Molecular Dynamics Simulations Of Biological Macromolecules

生物大分子的分子动力学模拟

• 批准号: 10008753
• 负责人: Bernard R Brooks
• 金额: $ 94.88万
• 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/10008753
• 关键词: ATP Hydrolysis; Active Sites; Address; Adopted; Affect; Affinity; Animal Sources; Antifungal Agents; Aspartic Endopeptidases; Basic Science; Binding; Binding Sites; Biological; Biophysics; Candida albicans; Cell Membrane Permeability; Cell physiology; Cells; Cleaved cell; Complex; Computational Biology; Cryoelectron Microscopy; Crystallization; Databases; Defense Mechanisms; Dependence; Development; Dimerization; Disease; Docking; Electron Microscopy; Electrons; Electrophysiology (science); Enzyme Stability; Enzymes; Evaluation; Exhibits; Family; Free Energy; Gene Expression Profiling; Glutamates; Glycols; HIV-1; Head; Human; Image Analysis; Inflammatory; Ion Channel; Ionic Strengths; Ions; Kinesin; Laboratories; Lead; Malignant Neoplasms; Maps; Mediating; Meiosis; Methods; Microtubules; Mitosis; Modeling; Molecular; Molecular Conformation; Molecular Motors; Motion; Motor; Movement; Mucous Membrane; Mutagenesis; Mutation; National Heart, Lung, and Blood Institute; Nuclear; Octanols; Partition Coefficient; Pathway interactions; Peptides; Pharmaceutical Preparations; Phase; Phosphorylation; Phosphotransferases; Physiological; Plant Sources; Play; Power stroke; Property; Protein Kinase; Proteins; Protons; Quantum Mechanics; Research; Research Project Grants; Resolution; Roentgen Rays; Role; Saliva; Sampling; Science; Scientist; Serine; Signal Pathway; Signal Transduction; Sodium Channel; Solvents; Source; Stroke; Structure; Structure-Activity Relationship; Surface; System; Techniques; Temperature; Testing; Thermodynamics; Time; Toxin; Tyrosine; Vertebral column; Virus Diseases; Walking; Water; aqueous; biophysical properties; blind; deep learning; design; dimer; drug efficacy; enzyme activity; enzyme structure; experimental study; flexibility; histatin 5; inhibitor/antagonist; insight; interest; intermolecular interaction; macromolecule; microscopic imaging; molecular dynamics; molecular mechanics; molecular modeling; mutant; pathogen; programs; protein complex; protein protein interaction; protonation; quantum; response; simulation; small molecule; sodium ion; theories; tool; voltage

pH dependance of a Na channel Sodium ion channels play an important role in electrical signaling in cells; as such they are the targets of many drugs, as well as naturally occurring toxins from plant and animal sources. Inhibition and/or improper functioning of these channels due to mutation can lead to disease. The passage of sodium ions through bacterial voltage-gated sodium ion channels are controlled by a selectivity filter (SF) comprised of four glutamate residues. While it is known that the protonation state of the SF residues can alter the ability to ferry sodium ions, the existence of multiple proton binding sites in these channels makes it challenging to interpret the results of mutagenesis/electrophysiological experiments. Molecular dynamics (MD) simulations at constant pH offer a way to study pH-dependent effects with atomic-level detail. Na channels exhibit a decrease in conductance with lowering of pH. The selectivity filter (SF) of bacterial Na channels consists of four glutamate residues. The protonation states in the SF has been shown to modulate the number of bound Na+ ions, and most likely the conductivity. We study the protonation states in the SF of a bacterial Na channel through molecular dynamics, free energy perturbation as well as constant pH simulations. The simulations show that the number of bound ions influences the protonation state of the SF. With 2 or 3 ions bound, at physiological pH, the SF is most likely in fully deprotonated state, and possibly also the singly protonated state. With 1 or 0 ions bound, the doubly protonated state can also get populated. We are currently investigating the pH dependence of conductance of a bacterial ion channel (NavMs) which is known to exhibit a decrease in conductance with lowering of pH. Ionic Strength Induced Protein-Protein Interactions Protein kinases are dynamic and can adopt many conformational states, including active, inactive, and intermediate states which can represent an array of structural features that distinguish the ability of the protein to bind other molecules. Revealing the transitions between the conformational states of protein complexes is critical for effective rational design, as it would allow deeper insights into the structure function properties. Improper signaling of the nuclear factor-B (NF-B) pathway plays a critical role in many inflammatory disease states including cancer, stroke, and viral infections. While the signaling pathways are known, how these molecular mechanisms respond to changes in the intracellular microenvironment such as pH, ionic strength, and temperature, remains elusive. Molecular dynamics simulations were used to investigate how mutations and the ionic strength affect dimerization of the protein assembly to probe the affinity for tyrosine and serine phosphorylation activation mechanisms. Intermolecular interactions, thermodynamic properties, and conformational changes were compared among the inactive, active, and null states of the kinase. Results suggest that the multimeric assembly mediates a global stability for the enzyme that influences the activity of IKK and offers insight into which activation mechanism is preferred. Kinesin walking mechanism from SGLD simulations. Kinesin belongs to a family of molecular motors characterized by unidirectional movement along microtubules from the center of a cell to its periphery. Kinesin converts the energy of ATP hydrolysis into stepping movement along microtubules, which supports several vital cellular functions including mitosis, meiosis, and the transport of cellular cargo. Because kinesin is a fundamental protein, further research on the topic will provide important information as to how it functions. Combined with low resolution electron microscopic images, self-guided Langevin dynamics simulations are performed to study molecular motion and conformational change of kinesin motor domain in water and binding with microtubule. SGLD enable simulation to reach the time scale required for conformational change to understand the role of ATP binding and interaction with microtubules. Through flexible fitting of two newly release cryo-EM maps, we derived atomic structures of the kinesin dimer-microtubule complexes in both two-head-bound and one-head bound states. To identify which head generating the cargo moving force, we designed atomic force simulations to examine the responses of the two heads to dragging forces. Our simulation results show the leading head can provide a necessary force to perform the power stroke while the trailing head cannot stand for even a 5pN dragging force. A structure comparison between two-head-bound and one-head bound states also supports the conclusion that the leading head is the source of the cargo moving force. Also, in this study, through molecular simulations and free energy calculations, we found that in aqueous solution, kinesin favors an extended form with its microtubule-binding interface (MTBI) motif unfolded, as seen in a recent x-ray structure of kinesin-8. The transition between the extended and compact forms, the structural differences of the leading and trailing heads, and atomic force simulations lead us to a completely new mechanism by which kinesin dimers walk on microtubules. Mechanism of degradation of Histatin 5 peptide by Secreted Aspartic Protease (SAPS) of C. Albicans: Candida Albicans is a fungal opportunistic pathogen that commonly colonizes mucosal surfaces. Histatin 5 (Hst-5) is a 24 residue peptide in human saliva that has strong antifungal activity against C. Albicans. However, the pathogen has Secreted Aspartic Protease (SAPS) enzyme as part of its defense mechanism that cleaves Histatin 5 in a Lys residue and mutation of Lys to either Arg leads to intact peptide. We are studying the mechanism of cleavage of this enzyme and the difference between wild type and the Arg mutant that leads to decreased activity of enzyme. Crystal structure of the enzyme is in complex with an inhibitor. In order to dock the peptide to active site of protein we have removed the inhibitor and ran MD simulation on the enzyme and then docked the peptide (Hst5) to the active site of SAPS. We are using replica exchange umbrella sampling (REUS) to obtain the binding free energy of the peptide by pulling the peptide from the active site to bulk water phase. It is shown that most aspartic protease enzymes such as HIV-1 nucleophilic attack of water molecule activated by Asp residue in enzyme initiates the formation of gem-diol intermediate state in the backbone of peptide which lead to its cleavage. The suitable structure for cleavage of peptide which involves a water molecule is obtained from REUS simulation. Next, we are going to use QM/MM with a high level DFT in Quantum level to investigate the mechanism of cleavage of the enzyme. Prediction of water/octanol partition coefficients for the SAMPL6 blind challenge, Part 2 The water-octanol partition coefficient, log P, is an important parameter for efficacy of drug-like small molecules and an important intermediate for estimating log D and membrane permeability. We used three different approaches for our predictions: classical molecular mechanics using off-the-shelf as well as re-optimized molecular models (MM), implicit-solvent quantum mechanics with different basis sets and different levels of theory (QM), and deep learning from online databases (ML). The results were satisfactory: the three methods predicted log P for 11 molecules with a mean absolute error of 0.7 (MM), 1.0 (QM), and 0.5 (ML) and an RMSE of 0.8 (MM), 1.1 (QM), and 0.6 (ML).

Na 通道的 pH 依赖性 钠离子通道在细胞电信号传导中发挥重要作用；因此，它们是许多药物以及植物和动物来源的天然毒素的目标。由于突变而导致这些通道的抑制和/或功能异常可能导致疾病。钠离子通过细菌电压门控钠离子通道的通道由由四个谷氨酸残基组成的选择性过滤器 (SF) 控制。虽然已知 SF 残基的质子化状态可以改变转运钠离子的能力，但这些通道中多个质子结合位点的存在使得解释诱变/电生理实验的结果具有挑战性。恒定 pH 条件下的分子动力学 (MD) 模拟提供了一种通过原子级细节研究 pH 依赖性效应的方法。 Na 通道的电导随着 pH 值的降低而降低。细菌Na通道的选择性过滤器（SF）由四个谷氨酸残基组成。 SF 中的质子化状态已被证明可以调节结合的 Na+ 离子的数量，并且很可能调节电导率。我们通过分子动力学、自由能扰动以及恒定 pH 模拟来研究细菌 Na 通道 SF 中的质子化状态。模拟表明，结合离子的数量影响 SF 的质子化状态。当 2 或 3 个离子结合时，在生理 pH 值下，SF 最有可能处于完全去质子化状态，也可能处于单质子化状态。当有 1 个或 0 个离子结合时，双质子化状态也可以得到填充。我们目前正在研究细菌离子通道 (NavMs) 电导的 pH 依赖性，已知该通道的电导随着 pH 值的降低而降低。 离子强度诱导蛋白质-蛋白质相互作用 蛋白激酶是动态的，可以采用多种构象状态，包括活性、非活性和中间状态，这些状态可以代表一系列区分蛋白质结合其他分子的能力的结构特征。揭示蛋白质复合物构象状态之间的转变对于有效的合理设计至关重要，因为它将允许更深入地了解结构功能特性。核因子 B (NF-B) 通路的不当信号传导在许多炎症性疾病中发挥着关键作用，包括癌症、中风和病毒感染。虽然信号传导途径已知，但这些分子机制如何响应细胞内微环境（例如 pH、离子强度和温度）的变化仍然难以捉摸。使用分子动力学模拟来研究突变和离子强度如何影响蛋白质组装的二聚化，以探测酪氨酸和丝氨酸磷酸化激活机制的亲和力。比较了激酶的非活性、活性和无效状态之间的分子间相互作用、热力学性质和构象变化。结果表明，多聚体组装介导了影响 IKK 活性的酶的整体稳定性，并提供了对哪种激活机制是首选的见解。 SGLD 模拟中的驱动蛋白行走机制。 驱动蛋白属于分子马达家族，其特征是沿着微管从细胞中心到其外围进行单向运动。驱动蛋白将 ATP 水解的能量转化为沿着微管的步进运动，支持多种重要的细胞功能，包括有丝分裂、减数分裂和细胞货物运输。由于驱动蛋白是一种基本蛋白质，因此对该主题的进一步研究将提供有关其功能的重要信息。结合低分辨率电子显微镜图像，进行自引导朗之万动力学模拟，研究水中驱动蛋白运动域的分子运动和构象变化以及与微管的结合。 SGLD 使模拟能够达到构象变化所需的时间尺度，以了解 ATP 结合以及与微管相互作用的作用。通过灵活拟合两个新发布的冷冻电镜图，我们得出了双头结合和单头结合状态下驱动蛋白二聚体-微管复合物的原子结构。为了确定哪个头产生货物移动力，我们设计了原子力模拟来检查两个头对拖曳力的响应。我们的模拟结果表明，前头可以提供执行动力冲程所需的力，而后头甚至无法承受 5pN 的拖动力。双头束缚状态和单头束缚状态的结构比较也支持了前头是货物移动力来源的结论。此外，在这项研究中，通过分子模拟和自由能计算，我们发现在水溶液中，驱动蛋白有利于其微管结合界面（MTBI）基序展开的延伸形式，如最近驱动蛋白的X射线结构所示- 8. 延伸形式和紧凑形式之间的转变、前导头和尾随头的结构差异以及原子力模拟使我们发现了驱动蛋白二聚体在微管上行走的全新机制。 白色念珠菌分泌性天冬氨酸蛋白酶 (SAPS) 降解组氨酸 5 肽的机制： 白色念珠菌是一种真菌机会致病菌，通常定植于粘膜表面。组蛋白 5 (Hst-5) 是人类唾液中的一种 24 残基肽，对白色念珠菌具有很强的抗真菌活性。然而，病原体具有分泌性天冬氨酸蛋白酶 (SAPS) 作为其防御机制的一部分，该酶会裂解 Lys 残基中的组蛋白 5，并且 Lys 突变为任一 Arg 都会导致完整的肽。我们正在研究这种酶的裂解机制以及野生型和精氨酸突变体之间导致酶活性降低的差异。酶的晶体结构与抑制剂复合。为了将肽对接至蛋白质的活性位点，我们去除了抑制剂并对酶进行 MD 模拟，然后将肽 (Hst5) 对接至 SAPS 的活性位点。我们使用复制品交换伞采样 (REUS)，通过将肽从活性位点拉至本体水相来获得肽的结合自由能。结果表明，大多数天冬氨酸蛋白酶，例如HIV-1，通过酶中的Asp残基激活水分子的亲核攻击，引发肽主链中偕二醇中间态的形成，从而导致其裂解。从 REUS 模拟中获得了适合切割涉及水分子的肽的结构。接下来，我们将使用量子水平上高水平DFT的QM/MM来研究酶的裂解机制。 SAMPL6 盲挑战的水/辛醇分配系数预测，第 2 部分 水-辛醇分配系数 log P 是药物样小分子功效的重要参数，也是估计 log D 和膜渗透性的重要中间值。我们使用三种不同的方法进行预测：使用现成的经典分子力学以及重新优化的分子模型（MM）、具有不同基础集和不同理论水平（QM）的隐式溶剂量子力学以及深度量子力学。从在线数据库（ML）中学习。结果令人满意：三种方法预测 11 个分子的 log P，平均绝对误差为 0.7 (MM)、1.0 (QM) 和 0.5 (ML)，RMSE 为 0.8 (MM)、1.1 (QM) 和0.6（毫升）。