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Discerning the structure and energy of multiple transition states in protein folding using psi-analysis.

Abstract：

:We quantify the degree to which folding occurs along a complex landscape with structurally distinct pathways using psi-analysis in combination with a protein engineering method that identifies native, non-covalent polypeptide interactions and their relative populations at the rate-limiting step. By probing the proximity of two specific partners, this method is extremely well-suited for comparison to theoretical simulations. Using ubiquitin as a model system, we detect individual pathways with site-resolved resolution, demonstrating that the protein folds through a native-like transition state ensemble with a common nucleus that contains heterogeneous features on its periphery. The consensus transition state topology has part of the major helix docked against four properly aligned beta-strands. However, structural heterogeneity exists in the transition state ensemble, wherein peripheral regions are differentially populated according to their relative stability. Pathway diversity reflects the variable order of formation of these peripheral elements, which radiate outward from the common nucleus. These results, which show only moderate agreement with traditional mutational phi-analysis, provide an extraordinarily detailed and quantitative description of protein folding.

journal_name

J Mol Biol

journal_title

Journal of molecular biology

authors

Krantz BA,Dothager RS,Sosnick TR

doi

10.1016/j.jmb.2004.01.018

keywords:

subject

Has Abstract

pub_date

2004-03-19 00:00:00

pages

463-75

issue

2

eissn

0022-2836

issn

1089-8638

pii

S0022283604000300

journal_volume

337

pub_type

杂志文章

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