用于蛋白质二级结构元件计算机模拟组装的漏斗塑形
Funnel sculpting for in silico assembly of secondary structure elements of proteins.
作者信息
Fain Boris, Levitt Michael
机构信息
Department of Structural Biology, Stanford University, Stanford, CA 94305, USA.
出版信息
Proc Natl Acad Sci U S A. 2003 Sep 16;100(19):10700-5. doi: 10.1073/pnas.1732312100. Epub 2003 Aug 18.
Abstract
We present a method for designing a funnel-shaped free-energy surface that reproducibly assembles secondary structure elements of proteins into their native conformations from a random extended configuration. Assuming a priori knowledge of secondary structure, our method can design a funnel-shaped surface for folding of alpha, beta, and alphabeta structures individually. We design energy surfaces that fold up to five unrelated sequences with the same energy parameters. We develop a measure of the foldability of an energy landscape in silico and present an alternative way to view energy landscapes.
摘要
我们提出了一种设计漏斗形自由能表面的方法，该方法可将蛋白质的二级结构元件从随机伸展构型可重复地组装成其天然构象。假设二级结构具有先验知识，我们的方法可以分别为α、β和αβ结构的折叠设计漏斗形表面。我们设计的能量表面能够以相同的能量参数折叠多达五个不相关的序列。我们开发了一种在计算机上衡量能量景观可折叠性的方法，并提出了一种观察能量景观的替代方法。
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