DYNAMICS AND RIGIDITY/FLEXIBILITY OF THERMOPHILIC AND MESOPHILIC PROTEINS

嗜热和嗜温蛋白质的动力学和刚性/柔性

• 批准号: 8171774
• 负责人: MARIA G KURNIKOVA
• 金额: $ 0.11万
• 依托单位: CARNEGIE-MELLON UNIVERSITY
• 依托单位国家: 美国
• 财政年份: 2010
• 资助国家: 美国
• 起止时间: 2010-08-01 至 2013-07-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/8171774
• 关键词: Computer Retrieval of Information on Scientific Projects Database; Funding; Genets; Goals; Grant; Graph; Homologous Protein; Hydrogen Bonding; Institution; Methods; Molecular Models; Muscle Rigidity; Physics; Property; Proteins; Research; Research Personnel; Resources; Sodium Chloride; Solutions; Source; Structure; Triad Acrylic Resin; United States National Institutes of Health; alpha helix; arginylglutamate; base; flexibility; lysylglutamic acid; molecular dynamics; molecular modeling; protein structure; theories

This subproject is one of many research subprojects utilizing the resources provided by a Center grant funded by NIH/NCRR. The subproject and investigator (PI) may have received primary funding from another NIH source, and thus could be represented in other CRISP entries. The institution listed is for the Center, which is not necessarily the institution for the investigator. The goals of this project is to systematically investigate how rigidity/flexibility varies among homologous structural domains of thermophilic and mesophilic proteins, to understand whether the rigidity/flexibility of thermophilic and mesophilic proteins correlate with their stability, and whether both properties are controlled by the same structural determinants. The method used in this study is a hierarchical physics based molecular modeling approach termed MD/FIRST (Mamonova, Phys. Biol. 2005), which combines the molecular dynamics (MD) simulations of a native structure protein in solution with a rigid cluster decomposition method FIRST based on the graph theory (Jacobs, Proteins: Struct., Funct., Genet. 2001). Using this approach we found that there are two groups of proteins. First one is characterized the salt bridge or ionic network. This network includes salt bridge triads Agr-Glu_Lys, Arg-Glu-Arg or salt bridges (like Arg-Glu) connected with hydrogen bonds. This ionic network accumulates alpha helixes and rigidifies the structure. The second groups can be characterized by the single salt bridges and h-bonds or small ionic clusters. Such difference in the network of salt bridges results in different flexibility of homologous protein. MD/FIRST approach allows for characterizing structural features in atomic detail that determine the rigidity/flexibility of a protein structure.

该副本是利用众多研究子项目之一 由NIH/NCRR资助的中心赠款提供的资源。子弹和 调查员（PI）可能已经从其他NIH来源获得了主要资金， 因此可以在其他清晰的条目中代表。列出的机构是 对于中心，这不一定是调查员的机构。 该项目的目标是系统地研究嗜热和嗜嗜蛋白质的同源结构结构域之间的刚性/柔韧性如何变化，以了解嗜热和嗜嗜蛋白的刚度/柔韧性是否与其稳定性相关，以及两种特性是否由同一结构确定剂控制。这项研究中使用的方法是一种基于层次物理学的分子建模方法，称为MD/First（Mamonova，Phys。Biol。2005），该方法结合了溶液中的分子动力学（MD）模拟溶液中的分子动力学（MD）模拟与刚性群集分解方法的基于图形论点（jacobs，prot，prot，proteins，proteins，proteins offorment officin：jacobs，prot proteins，proteins，proteins，proteins of tograls：jacobs，proteins：struce of struct of struct of struct of funct of contruct of centent。使用这种方法，我们发现有两组蛋白质。首先是盐桥或离子网络的特征。该网络包括与氢键相连的盐桥三合会agr-glu_lys，arg-glu-arg或盐桥（如Arg-Glu）。该离子网络积累了α螺旋并将结构固化。第二组可以以单盐桥和H键或小离子簇为特征。盐桥网络中的这种差异导致同源蛋白的灵活性不同。 MD/第一种方法允许在原子细节中表征结构特征，以确定蛋白质结构的刚度/灵活性。