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Proteins. 2004 Apr 1;55(1):107-14.

Funnel-like organization in sequence space determines the distributions of protein stability and folding rate preferred by evolution.

Author information

1
Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut 06520, USA. yuxia@bioinfo.mbb.yale.edu

Abstract

To understand the physical and evolutionary determinants of protein folding, we map out the complete organization of thermodynamic and kinetic properties for protein sequences that share the same fold. The exhaustive nature of our study necessitates using simplified models of protein folding. We obtain a stability map and a folding rate map in sequence space. Comparison of the two maps reveals a common organizational principle: optimality decreases more or less uniformly with distance from the optimal sequence in the sequence space. This gives a funnel-shaped optimality surface. Evolutionary dynamics of a sequence population on these two maps reveal how the simple organization of sequence space affects the distributions of stability and folding rate preferred by evolution.

PMID:
14997545
PMCID:
PMC2745081
DOI:
10.1002/prot.10563
[Indexed for MEDLINE]
Free PMC Article

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