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Fold Des. 1997;2(4):247-59.

Simultaneous and coupled energy optimization of homologous proteins: a new tool for structure prediction.

Author information

  • 1Department of Physical Chemistry, Fritz Haber Research Center for Molecular Dynamics, Hebrew University, Givaat Ram, Jerusalem, Israel.

Abstract

BACKGROUND:

Homology-based modeling and global optimization of energy are two complementary approaches to prediction of protein structures. A combination of the two approaches is proposed in which a novel component is added to the energy and forces similarity between homologous proteins.

RESULTS:

The combination was tested for two families: pancreatic hormones and homeodomains. The simulated lowest-energy structure of the pancreatic hormones is a reasonable approximation to the native fold. The lowest-energy structure of the homeodomains has 80% of the native contacts, but the helices are not packed correctly. The fourth lowest energy structure of the homeodomains has the correct helix packing (RMS 5.4 A and 82% of the correct contacts). Optimizations of a single protein of the family yield considerably worse structures.

CONCLUSIONS:

Use of coupled homologous proteins in the search for the native fold is more successful than the folding of a single protein in the family.

PMID:
9269565
[PubMed - indexed for MEDLINE]
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