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q-bio.BM/0505032

From: Antonio Trovato [view email]
Date: Tue, 17 May 2005 11:37:11 GMT   (148kb)

Geometrical model for the native-state folds of proteins

Authors: Trinh X. Hoang, Antonio Trovato, Flavio Seno, Jayanth R. Banavar, Amos Maritan

Comments: 12 pages, 3 figures

Subj-class: Biomolecules

Journal-ref: Biophys. Chem. 115 (2005), 289-294

DOI: 10.1016/j.bpc.2004.12.036

We recently introduced a physical model [Hoang et al., P. Natl. Acad. Sci. USA (2004), Banavar et al., Phys. Rev. E (2004)] for proteins which incorporates, in an approximate manner, several key features such as the inherent anisotropy of a chain molecule, the geometrical and energetic constraints placed by the hydrogen bonds and sterics, and the role played by hydrophobicity. Within this framework, marginally compact conformations resembling the native state folds of proteins emerge as broad competing minima in the free energy landscape even for a homopolymer. Here we show how the introduction of sequence heterogeneity using a simple scheme of just two types of amino acids, hydrophobic (H) and polar (P), and sequence design allows a selected putative native fold to become the free energy minimum at low temperature. The folding transition exhibits thermodynamic cooperativity, if one neglects the degeneracy between two different low energy conformations sharing the same fold topology.

Seno, Banavar, Maritanの組み合わせはちょっと気になる


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