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Protein oligomerization through domain swapping: role of inter-molecular interactions and protein concentration.

Abstract：

:Domain swapping has been shown to be an important mechanism controlling multiprotein assembly and has been suggested recently as a possible mechanism underlying protein aggregation. Understanding oligomerization via domain swapping is therefore of theoretical and practical importance. By using a symmetrized structure-based (Gō) model, we demonstrate that in the free-energy landscape of domain swapping, a large free-energy barrier separates monomeric and domain-swapped dimeric configurations. We investigate the effect of finite monomer concentration, by implementing a new semi-analytical method, which involves computing the second virial coefficient, a thermodynamic indicator of inter-molecular interactions. This method, together with the symmetrized structure-based (Gō) model, minimizes the need for expensive many-protein simulations, providing a convenient framework to investigate concentration effect. Finally, we perform direct simulations of domain-swapped trimer formation, showing that this modeling approach can be used for higher-order oligomers.

journal_name

J Mol Biol

journal_title

Journal of molecular biology

authors

Yang S,Levine H,Onuchic JN

doi

10.1016/j.jmb.2005.06.062

keywords:

subject

Has Abstract

pub_date

2005-09-09 00:00:00

pages

202-11

issue

1

eissn

0022-2836

issn

1089-8638

pii

S0022-2836(05)00746-1

journal_volume

352

pub_type

杂志文章

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