Skliros Aris, Zimmermann Michael T, Chakraborty Debkanta, Saraswathi Saras, Katebi Ataur R, Leelananda Sumudu P, Kloczkowski Andrzej, Jernigan Robert L
L. H. Baker Center for Bioinformatics and Biological Statistics, Iowa State University, Ames, IA 50011, USA. Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, IA 50011, USA.
Phys Biol. 2012 Feb;9(1):014001. doi: 10.1088/1478-3975/9/1/014001. Epub 2012 Feb 7.
Loops in proteins that connect secondary structures such as alpha-helix and beta-sheet, are often on the surface and may play a critical role in some functions of a protein. The mobility of loops is central for the motional freedom and flexibility requirements of active-site loops and may play a critical role for some functions. The structures and behaviors of loops have not been studied much in the context of the whole structure and its overall motions, especially how these might be coupled. Here we investigate loop motions by using coarse-grained structures (C(α) atoms only) to solve the motions of the system by applying Lagrange equations with elastic network models to learn about which loops move in an independent fashion and which move in coordination with domain motions, faster and slower, respectively. The normal modes of the system are calculated using eigen-decomposition of the stiffness matrix. The contribution of individual modes and groups of modes is investigated for their effects on all residues in each loop by using Fourier analyses. Our results indicate overall that the motions of functional sets of loops behave in similar ways as the whole structure. But overall only a relatively few loops move in coordination with the dominant slow modes of motion, and these are often closely related to function.
连接α-螺旋和β-折叠等二级结构的蛋白质环通常位于表面，可能在蛋白质的某些功能中起关键作用。环的流动性对于活性位点环的运动自由度和灵活性要求至关重要，并且可能在某些功能中起关键作用。在整个结构及其整体运动的背景下，环的结构和行为尚未得到充分研究，尤其是它们如何相互耦合。在这里，我们通过使用粗粒度结构（仅C(α)原子）来研究环的运动，通过应用带有弹性网络模型的拉格朗日方程来求解系统的运动，以了解哪些环以独立方式移动，哪些环分别与结构域运动协同移动，速度有快有慢。系统的正常模式通过刚度矩阵的特征分解来计算。通过傅里叶分析研究单个模式和模式组对每个环中所有残基的影响。我们的结果总体表明，功能性环集的运动与整个结构的行为方式相似。但总体而言，只有相对较少的环与占主导地位的慢运动模式协同移动，并且这些环通常与功能密切相关。
