PROTEIN PHYSICSPROTEIN PHYSICS
LECTURE 13-16LECTURE 13-16
- Structures of water-soluble globular proteins- Structures of water-soluble globular proteins- Physical selection of protein structures- Physical selection of protein structures- Structural classification of proteins- Structural classification of proteins
FibrousFibrous
H-bondsH-bonds & & hydrophobicshydrophobics
MembraneMembrane
________
Globular proteinsGlobular proteins (water-soluble) (water-soluble)
domain 1 domain 2domain 1 domain 2
single-domain single-domain globular proteinglobular protein
fold stack
Secondary structures (Secondary structures (-helices-helices, , -strands-strands) are ) are the most rigid and conserved details of proteins; the most rigid and conserved details of proteins; they are determined with the smallest errors andthey are determined with the smallest errors and
form a basis of protein classificationform a basis of protein classification
X-RAYX-RAYOne protein, various crystallizations
NMRNMR Structures, compatible with one NMR experiment
HomologousHomologous (closely related) (closely related)
proteinsproteins
Homologous proteins have similar folds.Homologous proteins have similar folds.True, but trivial. True, but trivial. NON-trivial:NON-trivial:Many NON-homologous proteins have similar folds.Many NON-homologous proteins have similar folds.
Hemo-Hemo-globinglobin
Hemo-Hemo-globinglobin
-proteins-proteins
-sheets:-sheets: usually, twisted usually, twisted (usually, right-) (usually, right-)
H-bonds: within sheetsH-bonds: within sheetsHydrophobics: between sheetsHydrophobics: between sheets
________
Orthogonal packing Aligned packing Orthogonal packing Aligned packing of of -sheets of -sheets of -sheets -sheets
sandwichessandwiches&&
cylinderscylinders
orthogonal packing orthogonal packing of one rolled of one rolled -sheet-sheet
Retinol-binding proteinRetinol-binding protein
Trypsin-like SER-protease Acid-proteaseTrypsin-like SER-protease Acid-protease orthogonal packings of orthogonal packings of -sheets-sheets
22
11
44
55
5’5’66332’2’
22
11
44
55
662’2’ 33 5’5’
IG-fold:IG-fold: aligned packing of aligned packing of -sheets-sheets
Greek key 2::5Greek key 2::5 Greek key 3::6Greek key 3::6
11
22
3344
55
66 77
non-crossed loopsnon-crossed loops
-sandwich-sandwichInterlocked pairs:Interlocked pairs:center of sandwichcenter of sandwich
Greek key: Greek key: edge of sandwichedge of sandwich
Hydrophobic surfaces Hydrophobic surfaces of sheets of the sandwichof sheets of the sandwich
aligned packingsaligned packings of of -sheets-sheets
a) different: a) different: only topologies only topologies
b) equal: b) equal: even even
topologytopology
66 5588 33
221166 33 88 11
2266
33
88
11
-crystallin CAB cpSTNV
aligned packing aligned packing of of -sheets-sheets
6-bladed propeller6-bladed propeller
neuraminidase neuraminidase
UNusual LEFTLEFT-HANDED -HANDED
chain turns chain turns (AND (AND NONO
TWIST!)TWIST!)
Left-handed Left-handed -prism:-prism: Acyl transferaseAcyl transferase Right-handed Right-handed -prism:-prism: Pectate lyasePectate lyase
Usual RIGHTRIGHT-HANDED -HANDED
chain turns chain turns (AND (AND RIGHTRIGHT -TWIST!)-TWIST!)
______________________________________________________________________________________TOPOLOGY of chain turns between parallel -strands
-proteins-proteins
H-bonds: within helicesH-bonds: within helices & & Hydrophobics: between helicesHydrophobics: between helices
Quasi-cylindrical core Quasi-cylindrical core (in fibrous)(in fibrous)
Quasi-flat coreQuasi-flat core Quasi-spherical coreQuasi-spherical coreMOST COMMONMOST COMMON
Orthogonal packingOrthogonal packing Similar to orthogonalSimilar to orthogonalof LONG of LONG -helices-helices packing of packing of -sheets-sheets
Aligned packingAligned packing Similar to alignedSimilar to alignedof LONG of LONG -helices-helices packing of packing of -sheets-sheets
Quasi-sphericalQuasi-sphericalpolyhedrapolyhedra
Quasi-Quasi-spherical spherical
core:core:MOST COMMONMOST COMMON
no loop turns of ~360no loop turns of ~360oo
no loop crossingsno loop crossings
Packing of ridgesPacking of ridges: :
““0-4” & “0-4”: -500-4” & “0-4”: -5000
““0-4” & “1-4”: +200-4” & “1-4”: +2000
IDEAL POLYHEDRAIDEAL POLYHEDRA
-60-600 0 -50 -500 0 +60+600 0 +20 +2000
* ** *
CLOSE PACKINGCLOSE PACKING
// proteins proteins
H-bonds: within helices & sheetsH-bonds: within helices & sheetsHydrophobics: between helices & sheetsHydrophobics: between helices & sheets
TIM barrel Rossmann foldTIM barrel Rossmann fold
and and layers layers rightright-handed-handed superhelicessuperhelices
Regular secondary structure Regular secondary structure sequence:sequence:
Classification ofClassification of-barrels:-barrels:““share number” Sshare number” Sand and strand number N.strand number N.Here: S=8, N=8Here: S=8, N=8
StandardStandardactive siteactive siteposition is position is given bygiven bythe archi-the archi-tecturetecture
NN NN NN NN
++ proteins proteins
H-bonds: within helices & sheetsH-bonds: within helices & sheetsHydrophobics: between helices & sheetsHydrophobics: between helices & sheets
++::a) A kind of regularity in the secondarya) A kind of regularity in the secondary structure sequence:structure sequence:
FerridoxinFerridoxinfoldfold
++::b) Secondary structure sequence:b) Secondary structure sequence: composed of irregular blocks, e.g.: composed of irregular blocks, e.g.:
Nuclease fold Nuclease fold (“Russian doll effect”)(“Russian doll effect”)
OB-foldOB-fold of the of the -subdomain -subdomain of nucleaseof nuclease
11
1’1’
33
55 44
22
J.Richardson, 1977J.Richardson, 1977
TYPICALTYPICALFOLDING PATTERNSFOLDING PATTERNS
EMPIRICAL RULESEMPIRICAL RULESseparateseparate and and layers layers rightright--handedhanded superhelicessuperhelices
no large, ~360no large, ~360oo turns turns no loop crossingsno loop crossings
Lost H-bonds: defect!Lost H-bonds: defect!
NO ‘defects’NO ‘defects’
RESULT:RESULT:NARROW SET NARROW SET
OF PREDOMINANT FOLDING PATTERNSOF PREDOMINANT FOLDING PATTERNSthese are those that have no ‘defects’these are those that have no ‘defects’
GlobularGlobulardomainsdomains
CCAATTHH
SSCCOOPP
Efimov’s “trees”Efimov’s “trees”
80/20 LAW:80/20 LAW:
EMPIRICAL RULES for FREQUENT FOLDSEMPIRICAL RULES for FREQUENT FOLDSand and structures, structures, rightright-handed-handedseparate separate and and layers superhelices layers superhelices
no large (360-degree) turnsno large (360-degree) turns no loop crossingno loop crossing
Lost H-bonds: defect!Lost H-bonds: defect!
Unusual foldUnusual fold(no(no , almost no, almost no structure: structure: bad for stabilitybad for stability) -) -
BUT: very special sequenceBUT: very special sequence (very many Cysteins, and therefore (very many Cysteins, and therefore
very many S-S bonds)very many S-S bonds)
e.g.:e.g.:
UnusualUnusual fold (GFP):fold (GFP):helix insidehelix inside
UsualUsual folds: folds:helices outsidehelices outside
What is more usual:What is more usual:sequence providingsequence providing inside orinside orinside?inside?
N>150N>150
__________
________
Miller,Miller,Janin,Janin,ChothiaChothia19841984
Example:Example:
SmallSmallproteinproteindetailsdetails
THEORYTHEORYClosedClosedsystem:system:energy energy E = constE = const
CONSIDER: 1 state of “small part” with CONSIDER: 1 state of “small part” with & all & all states of thermostat with E-states of thermostat with E-.. M(E- M(E-) = 1) = 1 •• MMthth(E-(E-) )
SStt(E-(E-) = ) = k k •• ln[Mln[Mtt(E-(E-)] )] S Stt(E) - (E) - ••(dS(dStt/dE)|/dE)|E E
MMtt(E-(E-) = exp[S) = exp[Stt(E)/(E)/kk] ] • • exp[-exp[-••(dS(dStt/dE)|/dE)|EE//kk]]
WHAT IS “TEMPERATURE”?WHAT IS “TEMPERATURE”?
S ~S ~ ln[M]ln[M]
Thus: d[ln(MThus: d[ln(Mtt)]/dE = 1/kT)]/dE = 1/kT
Protein structure is stable, Protein structure is stable, if its free energy is below some thresholdif its free energy is below some threshold
For example:For example: below that of completely unfolded chain;below that of completely unfolded chain;or:or:below that of any other globular structurebelow that of any other globular structure
““Multitude principle”Multitude principle” for physical selection of folds for physical selection of folds of globular proteins of globular proteins ((nownow: “designability”): “designability”)::
the more sequences fit the given the more sequences fit the given architecture without destroying its stability, architecture without destroying its stability, the higher the occurrence of this the higher the occurrence of this architecture in natural proteins. architecture in natural proteins.
GlobularGlobulardomainsdomains CC
AATTHH
SSCCOOPP
RATIONAL STRUCTURAL CLASSIFICATION OF PROTEINSRATIONAL STRUCTURAL CLASSIFICATION OF PROTEINS
- Structures of water-soluble globular proteins- Structures of water-soluble globular proteins- Physical selection of protein structures- Physical selection of protein structures: : min. of defectsmin. of defects!!- Rational structural classification of proteins- Rational structural classification of proteins