-H
Structural Classification of Proteins (SCOP)Authors Alexey G Murzin Loredana Lo Conte Bartlett G Ailey Steven E Brenner Tim J P Hubbard and Cyrus Chothia Reference Murzin A G Brenner S E Hubbard T Chothia C (1995) SCOP a structural classification of proteins database for the investigation of sequences and structures J Mol Biol 247 536-540Classes
1All alpha proteins (151) 2All beta proteins (111) 3Alpha and beta proteins (ab) (117) Mainly parallel beta sheets (beta-alpha-beta units) 4Alpha and beta proteins (a+b) (212) Mainly antiparallel beta sheets (segregated alpha and beta regions) 5Multi-domain proteins (alpha and beta) (39) Folds consisting of two or more domains belonging to different classes 6Membrane and cell surface proteins and peptides (12) Does not include proteins in the immune system 7Small proteins (59) Usually dominated by metal ligand heme andor disulfide bridges 8Coiled coil proteins (5) Not a true class 9Low resolution protein structures (17) Not a true class 10Peptides (95) Peptides and fragments Not a true class 11Designed proteins (36) Experimental structures of proteins with essentially non-natural sequences Not a true class
Membrane protein topology
Paradosso di Levinthalbull Proteina di 100 residuibull Due gradi di libertarsquo torsionaliresiduo (phipsi)bull 3 conformazioni accessibili per ogni grado dilibertarsquo torsionalebull 1048774 32x100 possibili conformazionibull 1013 conformazioni esploratesecbull Tempo richiesto per esplorare tutte leconformazioni t = 20 x 109 anni bull Le proteine si devono ripiegare seguendo uncammino definito caratterizzato da conformazionivia via piursquo stabili (diminuizione di G)
Ipotetica modalitagrave di ripiegamento di una struttura a
forcina per formare la struttura a chiave greca I filamenti 2 e 3
si ripiegano sugli altri due in modo che il filamento 2 viene ad essere allineato e antiparallelo al
filamento 1
Gamma-crystallin has two domains each of which is an eight- stranded -barrel-type structure composed of two Greek keys In fact the structure is more accurately described as consisting of two -sheets one consisting of strands 2147 (white) and the other of strands 6583 (red) as indicated in the diagram
Gamma-crystallin
Aligned and orthogonal sandwiches
Diagram of this -sheet arrangement in the Lipocalin family which binds small molecules between the sheets of the sandwich
barrels
Strutture alfabeta
topologies The most regular and common domain structures consist of repeating -- supersecondary units such that the outer layer of the structure is composed of helices packing against a central core of parallel -sheets These folds are called or wound Many enzymes including all those involved in glycolysis are structures Most proteins are cytosolicThe -- is always right-handed In structures there is a repetition of this arrangement giving a ---etc sequence The strands are parallel and hydrogen bonded to each other while the helices are all parallel to each other and are antiparallel to the strands Thus the helices form a layer packing against the sheetThe ---- subunit often present in nucleotide-binding proteins is named the Rossman Fold after Michael Rossman (Rao and Rossman1973)
Beta-alfa-beta destrorsa Beta-alfa-beta sinistrorsa
Alfa-eliche sul medesimo piano del foglietto beta
Alfa-eliche su piani opposti del foglietto beta
Elica di collegamento
barrels
Consider a sequence of eight - motifsIf the first strand hydrogen bonds to the last then the structure closes on itself forming a barrel-like structure
Enzima triosofosfato isomerasi
Struttura a ldquoTIM barrelrdquo
Enzima lattato deidrogenasi
Rossman Fold
In tutte le strutture a botte il sito attivo si trova in una tasca formata dalle regioni loop che collegano le estremitagrave carbossiliche dei filamenti beta con le adiacenti alfa eliche
Nei domini con struttura aperta ruotata il sito attivo si trova in una fessura localizzata esternamente allrsquoestremitagrave carbossilica del filamenti Questa fessura egrave formata da due regioni loop adiacenti che collegano i due filamenti con eliche presenti su facce opposte del foglietto
Adenilato chinasiflavodossina
Punti di inversione topologica (topological switch points)
Strutture alfabeta
I) TIM barrel
II) a)Struttura aperta e ruotata (di tipo parallelo o misto) - b) Rossmann fold
III) horseshoe (ferro di cavallo)
Alpha+Beta Topologies
bullRibonuclease-H
Structural Classification of Proteins (SCOP)Authors Alexey G Murzin Loredana Lo Conte Bartlett G Ailey Steven E Brenner Tim J P Hubbard and Cyrus Chothia Reference Murzin A G Brenner S E Hubbard T Chothia C (1995) SCOP a structural classification of proteins database for the investigation of sequences and structures J Mol Biol 247 536-540Classes
1All alpha proteins (151) 2All beta proteins (111) 3Alpha and beta proteins (ab) (117) Mainly parallel beta sheets (beta-alpha-beta units) 4Alpha and beta proteins (a+b) (212) Mainly antiparallel beta sheets (segregated alpha and beta regions) 5Multi-domain proteins (alpha and beta) (39) Folds consisting of two or more domains belonging to different classes 6Membrane and cell surface proteins and peptides (12) Does not include proteins in the immune system 7Small proteins (59) Usually dominated by metal ligand heme andor disulfide bridges 8Coiled coil proteins (5) Not a true class 9Low resolution protein structures (17) Not a true class 10Peptides (95) Peptides and fragments Not a true class 11Designed proteins (36) Experimental structures of proteins with essentially non-natural sequences Not a true class
Membrane protein topology
Paradosso di Levinthalbull Proteina di 100 residuibull Due gradi di libertarsquo torsionaliresiduo (phipsi)bull 3 conformazioni accessibili per ogni grado dilibertarsquo torsionalebull 1048774 32x100 possibili conformazionibull 1013 conformazioni esploratesecbull Tempo richiesto per esplorare tutte leconformazioni t = 20 x 109 anni bull Le proteine si devono ripiegare seguendo uncammino definito caratterizzato da conformazionivia via piursquo stabili (diminuizione di G)
Gamma-crystallin has two domains each of which is an eight- stranded -barrel-type structure composed of two Greek keys In fact the structure is more accurately described as consisting of two -sheets one consisting of strands 2147 (white) and the other of strands 6583 (red) as indicated in the diagram
Gamma-crystallin
Aligned and orthogonal sandwiches
Diagram of this -sheet arrangement in the Lipocalin family which binds small molecules between the sheets of the sandwich
barrels
Strutture alfabeta
topologies The most regular and common domain structures consist of repeating -- supersecondary units such that the outer layer of the structure is composed of helices packing against a central core of parallel -sheets These folds are called or wound Many enzymes including all those involved in glycolysis are structures Most proteins are cytosolicThe -- is always right-handed In structures there is a repetition of this arrangement giving a ---etc sequence The strands are parallel and hydrogen bonded to each other while the helices are all parallel to each other and are antiparallel to the strands Thus the helices form a layer packing against the sheetThe ---- subunit often present in nucleotide-binding proteins is named the Rossman Fold after Michael Rossman (Rao and Rossman1973)
Beta-alfa-beta destrorsa Beta-alfa-beta sinistrorsa
Alfa-eliche sul medesimo piano del foglietto beta
Alfa-eliche su piani opposti del foglietto beta
Elica di collegamento
barrels
Consider a sequence of eight - motifsIf the first strand hydrogen bonds to the last then the structure closes on itself forming a barrel-like structure
Enzima triosofosfato isomerasi
Struttura a ldquoTIM barrelrdquo
Enzima lattato deidrogenasi
Rossman Fold
In tutte le strutture a botte il sito attivo si trova in una tasca formata dalle regioni loop che collegano le estremitagrave carbossiliche dei filamenti beta con le adiacenti alfa eliche
Nei domini con struttura aperta ruotata il sito attivo si trova in una fessura localizzata esternamente allrsquoestremitagrave carbossilica del filamenti Questa fessura egrave formata da due regioni loop adiacenti che collegano i due filamenti con eliche presenti su facce opposte del foglietto
Adenilato chinasiflavodossina
Punti di inversione topologica (topological switch points)
Strutture alfabeta
I) TIM barrel
II) a)Struttura aperta e ruotata (di tipo parallelo o misto) - b) Rossmann fold
III) horseshoe (ferro di cavallo)
Alpha+Beta Topologies
bullRibonuclease-H
Structural Classification of Proteins (SCOP)Authors Alexey G Murzin Loredana Lo Conte Bartlett G Ailey Steven E Brenner Tim J P Hubbard and Cyrus Chothia Reference Murzin A G Brenner S E Hubbard T Chothia C (1995) SCOP a structural classification of proteins database for the investigation of sequences and structures J Mol Biol 247 536-540Classes
1All alpha proteins (151) 2All beta proteins (111) 3Alpha and beta proteins (ab) (117) Mainly parallel beta sheets (beta-alpha-beta units) 4Alpha and beta proteins (a+b) (212) Mainly antiparallel beta sheets (segregated alpha and beta regions) 5Multi-domain proteins (alpha and beta) (39) Folds consisting of two or more domains belonging to different classes 6Membrane and cell surface proteins and peptides (12) Does not include proteins in the immune system 7Small proteins (59) Usually dominated by metal ligand heme andor disulfide bridges 8Coiled coil proteins (5) Not a true class 9Low resolution protein structures (17) Not a true class 10Peptides (95) Peptides and fragments Not a true class 11Designed proteins (36) Experimental structures of proteins with essentially non-natural sequences Not a true class
Membrane protein topology
Paradosso di Levinthalbull Proteina di 100 residuibull Due gradi di libertarsquo torsionaliresiduo (phipsi)bull 3 conformazioni accessibili per ogni grado dilibertarsquo torsionalebull 1048774 32x100 possibili conformazionibull 1013 conformazioni esploratesecbull Tempo richiesto per esplorare tutte leconformazioni t = 20 x 109 anni bull Le proteine si devono ripiegare seguendo uncammino definito caratterizzato da conformazionivia via piursquo stabili (diminuizione di G)
Aligned and orthogonal sandwiches
Diagram of this -sheet arrangement in the Lipocalin family which binds small molecules between the sheets of the sandwich
barrels
Strutture alfabeta
topologies The most regular and common domain structures consist of repeating -- supersecondary units such that the outer layer of the structure is composed of helices packing against a central core of parallel -sheets These folds are called or wound Many enzymes including all those involved in glycolysis are structures Most proteins are cytosolicThe -- is always right-handed In structures there is a repetition of this arrangement giving a ---etc sequence The strands are parallel and hydrogen bonded to each other while the helices are all parallel to each other and are antiparallel to the strands Thus the helices form a layer packing against the sheetThe ---- subunit often present in nucleotide-binding proteins is named the Rossman Fold after Michael Rossman (Rao and Rossman1973)
Beta-alfa-beta destrorsa Beta-alfa-beta sinistrorsa
Alfa-eliche sul medesimo piano del foglietto beta
Alfa-eliche su piani opposti del foglietto beta
Elica di collegamento
barrels
Consider a sequence of eight - motifsIf the first strand hydrogen bonds to the last then the structure closes on itself forming a barrel-like structure
Enzima triosofosfato isomerasi
Struttura a ldquoTIM barrelrdquo
Enzima lattato deidrogenasi
Rossman Fold
In tutte le strutture a botte il sito attivo si trova in una tasca formata dalle regioni loop che collegano le estremitagrave carbossiliche dei filamenti beta con le adiacenti alfa eliche
Nei domini con struttura aperta ruotata il sito attivo si trova in una fessura localizzata esternamente allrsquoestremitagrave carbossilica del filamenti Questa fessura egrave formata da due regioni loop adiacenti che collegano i due filamenti con eliche presenti su facce opposte del foglietto
Adenilato chinasiflavodossina
Punti di inversione topologica (topological switch points)
Strutture alfabeta
I) TIM barrel
II) a)Struttura aperta e ruotata (di tipo parallelo o misto) - b) Rossmann fold
III) horseshoe (ferro di cavallo)
Alpha+Beta Topologies
bullRibonuclease-H
Structural Classification of Proteins (SCOP)Authors Alexey G Murzin Loredana Lo Conte Bartlett G Ailey Steven E Brenner Tim J P Hubbard and Cyrus Chothia Reference Murzin A G Brenner S E Hubbard T Chothia C (1995) SCOP a structural classification of proteins database for the investigation of sequences and structures J Mol Biol 247 536-540Classes
1All alpha proteins (151) 2All beta proteins (111) 3Alpha and beta proteins (ab) (117) Mainly parallel beta sheets (beta-alpha-beta units) 4Alpha and beta proteins (a+b) (212) Mainly antiparallel beta sheets (segregated alpha and beta regions) 5Multi-domain proteins (alpha and beta) (39) Folds consisting of two or more domains belonging to different classes 6Membrane and cell surface proteins and peptides (12) Does not include proteins in the immune system 7Small proteins (59) Usually dominated by metal ligand heme andor disulfide bridges 8Coiled coil proteins (5) Not a true class 9Low resolution protein structures (17) Not a true class 10Peptides (95) Peptides and fragments Not a true class 11Designed proteins (36) Experimental structures of proteins with essentially non-natural sequences Not a true class
Membrane protein topology
Paradosso di Levinthalbull Proteina di 100 residuibull Due gradi di libertarsquo torsionaliresiduo (phipsi)bull 3 conformazioni accessibili per ogni grado dilibertarsquo torsionalebull 1048774 32x100 possibili conformazionibull 1013 conformazioni esploratesecbull Tempo richiesto per esplorare tutte leconformazioni t = 20 x 109 anni bull Le proteine si devono ripiegare seguendo uncammino definito caratterizzato da conformazionivia via piursquo stabili (diminuizione di G)
Diagram of this -sheet arrangement in the Lipocalin family which binds small molecules between the sheets of the sandwich
barrels
Strutture alfabeta
topologies The most regular and common domain structures consist of repeating -- supersecondary units such that the outer layer of the structure is composed of helices packing against a central core of parallel -sheets These folds are called or wound Many enzymes including all those involved in glycolysis are structures Most proteins are cytosolicThe -- is always right-handed In structures there is a repetition of this arrangement giving a ---etc sequence The strands are parallel and hydrogen bonded to each other while the helices are all parallel to each other and are antiparallel to the strands Thus the helices form a layer packing against the sheetThe ---- subunit often present in nucleotide-binding proteins is named the Rossman Fold after Michael Rossman (Rao and Rossman1973)
Beta-alfa-beta destrorsa Beta-alfa-beta sinistrorsa
Alfa-eliche sul medesimo piano del foglietto beta
Alfa-eliche su piani opposti del foglietto beta
Elica di collegamento
barrels
Consider a sequence of eight - motifsIf the first strand hydrogen bonds to the last then the structure closes on itself forming a barrel-like structure
Enzima triosofosfato isomerasi
Struttura a ldquoTIM barrelrdquo
Enzima lattato deidrogenasi
Rossman Fold
In tutte le strutture a botte il sito attivo si trova in una tasca formata dalle regioni loop che collegano le estremitagrave carbossiliche dei filamenti beta con le adiacenti alfa eliche
Nei domini con struttura aperta ruotata il sito attivo si trova in una fessura localizzata esternamente allrsquoestremitagrave carbossilica del filamenti Questa fessura egrave formata da due regioni loop adiacenti che collegano i due filamenti con eliche presenti su facce opposte del foglietto
Adenilato chinasiflavodossina
Punti di inversione topologica (topological switch points)
Strutture alfabeta
I) TIM barrel
II) a)Struttura aperta e ruotata (di tipo parallelo o misto) - b) Rossmann fold
III) horseshoe (ferro di cavallo)
Alpha+Beta Topologies
bullRibonuclease-H
Structural Classification of Proteins (SCOP)Authors Alexey G Murzin Loredana Lo Conte Bartlett G Ailey Steven E Brenner Tim J P Hubbard and Cyrus Chothia Reference Murzin A G Brenner S E Hubbard T Chothia C (1995) SCOP a structural classification of proteins database for the investigation of sequences and structures J Mol Biol 247 536-540Classes
1All alpha proteins (151) 2All beta proteins (111) 3Alpha and beta proteins (ab) (117) Mainly parallel beta sheets (beta-alpha-beta units) 4Alpha and beta proteins (a+b) (212) Mainly antiparallel beta sheets (segregated alpha and beta regions) 5Multi-domain proteins (alpha and beta) (39) Folds consisting of two or more domains belonging to different classes 6Membrane and cell surface proteins and peptides (12) Does not include proteins in the immune system 7Small proteins (59) Usually dominated by metal ligand heme andor disulfide bridges 8Coiled coil proteins (5) Not a true class 9Low resolution protein structures (17) Not a true class 10Peptides (95) Peptides and fragments Not a true class 11Designed proteins (36) Experimental structures of proteins with essentially non-natural sequences Not a true class
Membrane protein topology
Paradosso di Levinthalbull Proteina di 100 residuibull Due gradi di libertarsquo torsionaliresiduo (phipsi)bull 3 conformazioni accessibili per ogni grado dilibertarsquo torsionalebull 1048774 32x100 possibili conformazionibull 1013 conformazioni esploratesecbull Tempo richiesto per esplorare tutte leconformazioni t = 20 x 109 anni bull Le proteine si devono ripiegare seguendo uncammino definito caratterizzato da conformazionivia via piursquo stabili (diminuizione di G)
barrels
Strutture alfabeta
topologies The most regular and common domain structures consist of repeating -- supersecondary units such that the outer layer of the structure is composed of helices packing against a central core of parallel -sheets These folds are called or wound Many enzymes including all those involved in glycolysis are structures Most proteins are cytosolicThe -- is always right-handed In structures there is a repetition of this arrangement giving a ---etc sequence The strands are parallel and hydrogen bonded to each other while the helices are all parallel to each other and are antiparallel to the strands Thus the helices form a layer packing against the sheetThe ---- subunit often present in nucleotide-binding proteins is named the Rossman Fold after Michael Rossman (Rao and Rossman1973)
Beta-alfa-beta destrorsa Beta-alfa-beta sinistrorsa
Alfa-eliche sul medesimo piano del foglietto beta
Alfa-eliche su piani opposti del foglietto beta
Elica di collegamento
barrels
Consider a sequence of eight - motifsIf the first strand hydrogen bonds to the last then the structure closes on itself forming a barrel-like structure
Enzima triosofosfato isomerasi
Struttura a ldquoTIM barrelrdquo
Enzima lattato deidrogenasi
Rossman Fold
In tutte le strutture a botte il sito attivo si trova in una tasca formata dalle regioni loop che collegano le estremitagrave carbossiliche dei filamenti beta con le adiacenti alfa eliche
Nei domini con struttura aperta ruotata il sito attivo si trova in una fessura localizzata esternamente allrsquoestremitagrave carbossilica del filamenti Questa fessura egrave formata da due regioni loop adiacenti che collegano i due filamenti con eliche presenti su facce opposte del foglietto
Adenilato chinasiflavodossina
Punti di inversione topologica (topological switch points)
Strutture alfabeta
I) TIM barrel
II) a)Struttura aperta e ruotata (di tipo parallelo o misto) - b) Rossmann fold
III) horseshoe (ferro di cavallo)
Alpha+Beta Topologies
bullRibonuclease-H
Structural Classification of Proteins (SCOP)Authors Alexey G Murzin Loredana Lo Conte Bartlett G Ailey Steven E Brenner Tim J P Hubbard and Cyrus Chothia Reference Murzin A G Brenner S E Hubbard T Chothia C (1995) SCOP a structural classification of proteins database for the investigation of sequences and structures J Mol Biol 247 536-540Classes
1All alpha proteins (151) 2All beta proteins (111) 3Alpha and beta proteins (ab) (117) Mainly parallel beta sheets (beta-alpha-beta units) 4Alpha and beta proteins (a+b) (212) Mainly antiparallel beta sheets (segregated alpha and beta regions) 5Multi-domain proteins (alpha and beta) (39) Folds consisting of two or more domains belonging to different classes 6Membrane and cell surface proteins and peptides (12) Does not include proteins in the immune system 7Small proteins (59) Usually dominated by metal ligand heme andor disulfide bridges 8Coiled coil proteins (5) Not a true class 9Low resolution protein structures (17) Not a true class 10Peptides (95) Peptides and fragments Not a true class 11Designed proteins (36) Experimental structures of proteins with essentially non-natural sequences Not a true class
Membrane protein topology
Paradosso di Levinthalbull Proteina di 100 residuibull Due gradi di libertarsquo torsionaliresiduo (phipsi)bull 3 conformazioni accessibili per ogni grado dilibertarsquo torsionalebull 1048774 32x100 possibili conformazionibull 1013 conformazioni esploratesecbull Tempo richiesto per esplorare tutte leconformazioni t = 20 x 109 anni bull Le proteine si devono ripiegare seguendo uncammino definito caratterizzato da conformazionivia via piursquo stabili (diminuizione di G)
Strutture alfabeta
topologies The most regular and common domain structures consist of repeating -- supersecondary units such that the outer layer of the structure is composed of helices packing against a central core of parallel -sheets These folds are called or wound Many enzymes including all those involved in glycolysis are structures Most proteins are cytosolicThe -- is always right-handed In structures there is a repetition of this arrangement giving a ---etc sequence The strands are parallel and hydrogen bonded to each other while the helices are all parallel to each other and are antiparallel to the strands Thus the helices form a layer packing against the sheetThe ---- subunit often present in nucleotide-binding proteins is named the Rossman Fold after Michael Rossman (Rao and Rossman1973)
Beta-alfa-beta destrorsa Beta-alfa-beta sinistrorsa
Alfa-eliche sul medesimo piano del foglietto beta
Alfa-eliche su piani opposti del foglietto beta
Elica di collegamento
barrels
Consider a sequence of eight - motifsIf the first strand hydrogen bonds to the last then the structure closes on itself forming a barrel-like structure
Enzima triosofosfato isomerasi
Struttura a ldquoTIM barrelrdquo
Enzima lattato deidrogenasi
Rossman Fold
In tutte le strutture a botte il sito attivo si trova in una tasca formata dalle regioni loop che collegano le estremitagrave carbossiliche dei filamenti beta con le adiacenti alfa eliche
Nei domini con struttura aperta ruotata il sito attivo si trova in una fessura localizzata esternamente allrsquoestremitagrave carbossilica del filamenti Questa fessura egrave formata da due regioni loop adiacenti che collegano i due filamenti con eliche presenti su facce opposte del foglietto
Adenilato chinasiflavodossina
Punti di inversione topologica (topological switch points)
Strutture alfabeta
I) TIM barrel
II) a)Struttura aperta e ruotata (di tipo parallelo o misto) - b) Rossmann fold
III) horseshoe (ferro di cavallo)
Alpha+Beta Topologies
bullRibonuclease-H
Structural Classification of Proteins (SCOP)Authors Alexey G Murzin Loredana Lo Conte Bartlett G Ailey Steven E Brenner Tim J P Hubbard and Cyrus Chothia Reference Murzin A G Brenner S E Hubbard T Chothia C (1995) SCOP a structural classification of proteins database for the investigation of sequences and structures J Mol Biol 247 536-540Classes
1All alpha proteins (151) 2All beta proteins (111) 3Alpha and beta proteins (ab) (117) Mainly parallel beta sheets (beta-alpha-beta units) 4Alpha and beta proteins (a+b) (212) Mainly antiparallel beta sheets (segregated alpha and beta regions) 5Multi-domain proteins (alpha and beta) (39) Folds consisting of two or more domains belonging to different classes 6Membrane and cell surface proteins and peptides (12) Does not include proteins in the immune system 7Small proteins (59) Usually dominated by metal ligand heme andor disulfide bridges 8Coiled coil proteins (5) Not a true class 9Low resolution protein structures (17) Not a true class 10Peptides (95) Peptides and fragments Not a true class 11Designed proteins (36) Experimental structures of proteins with essentially non-natural sequences Not a true class
Membrane protein topology
Paradosso di Levinthalbull Proteina di 100 residuibull Due gradi di libertarsquo torsionaliresiduo (phipsi)bull 3 conformazioni accessibili per ogni grado dilibertarsquo torsionalebull 1048774 32x100 possibili conformazionibull 1013 conformazioni esploratesecbull Tempo richiesto per esplorare tutte leconformazioni t = 20 x 109 anni bull Le proteine si devono ripiegare seguendo uncammino definito caratterizzato da conformazionivia via piursquo stabili (diminuizione di G)
topologies The most regular and common domain structures consist of repeating -- supersecondary units such that the outer layer of the structure is composed of helices packing against a central core of parallel -sheets These folds are called or wound Many enzymes including all those involved in glycolysis are structures Most proteins are cytosolicThe -- is always right-handed In structures there is a repetition of this arrangement giving a ---etc sequence The strands are parallel and hydrogen bonded to each other while the helices are all parallel to each other and are antiparallel to the strands Thus the helices form a layer packing against the sheetThe ---- subunit often present in nucleotide-binding proteins is named the Rossman Fold after Michael Rossman (Rao and Rossman1973)
Beta-alfa-beta destrorsa Beta-alfa-beta sinistrorsa
Alfa-eliche sul medesimo piano del foglietto beta
Alfa-eliche su piani opposti del foglietto beta
Elica di collegamento
barrels
Consider a sequence of eight - motifsIf the first strand hydrogen bonds to the last then the structure closes on itself forming a barrel-like structure
Enzima triosofosfato isomerasi
Struttura a ldquoTIM barrelrdquo
Enzima lattato deidrogenasi
Rossman Fold
In tutte le strutture a botte il sito attivo si trova in una tasca formata dalle regioni loop che collegano le estremitagrave carbossiliche dei filamenti beta con le adiacenti alfa eliche
Nei domini con struttura aperta ruotata il sito attivo si trova in una fessura localizzata esternamente allrsquoestremitagrave carbossilica del filamenti Questa fessura egrave formata da due regioni loop adiacenti che collegano i due filamenti con eliche presenti su facce opposte del foglietto
Adenilato chinasiflavodossina
Punti di inversione topologica (topological switch points)
Strutture alfabeta
I) TIM barrel
II) a)Struttura aperta e ruotata (di tipo parallelo o misto) - b) Rossmann fold
III) horseshoe (ferro di cavallo)
Alpha+Beta Topologies
bullRibonuclease-H
Structural Classification of Proteins (SCOP)Authors Alexey G Murzin Loredana Lo Conte Bartlett G Ailey Steven E Brenner Tim J P Hubbard and Cyrus Chothia Reference Murzin A G Brenner S E Hubbard T Chothia C (1995) SCOP a structural classification of proteins database for the investigation of sequences and structures J Mol Biol 247 536-540Classes
1All alpha proteins (151) 2All beta proteins (111) 3Alpha and beta proteins (ab) (117) Mainly parallel beta sheets (beta-alpha-beta units) 4Alpha and beta proteins (a+b) (212) Mainly antiparallel beta sheets (segregated alpha and beta regions) 5Multi-domain proteins (alpha and beta) (39) Folds consisting of two or more domains belonging to different classes 6Membrane and cell surface proteins and peptides (12) Does not include proteins in the immune system 7Small proteins (59) Usually dominated by metal ligand heme andor disulfide bridges 8Coiled coil proteins (5) Not a true class 9Low resolution protein structures (17) Not a true class 10Peptides (95) Peptides and fragments Not a true class 11Designed proteins (36) Experimental structures of proteins with essentially non-natural sequences Not a true class
Membrane protein topology
Paradosso di Levinthalbull Proteina di 100 residuibull Due gradi di libertarsquo torsionaliresiduo (phipsi)bull 3 conformazioni accessibili per ogni grado dilibertarsquo torsionalebull 1048774 32x100 possibili conformazionibull 1013 conformazioni esploratesecbull Tempo richiesto per esplorare tutte leconformazioni t = 20 x 109 anni bull Le proteine si devono ripiegare seguendo uncammino definito caratterizzato da conformazionivia via piursquo stabili (diminuizione di G)
Beta-alfa-beta destrorsa Beta-alfa-beta sinistrorsa
Alfa-eliche sul medesimo piano del foglietto beta
Alfa-eliche su piani opposti del foglietto beta
Elica di collegamento
barrels
Consider a sequence of eight - motifsIf the first strand hydrogen bonds to the last then the structure closes on itself forming a barrel-like structure
Enzima triosofosfato isomerasi
Struttura a ldquoTIM barrelrdquo
Enzima lattato deidrogenasi
Rossman Fold
In tutte le strutture a botte il sito attivo si trova in una tasca formata dalle regioni loop che collegano le estremitagrave carbossiliche dei filamenti beta con le adiacenti alfa eliche
Nei domini con struttura aperta ruotata il sito attivo si trova in una fessura localizzata esternamente allrsquoestremitagrave carbossilica del filamenti Questa fessura egrave formata da due regioni loop adiacenti che collegano i due filamenti con eliche presenti su facce opposte del foglietto
Adenilato chinasiflavodossina
Punti di inversione topologica (topological switch points)
Strutture alfabeta
I) TIM barrel
II) a)Struttura aperta e ruotata (di tipo parallelo o misto) - b) Rossmann fold
III) horseshoe (ferro di cavallo)
Alpha+Beta Topologies
bullRibonuclease-H
Structural Classification of Proteins (SCOP)Authors Alexey G Murzin Loredana Lo Conte Bartlett G Ailey Steven E Brenner Tim J P Hubbard and Cyrus Chothia Reference Murzin A G Brenner S E Hubbard T Chothia C (1995) SCOP a structural classification of proteins database for the investigation of sequences and structures J Mol Biol 247 536-540Classes
1All alpha proteins (151) 2All beta proteins (111) 3Alpha and beta proteins (ab) (117) Mainly parallel beta sheets (beta-alpha-beta units) 4Alpha and beta proteins (a+b) (212) Mainly antiparallel beta sheets (segregated alpha and beta regions) 5Multi-domain proteins (alpha and beta) (39) Folds consisting of two or more domains belonging to different classes 6Membrane and cell surface proteins and peptides (12) Does not include proteins in the immune system 7Small proteins (59) Usually dominated by metal ligand heme andor disulfide bridges 8Coiled coil proteins (5) Not a true class 9Low resolution protein structures (17) Not a true class 10Peptides (95) Peptides and fragments Not a true class 11Designed proteins (36) Experimental structures of proteins with essentially non-natural sequences Not a true class
Membrane protein topology
Paradosso di Levinthalbull Proteina di 100 residuibull Due gradi di libertarsquo torsionaliresiduo (phipsi)bull 3 conformazioni accessibili per ogni grado dilibertarsquo torsionalebull 1048774 32x100 possibili conformazionibull 1013 conformazioni esploratesecbull Tempo richiesto per esplorare tutte leconformazioni t = 20 x 109 anni bull Le proteine si devono ripiegare seguendo uncammino definito caratterizzato da conformazionivia via piursquo stabili (diminuizione di G)
Alfa-eliche sul medesimo piano del foglietto beta
Alfa-eliche su piani opposti del foglietto beta
Elica di collegamento
barrels
Consider a sequence of eight - motifsIf the first strand hydrogen bonds to the last then the structure closes on itself forming a barrel-like structure
Enzima triosofosfato isomerasi
Struttura a ldquoTIM barrelrdquo
Enzima lattato deidrogenasi
Rossman Fold
In tutte le strutture a botte il sito attivo si trova in una tasca formata dalle regioni loop che collegano le estremitagrave carbossiliche dei filamenti beta con le adiacenti alfa eliche
Nei domini con struttura aperta ruotata il sito attivo si trova in una fessura localizzata esternamente allrsquoestremitagrave carbossilica del filamenti Questa fessura egrave formata da due regioni loop adiacenti che collegano i due filamenti con eliche presenti su facce opposte del foglietto
Adenilato chinasiflavodossina
Punti di inversione topologica (topological switch points)
Strutture alfabeta
I) TIM barrel
II) a)Struttura aperta e ruotata (di tipo parallelo o misto) - b) Rossmann fold
III) horseshoe (ferro di cavallo)
Alpha+Beta Topologies
bullRibonuclease-H
Structural Classification of Proteins (SCOP)Authors Alexey G Murzin Loredana Lo Conte Bartlett G Ailey Steven E Brenner Tim J P Hubbard and Cyrus Chothia Reference Murzin A G Brenner S E Hubbard T Chothia C (1995) SCOP a structural classification of proteins database for the investigation of sequences and structures J Mol Biol 247 536-540Classes
1All alpha proteins (151) 2All beta proteins (111) 3Alpha and beta proteins (ab) (117) Mainly parallel beta sheets (beta-alpha-beta units) 4Alpha and beta proteins (a+b) (212) Mainly antiparallel beta sheets (segregated alpha and beta regions) 5Multi-domain proteins (alpha and beta) (39) Folds consisting of two or more domains belonging to different classes 6Membrane and cell surface proteins and peptides (12) Does not include proteins in the immune system 7Small proteins (59) Usually dominated by metal ligand heme andor disulfide bridges 8Coiled coil proteins (5) Not a true class 9Low resolution protein structures (17) Not a true class 10Peptides (95) Peptides and fragments Not a true class 11Designed proteins (36) Experimental structures of proteins with essentially non-natural sequences Not a true class
Membrane protein topology
Paradosso di Levinthalbull Proteina di 100 residuibull Due gradi di libertarsquo torsionaliresiduo (phipsi)bull 3 conformazioni accessibili per ogni grado dilibertarsquo torsionalebull 1048774 32x100 possibili conformazionibull 1013 conformazioni esploratesecbull Tempo richiesto per esplorare tutte leconformazioni t = 20 x 109 anni bull Le proteine si devono ripiegare seguendo uncammino definito caratterizzato da conformazionivia via piursquo stabili (diminuizione di G)
barrels
Consider a sequence of eight - motifsIf the first strand hydrogen bonds to the last then the structure closes on itself forming a barrel-like structure
Enzima triosofosfato isomerasi
Struttura a ldquoTIM barrelrdquo
Enzima lattato deidrogenasi
Rossman Fold
In tutte le strutture a botte il sito attivo si trova in una tasca formata dalle regioni loop che collegano le estremitagrave carbossiliche dei filamenti beta con le adiacenti alfa eliche
Nei domini con struttura aperta ruotata il sito attivo si trova in una fessura localizzata esternamente allrsquoestremitagrave carbossilica del filamenti Questa fessura egrave formata da due regioni loop adiacenti che collegano i due filamenti con eliche presenti su facce opposte del foglietto
Adenilato chinasiflavodossina
Punti di inversione topologica (topological switch points)
Strutture alfabeta
I) TIM barrel
II) a)Struttura aperta e ruotata (di tipo parallelo o misto) - b) Rossmann fold
III) horseshoe (ferro di cavallo)
Alpha+Beta Topologies
bullRibonuclease-H
Structural Classification of Proteins (SCOP)Authors Alexey G Murzin Loredana Lo Conte Bartlett G Ailey Steven E Brenner Tim J P Hubbard and Cyrus Chothia Reference Murzin A G Brenner S E Hubbard T Chothia C (1995) SCOP a structural classification of proteins database for the investigation of sequences and structures J Mol Biol 247 536-540Classes
1All alpha proteins (151) 2All beta proteins (111) 3Alpha and beta proteins (ab) (117) Mainly parallel beta sheets (beta-alpha-beta units) 4Alpha and beta proteins (a+b) (212) Mainly antiparallel beta sheets (segregated alpha and beta regions) 5Multi-domain proteins (alpha and beta) (39) Folds consisting of two or more domains belonging to different classes 6Membrane and cell surface proteins and peptides (12) Does not include proteins in the immune system 7Small proteins (59) Usually dominated by metal ligand heme andor disulfide bridges 8Coiled coil proteins (5) Not a true class 9Low resolution protein structures (17) Not a true class 10Peptides (95) Peptides and fragments Not a true class 11Designed proteins (36) Experimental structures of proteins with essentially non-natural sequences Not a true class
Membrane protein topology
Paradosso di Levinthalbull Proteina di 100 residuibull Due gradi di libertarsquo torsionaliresiduo (phipsi)bull 3 conformazioni accessibili per ogni grado dilibertarsquo torsionalebull 1048774 32x100 possibili conformazionibull 1013 conformazioni esploratesecbull Tempo richiesto per esplorare tutte leconformazioni t = 20 x 109 anni bull Le proteine si devono ripiegare seguendo uncammino definito caratterizzato da conformazionivia via piursquo stabili (diminuizione di G)
Enzima triosofosfato isomerasi
Struttura a ldquoTIM barrelrdquo
Enzima lattato deidrogenasi
Rossman Fold
In tutte le strutture a botte il sito attivo si trova in una tasca formata dalle regioni loop che collegano le estremitagrave carbossiliche dei filamenti beta con le adiacenti alfa eliche
Nei domini con struttura aperta ruotata il sito attivo si trova in una fessura localizzata esternamente allrsquoestremitagrave carbossilica del filamenti Questa fessura egrave formata da due regioni loop adiacenti che collegano i due filamenti con eliche presenti su facce opposte del foglietto
Adenilato chinasiflavodossina
Punti di inversione topologica (topological switch points)
Strutture alfabeta
I) TIM barrel
II) a)Struttura aperta e ruotata (di tipo parallelo o misto) - b) Rossmann fold
III) horseshoe (ferro di cavallo)
Alpha+Beta Topologies
bullRibonuclease-H
Structural Classification of Proteins (SCOP)Authors Alexey G Murzin Loredana Lo Conte Bartlett G Ailey Steven E Brenner Tim J P Hubbard and Cyrus Chothia Reference Murzin A G Brenner S E Hubbard T Chothia C (1995) SCOP a structural classification of proteins database for the investigation of sequences and structures J Mol Biol 247 536-540Classes
1All alpha proteins (151) 2All beta proteins (111) 3Alpha and beta proteins (ab) (117) Mainly parallel beta sheets (beta-alpha-beta units) 4Alpha and beta proteins (a+b) (212) Mainly antiparallel beta sheets (segregated alpha and beta regions) 5Multi-domain proteins (alpha and beta) (39) Folds consisting of two or more domains belonging to different classes 6Membrane and cell surface proteins and peptides (12) Does not include proteins in the immune system 7Small proteins (59) Usually dominated by metal ligand heme andor disulfide bridges 8Coiled coil proteins (5) Not a true class 9Low resolution protein structures (17) Not a true class 10Peptides (95) Peptides and fragments Not a true class 11Designed proteins (36) Experimental structures of proteins with essentially non-natural sequences Not a true class
Membrane protein topology
Paradosso di Levinthalbull Proteina di 100 residuibull Due gradi di libertarsquo torsionaliresiduo (phipsi)bull 3 conformazioni accessibili per ogni grado dilibertarsquo torsionalebull 1048774 32x100 possibili conformazionibull 1013 conformazioni esploratesecbull Tempo richiesto per esplorare tutte leconformazioni t = 20 x 109 anni bull Le proteine si devono ripiegare seguendo uncammino definito caratterizzato da conformazionivia via piursquo stabili (diminuizione di G)
In tutte le strutture a botte il sito attivo si trova in una tasca formata dalle regioni loop che collegano le estremitagrave carbossiliche dei filamenti beta con le adiacenti alfa eliche
Nei domini con struttura aperta ruotata il sito attivo si trova in una fessura localizzata esternamente allrsquoestremitagrave carbossilica del filamenti Questa fessura egrave formata da due regioni loop adiacenti che collegano i due filamenti con eliche presenti su facce opposte del foglietto
Adenilato chinasiflavodossina
Punti di inversione topologica (topological switch points)
Strutture alfabeta
I) TIM barrel
II) a)Struttura aperta e ruotata (di tipo parallelo o misto) - b) Rossmann fold
III) horseshoe (ferro di cavallo)
Alpha+Beta Topologies
bullRibonuclease-H
Structural Classification of Proteins (SCOP)Authors Alexey G Murzin Loredana Lo Conte Bartlett G Ailey Steven E Brenner Tim J P Hubbard and Cyrus Chothia Reference Murzin A G Brenner S E Hubbard T Chothia C (1995) SCOP a structural classification of proteins database for the investigation of sequences and structures J Mol Biol 247 536-540Classes
1All alpha proteins (151) 2All beta proteins (111) 3Alpha and beta proteins (ab) (117) Mainly parallel beta sheets (beta-alpha-beta units) 4Alpha and beta proteins (a+b) (212) Mainly antiparallel beta sheets (segregated alpha and beta regions) 5Multi-domain proteins (alpha and beta) (39) Folds consisting of two or more domains belonging to different classes 6Membrane and cell surface proteins and peptides (12) Does not include proteins in the immune system 7Small proteins (59) Usually dominated by metal ligand heme andor disulfide bridges 8Coiled coil proteins (5) Not a true class 9Low resolution protein structures (17) Not a true class 10Peptides (95) Peptides and fragments Not a true class 11Designed proteins (36) Experimental structures of proteins with essentially non-natural sequences Not a true class
Membrane protein topology
Paradosso di Levinthalbull Proteina di 100 residuibull Due gradi di libertarsquo torsionaliresiduo (phipsi)bull 3 conformazioni accessibili per ogni grado dilibertarsquo torsionalebull 1048774 32x100 possibili conformazionibull 1013 conformazioni esploratesecbull Tempo richiesto per esplorare tutte leconformazioni t = 20 x 109 anni bull Le proteine si devono ripiegare seguendo uncammino definito caratterizzato da conformazionivia via piursquo stabili (diminuizione di G)
Nei domini con struttura aperta ruotata il sito attivo si trova in una fessura localizzata esternamente allrsquoestremitagrave carbossilica del filamenti Questa fessura egrave formata da due regioni loop adiacenti che collegano i due filamenti con eliche presenti su facce opposte del foglietto
Adenilato chinasiflavodossina
Punti di inversione topologica (topological switch points)
Strutture alfabeta
I) TIM barrel
II) a)Struttura aperta e ruotata (di tipo parallelo o misto) - b) Rossmann fold
III) horseshoe (ferro di cavallo)
Alpha+Beta Topologies
bullRibonuclease-H
Structural Classification of Proteins (SCOP)Authors Alexey G Murzin Loredana Lo Conte Bartlett G Ailey Steven E Brenner Tim J P Hubbard and Cyrus Chothia Reference Murzin A G Brenner S E Hubbard T Chothia C (1995) SCOP a structural classification of proteins database for the investigation of sequences and structures J Mol Biol 247 536-540Classes
1All alpha proteins (151) 2All beta proteins (111) 3Alpha and beta proteins (ab) (117) Mainly parallel beta sheets (beta-alpha-beta units) 4Alpha and beta proteins (a+b) (212) Mainly antiparallel beta sheets (segregated alpha and beta regions) 5Multi-domain proteins (alpha and beta) (39) Folds consisting of two or more domains belonging to different classes 6Membrane and cell surface proteins and peptides (12) Does not include proteins in the immune system 7Small proteins (59) Usually dominated by metal ligand heme andor disulfide bridges 8Coiled coil proteins (5) Not a true class 9Low resolution protein structures (17) Not a true class 10Peptides (95) Peptides and fragments Not a true class 11Designed proteins (36) Experimental structures of proteins with essentially non-natural sequences Not a true class
Membrane protein topology
Paradosso di Levinthalbull Proteina di 100 residuibull Due gradi di libertarsquo torsionaliresiduo (phipsi)bull 3 conformazioni accessibili per ogni grado dilibertarsquo torsionalebull 1048774 32x100 possibili conformazionibull 1013 conformazioni esploratesecbull Tempo richiesto per esplorare tutte leconformazioni t = 20 x 109 anni bull Le proteine si devono ripiegare seguendo uncammino definito caratterizzato da conformazionivia via piursquo stabili (diminuizione di G)
Adenilato chinasiflavodossina
Punti di inversione topologica (topological switch points)
Strutture alfabeta
I) TIM barrel
II) a)Struttura aperta e ruotata (di tipo parallelo o misto) - b) Rossmann fold
III) horseshoe (ferro di cavallo)
Alpha+Beta Topologies
bullRibonuclease-H
Structural Classification of Proteins (SCOP)Authors Alexey G Murzin Loredana Lo Conte Bartlett G Ailey Steven E Brenner Tim J P Hubbard and Cyrus Chothia Reference Murzin A G Brenner S E Hubbard T Chothia C (1995) SCOP a structural classification of proteins database for the investigation of sequences and structures J Mol Biol 247 536-540Classes
1All alpha proteins (151) 2All beta proteins (111) 3Alpha and beta proteins (ab) (117) Mainly parallel beta sheets (beta-alpha-beta units) 4Alpha and beta proteins (a+b) (212) Mainly antiparallel beta sheets (segregated alpha and beta regions) 5Multi-domain proteins (alpha and beta) (39) Folds consisting of two or more domains belonging to different classes 6Membrane and cell surface proteins and peptides (12) Does not include proteins in the immune system 7Small proteins (59) Usually dominated by metal ligand heme andor disulfide bridges 8Coiled coil proteins (5) Not a true class 9Low resolution protein structures (17) Not a true class 10Peptides (95) Peptides and fragments Not a true class 11Designed proteins (36) Experimental structures of proteins with essentially non-natural sequences Not a true class
Membrane protein topology
Paradosso di Levinthalbull Proteina di 100 residuibull Due gradi di libertarsquo torsionaliresiduo (phipsi)bull 3 conformazioni accessibili per ogni grado dilibertarsquo torsionalebull 1048774 32x100 possibili conformazionibull 1013 conformazioni esploratesecbull Tempo richiesto per esplorare tutte leconformazioni t = 20 x 109 anni bull Le proteine si devono ripiegare seguendo uncammino definito caratterizzato da conformazionivia via piursquo stabili (diminuizione di G)
Strutture alfabeta
I) TIM barrel
II) a)Struttura aperta e ruotata (di tipo parallelo o misto) - b) Rossmann fold
III) horseshoe (ferro di cavallo)
Alpha+Beta Topologies
bullRibonuclease-H
Structural Classification of Proteins (SCOP)Authors Alexey G Murzin Loredana Lo Conte Bartlett G Ailey Steven E Brenner Tim J P Hubbard and Cyrus Chothia Reference Murzin A G Brenner S E Hubbard T Chothia C (1995) SCOP a structural classification of proteins database for the investigation of sequences and structures J Mol Biol 247 536-540Classes
1All alpha proteins (151) 2All beta proteins (111) 3Alpha and beta proteins (ab) (117) Mainly parallel beta sheets (beta-alpha-beta units) 4Alpha and beta proteins (a+b) (212) Mainly antiparallel beta sheets (segregated alpha and beta regions) 5Multi-domain proteins (alpha and beta) (39) Folds consisting of two or more domains belonging to different classes 6Membrane and cell surface proteins and peptides (12) Does not include proteins in the immune system 7Small proteins (59) Usually dominated by metal ligand heme andor disulfide bridges 8Coiled coil proteins (5) Not a true class 9Low resolution protein structures (17) Not a true class 10Peptides (95) Peptides and fragments Not a true class 11Designed proteins (36) Experimental structures of proteins with essentially non-natural sequences Not a true class
Membrane protein topology
Paradosso di Levinthalbull Proteina di 100 residuibull Due gradi di libertarsquo torsionaliresiduo (phipsi)bull 3 conformazioni accessibili per ogni grado dilibertarsquo torsionalebull 1048774 32x100 possibili conformazionibull 1013 conformazioni esploratesecbull Tempo richiesto per esplorare tutte leconformazioni t = 20 x 109 anni bull Le proteine si devono ripiegare seguendo uncammino definito caratterizzato da conformazionivia via piursquo stabili (diminuizione di G)
Alpha+Beta Topologies
bullRibonuclease-H
Structural Classification of Proteins (SCOP)Authors Alexey G Murzin Loredana Lo Conte Bartlett G Ailey Steven E Brenner Tim J P Hubbard and Cyrus Chothia Reference Murzin A G Brenner S E Hubbard T Chothia C (1995) SCOP a structural classification of proteins database for the investigation of sequences and structures J Mol Biol 247 536-540Classes
1All alpha proteins (151) 2All beta proteins (111) 3Alpha and beta proteins (ab) (117) Mainly parallel beta sheets (beta-alpha-beta units) 4Alpha and beta proteins (a+b) (212) Mainly antiparallel beta sheets (segregated alpha and beta regions) 5Multi-domain proteins (alpha and beta) (39) Folds consisting of two or more domains belonging to different classes 6Membrane and cell surface proteins and peptides (12) Does not include proteins in the immune system 7Small proteins (59) Usually dominated by metal ligand heme andor disulfide bridges 8Coiled coil proteins (5) Not a true class 9Low resolution protein structures (17) Not a true class 10Peptides (95) Peptides and fragments Not a true class 11Designed proteins (36) Experimental structures of proteins with essentially non-natural sequences Not a true class
Membrane protein topology
Paradosso di Levinthalbull Proteina di 100 residuibull Due gradi di libertarsquo torsionaliresiduo (phipsi)bull 3 conformazioni accessibili per ogni grado dilibertarsquo torsionalebull 1048774 32x100 possibili conformazionibull 1013 conformazioni esploratesecbull Tempo richiesto per esplorare tutte leconformazioni t = 20 x 109 anni bull Le proteine si devono ripiegare seguendo uncammino definito caratterizzato da conformazionivia via piursquo stabili (diminuizione di G)
Structural Classification of Proteins (SCOP)Authors Alexey G Murzin Loredana Lo Conte Bartlett G Ailey Steven E Brenner Tim J P Hubbard and Cyrus Chothia Reference Murzin A G Brenner S E Hubbard T Chothia C (1995) SCOP a structural classification of proteins database for the investigation of sequences and structures J Mol Biol 247 536-540Classes
1All alpha proteins (151) 2All beta proteins (111) 3Alpha and beta proteins (ab) (117) Mainly parallel beta sheets (beta-alpha-beta units) 4Alpha and beta proteins (a+b) (212) Mainly antiparallel beta sheets (segregated alpha and beta regions) 5Multi-domain proteins (alpha and beta) (39) Folds consisting of two or more domains belonging to different classes 6Membrane and cell surface proteins and peptides (12) Does not include proteins in the immune system 7Small proteins (59) Usually dominated by metal ligand heme andor disulfide bridges 8Coiled coil proteins (5) Not a true class 9Low resolution protein structures (17) Not a true class 10Peptides (95) Peptides and fragments Not a true class 11Designed proteins (36) Experimental structures of proteins with essentially non-natural sequences Not a true class
Membrane protein topology
Paradosso di Levinthalbull Proteina di 100 residuibull Due gradi di libertarsquo torsionaliresiduo (phipsi)bull 3 conformazioni accessibili per ogni grado dilibertarsquo torsionalebull 1048774 32x100 possibili conformazionibull 1013 conformazioni esploratesecbull Tempo richiesto per esplorare tutte leconformazioni t = 20 x 109 anni bull Le proteine si devono ripiegare seguendo uncammino definito caratterizzato da conformazionivia via piursquo stabili (diminuizione di G)
Membrane protein topology
Paradosso di Levinthalbull Proteina di 100 residuibull Due gradi di libertarsquo torsionaliresiduo (phipsi)bull 3 conformazioni accessibili per ogni grado dilibertarsquo torsionalebull 1048774 32x100 possibili conformazionibull 1013 conformazioni esploratesecbull Tempo richiesto per esplorare tutte leconformazioni t = 20 x 109 anni bull Le proteine si devono ripiegare seguendo uncammino definito caratterizzato da conformazionivia via piursquo stabili (diminuizione di G)
Paradosso di Levinthalbull Proteina di 100 residuibull Due gradi di libertarsquo torsionaliresiduo (phipsi)bull 3 conformazioni accessibili per ogni grado dilibertarsquo torsionalebull 1048774 32x100 possibili conformazionibull 1013 conformazioni esploratesecbull Tempo richiesto per esplorare tutte leconformazioni t = 20 x 109 anni bull Le proteine si devono ripiegare seguendo uncammino definito caratterizzato da conformazionivia via piursquo stabili (diminuizione di G)