Arikawa Keisuke
Department of Mechanical Engineering Kanagawa Institute of Technology, Atsugi, Kanagawa 243-0292, Japan.
Biophys Physicobiol. 2018 Feb 27;15:58-74. doi: 10.2142/biophysico.15.0_58. eCollection 2018.
We propose methods for directly analyzing structural compliance (SC) properties of elastic network models of proteins, and we also propose methods for extracting information about motion properties from the SC properties. The analysis of SC properties involves describing the relationships between the applied forces and the deformations. When decomposing the motion according to the magnitude of SC (SC mode decomposition), we can obtain information about the motion properties under the assumption that the lower SC mode motions or the softer motions occur easily. For practical applications, the methods are formulated in a general form. The parts where forces are applied and those where deformations are evaluated are separated from each other for enabling the analyses of allosteric interactions between the specified parts. The parts are specified not only by the points but also by the groups of points (the groups are treated as flexible bodies). In addition, we propose methods for quantitatively evaluating the properties based on the screw theory and the considerations of the algebraic structures of the basic equations expressing the SC properties. These methods enable quantitative discussions about the relationships between the SC mode motions and the motions estimated from two different conformations; they also help identify the key parts that play important roles for the motions by comparing the SC properties with those of partially constrained models. As application examples, lactoferrin and ATCase are analyzed. The results show that we can understand their motion properties through their lower SC mode motions or the softer motions.
我们提出了直接分析蛋白质弹性网络模型的结构柔顺性（SC）特性的方法，并且还提出了从SC特性中提取有关运动特性信息的方法。SC特性分析涉及描述外力与变形之间的关系。当根据SC的大小对运动进行分解（SC模式分解）时，在较低SC模式运动或较柔和运动更容易发生的假设下，我们可以获得有关运动特性的信息。对于实际应用，这些方法以通用形式制定。施加力的部分和评估变形的部分相互分开，以便能够分析指定部分之间的变构相互作用。这些部分不仅由点指定，还由点组指定（这些组被视为柔性体）。此外，我们提出了基于螺旋理论和对表达SC特性的基本方程代数结构的考虑来定量评估特性的方法。这些方法能够对SC模式运动与从两种不同构象估计的运动之间的关系进行定量讨论；通过将SC特性与部分约束模型的特性进行比较，它们还有助于识别对运动起重要作用的关键部分。作为应用实例，对乳铁蛋白和天冬氨酸转氨甲酰酶进行了分析。结果表明，我们可以通过它们的较低SC模式运动或较柔和运动来了解它们的运动特性。
