Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Prague, Czech Republic.
J Phys Chem A. 2011 Oct 20;115(41):11455-65. doi: 10.1021/jp2065612. Epub 2011 Sep 30.
Effective simulations of proteins, their complexes, and other amino-acid polymers such as peptides or peptoids are critically dependent on the performance of the simulation methods and their ability to map the conformational space of the molecule in question. The most important step in this process is the choice of the coordinates in which the conformational sampling will be executed and their uniqueness regarding the capability to unambiguously determine the energy minimum on the free-energy hypersurface. In the presented study, we show that metadynamics and chosen collective coordinates-the principal moments of the tensors of gyration and inertia, the principal radii of gyration around the principal axes, asphericity, acylindricity, and anisotropy-can be used as a powerful combination to map the conformational space of peptides and proteins. We show that the combination of these coordinates with metadynamics produces a powerful tool for the study of biologically relevant molecules.
有效的蛋白质、蛋白质复合物以及其他氨基酸聚合物（如肽或拟肽）的模拟，严重依赖于模拟方法的性能及其映射分子构象空间的能力。在这个过程中，最重要的一步是选择坐标，在这些坐标中执行构象采样，并且这些坐标在确定自由能超曲面上的能量最小值的能力方面是独一无二的。在本研究中，我们表明，元动力学和所选的集体坐标——回转张量和惯性张量的主矩、主转动惯量半径、各向异性、非圆柱度和各向异性，可以作为一种强大的组合，来映射肽和蛋白质的构象空间。我们表明，将这些坐标与元动力学相结合，为研究具有生物学相关性的分子提供了一种强大的工具。
