MOLECULAR SIMULATION STUDIES OF BIOLOGICAL MOLECULES

生物分子的分子模拟研究

• 批准号: 6282497
• 负责人: DAVID L BEVERIDGE
• 金额: $ 1.19万
• 依托单位: MELLON PITTS CORPORATION (MPC CORP)
• 依托单位国家: 美国
• 财政年份: 1998
• 资助国家: 美国
• 起止时间: 1998-08-01 至 1999-07-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/6282497
• 关键词: biological products; biomedical resource; computers

We request herein continuation support for the study of the structure and dynamics of biological macromolecules using Molecular Dynamics (MD) and Monte Carlo (MC) computer simulation methods. The focus of our research involves development and robust simulation protocols for application to the above systems, detailed characterization of the ensuing trajectories and establishment of the feasibility, accuracy and limitations of the MC methodology as applied to these systems. The studies proposed herein will focus in four areas: a) critical assessment of the applicability of current M simulation protocols to longer DNA oligonucleotides, varying in length from about 17-30 base pairs; b) dynamical structure of DNA sequences important in the regulation of physiological processes through bending and/or protein recognition and c) structural studies and mechanistic implications derived from solution simulations of an enzyme complexed with an inhibitor/substrate and d) MD/MC simulations of proteins involved in DNA sequence recognition that are significant towards understanding the molecular basis of gene expression. The emphasis in our projects is on detailed structural characterization based on a variety of force fields, scrutinization of the results with crystallographic, NMR and other available experimental data, identifying and analyzing substates and development of state of the art graphical analysis tools.

我们在此请求继续支持该研究 使用分子生物学研究生物大分子的结构和动力学 动力学（MD）和蒙特卡罗（MC）计算机模拟方法。 这 我们研究的重点涉及开发和鲁棒模拟 适用于上述系统的协议，详细 随后的轨迹的特征和建立 所应用的 MC 方法的可行性、准确性和局限性 到这些系统。 本文提出的研究将集中在四个方面 领域： a) 对当前 M 的适用性进行严格评估 不同长度的较长 DNA 寡核苷酸的模拟方案 约17-30个碱基对； b) DNA序列的动态结构 通过弯曲调节生理过程很重要 和/或蛋白质识别和 c) 结构研究和机制 来自酶复合物溶液模拟的影响 使用抑制剂/底物和 d) 蛋白质的 MD/MC 模拟 参与 DNA 序列识别，这对于 了解基因表达的分子基础。 重点在于 我们的项目是基于详细的结构特征 各种力场，仔细检查结果 晶体学、核磁共振和其他可用的实验数据， 识别和分析子状态以及状态的发展 艺术图形分析工具。