Experimental Benchmarks for Protein/Water Force Fields

蛋白质/水力场的实验基准

• 批准号: 6877211
• 负责人: Teresa L. Head-Gordon
• 金额: $ 24.84万
• 依托单位: UNIVERSITY OF CALIFORNIA BERKELEY
• 依托单位国家: 美国
• 财政年份: 2002
• 资助国家: 美国
• 起止时间: 2002-04-01 至 2007-03-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/6877211
• 关键词: aminoacid; analytical method; atmospheric pressure; chemical hydration; chemical stability; chemical structure function; computer simulation; intermolecular interaction; lactalbumin; low angle X ray diffraction analysis; lysozyme; mathematics; model design /development; molecular dynamics; molecular site; neutron diffraction; physical model; protein folding; proteins; stoichiometry; structural biology; technology /technique development; temperature; thermodynamics; water; water solution

DESCRIPTION (provided by applicant): We seek support for a combined theoretical and experimental program that will advance our solution scattering experiments, molecular dynamics simulations, and theoretical analysis expertise, further into the area of pure water and aqueous hydration for both model protein systems and for molten globule proteins. We propose to conduct high quality scattering experiments and appropriate theoretical analysis on pure water away from ambient conditions, and to study aqueous amino acid monomer solutions using simulations and scattering experiments to determine the free energy of association of a variety of monomeric and some trimeric amino acids in water. The experimentally determined solvation of amino acid monomers will be extended to real protein chains by considering the role of hydration in stabilizing molten globule intermediates of various lysozymes and a-lactalbumin. We propose to simulate and perform neutron solution scattering experiments on labeled forms of both the native and molten globule forms of the lysozyme fold class to experimentally determine differences in intensity that arise from different structural organization of the hydrophobic core under native and molten globule conditions. The benchinarking of protein simulations as to the quality of the underlying empirical force fields is naturally addressed in the simulation and experimental research proposed here.

描述（由申请人提供）：我们寻求支持合并理论的支持 和实验计划，可以推进我们的解决方案散射实验， 分子动力学模拟和理论分析专业知识，进一步 进入两种模型蛋白的纯水和水合水的区域 系统和熔融球蛋白。我们建议进行高质量 散射实验和对纯净水的适当理论分析 从环境条件下研究氨基酸单体溶液 使用模拟和散射实验来确定 水中各种单体和一些三聚体氨基酸的关联。 将扩展实验确定的氨基酸单体溶剂化 通过考虑水合在稳定中的作用来实现真实蛋白质链 各种溶菌酶和A-乳蛋白的熔融球中间体。我们建议 模拟和执行标记的中子溶液散射实验 溶菌酶折叠类的天然和熔融球的形式 实验确定由不同的强度差异 疏水核的结构组织在天然和熔融球下 状况。关于蛋白质模拟的替补公告 在模拟中自然解决了基本的经验力领域 实验研究在这里提出。

项目成果

Hydration dynamics near a model protein surface.

• DOI: 10.1016/s0006-3495(04)74252-6
• 发表时间: 2004-03
• 期刊: Biophysical journal
• 影响因子: 3.4
• 作者: D. Russo;Greg L. Hura;T. Head‐Gordon

Effects of hydration water on protein methyl group dynamics in solution.

水合水对溶液中蛋白质甲基动力学的影响。

• DOI: 10.1103/physreve.75.040902
• 发表时间: 2007
• 期刊: Physical review. E, Statistical, nonlinear, and soft matter physics
• 作者: Russo,Daniela;Hura,GregL;Copley,JohnRD
• 通讯作者: Copley,JohnRD

Molecular view of water dynamics near model peptides.

• DOI: 10.1021/jp051137k
• 发表时间: 2005-07
• 期刊: The journal of physical chemistry. B
• 作者: D. Russo;R. Murarka;J. Copley;T. Head‐Gordon