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Elastic properties of proteins: insight on the folding process and evolutionary selection of native structures.

Abstract：

:We carry out a theoretical study of the vibrational and relaxation properties of naturally occurring proteins with the purpose of characterizing both the folding and equilibrium thermodynamics. By means of a suitable model, we provide a full characterization of the spectrum and eigenmodes of vibration at various temperatures by merely exploiting the knowledge of the protein native structure. It is shown that the rate at which perturbations decay at the folding transition correlates well with experimental folding rates. This validation is carried out on a list of about 30 two-state folders. Furthermore, the qualitative analysis of residues mean square displacements (shown to reproduce crystallographic data accurately) provides a reliable and statistically accurate method to identify crucial folding sites/contacts. This novel strategy is validated against clinical data for human immunodeficiency virus type 1 (HIV-1) protease. Finally, we compare the spectra and eigenmodes of vibration of natural proteins against randomly generated compact structures and regular random graphs. The comparison reveals a distinctive enhanced flexibility of natural structures accompanied by slow relaxation times at the folding temperature. The fact that these properties are connected intimately to the presence and assembly of secondary motifs hints at the special criteria adopted by evolution in the selection of viable folds.

journal_name

J Mol Biol

journal_title

Journal of molecular biology

authors

Micheletti C,Lattanzi G,Maritan A

doi

10.1016/s0022-2836(02)00710-6

keywords:

subject

Has Abstract

pub_date

2002-08-30 00:00:00

pages

909-21

issue

5

eissn

0022-2836

issn

1089-8638

pii

S0022283602007106

journal_volume

321

pub_type

杂志文章

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