protein physics lecture 13-16

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