Sen Taner Z, Feng Yaping, Garcia John V, Kloczkowski Andrzej, Jernigan Robert L
L. H. Baker Center for Bioinformatics and Biological Statistics, Iowa State University, Ames, IA 50011-3020.
J Chem Theory Comput. 2006;2(3):696-704. doi: 10.1021/ct600060d.
Coarse-grained elastic network models have been successful in determining functionally relevant collective motions. The level of coarse-graining, however, has usually focused on the level of one point per residue. In this work, we compare the applicability of elastic network models over a broader range of representational scales. We apply normal mode analysis for multiple scales on a high-resolution protein data set using various cutoff radii to define the residues considered to be interacting, or the extent of cooperativity of their motions. These scales include the residue-, atomic-, proton-, and explicit solvent-levels. Interestingly, atomic, proton, and explicit solvent level calculations all provide similar results at the same cutoff value, with the computed mean-square fluctuations showing only a slightly higher correlation (0.61) with the experimental temperature factors from crystallography than the results of the residue-level coarse-graining. The qualitative behavior of each level of coarse graining is similar at different cutoff values. The correlations between these fluctuations and the number of internal contacts improve with increased cutoff values. Our results demonstrate that atomic level elastic network models provide an improved representation for the collective motions of proteins compared to the coarse-grained models.
粗粒度弹性网络模型在确定功能相关的集体运动方面已取得成功。然而，粗粒度的程度通常集中在每个残基一个点的水平上。在这项工作中，我们比较了弹性网络模型在更广泛的表示尺度范围内的适用性。我们使用各种截止半径对高分辨率蛋白质数据集进行多尺度的正常模式分析，以定义被认为相互作用的残基，或其运动的协同程度。这些尺度包括残基水平、原子水平、质子水平和显式溶剂水平。有趣的是，原子、质子和显式溶剂水平的计算在相同截止值下都提供了相似的结果，计算得到的均方波动与晶体学实验温度因子的相关性仅略高于残基水平粗粒度的结果（0.61）。在不同截止值下，每个粗粒度水平的定性行为相似。这些波动与内部接触数量之间的相关性随着截止值的增加而提高。我们的结果表明，与粗粒度模型相比，原子水平的弹性网络模型为蛋白质的集体运动提供了更好的表示。
