Residue packing in proteins: Uniform distribution on a coarse-grained scale
Residue packing in proteins: Uniform distribution on a coarse-grained scale
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DOI：
10.1063/1.1432502
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发表时间：
2002-02-01
影响因子：
4.4
通讯作者：
Bahar, I
中科院分区：
文献类型：
--
作者：
Bagci, Z;Jernigan, RL;Bahar, I
蛋白质中残基的高堆积密度应该以某种顺序表现出来；到目前为止，这种堆积顺序还没有得到彻底的表征。蛋白质的堆积规律性很重要，因为蛋白质的内部组织可以对功能动力学产生主导作用，并有助于结构的设计、模拟和评估。打包度量还可以让我们了解正常的序列可变性，随着基因组数据的积累，这个问题变得越来越重要。其他研究表明，堆积密度、序列保守性和折叠成核之间可能存在相关性[O.B.Ptitsyn，J.Mol.比奥尔。278,655(1998)]，都强调了包装的重要性。在这里，来自蛋白质数据库结构的残基簇，每个由一个中心残基和位于第一配位壳内的所有邻居组成，被严格地重新定向并在自洽优化中叠加。在粗粒尺度上(每个残基一个位点)检查时，发现大约三分之二的残基遵循以面为中心的立方体填充的相对取向偏好，而其余三分之一占据随机位置。观察到的规律性在核心残基的最佳叠加后变得更加明显，似乎是在粗粒尺度上通过疏水聚集和体积排除对每个残基周围的配位空间进行均匀采样的结果，以获得接近相同球体的普遍最接近的堆积密度。(C)2002年美国物理研究所。
The high packing density of residues in proteins ought to be manifested in some order; to date this packing order has not been thoroughly characterized. The packing regularity in proteins is important because the internal organization of proteins can have a dominant effect on functional dynamics, and it can aid in the design, simulation and evaluation of structures. Packing metrics could also inform us about normal sequence variability, an issue that, with the accumulating genome data, becomes increasingly important. Other studies, indicating a possible correlation between packing density, sequence conservation, and folding nucleation [O. B. Ptitsyn, J. Mol. Biol. 278, 655 (1998)], have emphasized the importance of packing. Here, residue clusters from protein databank structures, each comprised of a central residue and all neighbors located within the first coordination shell, have been rigidly re-oriented and superimposed in a self-consistent optimization. About two-thirds of residues are found to follow approximately the relative orientation preferences of face-centered-cubic packing, when examined on a coarse-grained scale (one site per residue), while the remaining one-third occupy random positions. The observed regularity, which becomes more pronounced after optimal superimposition of core residues, appears to be the result of uniform sampling of the coordination space around each residue on a coarse-grained scale with hydrophobic clustering and volume exclusion, to achieve packing densities close to that of the universal closest packing of identical spheres. (C) 2002 American Institute of Physics.