Protein Physics Protein Physics Protein Physics Protein Physics A. V. Finkelstein & O. B. Ptitsyn LECTURE 13 LECTURE 13 porin
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Transcript
Protein PhysicsProtein PhysicsProtein PhysicsProtein PhysicsA V Finkelstein amp
O B PtitsynLECTURE 13LECTURE 13
porin
One Classification of Proteins1Fibrous Proteins - mostly structural proteins
- an elongated unidimensional structure
2Membrane Proteins
g
- reside within the cellular amp intracellular membrane- transport molecules in and out of the cell
3Globular Proteins - short chains packed into a compact 25-40Aring globule- closely folded structurey- water soluble proteins- Ex egg albumin hemoglobin many enzymes
Globular Proteins amp Domainsbull Short chains packed into a globule
as tightly as organic molecules in a crystalin a crystal
Primary structurey
Secondary structures bullDomain sizes 20 -692 average ~ 100 residuesbullE h f th f ld i di id lly
Super-secondary structures (motifs)
bullEach of them folds individuallybullContain a hydrophobic core built from sheets and helices connected by loop regions
structures (motifs)
DomainsDomains
Multi-domain proteins(Tertiary structure)
γ-crystallin
XX--RAYRAY One protein various One protein various
NMRNMRStructures compatible Structures compatible p p
crystallizationcrystallization p p
with one NMR experimentwith one NMR experiment
Secondary structures (Secondary structures (αα--heliceshelices ββ--strandsstrands) are) areSecondary structures (Secondary structures (αα--heliceshelices ββ--strandsstrands) are ) are the most rigid details of proteins the most rigid details of proteins
they are determined with the smallest errorsthey are determined with the smallest errors
One protein various One protein various crystallizationcrystallization
Homologous (closely Homologous (closely related) proteinsrelated) proteins
Secondary structures (Secondary structures (αα--heliceshelices ββ--strandsstrands))Secondary structures (Secondary structures (αα heliceshelices ββ strandsstrands) ) are most conserved structural elements are most conserved structural elements They form a basis of protein classificationThey form a basis of protein classification
HH HHHemoHemo--globinglobin
HemoHemo--globinglobin
H l i h i il f ldH l i h i il f ldHomologous proteins have similar foldsHomologous proteins have similar foldsTrue but trivial True but trivial NONNON t i i lt i i lNONNON--trivialtrivialMany NONMany NON--homologous proteins have similar foldshomologous proteins have similar folds
Structural Classes of Globular ProteinsDomains1 ldquopurerdquo-α - a core built exclusively from alpha-helices2 ldquopurerdquo-β - a core built exclusively from (mostly antiparallel) beta-sheets3 ldquomixedrdquo αβ mixture of ldquopurerdquo α and ldquopurerdquo β3 mixed -αβ - mixture of pure -α and pure -β4 α+β - built from combinations of β-α-β motifs
Further Simplified Models of Protein Structures
Architecture of protein
Topology of
Fold Folding Pattern Packing
Topology of protein
Level of Simplification
Usefulness classification and outlining their typical features
β-proteinsbull Mostly antiparallel arrangement bull Two sheets packed against each other
bull Basic packing types Top views
Orthogonal Packing Aligned PackingBottom views
β-barrelcylinderβ y
Retinol-binding protein
PorinPorinβ-hairpin
Meander (up amp down) motifβ-hairpin
55 55Acid protease
11
445rsquo5rsquo66332rsquo2rsquo11
44662rsquo2rsquo 33 5rsquo5rsquo
22
1122
11
Serine proteaseSerine protease
Topology Diagramsp gy g
Greek keymotif
O l i l
Greek keyOverlapping loop
uncommon
β-proteinsβ pSo far hellip
bull Packing types orthogonal amp alignedbull Structural architecturesβ-barrel
bull Motifs present in structural architecturesbull Motifs present in structural architectures(super-secondary structures) β-hairpin meander greek kemeander greek key
β-sandwichβ sandwich
2255 22
44
55
66 773344 66 77Greek key 2 - 5
Greek key 3 - 6Bottom view
+ N-end11
y C-endldquocomplete Greek keyrdquo
Immunoglobulin κ
2211 2266 55 88 33
221166 33 88 11
2266
3388
1188
γ-crystallin β catabolite activating
protein virus coat proteinprotein
Greek key amp Jelly roll
Greek key
Jelly roll
β-proteinsβ pSo far hellip
bull Packing types orthogonal amp alignedbull Structural architecturesβ-barrel β-sandwich
bull Motifs present in structural architecturesbull Motifs present in structural architectures(super-secondary structures) β-hairpin meander greek ke jell rollmeander greek key jelly roll
β-propeller β p p
multi-blade (45678) propeller =
three β-sandwiches
Neuraminidase
β-prism(helix)β p ( )bull Formed by three parallel (unusual) beta-sheets
Acyl-transferase(left-handed helix)
Pectate lyase(right-handed helix)
uncommoncommon
Possible topologies composed of four β-strands
Meander G k kMeander Greek keysEfimovrsquos ldquoabcd ldquo structures
Spatial structures with the same Greek key topology
β-proteinsβ proteins
bull Built up from mostly antiparallel β-strands (based on β-hairpins)
bull Packing types orthogonal amp alignedbull Structural architecturesSt uctu a a c tectu esβ-barrel β-sandwich β-propeller β-prism
bull Motifs present in structural architecturesbull Motifs present in structural architectures(super-secondary structures)β-hairpin meander greek key jelly rollhellip
One Classification of Proteins1Fibrous Proteins - mostly structural proteins
- an elongated unidimensional structure
2Membrane Proteins
g
- reside within the cellular amp intracellular membrane- transport molecules in and out of the cell
3Globular Proteins - short chains packed into a compact 25-40Aring globule- closely folded structurey- water soluble proteins- Ex egg albumin hemoglobin many enzymes
Globular Proteins amp Domainsbull Short chains packed into a globule
as tightly as organic molecules in a crystalin a crystal
Primary structurey
Secondary structures bullDomain sizes 20 -692 average ~ 100 residuesbullE h f th f ld i di id lly
Super-secondary structures (motifs)
bullEach of them folds individuallybullContain a hydrophobic core built from sheets and helices connected by loop regions
structures (motifs)
DomainsDomains
Multi-domain proteins(Tertiary structure)
γ-crystallin
XX--RAYRAY One protein various One protein various
NMRNMRStructures compatible Structures compatible p p
crystallizationcrystallization p p
with one NMR experimentwith one NMR experiment
Secondary structures (Secondary structures (αα--heliceshelices ββ--strandsstrands) are) areSecondary structures (Secondary structures (αα--heliceshelices ββ--strandsstrands) are ) are the most rigid details of proteins the most rigid details of proteins
they are determined with the smallest errorsthey are determined with the smallest errors
One protein various One protein various crystallizationcrystallization
Homologous (closely Homologous (closely related) proteinsrelated) proteins
Secondary structures (Secondary structures (αα--heliceshelices ββ--strandsstrands))Secondary structures (Secondary structures (αα heliceshelices ββ strandsstrands) ) are most conserved structural elements are most conserved structural elements They form a basis of protein classificationThey form a basis of protein classification
HH HHHemoHemo--globinglobin
HemoHemo--globinglobin
H l i h i il f ldH l i h i il f ldHomologous proteins have similar foldsHomologous proteins have similar foldsTrue but trivial True but trivial NONNON t i i lt i i lNONNON--trivialtrivialMany NONMany NON--homologous proteins have similar foldshomologous proteins have similar folds
Structural Classes of Globular ProteinsDomains1 ldquopurerdquo-α - a core built exclusively from alpha-helices2 ldquopurerdquo-β - a core built exclusively from (mostly antiparallel) beta-sheets3 ldquomixedrdquo αβ mixture of ldquopurerdquo α and ldquopurerdquo β3 mixed -αβ - mixture of pure -α and pure -β4 α+β - built from combinations of β-α-β motifs
Further Simplified Models of Protein Structures
Architecture of protein
Topology of
Fold Folding Pattern Packing
Topology of protein
Level of Simplification
Usefulness classification and outlining their typical features
β-proteinsbull Mostly antiparallel arrangement bull Two sheets packed against each other
bull Basic packing types Top views
Orthogonal Packing Aligned PackingBottom views
β-barrelcylinderβ y
Retinol-binding protein
PorinPorinβ-hairpin
Meander (up amp down) motifβ-hairpin
55 55Acid protease
11
445rsquo5rsquo66332rsquo2rsquo11
44662rsquo2rsquo 33 5rsquo5rsquo
22
1122
11
Serine proteaseSerine protease
Topology Diagramsp gy g
Greek keymotif
O l i l
Greek keyOverlapping loop
uncommon
β-proteinsβ pSo far hellip
bull Packing types orthogonal amp alignedbull Structural architecturesβ-barrel
bull Motifs present in structural architecturesbull Motifs present in structural architectures(super-secondary structures) β-hairpin meander greek kemeander greek key
β-sandwichβ sandwich
2255 22
44
55
66 773344 66 77Greek key 2 - 5
Greek key 3 - 6Bottom view
+ N-end11
y C-endldquocomplete Greek keyrdquo
Immunoglobulin κ
2211 2266 55 88 33
221166 33 88 11
2266
3388
1188
γ-crystallin β catabolite activating
protein virus coat proteinprotein
Greek key amp Jelly roll
Greek key
Jelly roll
β-proteinsβ pSo far hellip
bull Packing types orthogonal amp alignedbull Structural architecturesβ-barrel β-sandwich
bull Motifs present in structural architecturesbull Motifs present in structural architectures(super-secondary structures) β-hairpin meander greek ke jell rollmeander greek key jelly roll
β-propeller β p p
multi-blade (45678) propeller =
three β-sandwiches
Neuraminidase
β-prism(helix)β p ( )bull Formed by three parallel (unusual) beta-sheets
Acyl-transferase(left-handed helix)
Pectate lyase(right-handed helix)
uncommoncommon
Possible topologies composed of four β-strands
Meander G k kMeander Greek keysEfimovrsquos ldquoabcd ldquo structures
Spatial structures with the same Greek key topology
β-proteinsβ proteins
bull Built up from mostly antiparallel β-strands (based on β-hairpins)
bull Packing types orthogonal amp alignedbull Structural architecturesSt uctu a a c tectu esβ-barrel β-sandwich β-propeller β-prism
bull Motifs present in structural architecturesbull Motifs present in structural architectures(super-secondary structures)β-hairpin meander greek key jelly rollhellip
Globular Proteins amp Domainsbull Short chains packed into a globule
as tightly as organic molecules in a crystalin a crystal
Primary structurey
Secondary structures bullDomain sizes 20 -692 average ~ 100 residuesbullE h f th f ld i di id lly
Super-secondary structures (motifs)
bullEach of them folds individuallybullContain a hydrophobic core built from sheets and helices connected by loop regions
structures (motifs)
DomainsDomains
Multi-domain proteins(Tertiary structure)
γ-crystallin
XX--RAYRAY One protein various One protein various
NMRNMRStructures compatible Structures compatible p p
crystallizationcrystallization p p
with one NMR experimentwith one NMR experiment
Secondary structures (Secondary structures (αα--heliceshelices ββ--strandsstrands) are) areSecondary structures (Secondary structures (αα--heliceshelices ββ--strandsstrands) are ) are the most rigid details of proteins the most rigid details of proteins
they are determined with the smallest errorsthey are determined with the smallest errors
One protein various One protein various crystallizationcrystallization
Homologous (closely Homologous (closely related) proteinsrelated) proteins
Secondary structures (Secondary structures (αα--heliceshelices ββ--strandsstrands))Secondary structures (Secondary structures (αα heliceshelices ββ strandsstrands) ) are most conserved structural elements are most conserved structural elements They form a basis of protein classificationThey form a basis of protein classification
HH HHHemoHemo--globinglobin
HemoHemo--globinglobin
H l i h i il f ldH l i h i il f ldHomologous proteins have similar foldsHomologous proteins have similar foldsTrue but trivial True but trivial NONNON t i i lt i i lNONNON--trivialtrivialMany NONMany NON--homologous proteins have similar foldshomologous proteins have similar folds
Structural Classes of Globular ProteinsDomains1 ldquopurerdquo-α - a core built exclusively from alpha-helices2 ldquopurerdquo-β - a core built exclusively from (mostly antiparallel) beta-sheets3 ldquomixedrdquo αβ mixture of ldquopurerdquo α and ldquopurerdquo β3 mixed -αβ - mixture of pure -α and pure -β4 α+β - built from combinations of β-α-β motifs
Further Simplified Models of Protein Structures
Architecture of protein
Topology of
Fold Folding Pattern Packing
Topology of protein
Level of Simplification
Usefulness classification and outlining their typical features
β-proteinsbull Mostly antiparallel arrangement bull Two sheets packed against each other
bull Basic packing types Top views
Orthogonal Packing Aligned PackingBottom views
β-barrelcylinderβ y
Retinol-binding protein
PorinPorinβ-hairpin
Meander (up amp down) motifβ-hairpin
55 55Acid protease
11
445rsquo5rsquo66332rsquo2rsquo11
44662rsquo2rsquo 33 5rsquo5rsquo
22
1122
11
Serine proteaseSerine protease
Topology Diagramsp gy g
Greek keymotif
O l i l
Greek keyOverlapping loop
uncommon
β-proteinsβ pSo far hellip
bull Packing types orthogonal amp alignedbull Structural architecturesβ-barrel
bull Motifs present in structural architecturesbull Motifs present in structural architectures(super-secondary structures) β-hairpin meander greek kemeander greek key
β-sandwichβ sandwich
2255 22
44
55
66 773344 66 77Greek key 2 - 5
Greek key 3 - 6Bottom view
+ N-end11
y C-endldquocomplete Greek keyrdquo
Immunoglobulin κ
2211 2266 55 88 33
221166 33 88 11
2266
3388
1188
γ-crystallin β catabolite activating
protein virus coat proteinprotein
Greek key amp Jelly roll
Greek key
Jelly roll
β-proteinsβ pSo far hellip
bull Packing types orthogonal amp alignedbull Structural architecturesβ-barrel β-sandwich
bull Motifs present in structural architecturesbull Motifs present in structural architectures(super-secondary structures) β-hairpin meander greek ke jell rollmeander greek key jelly roll
β-propeller β p p
multi-blade (45678) propeller =
three β-sandwiches
Neuraminidase
β-prism(helix)β p ( )bull Formed by three parallel (unusual) beta-sheets
Acyl-transferase(left-handed helix)
Pectate lyase(right-handed helix)
uncommoncommon
Possible topologies composed of four β-strands
Meander G k kMeander Greek keysEfimovrsquos ldquoabcd ldquo structures
Spatial structures with the same Greek key topology
β-proteinsβ proteins
bull Built up from mostly antiparallel β-strands (based on β-hairpins)
bull Packing types orthogonal amp alignedbull Structural architecturesSt uctu a a c tectu esβ-barrel β-sandwich β-propeller β-prism
bull Motifs present in structural architecturesbull Motifs present in structural architectures(super-secondary structures)β-hairpin meander greek key jelly rollhellip
XX--RAYRAY One protein various One protein various
NMRNMRStructures compatible Structures compatible p p
crystallizationcrystallization p p
with one NMR experimentwith one NMR experiment
Secondary structures (Secondary structures (αα--heliceshelices ββ--strandsstrands) are) areSecondary structures (Secondary structures (αα--heliceshelices ββ--strandsstrands) are ) are the most rigid details of proteins the most rigid details of proteins
they are determined with the smallest errorsthey are determined with the smallest errors
One protein various One protein various crystallizationcrystallization
Homologous (closely Homologous (closely related) proteinsrelated) proteins
Secondary structures (Secondary structures (αα--heliceshelices ββ--strandsstrands))Secondary structures (Secondary structures (αα heliceshelices ββ strandsstrands) ) are most conserved structural elements are most conserved structural elements They form a basis of protein classificationThey form a basis of protein classification
HH HHHemoHemo--globinglobin
HemoHemo--globinglobin
H l i h i il f ldH l i h i il f ldHomologous proteins have similar foldsHomologous proteins have similar foldsTrue but trivial True but trivial NONNON t i i lt i i lNONNON--trivialtrivialMany NONMany NON--homologous proteins have similar foldshomologous proteins have similar folds
Structural Classes of Globular ProteinsDomains1 ldquopurerdquo-α - a core built exclusively from alpha-helices2 ldquopurerdquo-β - a core built exclusively from (mostly antiparallel) beta-sheets3 ldquomixedrdquo αβ mixture of ldquopurerdquo α and ldquopurerdquo β3 mixed -αβ - mixture of pure -α and pure -β4 α+β - built from combinations of β-α-β motifs
Further Simplified Models of Protein Structures
Architecture of protein
Topology of
Fold Folding Pattern Packing
Topology of protein
Level of Simplification
Usefulness classification and outlining their typical features
β-proteinsbull Mostly antiparallel arrangement bull Two sheets packed against each other
bull Basic packing types Top views
Orthogonal Packing Aligned PackingBottom views
β-barrelcylinderβ y
Retinol-binding protein
PorinPorinβ-hairpin
Meander (up amp down) motifβ-hairpin
55 55Acid protease
11
445rsquo5rsquo66332rsquo2rsquo11
44662rsquo2rsquo 33 5rsquo5rsquo
22
1122
11
Serine proteaseSerine protease
Topology Diagramsp gy g
Greek keymotif
O l i l
Greek keyOverlapping loop
uncommon
β-proteinsβ pSo far hellip
bull Packing types orthogonal amp alignedbull Structural architecturesβ-barrel
bull Motifs present in structural architecturesbull Motifs present in structural architectures(super-secondary structures) β-hairpin meander greek kemeander greek key
β-sandwichβ sandwich
2255 22
44
55
66 773344 66 77Greek key 2 - 5
Greek key 3 - 6Bottom view
+ N-end11
y C-endldquocomplete Greek keyrdquo
Immunoglobulin κ
2211 2266 55 88 33
221166 33 88 11
2266
3388
1188
γ-crystallin β catabolite activating
protein virus coat proteinprotein
Greek key amp Jelly roll
Greek key
Jelly roll
β-proteinsβ pSo far hellip
bull Packing types orthogonal amp alignedbull Structural architecturesβ-barrel β-sandwich
bull Motifs present in structural architecturesbull Motifs present in structural architectures(super-secondary structures) β-hairpin meander greek ke jell rollmeander greek key jelly roll
β-propeller β p p
multi-blade (45678) propeller =
three β-sandwiches
Neuraminidase
β-prism(helix)β p ( )bull Formed by three parallel (unusual) beta-sheets
Acyl-transferase(left-handed helix)
Pectate lyase(right-handed helix)
uncommoncommon
Possible topologies composed of four β-strands
Meander G k kMeander Greek keysEfimovrsquos ldquoabcd ldquo structures
Spatial structures with the same Greek key topology
β-proteinsβ proteins
bull Built up from mostly antiparallel β-strands (based on β-hairpins)
bull Packing types orthogonal amp alignedbull Structural architecturesSt uctu a a c tectu esβ-barrel β-sandwich β-propeller β-prism
bull Motifs present in structural architecturesbull Motifs present in structural architectures(super-secondary structures)β-hairpin meander greek key jelly rollhellip
One protein various One protein various crystallizationcrystallization
Homologous (closely Homologous (closely related) proteinsrelated) proteins
Secondary structures (Secondary structures (αα--heliceshelices ββ--strandsstrands))Secondary structures (Secondary structures (αα heliceshelices ββ strandsstrands) ) are most conserved structural elements are most conserved structural elements They form a basis of protein classificationThey form a basis of protein classification
HH HHHemoHemo--globinglobin
HemoHemo--globinglobin
H l i h i il f ldH l i h i il f ldHomologous proteins have similar foldsHomologous proteins have similar foldsTrue but trivial True but trivial NONNON t i i lt i i lNONNON--trivialtrivialMany NONMany NON--homologous proteins have similar foldshomologous proteins have similar folds
Structural Classes of Globular ProteinsDomains1 ldquopurerdquo-α - a core built exclusively from alpha-helices2 ldquopurerdquo-β - a core built exclusively from (mostly antiparallel) beta-sheets3 ldquomixedrdquo αβ mixture of ldquopurerdquo α and ldquopurerdquo β3 mixed -αβ - mixture of pure -α and pure -β4 α+β - built from combinations of β-α-β motifs
Further Simplified Models of Protein Structures
Architecture of protein
Topology of
Fold Folding Pattern Packing
Topology of protein
Level of Simplification
Usefulness classification and outlining their typical features
β-proteinsbull Mostly antiparallel arrangement bull Two sheets packed against each other
bull Basic packing types Top views
Orthogonal Packing Aligned PackingBottom views
β-barrelcylinderβ y
Retinol-binding protein
PorinPorinβ-hairpin
Meander (up amp down) motifβ-hairpin
55 55Acid protease
11
445rsquo5rsquo66332rsquo2rsquo11
44662rsquo2rsquo 33 5rsquo5rsquo
22
1122
11
Serine proteaseSerine protease
Topology Diagramsp gy g
Greek keymotif
O l i l
Greek keyOverlapping loop
uncommon
β-proteinsβ pSo far hellip
bull Packing types orthogonal amp alignedbull Structural architecturesβ-barrel
bull Motifs present in structural architecturesbull Motifs present in structural architectures(super-secondary structures) β-hairpin meander greek kemeander greek key
β-sandwichβ sandwich
2255 22
44
55
66 773344 66 77Greek key 2 - 5
Greek key 3 - 6Bottom view
+ N-end11
y C-endldquocomplete Greek keyrdquo
Immunoglobulin κ
2211 2266 55 88 33
221166 33 88 11
2266
3388
1188
γ-crystallin β catabolite activating
protein virus coat proteinprotein
Greek key amp Jelly roll
Greek key
Jelly roll
β-proteinsβ pSo far hellip
bull Packing types orthogonal amp alignedbull Structural architecturesβ-barrel β-sandwich
bull Motifs present in structural architecturesbull Motifs present in structural architectures(super-secondary structures) β-hairpin meander greek ke jell rollmeander greek key jelly roll
β-propeller β p p
multi-blade (45678) propeller =
three β-sandwiches
Neuraminidase
β-prism(helix)β p ( )bull Formed by three parallel (unusual) beta-sheets
Acyl-transferase(left-handed helix)
Pectate lyase(right-handed helix)
uncommoncommon
Possible topologies composed of four β-strands
Meander G k kMeander Greek keysEfimovrsquos ldquoabcd ldquo structures
Spatial structures with the same Greek key topology
β-proteinsβ proteins
bull Built up from mostly antiparallel β-strands (based on β-hairpins)
bull Packing types orthogonal amp alignedbull Structural architecturesSt uctu a a c tectu esβ-barrel β-sandwich β-propeller β-prism
bull Motifs present in structural architecturesbull Motifs present in structural architectures(super-secondary structures)β-hairpin meander greek key jelly rollhellip
HH HHHemoHemo--globinglobin
HemoHemo--globinglobin
H l i h i il f ldH l i h i il f ldHomologous proteins have similar foldsHomologous proteins have similar foldsTrue but trivial True but trivial NONNON t i i lt i i lNONNON--trivialtrivialMany NONMany NON--homologous proteins have similar foldshomologous proteins have similar folds
Structural Classes of Globular ProteinsDomains1 ldquopurerdquo-α - a core built exclusively from alpha-helices2 ldquopurerdquo-β - a core built exclusively from (mostly antiparallel) beta-sheets3 ldquomixedrdquo αβ mixture of ldquopurerdquo α and ldquopurerdquo β3 mixed -αβ - mixture of pure -α and pure -β4 α+β - built from combinations of β-α-β motifs
Further Simplified Models of Protein Structures
Architecture of protein
Topology of
Fold Folding Pattern Packing
Topology of protein
Level of Simplification
Usefulness classification and outlining their typical features
β-proteinsbull Mostly antiparallel arrangement bull Two sheets packed against each other
bull Basic packing types Top views
Orthogonal Packing Aligned PackingBottom views
β-barrelcylinderβ y
Retinol-binding protein
PorinPorinβ-hairpin
Meander (up amp down) motifβ-hairpin
55 55Acid protease
11
445rsquo5rsquo66332rsquo2rsquo11
44662rsquo2rsquo 33 5rsquo5rsquo
22
1122
11
Serine proteaseSerine protease
Topology Diagramsp gy g
Greek keymotif
O l i l
Greek keyOverlapping loop
uncommon
β-proteinsβ pSo far hellip
bull Packing types orthogonal amp alignedbull Structural architecturesβ-barrel
bull Motifs present in structural architecturesbull Motifs present in structural architectures(super-secondary structures) β-hairpin meander greek kemeander greek key
β-sandwichβ sandwich
2255 22
44
55
66 773344 66 77Greek key 2 - 5
Greek key 3 - 6Bottom view
+ N-end11
y C-endldquocomplete Greek keyrdquo
Immunoglobulin κ
2211 2266 55 88 33
221166 33 88 11
2266
3388
1188
γ-crystallin β catabolite activating
protein virus coat proteinprotein
Greek key amp Jelly roll
Greek key
Jelly roll
β-proteinsβ pSo far hellip
bull Packing types orthogonal amp alignedbull Structural architecturesβ-barrel β-sandwich
bull Motifs present in structural architecturesbull Motifs present in structural architectures(super-secondary structures) β-hairpin meander greek ke jell rollmeander greek key jelly roll
β-propeller β p p
multi-blade (45678) propeller =
three β-sandwiches
Neuraminidase
β-prism(helix)β p ( )bull Formed by three parallel (unusual) beta-sheets
Acyl-transferase(left-handed helix)
Pectate lyase(right-handed helix)
uncommoncommon
Possible topologies composed of four β-strands
Meander G k kMeander Greek keysEfimovrsquos ldquoabcd ldquo structures
Spatial structures with the same Greek key topology
β-proteinsβ proteins
bull Built up from mostly antiparallel β-strands (based on β-hairpins)
bull Packing types orthogonal amp alignedbull Structural architecturesSt uctu a a c tectu esβ-barrel β-sandwich β-propeller β-prism
bull Motifs present in structural architecturesbull Motifs present in structural architectures(super-secondary structures)β-hairpin meander greek key jelly rollhellip
Structural Classes of Globular ProteinsDomains1 ldquopurerdquo-α - a core built exclusively from alpha-helices2 ldquopurerdquo-β - a core built exclusively from (mostly antiparallel) beta-sheets3 ldquomixedrdquo αβ mixture of ldquopurerdquo α and ldquopurerdquo β3 mixed -αβ - mixture of pure -α and pure -β4 α+β - built from combinations of β-α-β motifs
Further Simplified Models of Protein Structures
Architecture of protein
Topology of
Fold Folding Pattern Packing
Topology of protein
Level of Simplification
Usefulness classification and outlining their typical features
β-proteinsbull Mostly antiparallel arrangement bull Two sheets packed against each other
bull Basic packing types Top views
Orthogonal Packing Aligned PackingBottom views
β-barrelcylinderβ y
Retinol-binding protein
PorinPorinβ-hairpin
Meander (up amp down) motifβ-hairpin
55 55Acid protease
11
445rsquo5rsquo66332rsquo2rsquo11
44662rsquo2rsquo 33 5rsquo5rsquo
22
1122
11
Serine proteaseSerine protease
Topology Diagramsp gy g
Greek keymotif
O l i l
Greek keyOverlapping loop
uncommon
β-proteinsβ pSo far hellip
bull Packing types orthogonal amp alignedbull Structural architecturesβ-barrel
bull Motifs present in structural architecturesbull Motifs present in structural architectures(super-secondary structures) β-hairpin meander greek kemeander greek key
β-sandwichβ sandwich
2255 22
44
55
66 773344 66 77Greek key 2 - 5
Greek key 3 - 6Bottom view
+ N-end11
y C-endldquocomplete Greek keyrdquo
Immunoglobulin κ
2211 2266 55 88 33
221166 33 88 11
2266
3388
1188
γ-crystallin β catabolite activating
protein virus coat proteinprotein
Greek key amp Jelly roll
Greek key
Jelly roll
β-proteinsβ pSo far hellip
bull Packing types orthogonal amp alignedbull Structural architecturesβ-barrel β-sandwich
bull Motifs present in structural architecturesbull Motifs present in structural architectures(super-secondary structures) β-hairpin meander greek ke jell rollmeander greek key jelly roll
β-propeller β p p
multi-blade (45678) propeller =
three β-sandwiches
Neuraminidase
β-prism(helix)β p ( )bull Formed by three parallel (unusual) beta-sheets
Acyl-transferase(left-handed helix)
Pectate lyase(right-handed helix)
uncommoncommon
Possible topologies composed of four β-strands
Meander G k kMeander Greek keysEfimovrsquos ldquoabcd ldquo structures
Spatial structures with the same Greek key topology
β-proteinsβ proteins
bull Built up from mostly antiparallel β-strands (based on β-hairpins)
bull Packing types orthogonal amp alignedbull Structural architecturesSt uctu a a c tectu esβ-barrel β-sandwich β-propeller β-prism
bull Motifs present in structural architecturesbull Motifs present in structural architectures(super-secondary structures)β-hairpin meander greek key jelly rollhellip
β-proteinsbull Mostly antiparallel arrangement bull Two sheets packed against each other
bull Basic packing types Top views
Orthogonal Packing Aligned PackingBottom views
β-barrelcylinderβ y
Retinol-binding protein
PorinPorinβ-hairpin
Meander (up amp down) motifβ-hairpin
55 55Acid protease
11
445rsquo5rsquo66332rsquo2rsquo11
44662rsquo2rsquo 33 5rsquo5rsquo
22
1122
11
Serine proteaseSerine protease
Topology Diagramsp gy g
Greek keymotif
O l i l
Greek keyOverlapping loop
uncommon
β-proteinsβ pSo far hellip
bull Packing types orthogonal amp alignedbull Structural architecturesβ-barrel
bull Motifs present in structural architecturesbull Motifs present in structural architectures(super-secondary structures) β-hairpin meander greek kemeander greek key
β-sandwichβ sandwich
2255 22
44
55
66 773344 66 77Greek key 2 - 5
Greek key 3 - 6Bottom view
+ N-end11
y C-endldquocomplete Greek keyrdquo
Immunoglobulin κ
2211 2266 55 88 33
221166 33 88 11
2266
3388
1188
γ-crystallin β catabolite activating
protein virus coat proteinprotein
Greek key amp Jelly roll
Greek key
Jelly roll
β-proteinsβ pSo far hellip
bull Packing types orthogonal amp alignedbull Structural architecturesβ-barrel β-sandwich
bull Motifs present in structural architecturesbull Motifs present in structural architectures(super-secondary structures) β-hairpin meander greek ke jell rollmeander greek key jelly roll
β-propeller β p p
multi-blade (45678) propeller =
three β-sandwiches
Neuraminidase
β-prism(helix)β p ( )bull Formed by three parallel (unusual) beta-sheets
Acyl-transferase(left-handed helix)
Pectate lyase(right-handed helix)
uncommoncommon
Possible topologies composed of four β-strands
Meander G k kMeander Greek keysEfimovrsquos ldquoabcd ldquo structures
Spatial structures with the same Greek key topology
β-proteinsβ proteins
bull Built up from mostly antiparallel β-strands (based on β-hairpins)
bull Packing types orthogonal amp alignedbull Structural architecturesSt uctu a a c tectu esβ-barrel β-sandwich β-propeller β-prism
bull Motifs present in structural architecturesbull Motifs present in structural architectures(super-secondary structures)β-hairpin meander greek key jelly rollhellip
β-barrelcylinderβ y
Retinol-binding protein
PorinPorinβ-hairpin
Meander (up amp down) motifβ-hairpin
55 55Acid protease
11
445rsquo5rsquo66332rsquo2rsquo11
44662rsquo2rsquo 33 5rsquo5rsquo
22
1122
11
Serine proteaseSerine protease
Topology Diagramsp gy g
Greek keymotif
O l i l
Greek keyOverlapping loop
uncommon
β-proteinsβ pSo far hellip
bull Packing types orthogonal amp alignedbull Structural architecturesβ-barrel
bull Motifs present in structural architecturesbull Motifs present in structural architectures(super-secondary structures) β-hairpin meander greek kemeander greek key
β-sandwichβ sandwich
2255 22
44
55
66 773344 66 77Greek key 2 - 5
Greek key 3 - 6Bottom view
+ N-end11
y C-endldquocomplete Greek keyrdquo
Immunoglobulin κ
2211 2266 55 88 33
221166 33 88 11
2266
3388
1188
γ-crystallin β catabolite activating
protein virus coat proteinprotein
Greek key amp Jelly roll
Greek key
Jelly roll
β-proteinsβ pSo far hellip
bull Packing types orthogonal amp alignedbull Structural architecturesβ-barrel β-sandwich
bull Motifs present in structural architecturesbull Motifs present in structural architectures(super-secondary structures) β-hairpin meander greek ke jell rollmeander greek key jelly roll
β-propeller β p p
multi-blade (45678) propeller =
three β-sandwiches
Neuraminidase
β-prism(helix)β p ( )bull Formed by three parallel (unusual) beta-sheets
Acyl-transferase(left-handed helix)
Pectate lyase(right-handed helix)
uncommoncommon
Possible topologies composed of four β-strands
Meander G k kMeander Greek keysEfimovrsquos ldquoabcd ldquo structures
Spatial structures with the same Greek key topology
β-proteinsβ proteins
bull Built up from mostly antiparallel β-strands (based on β-hairpins)
bull Packing types orthogonal amp alignedbull Structural architecturesSt uctu a a c tectu esβ-barrel β-sandwich β-propeller β-prism
bull Motifs present in structural architecturesbull Motifs present in structural architectures(super-secondary structures)β-hairpin meander greek key jelly rollhellip
55 55Acid protease
11
445rsquo5rsquo66332rsquo2rsquo11
44662rsquo2rsquo 33 5rsquo5rsquo
22
1122
11
Serine proteaseSerine protease
Topology Diagramsp gy g
Greek keymotif
O l i l
Greek keyOverlapping loop
uncommon
β-proteinsβ pSo far hellip
bull Packing types orthogonal amp alignedbull Structural architecturesβ-barrel
bull Motifs present in structural architecturesbull Motifs present in structural architectures(super-secondary structures) β-hairpin meander greek kemeander greek key
β-sandwichβ sandwich
2255 22
44
55
66 773344 66 77Greek key 2 - 5
Greek key 3 - 6Bottom view
+ N-end11
y C-endldquocomplete Greek keyrdquo
Immunoglobulin κ
2211 2266 55 88 33
221166 33 88 11
2266
3388
1188
γ-crystallin β catabolite activating
protein virus coat proteinprotein
Greek key amp Jelly roll
Greek key
Jelly roll
β-proteinsβ pSo far hellip
bull Packing types orthogonal amp alignedbull Structural architecturesβ-barrel β-sandwich
bull Motifs present in structural architecturesbull Motifs present in structural architectures(super-secondary structures) β-hairpin meander greek ke jell rollmeander greek key jelly roll
β-propeller β p p
multi-blade (45678) propeller =
three β-sandwiches
Neuraminidase
β-prism(helix)β p ( )bull Formed by three parallel (unusual) beta-sheets
Acyl-transferase(left-handed helix)
Pectate lyase(right-handed helix)
uncommoncommon
Possible topologies composed of four β-strands
Meander G k kMeander Greek keysEfimovrsquos ldquoabcd ldquo structures
Spatial structures with the same Greek key topology
β-proteinsβ proteins
bull Built up from mostly antiparallel β-strands (based on β-hairpins)
bull Packing types orthogonal amp alignedbull Structural architecturesSt uctu a a c tectu esβ-barrel β-sandwich β-propeller β-prism
bull Motifs present in structural architecturesbull Motifs present in structural architectures(super-secondary structures)β-hairpin meander greek key jelly rollhellip
β-proteinsβ pSo far hellip
bull Packing types orthogonal amp alignedbull Structural architecturesβ-barrel
bull Motifs present in structural architecturesbull Motifs present in structural architectures(super-secondary structures) β-hairpin meander greek kemeander greek key
β-sandwichβ sandwich
2255 22
44
55
66 773344 66 77Greek key 2 - 5
Greek key 3 - 6Bottom view
+ N-end11
y C-endldquocomplete Greek keyrdquo
Immunoglobulin κ
2211 2266 55 88 33
221166 33 88 11
2266
3388
1188
γ-crystallin β catabolite activating
protein virus coat proteinprotein
Greek key amp Jelly roll
Greek key
Jelly roll
β-proteinsβ pSo far hellip
bull Packing types orthogonal amp alignedbull Structural architecturesβ-barrel β-sandwich
bull Motifs present in structural architecturesbull Motifs present in structural architectures(super-secondary structures) β-hairpin meander greek ke jell rollmeander greek key jelly roll
β-propeller β p p
multi-blade (45678) propeller =
three β-sandwiches
Neuraminidase
β-prism(helix)β p ( )bull Formed by three parallel (unusual) beta-sheets
Acyl-transferase(left-handed helix)
Pectate lyase(right-handed helix)
uncommoncommon
Possible topologies composed of four β-strands
Meander G k kMeander Greek keysEfimovrsquos ldquoabcd ldquo structures
Spatial structures with the same Greek key topology
β-proteinsβ proteins
bull Built up from mostly antiparallel β-strands (based on β-hairpins)
bull Packing types orthogonal amp alignedbull Structural architecturesSt uctu a a c tectu esβ-barrel β-sandwich β-propeller β-prism
bull Motifs present in structural architecturesbull Motifs present in structural architectures(super-secondary structures)β-hairpin meander greek key jelly rollhellip
β-sandwichβ sandwich
2255 22
44
55
66 773344 66 77Greek key 2 - 5
Greek key 3 - 6Bottom view
+ N-end11
y C-endldquocomplete Greek keyrdquo
Immunoglobulin κ
2211 2266 55 88 33
221166 33 88 11
2266
3388
1188
γ-crystallin β catabolite activating
protein virus coat proteinprotein
Greek key amp Jelly roll
Greek key
Jelly roll
β-proteinsβ pSo far hellip
bull Packing types orthogonal amp alignedbull Structural architecturesβ-barrel β-sandwich
bull Motifs present in structural architecturesbull Motifs present in structural architectures(super-secondary structures) β-hairpin meander greek ke jell rollmeander greek key jelly roll
β-propeller β p p
multi-blade (45678) propeller =
three β-sandwiches
Neuraminidase
β-prism(helix)β p ( )bull Formed by three parallel (unusual) beta-sheets
Acyl-transferase(left-handed helix)
Pectate lyase(right-handed helix)
uncommoncommon
Possible topologies composed of four β-strands
Meander G k kMeander Greek keysEfimovrsquos ldquoabcd ldquo structures
Spatial structures with the same Greek key topology
β-proteinsβ proteins
bull Built up from mostly antiparallel β-strands (based on β-hairpins)
bull Packing types orthogonal amp alignedbull Structural architecturesSt uctu a a c tectu esβ-barrel β-sandwich β-propeller β-prism
bull Motifs present in structural architecturesbull Motifs present in structural architectures(super-secondary structures)β-hairpin meander greek key jelly rollhellip
2211 2266 55 88 33
221166 33 88 11
2266
3388
1188
γ-crystallin β catabolite activating
protein virus coat proteinprotein
Greek key amp Jelly roll
Greek key
Jelly roll
β-proteinsβ pSo far hellip
bull Packing types orthogonal amp alignedbull Structural architecturesβ-barrel β-sandwich
bull Motifs present in structural architecturesbull Motifs present in structural architectures(super-secondary structures) β-hairpin meander greek ke jell rollmeander greek key jelly roll
β-propeller β p p
multi-blade (45678) propeller =
three β-sandwiches
Neuraminidase
β-prism(helix)β p ( )bull Formed by three parallel (unusual) beta-sheets
Acyl-transferase(left-handed helix)
Pectate lyase(right-handed helix)
uncommoncommon
Possible topologies composed of four β-strands
Meander G k kMeander Greek keysEfimovrsquos ldquoabcd ldquo structures
Spatial structures with the same Greek key topology
β-proteinsβ proteins
bull Built up from mostly antiparallel β-strands (based on β-hairpins)
bull Packing types orthogonal amp alignedbull Structural architecturesSt uctu a a c tectu esβ-barrel β-sandwich β-propeller β-prism
bull Motifs present in structural architecturesbull Motifs present in structural architectures(super-secondary structures)β-hairpin meander greek key jelly rollhellip
Greek key amp Jelly roll
Greek key
Jelly roll
β-proteinsβ pSo far hellip
bull Packing types orthogonal amp alignedbull Structural architecturesβ-barrel β-sandwich
bull Motifs present in structural architecturesbull Motifs present in structural architectures(super-secondary structures) β-hairpin meander greek ke jell rollmeander greek key jelly roll
β-propeller β p p
multi-blade (45678) propeller =
three β-sandwiches
Neuraminidase
β-prism(helix)β p ( )bull Formed by three parallel (unusual) beta-sheets
Acyl-transferase(left-handed helix)
Pectate lyase(right-handed helix)
uncommoncommon
Possible topologies composed of four β-strands
Meander G k kMeander Greek keysEfimovrsquos ldquoabcd ldquo structures
Spatial structures with the same Greek key topology
β-proteinsβ proteins
bull Built up from mostly antiparallel β-strands (based on β-hairpins)
bull Packing types orthogonal amp alignedbull Structural architecturesSt uctu a a c tectu esβ-barrel β-sandwich β-propeller β-prism
bull Motifs present in structural architecturesbull Motifs present in structural architectures(super-secondary structures)β-hairpin meander greek key jelly rollhellip
β-proteinsβ pSo far hellip
bull Packing types orthogonal amp alignedbull Structural architecturesβ-barrel β-sandwich
bull Motifs present in structural architecturesbull Motifs present in structural architectures(super-secondary structures) β-hairpin meander greek ke jell rollmeander greek key jelly roll
β-propeller β p p
multi-blade (45678) propeller =
three β-sandwiches
Neuraminidase
β-prism(helix)β p ( )bull Formed by three parallel (unusual) beta-sheets
Acyl-transferase(left-handed helix)
Pectate lyase(right-handed helix)
uncommoncommon
Possible topologies composed of four β-strands
Meander G k kMeander Greek keysEfimovrsquos ldquoabcd ldquo structures
Spatial structures with the same Greek key topology
β-proteinsβ proteins
bull Built up from mostly antiparallel β-strands (based on β-hairpins)
bull Packing types orthogonal amp alignedbull Structural architecturesSt uctu a a c tectu esβ-barrel β-sandwich β-propeller β-prism
bull Motifs present in structural architecturesbull Motifs present in structural architectures(super-secondary structures)β-hairpin meander greek key jelly rollhellip
β-propeller β p p
multi-blade (45678) propeller =
three β-sandwiches
Neuraminidase
β-prism(helix)β p ( )bull Formed by three parallel (unusual) beta-sheets
Acyl-transferase(left-handed helix)
Pectate lyase(right-handed helix)
uncommoncommon
Possible topologies composed of four β-strands
Meander G k kMeander Greek keysEfimovrsquos ldquoabcd ldquo structures
Spatial structures with the same Greek key topology
β-proteinsβ proteins
bull Built up from mostly antiparallel β-strands (based on β-hairpins)
bull Packing types orthogonal amp alignedbull Structural architecturesSt uctu a a c tectu esβ-barrel β-sandwich β-propeller β-prism
bull Motifs present in structural architecturesbull Motifs present in structural architectures(super-secondary structures)β-hairpin meander greek key jelly rollhellip
β-prism(helix)β p ( )bull Formed by three parallel (unusual) beta-sheets
Acyl-transferase(left-handed helix)
Pectate lyase(right-handed helix)
uncommoncommon
Possible topologies composed of four β-strands
Meander G k kMeander Greek keysEfimovrsquos ldquoabcd ldquo structures
Spatial structures with the same Greek key topology
β-proteinsβ proteins
bull Built up from mostly antiparallel β-strands (based on β-hairpins)
bull Packing types orthogonal amp alignedbull Structural architecturesSt uctu a a c tectu esβ-barrel β-sandwich β-propeller β-prism
bull Motifs present in structural architecturesbull Motifs present in structural architectures(super-secondary structures)β-hairpin meander greek key jelly rollhellip
Possible topologies composed of four β-strands
Meander G k kMeander Greek keysEfimovrsquos ldquoabcd ldquo structures
Spatial structures with the same Greek key topology
β-proteinsβ proteins
bull Built up from mostly antiparallel β-strands (based on β-hairpins)
bull Packing types orthogonal amp alignedbull Structural architecturesSt uctu a a c tectu esβ-barrel β-sandwich β-propeller β-prism
bull Motifs present in structural architecturesbull Motifs present in structural architectures(super-secondary structures)β-hairpin meander greek key jelly rollhellip
β-proteinsβ proteins
bull Built up from mostly antiparallel β-strands (based on β-hairpins)
bull Packing types orthogonal amp alignedbull Structural architecturesSt uctu a a c tectu esβ-barrel β-sandwich β-propeller β-prism
bull Motifs present in structural architecturesbull Motifs present in structural architectures(super-secondary structures)β-hairpin meander greek key jelly rollhellip
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