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 钠离子通道在细胞的电信号传导中起重要作用。因此，它们是许多药物的靶标，也是动植物来源的天然毒素。 由于突变引起的钠通道的抑制和/或功能不当会导致疾病。 在细菌电压门控钠通道中，钠离子通过孔的通过由由四个谷氨酸残基组成的选择性过滤器（SF）控制。通道中绑定的离子数量可能会有所不同，但平均约为2个。 我们已经在恒定pH和自由能扰动下显示了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。 在生理pH下，有2或3个离子结合，SF最有可能处于完全去质子的状态，也可能是单一质子化状态。有1或0离子绑定，倍增的质子化状态也可以被填充。基于完全开放通道的MD模拟，我们进一步表明，通道的电导量随着每个质子结合到SF而降低。因此，通道的电导依赖于pH，并且随着pH的降低而降低。我们还表明，电导取决于膜的脂质组成。调节通道电导的机制涉及栅极和SF的半径以及孔中的电场的变化。 白色念珠菌分泌的天冬氨酸蛋白酶（SAPS）降解组蛋白5肽的机理 该项目始于测试双连接原子（DLM）方法，以处理氨基酸上QM和MM区域之间的边界。通过最小化去除QM部分之前和之后分子偶极子之间的差异，可以优化氨基酸的MM链接原子的电荷。接下来，使用QM/mm方法研究了SAP-2的HST5裂解机理，主要产生的白色念珠菌的天冬氨酸蛋白酶以及突变对裂解过程的影响。将肽对接到SAP的活性位点是通过限制HST5上活性位点Aspartic（ASP）残基和赖氨酸（LYS）残基之间的距离来执行的。为了找到HST5及其突变体与SAP的结合之间的差异，我们通过将肽从活性位点拉到块状水相。结果显示HST5与SAP的结合的-11 kcal/mol自由能。量子区域的初始构象是通过在酶的肽和ASP之间放置谐波约束来获得的，并且观察到水分子占据了活性位点。反应的中间体和产物状态是通过量子区域的DFT水平的限制性QMMM优化产生的。该机制涉及四面体GEM-DOL中间状态，然后导致酰胺键水解。 CHARMM中的复制路径方法用于找到与Hartree Fock（HF）的QM区理论水平的过渡状态和最小能量路径（MEP），其基于6-31g基集。发现中间状态的形成是反应的限制步骤。但是，现在正在使用更高水平的理论和更复杂的基础集来确认这些结果。在下一步中，我们将使用优化的反应路径开始进行外差抽样，从而使我们能够找到反应的自由能。 通过MD模拟评估NCOV-2019与ACE2结合的临界序列热点： 截至2020年6月，新颖的冠状病毒（NCOV-2019）爆发使世界处于边缘状态，造成了数百万人的案件和成千上万的死亡，更不用说危机的社会和经济影响了。 NCOV-2019的尖峰蛋白通过将其受体结合结构域（RBD）与宿主细胞表面受体蛋白，血管紧张素转化剂酶（ACE2）结合到宿主细胞中的病毒体表面上。在这项研究中，我们提供了一种详细的结构机制，即NCOV-2019如何通过广泛的分子动力学（MD）模拟在2002年与ACE2识别和建立与ACE2及其与早期冠状病毒SARS-COV的差异。我们的结果表明，NCOV-2019 RBD与SARS-COV相关的ACE2具有明显高的ACE2结合，而SARS-COV与其更高的感染率相关。每个救济的自由能分解指出了NCOV-2019 RBD残基Lys417，Tyr505，GLN498，GLN493在结合ACE2中的关键作用。在世界各地的人类分离的NCOV-2019菌株的RBD中已经发现了许多突变。在这项研究中，我们调查了这些突变以及其他ALA扫描突变对RBD/ACE2复合物稳定性的影响。发现大多数天然发生的RBD突变要么略微增强，要么与ACE2具有与野生型NCOV-2019相同的结合亲和力。这意味着该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的努力都具有影响，因为这些突变可以充当抗体逃生突变体。此外，内部的ALA扫描和长时间尺度的MD模拟突出了残基在RBD和ACE2界面上的关键作用，这些作用可用作任何药物开发努力的潜在药物算体。从进化的角度来看，这项研究还确定了该病毒是如何从其前身SARS-COV演变而来的，以及如何进一步发展以变得更加感染。 探索SARS-COV-2中峰值糖蛋白的动态和网络分析 冠状病毒SARS-COV-2引起的持续大流行继续遭受对人类健康和全球经济的毁灭性后果。冠状病毒表面上的尖峰糖蛋白介导了其进入宿主细胞的进入，并且是所有抗体设计工作的目标，以中和该病毒。尖峰的聚糖护罩通过为任何抗体提供厚厚的糖涂层屏障来帮助病毒逃避人类的免疫反应。为了研究尖峰蛋白中聚糖的动态运动，我们在两个不同状态下对峰值蛋白进行了微秒长的MD模拟，这些状态与开放式或封闭构象中的受体结合结构域相对应。对这一长度模拟的分析表明，夹层器中相邻单体的N末端结构域进行了剪裁的运动。通过网络分析发现了多种聚糖在不同区域屏蔽峰值蛋白质中的作用。图理论中的中心度测量帮助我们确定了在网络中扮演本地或全球角色的聚糖。发现茎区域具有高的当地核心，从而有效地屏蔽了该领域。另一方面，可以在尖峰蛋白的顶点中发现违规行为，以结合和中和病毒。在聚糖网络中确定了几个聚糖（例如N234和N165）的作用。鉴定出具有高度在这些微区域的高度沟通的小域的微域，因此大多数抗体会与这些微区域之间的区域结合。抗体重叠分析揭示了聚糖微域以及单个聚糖，它们抑制了峰值蛋白上抗体表位的获取。我们的分析表明，当RBD处于开放状态时，峰值蛋白更容易受到抗体的影响。总体而言，这项研究的结果提供了对尖峰聚糖屏蔽层的详细了解，该盾牌必须考虑到任何合理抗体设计项目。