同源蛋白的同步和耦合能量优化:结构预测的新工具

Chen Keasar , Ron Elber , Jeffrey Skolnick
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引用次数: 16

摘要

背景:基于同源性的建模和能量全局优化是预测蛋白质结构的两种互补方法。提出了两种方法的结合,其中一种新的成分被添加到同源蛋白质之间的能量和力的相似性。结果:联合用药对胰腺激素和同位结构域两个家族进行了检测。模拟的胰腺激素的最低能量结构是对天然折叠的合理近似。同畴的最低能量结构具有80%的天然接触,但螺旋排列不正确。第四低能量的同位结构具有正确的螺旋填充(RMS为5.4 Å和82%的正确接触)。该家族的单个蛋白质的优化产生相当差的结构。结论:利用偶联同源蛋白寻找原生折叠比寻找家族中单个蛋白折叠更成功。
本文章由计算机程序翻译,如有差异,请以英文原文为准。
Simultaneous and coupled energy optimization of homologous proteins: a new tool for structure prediction

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 Å 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.

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