SIMULATING DYNAMICS AND ORIENTATIONS OF ENGINEERED SIDE CHAINS IN THE RESTRICTI

模拟限制条件下工程侧链的动力学和方向

• 批准号: 8364202
• 负责人: SUNIL K SAXENA
• 金额: $ 0.11万
• 依托单位: CARNEGIE-MELLON UNIVERSITY
• 依托单位国家: 美国
• 财政年份: 2011
• 资助国家: 美国
• 起止时间: 2011-09-15 至 2013-07-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/8364202
• 关键词: Base Pairing; Binding; Biomedical Research; DNA Restriction Enzymes; DNA Sequence; DNA Structure; Deoxyribonuclease EcoRI; Discrimination; Electron Spin Resonance Spectroscopy; Engineering; Exhibits; Funding; Goals; Grant; High Performance Computing; Hour; Knowledge; Label; Location; Measurement; Methods; Modeling; National Center for Research Resources; Paint; Principal Investigator; Procedures; Proteins; Research; Research Infrastructure; Resources; Role; Running; Sampling; Side; Simulate; Site; Source; Specificity; Spin Labels; Structure; System; Time; United States National Institutes of Health; Vertebral column; Work; biological systems; cost; molecular dynamics; protein structure; research study; simulation

This subproject is one of many research subprojects utilizing the resources provided by a Center grant funded by NIH/NCRR. Primary support for the subproject and the subproject's principal investigator may have been provided by other sources, including other NIH sources. The Total Cost listed for the subproject likely represents the estimated amount of Center infrastructure utilized by the subproject, not direct funding provided by the NCRR grant to the subproject or subproject staff. We request computing time and storage space on TeraGrid resources, specifically Pople, to run extensive parallel molecular dynamics simulations to determine the preferred orientations of a modified side chain of the restriction endonuclease EcoRI. EcoRI exhibits an extremely high binding specificity to a six base pair sequence of DNA, the structural origin of which was investigated using Electron Spin Resonance (ESR). In conjunction with site-directed spin labeling, which introduces a side chain containing a nitroxide label into the protein, distance measurements were performed on EcoRI to provide structural constraints of the system. In order to paint a more accurate picture of the structure and dynamics of the spin labeled locations of EcoRI from ESR measurements, knowledge of the average nitroxide side chain orientation is required. Initial attempts to model the nitroxide side chain using Monte Carlo rotamer search methods in combination with all-atom molecular dynamics have revealed discrepancies between experiment and simulation due to sampling restrictions. This request aims to establish a procedure where extensive MD simulations can be used to reproduce the distance between two nitroxide side chains, enabling the extraction of the C?-C? distance and distribution. The simulations will also allow a discrimination of the role of nitroxide side chain dynamics versus backbone dynamics on ESR lineshapes and distance distributions. We will run 10 parallel simulations at six different sites in the protein using two independent nitroxide force fields. By doubly labeling the crystal structure a total of 60 simulations will be run for 100 ns each to simulate the average nitroxide orientation and dynamics at different secondary structures in addition to investigating the effects of nitroxide parameterization on these observables. Our request of 480K CPU hours will provide the computational power needed to perform long runs that enable sufficient sampling of the nitroxide side chain. In this way, we will work towards our goal of developing an MD simulation procedure that can be applied to different biological systems to reliably model nitroxide side chain orientations and dynamics so that more atomistic details of the protein or DNA structure and dynamics can be better understood.

该副本是利用资源的众多研究子项目之一 由NIH/NCRR资助的中心赠款提供。对该子弹的主要支持 而且，副投影的主要研究员可能是其他来源提供的 包括其他NIH来源。 列出的总费用可能 代表subproject使用的中心基础架构的估计量， NCRR赠款不直接向子弹或副本人员提供的直接资金。 我们要求在Teragrid资源（特别是Pople）上计算时间和存储空间，以运行广泛的并行分子动力学模拟，以确定限制性核酸内切酶Ecori修改的侧链的首选方向。 ECORI对DNA的六个碱基对序列表现出极高的结合特异性，其结构起源是使用电子自旋共振（ESR）研究的。与位置定向的自旋标记结合使用，该标记将含有氮氧化标记的侧链引入蛋白质中，对ECORI进行了距离测量，以提供系统的结构约束。为了更准确地描绘出从ESR测量中旋转标记的ECORI位置的结构和动力学，需要了解平均氮氧化物侧链方向。最初使用蒙特卡洛旋转型搜索方法与全原子分子动力学结合使用硝酸侧链对氮氧化物进行建模的尝试揭示了由于采样限制而引起的实验和仿真之间的差异。该请求旨在建立一个程序，其中可以使用大量的MD模拟来重现两个氮氧化侧链之间的距离，从而可以提取C？-C？距离和分布。这些模拟还将允许歧视ESR线形和距离分布在ESR线路上的氮侧链动力学与骨干动力学的作用。我们将使用两个独立的氮氧化力场在蛋白质的六个不同位点运行10个平行模拟。通过双重标记晶体结构，总共将进行100 ns的总共60个模拟，以模拟不同二级结构在不同二级结构的平均氮氧化方向和动力学，此外还研究了氮氧化物参数化对这些可观察到的物体的影响。我们对480K CPU小时的要求将提供进行长途运行所需的计算能力，从而可以对氮氧化物侧链进行足够的采样。通过这种方式，我们将朝着开发MD模拟程序的目标努力，该过程可以应用于不同的生物系统，以可靠地对氮氧化物侧链方向和动力学进行可靠的模型，以便可以更好地理解蛋白质或DNA结构和动力学的更多原子细节。