PROTEIN PHYSICS LECTURE 15. Protein Structures & Physical Background of Their Natural Selection  Structures  Selection.

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Presentation transcript:

PROTEIN PHYSICS LECTURE 15

Protein Structures & Physical Background of Their Natural Selection  Structures  Selection

GlobulardomainsCATHSCOP

Efimov’s “trees”

We do not see difference of folds of globular proteins of pro- and eukariotes. However, we see that eukariotic proteins are larger, contain more domains, and are more modified. Adaptive evolution of protein structures: Microscopic adaptive changes; Domain duplication an divergence.

J.Richardson, 1977 TYPICAL FOLDING PATTERNS

EMPIRICAL RULES for FREQUENT FOLDS   and   structures, right-handed separate  and  layers superhelices no large (360-degree) turns no loop crossing Lost H-bonds: defect!

Unusual fold (no , almost no  structure) Special sequence (very many S-S bonds) RARE FOLDS, e.g.:

 -sheet: INSIDE

Unusual fold (GFP)

What is better:   inside or    inside?   N>150

_____ ____

Miller,Janin,Chothia1984 Example:Smallproteindetails

THEORYClosedsystem:energy E = const CONSIDER: 1 state of “small part” with  & all states of thermostat with E- . M(E-  ) = 1 M th (E-  ) S t (E-  ) = k ln[M t (E-  )]  S t (E) - (dS t /dE)| E M t (E-  ) = exp[S t (E)/k] exp[- (dS t /dE)| E /k] WHAT IS “TEMPERATURE”? S ~ ln[M] Thus: (dS t /dE)| E = 1/ T; d[ln(M t )]/dE = 1/kT

Protein structure is stable, if its free energy is below some threshold For example: below that of completely unfolded chain; or: below that of any other globular structure

“Multitude principle” for physical selection of folds of globular proteins (“designability”): the more sequences fit the given architecture without disturbing its stability, the higher the occurrence of this architecture in natural proteins.

Hydrophobic patterns necessary for secondary structures Secondary structure patterns (  3 turns, as in globular proteins) are randomly formed in random sequences