Molecular Dynamics Simulations Of Biological Macromolecu

生物大分子的分子动力学模拟

• 批准号: 6817669
• 负责人: BERNARD R BROOKS
• 金额: --
• 依托单位: NATIONAL HEART, LUNG, AND BLOOD INSTITUTE
• 依托单位国家: 美国
• 资助国家: 美国
• 起止时间: 至
• 项目状态: 未结题
• 来源: https://reporter.nih.gov/project-details/6817669
• 关键词: chemical models; computer simulation; lipid bilayer membrane; molecular chaperones; molecular dynamics; myosins; nuclear magnetic resonance spectroscopy; peptide structure; protein folding; protein structure function; structural biology

The Computational Biophysics Section studies problems of biological significance using several theoretical techniques: molecular dynamics, molecular mechanics, modeling, ab initio analysis of small molecule structure, and molecular graphics. These techniques are applied to a wide variety of macromolecular systems. Specific projects applied to molecules of biomedical interest uses molecular dynamics simulations to predict function or structures of peptides and proteins. Such projects include: - Modeling of Acanthamoeba Myosin II wildtype leucine zipper segment - The study of the catalytic mechanism of D5-3-Ketosteroid Isomerase using QM/MM methods - The study of the catalytic mechanism of N-acetyltransferase using QM/MM methods - The study of the catalytic mechanism of Chorismate Mutase using QM/MM methods Basic research is underway to provide a better understanding of macromolecular systems. The projects include studies of: - Examining chaperonin-mediated protein folding - NMR Shielding Tensor calculations - Lipid bilayer gel phase simulations - Investigating the environmental dependence of nucleic acid structure - Free energy calculations on the leucine zipper domain of yeast transcription factor GCN4 - Protein folding simulation studies - Solvation Free energy force of protein systems - Ligand binding dynamics - Microscopic details of rotational diffusion of perylene in organic solvents The GroEL/GroES chaperonin system facilitates protein folding through a complex cycle involving the capture and encapsulation of substrate proteins. We study the change in the microenvironment felt by substrate proteins as a result of GroEL structural transformations and the effect of peptide binding on the GroEL apical domain binding site and on the peptide. Microenvironment changes due to GroEL structural transformations during the cycle are studied by examining known structures of GroEL (T state), GroEL-7ATP (R) and GroEL-GroES-7ADP (R"). We find that large structural changes occur even prior to GroES binding, and are associated mostly with residues in the apical domain. Multiple sequence alignments show a strong conservation of the chemical character, rather than the residue type, of residues important for the chaperonin functions. We predict that mutations in several strongly conserved charged residues (Lys 262, Gly 252, and Asp 253) lead to reduced efficiency of the annealing action. Molecular dynamics simulations of a solvated apical domain, liganded to a 12-mer polypeptide or unliganded, yield information about the solvent effects and the chaperonin structural dynamics. Upon polypeptide binding, water is completely removed from the peptide binding site. The apical domain manifests a high flexibility at a pair of parallel helices, which execute a transverse translation to accommodate the peptide. This flexibility is reduced upon peptide binding, as shown by the reduced capacity of these two helices to establish hydrogen bonds with water. Charged residues at both ends of these helices, Lys 242, Glu 257, and Arg 268, are likely to play a significant role in peptide unbinding. Their destabilizing effect on the peptide-chaperonin interaction is shown by the reduced hydration compared to the unbound state and the formation of unstable hydrogen bonds to the peptide. These observations are supported by the reduction in surface area of Lys 242 and Glu 257 during the chaperonin cycle. The peptide, which is in a random coil conformation in solution, is forced to adopt a hairpin structure upon binding to apical domain. Protein folding mediated by chaperonin molecules is studied using computer simulations. Our focus is on the GroEL-GroES chaperonin complex of the Escherichia coli, for which the associated structures are known. High-performance scientific computing methods are used, such as coarse-grained and all-atom descriptions of proteins in conjunction with the state-of-the-art CHARMM simulation program. These studies elucidate the effect of chaperones on the protein structure, the mechanism of the chaperonin system, and the timescales in the chaperonin cycle. Ab initio calculations of NMR shielding tensors were performed for comparison with experimental studies for 1H and 15N nuclei. There was little correlation between calculated and experimental values for amide 1H, and role of factors such as basis set, and isotope effect were investigated as potential causes for the discrepancy. An 15N study is currently underway, using the 1H results as a starting point. Free energy calculations on the leucine zipper domain (GCN4-p1) of the yeast transcription factor GCN4 using Molecular Dynamics (MD) under physiological conditions and continuum models. The leucine zipper motif is a parallel left-handed supercoil composed of two a-helices. It is estimated that the native (parallel) alignment is energetically more stable than the non-native antiparallel alignment where electrostatic energies contribute significantly in the overall energetic picture of both orientation as well as to the preference of the parallel vs the antiparallel orientation. Modeling of Acanthamoeba Myosin II wildtype leucine zipper segment using molecular dynamics. This type of analysis has been extended to the modeling of acanthamoeba myosin II wildtype leucine zipper segment using molecular dynamics which examines free energy of solvation and helical packing, while evaluating different alignments of the myosin II wildtype leucine zipper segment. The results suggest likely mechanism for previously unexplained protein mutation behavior. Protein mechanisms are studied by examining different possible pathways in which the mechanism can proceed. This employs quantum mechanical/molecular mechanical techniques using our double link atom method with gaussian blur of MM charges. We have carried out QM/MM simulations N-acetyltransferase to determine whether a proton of the primary amine of serotonin is transferred via a water channel or His120 during catalysis. Similarly, we have examined D5-3-Ketosteroid Isomerase. This enzyme catalyzes the isomerization of the 5,6 double bond of D5-3-ketosteroid isomerase to the 4,5 position. In particular, examine h-bonding interactions between substrate D5-3-ketosteroid and the key residues, Tyr14 and Asp99 at both QM/MM and MM level. The beta-hairpin fold mechanism of a 9-residue peptide is studied through direct folding simulations in explicit water at native folding conditions. Self-guided molecular dynamics (SGMD) simulations have revealed a series of beta-hairpin folding events. For the first time, we successfully observed two-state protein folding phenomena. During these simulations, the peptide folds repeatedly into a major cluster of b-hairpin structures, which agree well with NMR experimental observations. These direct observation of the peptide folding at atomic detail provide us many clues of protein folding mechanism. We find hydration interaction plays a signigicant role in mediating protein folding. It is hydration confinement makes b-hairpin the only energetically favored structure for this peptide to fold.

计算生物物理学部分使用多种理论技术研究具有生物学意义的问题：分子动力学、分子力学、建模、小分子结构从头开始分析和分子图形。这些技术应用于多种大分子系统。 应用于生物医学分子的特定项目使用分子动力学模拟来预测肽和蛋白质的功能或结构。此类项目包括： - 棘阿米巴肌球蛋白 II 野生型亮氨酸拉链片段的建模 - 利用QM/MM方法研究D5-3-酮类固醇异构酶的催化机制 - 利用QM/MM方法研究N-乙酰转移酶的催化机制 - 利用QM/MM方法研究分支酸变位酶的催化机制 基础研究正在进行中，以更好地了解大分子系统。这些项目包括以下方面的研究： - 检查伴侣蛋白介导的蛋白质折叠 - NMR屏蔽张量计算 - 脂质双层凝胶相模拟 - 研究核酸结构的环境依赖性 - 酵母亮氨酸拉链结构域的自由能计算 转录因子GCN4 - 蛋白质折叠模拟研究 - 蛋白质系统的溶剂自由能 - 配体结合动力学 - 苝在有机溶剂中旋转扩散的微观细节 GroEL/GroES 伴侣蛋白系统通过涉及底物蛋白捕获和封装的复杂循环促进蛋白质折叠。我们研究了 GroEL 结构转变导致底物蛋白感受到的微环境的变化，以及肽结合对 GroEL 顶端结构域结合位点和肽的影响。通过检查 GroEL（T 状态）、GroEL-7ATP (R) 和 GroEL-GroES-7ADP (R") 的已知结构，研究了循环期间由 GroEL 结构转变引起的微环境变化。我们发现，甚至在 GroES 结合之前就发生了大的结构变化，并且主要与顶端结构域中的残基相关。多重序列比对显示出化学特征的强烈保守性，而不是残基类型， 对伴侣蛋白功能重要的残基。我们预测几个高度保守的带电残基（Lys 262、Gly 252 和 Asp 253）的突变会导致退火作用效率降低。对与 12 聚体多肽配体或未配体的溶剂化顶端结构域进行分子动力学模拟，可得到有关溶剂效应和伴侣蛋白结构动力学的信息。基于多肽 结合后，水从肽结合位点被完全除去。顶端结构域在一对平行螺旋处表现出高度的灵活性，其执行横向平移以容纳肽。这种灵活性在肽结合时会降低，如这两个螺旋与水建立氢键的能力降低所示。这些螺旋两端的带电残基 Lys 242、Glu 257 和 Arg 268 可能 在肽解结合中发挥重要作用。它们对肽-伴侣蛋白相互作用的不稳定作用表现为与未结合状态相比水合作用的减少以及与肽形成不稳定氢键。这些观察结果得到了伴侣蛋白循环期间 Lys 242 和 Glu 257 表面积减少的支持。该肽在溶液中呈无规卷曲构象，被迫采用 与顶端域结合后的发夹结构。使用计算机模拟研究伴侣蛋白分子介导的蛋白质折叠。我们的重点是大肠杆菌的 GroEL-GroES 伴侣蛋白复合物，其相关结构是已知的。使用高性能科学计算方法，例如结合最先进的 CHARMM 模拟对蛋白质进行粗粒度和全原子描述 程序。这些研究阐明了伴侣蛋白对蛋白质结构的影响、伴侣蛋白系统的机制以及伴侣蛋白循环的时间尺度。 对 NMR 屏蔽张量进行从头计算，以便与 1H 和 15N 核的实验研究进行比较。酰胺 1H 的计算值和实验值之间几乎没有相关性，并且研究了基础组和同位素效应等因素的作用作为差异的潜在原因。目前正在进行一项 15N 研究，以 1H 结果为起点。 在生理条件和连续体模型下，使用分子动力学 (MD) 对酵母转录因子 GCN4 的亮氨酸拉链结构域 (GCN4-p1) 进行自由能计算。亮氨酸拉链图案是由两个α螺旋组成的平行左手超螺旋。据估计，原生（平行）排列在能量上比非原生反平行排列更稳定，其中静电能对两个方向的整体能量图以及平行与反平行方向的偏好有显着贡献。 使用棘阿米巴肌球蛋白 II 野生型亮氨酸拉链片段建模 分子动力学。这种类型的分析已扩展到使用分子动力学对棘阿米巴肌球蛋白 II 野生型亮氨酸拉链片段进行建模，该分子动力学检查溶剂化和螺旋堆积的自由能，同时评估肌球蛋白 II 野生型亮氨酸拉链片段的不同排列。结果表明了先前无法解释的蛋白质突变行为的可能机制。 通过检查该机制可能进行的不同可能途径来研究蛋白质机制。这采用了量子力学/分子力学技术，使用我们的双链接原子方法和 MM 电荷的高斯模糊。我们对 N-乙酰转移酶进行了 QM/MM 模拟，以确定在催化过程中血清素伯胺的质子是否通过水通道或 His120 转移。同样，我们检查了 D5-3-酮类固醇异构酶。该酶催化 D5-3-酮类固醇异构酶的 5,6 双键异构化至 4,5 位。特别是，在 QM/MM 和 MM 水平上检查底物 D5-3-酮类固醇与关键残基 Tyr14 和 Asp99 之间的 h 键相互作用。 通过在天然折叠条件下在纯水中进行直接折叠模拟，研究了 9 个残基肽的 β-发夹折叠机制。自引导分子动力学（SGMD）模拟揭示了一系列β-发夹折叠事件。我们首次成功观察到两种状态的蛋白质折叠现象。在这些模拟过程中，肽反复折叠成 b 发夹结构的主要簇，这与 NMR 实验观察结果非常吻合。这些对原子细节上肽折叠的直接观察为我们提供了蛋白质折叠机制的许多线索。我们发现水合相互作用在介导蛋白质折叠中起着重要作用。正是水合限制使得 b-发夹成为该肽折叠的唯一能量上有利的结构。