Computer Simulation of Protein Structure and Kinetics

9418964 Doniach将开发用于表示溶液中多肽和蛋白质的构象动力学的新的计算机模拟技术。 这些技术将包括两个发展：使用过阻尼约束朗之万动力学来表示多肽链的动力学，其中考虑到肽的所有原子在笛卡尔空间中的位置和力;以及肽与溶剂的相互作用的表示的发展。 过阻尼约束朗之万动力学，这是最近发表的Gronbech-Jensen和Doniach，是通过投影出的力场，这将倾向于改变约束键长的所有组件，因此，在肽的主链和侧链的键角。 溶剂的处理将基于朗之万动力学方法来明确水分子，它们彼此之间以及与肽的相互作用，以及基于新的“平均场”方法来计算多肽的水合壳到距离表面原子8埃的距离。 这些新的技术将被应用到模拟的螺旋随机卷曲过渡在小的多肽链13至20个残基，这是已知的具有新生螺旋特性。 ***

9418964 Doniach New computer simulation techniques for representing the conformational kinetics of polypeptides and proteins in solution will be developed. These techniques will comprise two developments: the use of overdamped constrained Langevin dynamics to represent the kinetics of a polypeptide chain, in which the positions in Cartesian space and forces on all atoms of the peptide are taken into account; and the development of the representation of the interaction of the peptide with solvent. The overdamped constrained Langevin dynamics, which has recently been published by Gronbech-Jensen and Doniach, is obtained by projecting out all components of the force field which would tend to alter constrained bond lengths, and hence, bond angles in the peptide backbone and side chains. The treatment of solvent will be based both on a Langevin dynamics approach to explicit water molecules, their interactions between each other and with the peptide, and on a novel "mean-field" approach to the calculation of the hydration shell of a polypeptide out to a distance of 8 Angstrom from the surface atoms. These new techniques will be applied to the simulation of the helix-random coil transitions in small polypeptide chains 13 to 20 residues which are known to have nascent helix properties. ***