Suppr超能文献

一种利用化学键信息的α-碳粗粒度弹性网络模型的连接规则。

A connection rule for alpha-carbon coarse-grained elastic network models using chemical bond information.

作者信息

Jeong Jay I, Jang Yunho, Kim Moon K

机构信息

Department of Mechanical Engineering, The Johns Hopkins University, Baltimore, MD 21218, USA.

出版信息

J Mol Graph Model. 2006 Jan;24(4):296-306. doi: 10.1016/j.jmgm.2005.09.006. Epub 2005 Nov 11.

Abstract

A sparser but more efficient connection rule (called a bond-cutoff method) for a simplified alpha-carbon coarse-grained elastic network model is presented. One of conventional connection rules for elastic network models is the distance-cutoff method, where virtual springs connect an alpha-carbon with all neighbor alpha-carbons within predefined distance-cutoff value. However, though the maximum interaction distance between alpha-carbons is reported as 7 angstroms, this cutoff value can make the elastic network unstable in many cases of protein structures. Thus, a larger cutoff value (>11 angstroms) is often used to establish a stable elastic network model in previous researches. To overcome this problem, a connection rule for backbone model is proposed, which satisfies the minimum condition to stabilize an elastic network. Based on the backbone connections, each type of chemical interactions is considered and added to the elastic network model: disulfide bonds, hydrogen bonds, and salt-bridges. In addition, the van der Waals forces between alpha-carbons are modeled by using the distance-cutoff method. With the proposed connection rule, one can make an elastic network model with less than 7 angstroms distance cutoff, which can reveal protein flexibility more sharply. Moreover, the normal modes from the new elastic network model can reflect conformational changes of a given protein better than ones by the distance-cutoff method. This method can save the computational cost when calculating normal modes of a given protein structure, because it can reduce the total number of connections. As a validation, six example proteins are tested. Computational times and the overlap values between the conformational change and infinitesimal motion calculated by normal mode analysis are presented. Those animations are also available at UMass Morph Server (http://biomechanics.ecs.umass.edu/umms.html).

摘要

提出了一种用于简化的α-碳粗粒度弹性网络模型的更稀疏但更有效的连接规则(称为键截断方法)。弹性网络模型的传统连接规则之一是距离截断方法,其中虚拟弹簧将α-碳与预定义距离截断值内的所有相邻α-碳相连。然而,尽管据报道α-碳之间的最大相互作用距离为7埃,但在许多蛋白质结构情况下,这个截断值会使弹性网络不稳定。因此,在先前的研究中,通常使用更大的截断值(>11埃)来建立稳定的弹性网络模型。为了克服这个问题,提出了一种用于主链模型的连接规则,该规则满足稳定弹性网络的最小条件。基于主链连接,考虑每种类型的化学相互作用并将其添加到弹性网络模型中:二硫键、氢键和盐桥。此外,α-碳之间的范德华力通过距离截断方法进行建模。使用所提出的连接规则,可以构建一个距离截断小于7埃的弹性网络模型,该模型能够更清晰地揭示蛋白质的灵活性。此外,新弹性网络模型的正常模式比距离截断方法的模型能更好地反映给定蛋白质的构象变化。该方法在计算给定蛋白质结构的正常模式时可以节省计算成本,因为它可以减少连接总数。作为验证,对六个示例蛋白质进行了测试。给出了计算时间以及通过正常模式分析计算的构象变化与微小运动之间的重叠值。这些动画也可在马萨诸塞大学形态服务器(http://biomechanics.ecs.umass.edu/umms.html)上获取。

文献AI研究员

20分钟写一篇综述,助力文献阅读效率提升50倍。

立即体验

用中文搜PubMed

大模型驱动的PubMed中文搜索引擎

马上搜索

文档翻译

学术文献翻译模型,支持多种主流文档格式。

立即体验