Molecular Dynamics Simulations Of Biological Macromolecules

生物大分子的分子动力学模拟

• 批准号: 10262664
• 负责人: Bernard R Brooks
• 金额: $ 106.72万
• 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/10262664
• 关键词: 2019-nCoV; Active Sites; Address; Affinity; Amides; Amino Acids; Angiotensins; Animal Sources; Antibodies; Aspartic Endopeptidases; Basic Science; Binding; Biological; Biophysics; Candida albicans; Cell Surface Receptors; Cells; Cessation of life; Charge; Communication; Complex; Computational Biology; Coronavirus; Development; Disease; Disease Outbreaks; Docking; Electron Microscopy; Enzymes; Epitopes; Escape Mutant; Evaluation; Evolution; Free Energy; Gene Expression Profiling; Glutamates; Glycols; Glycoproteins; Health; Hot Spot; Human; Hydrolysis; Image Analysis; Immune response; Individual; Ions; Laboratories; Lead; Link; Lipids; Lysine; Measurement; Mediating; Membrane; Methodology; Methods; Modeling; Molecular Conformation; Motion; Multienzyme Complexes; Mutation; N-terminal; National Heart, Lung, and Blood Institute; Pathway Analysis; Peptides; Pharmaceutical Preparations; Phase; Physiological; Plant Sources; Play; Polysaccharides; Process; Proteins; Protons; Quantum Mechanics; Quantum Theory; Radial; Reaction; Research; Research Project Grants; Role; SARS coronavirus; Sampling; Scanning; Science; Scientist; Signal Transduction; Sodium Channel; Structure; Structure-Activity Relationship; Surface; System; Techniques; Testing; Thick; Toxin; Vaccine Design; Virion; Virus; Water; base; biophysical properties; design; drug development; economic impact; electric field; graph theory; histatin 5; in silico; infection rate; interest; macromolecule; molecular dynamics; molecular mechanics; molecular modeling; monomer; mutant; mutation screening; novel coronavirus; pandemic disease; pharmacophore; programs; quantum; receptor; receptor binding; restraint; simulation; small molecule; sodium ion; sugar; 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 sodium channels due to mutation can lead to disease. In bacterial voltage gated sodium channels, the passage of sodium ions through the pore is controlled by a selectivity filter (SF) comprised of four glutamate residues. The number of ions bound in the channel can vary, but is about 2 on average. We have shown with MD simulations at constant pH and with free energy perturbation that the pKa values of the four SF glutamate residues depend on the number of ions bound in the channel. 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. Based on the MD simulations of the fully open channel, we have further shown that the conductance of the channel decreases with each proton bound to the SF. Thus the conductance of the channel is pH dependent, and decreases with lowering of pH. We also show that the conductance depends on the lipid composition of the membrane. The mechanisms involved in modulation of the channel conductances involves changes in the radius of the gate and the SF, as well as the electric field in the pore. Mechanism of degradation of Histatin 5 peptide by Secreted Aspartic Protease (SAPS) of C. Albicans This project started with testing the double link atom (DLM) methodology to treat the boundary between QM and MM regions on Amino Acids. The charge of MM link atom for Amino Acids was optimized by minimizing the difference between the dipole of the molecule before and after removing the QM part. Next, mechanism of cleavage of Hst5 by Sap-2 the major produced Aspartic Protease of C. Albicans and the effect of mutation on the cleavage process was studied with QM/MM methodology. Docking the peptide to the active site of Saps is performed by restraining the distance between the active site aspartic (Asp) residues and the lysine (Lys) residue on Hst5. To find difference between binding of Hst5 and its mutants to SAP we performed replica exchange umbrella sampling (REUS) of the peptide by pulling the peptide from active site to bulk water phase. The results showed a -11 kcal/mol free energy of binding for Hst5 to SAP. Initial conformation for quantum region is obtained by putting a harmonic restraint between Lys of the peptide and Asp of the enzyme and it is observed that water molecules occupy the active site. Intermediate and product states of the reaction are produced by restrained QMMM optimization with DFT level of theory for quantum region. The mechanism involves a tetrahedral gem-diol intermediate state which then leads to amide bond hydrolysis. A replica path method in CHARMM was used to find transition state and minimum energy path (MEP) of the reaction with Hartree Fock (HF) level of theory of QM region with 6-31G basis set. It was found that the formation of the intermediate state is the limiting step of the reaction. However, a higher level of theory and a more complex basis set is now being used to confirm these results. In the next step, we will use the optimized reaction path to start an off-path sampling which allows us to find the free energy of the reaction. Critical Sequence Hot-spots for Binding of nCOV-2019 to ACE2 as Evaluated by MD simulations: The novel coronavirus (nCOV-2019) outbreak has put the world on edge, causing millions of cases and hundreds of thousands of deaths all around the world, as of June 2020, let alone the societal and economic impacts of the crisis. The spike protein of nCOV-2019 resides on the virions surface mediating coronavirus entry into host cells by binding its receptor binding domain (RBD) to the host cell surface receptor protein, angiotensin converter enzyme (ACE2). In this study we have provided a detailed structural mechanism of how nCOV-2019 recognizes and establishes contacts with ACE2 and its difference with an earlier coronavirus SARS-COV in 2002 via extensive molecular dynamics (MD) simulations. Our results showed that nCOV-2019 RBD binds ACE2 with a significantly higher affinity () than SARS-COV which correlates with its higher infection rate. A per-residue free energy decomposition pinpointed the critical role of nCOV-2019 RBD residues Lys417, Tyr505, Gln498, Gln493 in binding ACE2. Numerous mutations have been identified in the RBD of nCOV-2019 strains isolated from humans in different parts of the world. In this study, we investigated the effect of these mutations as well as other Ala-scanning mutations on the stability of RBD/ACE2 complex. It is found that most of the naturally occurring mutations to the RBD either slightly strengthen or have the same binding affinity to ACE2 as the wild-type nCOV-2019. This means the virus had sufficient binding affinity to its receptor at the beginning of the crisis. This also have implications for any vaccine design endeavors since these mutations could act as antibody escape mutants. Furthermore, in-silico Ala-scanning and long-timescale MD simulations, highlight the crucial role of the residues at the interface of RBD and ACE2 that may be used as potential pharmacophores for any drug development endeavors. From an evolutional perspective, this study also identifies how the virus has evolved from its predecessor SARS-COV and how it could further evolve to become even more infectious. Exploring dynamics and network analysis of spike glycoprotein in SARS-COV-2 The ongoing pandemic caused by coronavirus SARS-COV-2 continues to rage with devastating consequences on human health and global economy. A spike glycoprotein on the surface of coronavirus mediates its entry into host cells and is the target of all antibody design efforts to neutralize the virus. The glycan shield of the spike helps the virus to evade the human immune response by providing a thick sugar-coated barrier against any antibody. To study the dynamic motion of glycans in the spike protein we performed microsecond-long MD simulation on the spike protein in two different states that correspond to the receptor binding domain in open or closed conformations. Analysis of this microsecond-long simulation revealed a scissoring motion on the N-terminal domain of neighboring monomers in the trimer. Role of multiple glycans in shielding of spike protein in different regions were uncovered by a network analysis. Centrality measurements in graph theory helped us identify glycans that play local or global roles in the network. It was found that the stalk region glycans have high local centralities which give rise to an effective shielding of this domain. On the other hand, breaches can be found in the apex of the spike protein for antibodies to bind and neutralize the virus. Role of several glycan such as N234 and N165 were pinpointed in the network of glycan. Microdomains of glycans were identified featuring a high degree of intra-communication in these microdomains and therefore most antibodies would bind to regions between these microdomains. An antibody overlap analysis revealed the glycans microdomains as well as individual glycans that inhibit access to the antibody epitopes on the spike protein. Our analysis showed that the spike protein is more vulnerable to antibodies when the RBD is in the open state. Overall, the results of this study provide detailed understanding of the spike glycan shield which must be considered for any rational antibody design project.

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。 由于突变导致钠通道的抑制和/或功能异常可能导致疾病。 在细菌电压门控钠通道中，钠离子通过孔的通道由由四个谷氨酸残基组成的选择性过滤器 (SF) 控制。通道中结合的离子数量可能有所不同，但平均约为 2 个。 我们通过在恒定 pH 和自由能扰动下的 MD 模拟表明，四个 SF 谷氨酸残基的 pKa 值取决于通道中结合的离子数量。 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。基于完全开放通道的 MD 模拟，我们进一步表明，通道的电导随着每个质子与 SF 的结合而降低。因此，通道的电导与 pH 值相关，并且随着 pH 值的降低而降低。我们还表明电导取决于膜的脂质成分。通道电导调制涉及的机制涉及栅极和 SF 半径以及孔内电场的变化。 白色念珠菌分泌型天冬氨酸蛋白酶 (SAPS) 降解组氨酸 5 肽的机制 该项目首先测试双链原子 (DLM) 方法来处理氨基酸上 QM 和 MM 区域之间的边界。通过最小化去除 QM 部分前后分子偶极子之间的差异来优化氨基酸 MM 连接原子的电荷。接下来，利用QM/MM方法研究了白色念珠菌主要产生的天冬氨酸蛋白酶Sap-2切割Hst5的机制以及突变对切割过程的影响。通过限制 Hst5 上活性位点天冬氨酸 (Asp) 残基和赖氨酸 (Lys) 残基之间的距离，将肽与 Saps 活性位点对接。为了找出 Hst5 及其突变体与 SAP 结合之间的差异，我们通过将肽从活性位点拉至本体水相来对肽进行复制交换伞采样 (REUS)。结果显示 Hst5 与 SAP 的结合自由能为 -11 kcal/mol。通过在肽的Lys和酶的Asp之间进行调和约束获得量子区的初始构象，并且观察到水分子占据活性位点。反应的中间态和产物态是通过量子区域的 DFT 理论水平的约束 QMMM 优化产生的。该机制涉及四面体偕二醇中间态，然后导致酰胺键水解。 CHARMM中的复制路径方法用于寻找具有6-31G基组的QM区域理论的Hartree Fock（HF）水平反应的过渡态和最小能量路径（MEP）。研究发现中间态的形成是反应的限制步骤。然而，现在正在使用更高水平的理论和更复杂的基础集来证实这些结果。在下一步中，我们将使用优化的反应路径来启动路径外采样，这使我们能够找到反应的自由能。 MD 模拟评估 nCOV-2019 与 ACE2 结合的关键序列热点： 截至 2020 年 6 月，新型冠状病毒 (nCOV-2019) 的爆发让世界陷入紧张，在全世界造成数百万病例和数十万人死亡，更不用说这场危机的社会和经济影响了。 nCOV-2019 的刺突蛋白驻留在病毒粒子表面，通过将其受体结合域 (RBD) 与宿主细胞表面受体蛋白血管紧张素转化酶 (ACE2) 结合，介导冠状病毒进入宿主细胞。在这项研究中，我们通过广泛的分子动力学 (MD) 模拟，提供了 nCOV-2019 如何识别并与 ACE2 建立联系的详细结构机制，以及它与 2002 年早期冠状病毒 SARS-COV 的区别。我们的结果表明，nCOV-2019 RBD 与 ACE2 的结合亲和力明显高于 SARS-COV，这与其较高的感染率相关。每个残基的自由能分解确定了 nCOV-2019 RBD 残基 Lys417、Tyr505、Gln498、Gln493 在结合 ACE2 中的关键作用。在从世界不同地区的人类身上分离出的 nCOV-2019 毒株的 RBD 中发现了许多突变。在这项研究中，我们研究了这些突变以及其他丙氨酸扫描突变对 RBD/ACE2 复合物稳定性的影响。研究发现，大多数 RBD 天然发生的突变对 ACE2 的结合亲和力与野生型 nCOV-2019 略有增强或具有相同的结合亲和力。这意味着病毒在危机开始时与其受体具有足够的结合亲和力。这也对任何疫苗设计工作都有影响，因为这些突变可能充当抗体逃逸突变体。此外，计算机丙氨酸扫描和长时间尺度的 MD 模拟强调了 RBD 和 ACE2 界面残基的关键作用，这些残基可用作任何药物开发工作的潜在药效团。从进化的角度来看，这项研究还确定了该病毒如何从其前身 SARS-COV 进化而来，以及如何进一步进化以变得更具传染性。 探索 SARS-COV-2 中刺突糖蛋白的动力学和网络分析 由冠状病毒 SARS-COV-2 引起的持续流行病继续肆虐，对人类健康和全球经济造成毁灭性后果。冠状病毒表面的刺突糖蛋白介导其进入宿主细胞，是所有中和病毒的抗体设计工作的目标。刺突的聚糖屏蔽通过提供针对任何抗体的厚糖衣屏障，帮助病毒逃避人类免疫反应。为了研究刺突蛋白中聚糖的动态运动，我们对两种不同状态下的刺突蛋白进行了微秒长的 MD 模拟，这两种状态对应于开放或闭合构象的受体结合域。对这一微秒长模拟的分析揭示了三聚体中相邻单体的 N 末端结构域的剪切运动。通过网络分析揭示了多个聚糖在不同区域屏蔽刺突蛋白中的作用。图论中的中心性测量帮助我们识别在网络中发挥局部或全局作用的聚糖。研究发现，茎区聚糖具有较高的局部中心性，这导致了该结构域的有效屏蔽。另一方面，在刺突蛋白的顶端可以发现缺口，以便抗体结合并中和病毒。确定了多种聚糖（例如 N234 和 N165）在聚糖网络中的作用。聚糖的微域被鉴定为这些微域中具有高度的内部通信，因此大多数抗体会结合到这些微域之间的区域。抗体重叠分析揭示了聚糖微结构域以及抑制访问刺突蛋白上抗体表位的单个聚糖。我们的分析表明，当 RBD 处于开放状态时，刺突蛋白更容易受到抗体的影响。总的来说，这项研究的结果提供了对尖峰聚糖屏蔽的详细了解，任何合理的抗体设计项目都必须考虑这一点。