Computer Simulation of Protein Structure and Kinetics

蛋白质结构和动力学的计算机模拟

• 批准号: 9418964
• 负责人: Sebastian Doniach
• 金额: $ 27万
• 依托单位: Stanford University
• 依托单位国家: 美国
• 项目类别: Continuing Grant
• 财政年份: 1995
• 资助国家: 美国
• 起止时间: 1995-06-01 至 1998-09-30
• 项目状态: 已结题
• 来源: https://www.nsf.gov/awardsearch/showAward?AWD_ID=9418964&HistoricalAwards=false
• 关键词: Computer; Simulation; Protein; Structure; Kinetics

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. ***

将发展新的计算机模拟技术来表示多肽和蛋白质在溶液中的构象动力学。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，其中考虑了多肽在笛卡尔空间中的位置和所有原子上的力；以及多肽与溶剂相互作用表征的研究进展。最近由Gronbech-Jensen和Doniach发表的过阻尼约束朗格万动力学，是通过突出力场的所有分量得到的，这些分量会改变约束键的长度，从而改变肽主链和侧链的键角。溶剂的处理将基于langevan动力学方法来研究明确的水分子，它们之间的相互作用以及与肽的相互作用，以及一种新的“平均场”方法来计算距离表面原子8埃的多肽的水合壳。这些新技术将应用于13到20个残基的小多肽链的螺旋-随机线圈过渡的模拟，这些小多肽链已知具有新生的螺旋性质。＊＊＊