Potapov Alex, Stepanova Maria
Centre for Mathematical Biology, University of Alberta, Edmonton, Alberta, Canada.
Phys Rev E Stat Nonlin Soft Matter Phys. 2012 Feb;85(2 Pt 1):020901. doi: 10.1103/PhysRevE.85.020901. Epub 2012 Feb 13.
Understanding the physical mechanisms behind the folding and conformational dynamics of biomolecules is one of the major unsolved challenges of soft matter theory. In this contribution, a theoretical framework for biomolecular dynamics is introduced, employing selected aspects of statistical mechanics, dimensionality reduction, the perturbation theory, and the theory of matrices. Biomolecular dynamics is represented by time-dependent orthogonal conformational modes, the dynamics of the modes is investigated, and invariant properties that persist are identified. As an example, the dynamics of a human prion protein is considered. The theory provides a rigorous background for assessing the stable dynamical properties of biomolecules, such as their coarse-grained structure, through a multiscale approach using short subnanosecond segments of molecular dynamics trajectories. Furthermore, the paper offers a theoretical platform for models of conformational changes in macromolecules, which may allow complementing molecular dynamics simulations.
理解生物分子折叠和构象动力学背后的物理机制是软物质理论中尚未解决的主要挑战之一。在本文中，引入了一个生物分子动力学的理论框架，该框架采用了统计力学、降维、微扰理论和矩阵理论的某些方面。生物分子动力学由随时间变化的正交构象模式表示，研究了这些模式的动力学，并确定了持续存在的不变性质。作为一个例子，考虑了人类朊病毒蛋白的动力学。该理论为通过使用分子动力学轨迹的短亚纳秒片段的多尺度方法评估生物分子的稳定动力学性质（如它们的粗粒度结构）提供了严格的背景。此外，本文为大分子构象变化模型提供了一个理论平台，这可能有助于补充分子动力学模拟。
