Molecular simulation of protein folding in vivo

体内蛋白质折叠的分子模拟

• 批准号: 9188812
• 负责人: ADRIAN Hamilton ELCOCK
• 金额: $ 27.39万
• 依托单位: UNIVERSITY OF IOWA
• 依托单位国家: 美国
• 财政年份: 2009
• 资助国家: 美国
• 起止时间: 2009-09-21 至 2017-12-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/9188812
• 关键词: Agreement; Amino Acids; Behavior; Biophysics; Cells; Cereals; Code; Communities; Complement; Computer Simulation; Consultations; Crowding; Cytoplasm; Data; Diffusion; Environment; Escherichia coli; Event; Fluorescence; Fluorescence Recovery After Photobleaching; Goals; In Vitro; Kinetics; Knowledge; Lead; Measurement; Methodology; Methods; Mission; Modeling; Molecular; National Institute of General Medical Sciences; Nucleic Acids; Nucleotides; Prokaryotic Cells; Property; Proteins; Protocols documentation; Public Health; RNA; Radial; Resolution; Running; Sampling; Scheme; Series; Solvents; System; Techniques; Thermodynamics; Time; Work; aqueous; base; computer cluster; distributed memory; experimental study; flexibility; hydrodynamic model; in vivo; macromolecule; misfolded protein; molecular dynamics; nervous system disorder; novel; parallelization; protein folding; public health relevance; shared memory; simulation

DESCRIPTION (provided by applicant): An important current goal in molecular biophysics is to determine the extent to which protein behavior observed in vitro is reflective of that occurring in vivo. Experimental approaches based on "in-cell" NMR and fluorescence techniques are beginning to bridge the gaps in knowledge, but such studies can present significant technical challenges in terms of execution, resolution and interpretation; in addition, they typically allow only one or a few types of macromolecule to be studied at a time. To provide a complement to these experimental approaches, the purpose of this proposal is to develop a Brownian dynamics (BD) simulation method capable of modeling intracellular environments at a near-atomic level of resolution, and to apply the method to simulate key aspects of protein behavior in a model of the cytoplasm of the prokaryote Escherichia coli. The simulation method will allow all macromolecules to be treated as fully flexible, thereby allowing protein folding events in vivo to be modeled, and will provide a rigorous modeling of the hydrodynamic interactions that are crucial to include if the diffusional properties of macromolecules are to be accurately captured. Three Specific Aims will be pursued. In Aim 1, a comprehensive, parallelized coarse-grained (CG) BD simulation method will be completed that allows large-scale biomolecular systems to be modeled. The proposed work will involve (a) the implementation of a novel method for modeling hydrodynamic interactions on a very large scale, and (b) parallelization of the simulation code so that it runs efficiently on common distributed-memory computer clusters. In Aim 2, a comprehensive force field for use in CG simulations of protein/RNA systems will be derived for use with the simulation code developed in Aim 1. Importantly, parameterization of the force field will be performed in two fundamentally different ways: 'top down', using experimental data on the thermodynamics of weak macromolecular interactions, and 'bottom up', using all-atom, explicit-solvent molecular dynamics simulation data. In addition to being parameterized in a comprehensive way, the derived CG force field will be unique in also having its hydrodynamic parameters explicitly parameterized. Finally, in Aim 3, the methods developed in Aims 1 and 2 will be used to perform a series of simulation studies examining fundamental aspects of protein behavior in the highly crowded conditions encountered in vivo. BD simulations of protein folding thermodynamics in concentrated single-protein solutions will be compared with the results of H/D exchange measurements. BD simulations of protein diffusion in a model of the cytoplasm of E. coli will be aimed at reproducing in silico the results of 'in-cel' NMR and fluorescence-recovery-after-photobleaching (FRAP) experiments, also performed in E. coli. Finally, BD simulations of the thermodynamics and kinetics of protein folding in the E. coli cytoplasm will also be carried out and compared with corresponding experimental data. If successful, the methods developed and applied here will provide a fundamentally new view of macromolecular behavior in vivo that will be capable of rationalizing previously poorly understood experimental results and making directly testable predictions. Both the simulation code and its attendant force fields will be made freely available to the community.

描述（由申请人提供）：分子生物物理学的重要当前目标是确定在体外观察到的蛋白质行为的程度 体内。基于“细胞内” NMR和荧光技术的实验方法开始弥合知识的差距，但是这些研究可以在执行，解决和解释方面提出重大的技术挑战。此外，它们通常只允许一次研究一种或几种类型的大分子。为了提供这些实验方法的补充，该提案的目的是开发一种布朗动力学（BD）仿真方法，能够在近乎原子的分辨率水平上对细胞内环境进行建模，并应用该方法来模拟蛋白质行为的关键方面，以蛋白质行为的关键方面，在Prokaryote Escherichia coli的细胞质量模型中。模拟方法将使所有大分子都被视为完全柔韧性，从而允许对体内建模蛋白质折叠事件，并将提供对流体动力相互作用的严格建模，这些相互作用对于包括准确捕获了巨粒分子的扩散性能至关重要。将追求三个具体目标。在AIM 1中，将完成一种全面的，并行的粗粒（CG）BD模拟方法，允许对大规模的生物分子系统进行建模。拟议的工作将涉及（a）实施一种新型方法，以大规模地建模流体动力相互作用，以及（b）模拟代码的并行化，以便它在共同的分布式内存计算机群体上有效地运行。在AIM 2中，将在AIM 1中开发的仿真代码中使用一个全面的力领域用于CG蛋白质/RNA系统的模拟。重要的是，将使用两个根本不同的方式进行力场的参数化：使用对弱分子相互作用的热力学的实验数据，使用sim sim solict solect solict solict solict solict solict solict sol-art-art-art-art-art-art-art-art-sol-at-art-sol-at-art-art-art-art-sol-at-atity，除了以全面的方式进行参数化外，派生的CG力场还将在其流体动力学参数明确参数方面是唯一的。最后，在AIM 3中，AIMS 1和2中开发的方法将用于进行一系列模拟研究，研究在体内遇到的高度拥挤的条件下蛋白质行为的基本方面。将浓缩单蛋白溶液中蛋白质折叠热力学的BD模拟与H/D交换测量结果进行比较。大肠杆菌细胞质模型中蛋白质扩散的BD模拟将旨在在硅中繁殖“ cel” NMR和荧光恢复 - 经过光化（FRAP）实验的结果，也在大肠杆菌中进行。最后，还将对大肠杆菌细胞质中蛋白质折叠的热力学和动力学进行BD模拟，并将其与相应的实验数据进行比较。如果成功，此处开发和应用的方法将提供体内大分子行为的根本新观点，该观点将能够合理化以前了解的实验结果并进行直接测试的预测。模拟代码及其随之而来的部队场均可自由地向社区提供。

项目成果

A molecule-centered method for accelerating the calculation of hydrodynamic interactions in Brownian dynamics simulations containing many flexible biomolecules.

• DOI: 10.1021/ct400240w
• 发表时间: 2013-07-09
• 期刊: JOURNAL OF CHEMICAL THEORY AND COMPUTATION
• 影响因子: 5.5
• 作者: Elcock, Adrian H.

Residue-Specific Force Field (RSFF2) Improves the Modeling of Conformational Behavior of Peptides and Proteins.

• DOI: 10.1021/acs.jpclett.5b00654
• 发表时间: 2015-06-04
• 期刊: The journal of physical chemistry letters
• 作者: Li S;Elcock AH
• 通讯作者: Elcock AH

Models of macromolecular crowding effects and the need for quantitative comparisons with experiment.

• DOI: 10.1016/j.sbi.2010.01.008
• 发表时间: 2010-04
• 期刊: Current opinion in structural biology
• 影响因子: 6.8
• 作者: Elcock AH

Reparametrization of Protein Force Field Nonbonded Interactions Guided by Osmotic Coefficient Measurements from Molecular Dynamics Simulations.

• DOI: 10.1021/acs.jctc.6b01059
• 发表时间: 2017-04-11
• 期刊: Journal of chemical theory and computation
• 影响因子: 5.5
• 作者: Miller MS;Lay WK;Li S;Hacker WC;An J;Ren J;Elcock AH
• 通讯作者: Elcock AH

Molecular Dynamics Simulations of 441 Two-Residue Peptides in Aqueous Solution: Conformational Preferences and Neighboring Residue Effects with the Amber ff99SB-ildn-NMR Force Field.

水溶液中 441 个二残基肽的分子动力学模拟：Amber ff99SB-ildn-NMR 力场的构象偏好和邻近残基效应。

• DOI: 10.1021/ct5010966
• 发表时间: 2015
• 期刊: Journal of chemical theory and computation
• 影响因子: 5.5
• 作者: Li,Shuxiang;Andrews,CaseyT;Frembgen-Kesner,Tamara;Miller,MarkS;Siemonsma,StephenL;Collingsworth,TimothyD;Rockafellow,IsaacT;Ngo,NguyetAnh;Campbell,BradyA;Brown,ReidF;Guo,Chengxuan;Schrodt,Michael;Liu,Yu-Tsan;Elcock,Adria
• 通讯作者: Elcock,Adria