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首页> 外文期刊>Journal of Molecular Biology >Probing protein fold space with a simplified model
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Probing protein fold space with a simplified model

机译：用简化模型探测蛋白质折叠空间

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We probe the stability and near-native energy landscape of protein fold space using powerful conformational sampling methods together with simple reduced models and statistical potentials. Fold space is represented by a set of 280 protein domains spanning all topological classes and having a wide range of lengths (33-300 residues) amino acid composition and number of secondary structural elements. The degrees of freedom are taken as the loop torsion angles. This choice preserves the native secondary structure but allows the tertiary structure to change. The proteins are represented by three-point per residue, three-dimensional models with statistical potentials derived from a knowledge-based study of known protein structures. When this space is sampled by a combination of parallel tempering and equi-energy Monte Carlo, we find that the three-point model captures the known stability of protein native structures with stable energy basins that are near-native (all alpha: 4.77 angstrom, all beta: 2.93 angstrom, alpha/beta: 3.09 angstrom, alpha+beta: 4.89 angstrom on average and within 6 angstrom for 71.41%, 92.85%, 94.29% and 64.28% for all-alpha, all-beta, alpha/beta and alpha+beta, classes, respectively). Denatured structures also occur and these have interesting structural properties that shed light on the different landscape characteristics of alpha and beta folds. We find that alpha/beta proteins with alternating alpha and beta segments (such as the beta-barrel) are more stable than proteins in other fold classes. (c) 2007 Elsevier Ltd. All rights reserved.
机译：我们使用强大的构象采样方法以及简单的归约模型和统计潜力来探究蛋白质折叠空间的稳定性和近乎自然的能量格局。折叠空间由跨越所有拓扑类别的280个蛋白质域代表，并具有广泛的长度范围（33-300个残基）氨基酸组成和许多二级结构元件。自由度被当作环的扭转角。此选择保留了本机二级结构，但允许三级结构发生更改。蛋白质由每个残基的三点三维模型表示，具有潜在的统计潜力，这些潜力来自于已知蛋白质结构的基于知识的研究。当通过平行回火和等能量蒙特卡洛相结合的方式对该空间进行采样时，我们发现三点模型捕获了具有天然能量池的蛋白质天然结构的已知稳定性，该能量池接近自然（所有alpha：4.77埃，所有beta：平均71.41％，92.85％，94.29％和64.28％的平均beta：2.93埃，alpha / beta：平均3.09埃，alpha + beta：4.89埃，对于所有alpha，all-beta，alpha / beta和alpha + beta，分别是类）。变性结构也会发生，并且它们具有有趣的结构特性，这些特性揭示了α和β折叠的不同景观特征。我们发现具有交替的alpha和beta片段的alpha / beta蛋白（例如beta-barrel）比其他折叠类别的蛋白更稳定。 （c）2007 Elsevier Ltd.保留所有权利。

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