Molecular Dynamics Simulations Of Biological Macromolecules

生物大分子的分子动力学模拟

• 批准号: 7968988
• 负责人: Bernard R Brooks
• 金额: $ 67.12万
• 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/7968988
• 关键词: Acids; Active Sites; Address; Affinity; Agreement; Aspartate; Basic Science; Bathing; Behavior; Binding; Biological; Biophysics; Biopolymers; Blood Glucose; Boron; Boronic Acids; Bortezomib; C-Peptide; Caliber; Cancer Center; Carbon; Cells; Cereals; Charge; Chemical Structure; Chemicals; Chemistry; Chickens; Classification; Collaborations; Complex; Computational Biology; Computers; Core Protein; Coupling; Crystallization; DNA Sequence Rearrangement; Dependence; Development; Disease; Due Process; Electron Microscopy; Elements; Environment; Event; FDA approved; Friction; Future; Gene Expression; Heterogeneity; High temperature of physical object; Hydration status; Hydrogen; Image Analysis; Insulin; Investigation; Laboratories; Ligands; Marketing; Methods; Micrococcal Nuclease; Modeling; Molecular; Molecular Conformation; Molecular Models; Motion; Multiple Myeloma; Muramidase; Myosin ATPase; Myosin Type II; NMR Spectroscopy; Nanotubes; National Heart, Lung, and Blood Institute; Nature; Pathway interactions; Patients; Pattern; Peptides; Pharmaceutical Preparations; Phase; Philadelphia; Phosphorylation; Polymers; Power stroke; Property; Proteasome Inhibition; Protein C; Protein Dynamics; Proteins; Reaction; Refractory; Relapse; Research; Research Project Grants; Ribosomes; Sampling; Scallop; Science; Scientist; Series; Signal Transduction; Simulate; Solutions; Solvents; Structure; Structure-Activity Relationship; System; Techniques; Temperature; Testing; Time; Universities; Variant; Velcade; Vertebral column; Work; analog; biological systems; cancer therapy; chaperonin; conventional therapy; design; dimer; evaluation/testing; improved; inhibitor/antagonist; insight; interest; ionization; macromolecule; molecular dynamics; molecular mechanics; molecular modeling; monomer; multicatalytic endopeptidase complex; network models; nitrogen metabolism; nitrogen-regulated response proteins; novel; polyalanine; prevent; programs; protein folding; quantum; research study; simulation; small molecule; theories; therapy design; tool; trend; vibration

Protein folding and conformational search improvements Molecular simulations of protein folding at native conditions with atomic details can elucidate protein-folding events. To overcome the limitation in time scale, an enhanced simulation method, the self-guided molecular/Langevin dynamics (SGMD/SGLD) method was develope to boost systematic motion in molecular systems. This approach is capable of addressing slow events like crystallization, peptide folding, and molecular capturing. It allows us to directly access reversible protein folding events. Protein folding in the cell is not always a spontaneous process due to unproductive pathways of misfolding and aggregation. Chaperonin molecules prevent such off-pathway reactions and promote protein folding through spectacular ATP-driven cycles of binding and releasing substrate proteins. Protein folding in a confined environment. Coarse grained Langevin dynamics was used to examine the stability of different helix-forming sequences confined to a carbon nanotube. Several factors, including sequence, solvent conditions, strength (λ) of nanotube-peptide interactions, and the nanotube diameter (D), determine confinement-induced stability of helices. The results derived are in agreement with polymer theory. There is a strong sequence dependence as the strength of the λ increases. For an amphiphilic sequence, the helical stability increases with λ, whereas for polyalanine the diagram of states is a complex function of λ and D. Decreasing the size of the hydrophobic patch lining the nanotube, which mimics the chemical heterogeneity of the ribosome tunnel, increases the helical stability of the sequence. Our results provide a framework for interpreting the structure formation of peptides in the ribosome tunnel and transport of biopolymers through nanotubes. Protein switches. Many proteins involved in cellular signal transduction switch between inactive and active conformations upon binding or release of ligands. The switching between these conformations of nitrogen regulatory protein C(NtrC) is one of the key steps in bacterial nitrogen metabolism. The structures of the active and inactive forms of NtrC have recently been determined through NMR spectroscopy. NtrC becomes active through phosphorylation of an active site aspartate. We have used multiple SGLD simulations to study the dynamics of the active and the inactive conformation of NtrC. Calculations of pKa values with the finite difference Poisson-Boltzmann method have suggested that phosphorylation can change the pKa value of a His residue that is close to the active site, while SGLD simulations have suggested that phosphorylation combined with charging of this His can stabilize the ensemble of the active form structures. Furthermore the simulations suggested that the regulatory helix may change its conformation through a partial unfolding mechanism. This mechanism is at the core of cellular regulatory mechanisms. Coupling between ionization of internal groups and protein dynamics. Ionization of internal groups in proteins is at the core of energy transduction in biological systems. The ionization can trigger conformational rearrangements, which in turn can change the pKa values of ionizable groups. To study how the protein responds to the ionization of internal groups, we have performed a series of SGLD simulations of variants of staphylococcal nuclease (SN) in which ionizable groups are buried in the protein core. The work was performed in collaboration with Prof. Bertrand Garcia-Moreno at Johns Hopkins University, who has experimentally characterized a large number of variants of SN. The simulations have shown that the protein can respond to charging of internal groups through large scale reorganization of the backbone. They also suggested that such charging events can trigger increased hydration of these internal groups. This study emphasizes the difficulties in calculations of pKa values of internal groups: those of a simultaneous description of changes in hydration patterns and possibly large scale conformational rearrangements. Exploring myosin II efficiency using the Langevin Network Model (LNM). The Langevin Network Model was developed and used to study the power-stroke efficiency of scallop myosin II. Previous normal mode studies of this protein did not consider the effect of solvent friction on behavior. The Langevin Network Model improves upon these by combining the Elastic Network Model (ENM) with Langevin Modes to create a method to calculate protein vibrations in simulated solvent using a relatively small amount of computer time. This new method was used to study pre- and post-power stroke structures of scallop myosin II, along with chicken lysozyme and a 4-bead test system. The Rotne-Prager tensor was used to effect solvent friction for all systems. By comparing the Langevin modes with the frictionless ENM modes, this study showed that the critical power-stroke modes are relatively unperturbed by friction when compared with other modes of the myosin structures. This result can be used as a first step toward examining the structural efficiency of myosin II. Structure and Reaction Mechanisms of Boronic Acids. In collaboration with Charles W. Bock (Philadelphia University), Tony D. James (Bath University, UK), and George D. Markham (FoxChase Cancer Center), the chemical structure and reaction mechanisms of various boronic, borinic, and orthoboric acids have been investigated. Bortezomib (formerly known as PS-341, and marketed as VELCADE) is a novel dipeptidyl boronic acid inhibitor of the S26 proteasome that was recently approved by the FDA for the treatment of patients with relapsed multiple myeloma where the disease is refractory to conventional therapies. Ab initio calculations were performed in several LCB studies on boronic acids (BAs): the structural characterization of BA monomers and dimers; the nature of boron bonding was described (specifically dative, hydrogen, and multiple bonding); and proto- and oxidative-deboronation mechanisms in the solution phase were elucidated. These results provide much needed insight into boron chemistry that will help guide future QM/MM investigations on boronic acid inhibition of proteasomes that show significant promise in cancer therapy. Investigating the effects of a six residue connecting peptide on insulin stability. Insulin is a 51 residue dimer (Chain A 21 residues and Chain B 30 residues) that regulates blood glucose level. Recently a study134 showed improved stability of insulin where a six residue peptide (GGGPRR) was used to connect the C-terminus of the B-chain to the N-terminus of the A-chain. NMR experiments showed that resulting single chain insulin analog (SCI-57) has improved stability over wild type insulin with similar binding affinity. A more refined structure with less fluctuations was observed but the extent of the effects of the connecting peptide is not known. We used molecular dynamics simulations in explicit solvent to investigate the effects of this connecting peptide on insulin using CHARMM. SCI-57 and its two chain analog (2CA) were simulated at various temperatures (300K, 325K, 340K and 350K). Both chains maintained their native conformations at 300K with no significant NOE violations. 2CA shows more fluctuations at the terminal residues compared to SCI-57. At elevated temperatures SCI-57 still maintains its conformation where 2CA starts losing some of its secondary structure elements. For enhanced sampling SGLD simulations are being also performed that show similar trends as seen in the high temperature simulations for both systems. Specific interactions between both chains and the connecting peptide are still being investigated. This project has implications for therapy design.

蛋白质折叠和构象搜索改进 在自然条件下利用原子细节对蛋白质折叠进行分子模拟可以阐明蛋白质折叠事件。为了克服时间尺度的限制，开发了一种增强的模拟方法，即自引导分子/朗之万动力学（SGMD/SGLD）方法来促进分子系统中的系统运动。这种方法能够解决结晶、肽折叠和分子捕获等缓慢事件。它使我们能够直接了解可逆的蛋白质折叠事件。 由于错误折叠和聚集的非生产性途径，细胞中的蛋白质折叠并不总是自发过程。伴侣蛋白分子可防止此类偏离途径的反应，并通过 ATP 驱动的结合和释放底物蛋白的壮观循环促进蛋白质折叠。 蛋白质在有限环境中折叠。 粗粒朗之万动力学用于检查限制在碳纳米管内的不同螺旋形成序列的稳定性。几个因素，包括序列、溶剂条件、纳米管-肽相互作用的强度 (λ) 和纳米管直径 (D)，决定了限制诱导的螺旋稳定性。所得结果与聚合物理论一致。随着 λ 强度的增加，存在很强的序列依赖性。对于两亲性序列，螺旋稳定性随着 λ 的增加而增加，而对于聚丙氨酸，状态图是 λ 和 D 的复杂函数。减小纳米管内衬疏水斑块的尺寸（模拟核糖体隧道的化学异质性）会增加序列的螺旋稳定性。我们的结果为解释核糖体隧道中肽的结构形成以及生物聚合物通过纳米管的运输提供了一个框架。 蛋白质开关。 许多参与细胞信号转导的蛋白质在结合或释放配体时在非活性和活性构象之间切换。 氮调节蛋白C(NtrC)这些构象之间的转换是细菌氮代谢的关键步骤之一。最近通过核磁共振波谱法确定了 NtrC 的活性和非活性形式的结构。 NtrC 通过活性位点天冬氨酸的磷酸化而变得活跃。我们使用多次 SGLD 模拟来研究 NtrC 活性和非活性构象的动力学。 用有限差分Poisson-Boltzmann方法计算pKa值表明磷酸化可以改变靠近活性位点的His残基的pKa值，而SGLD模拟表明磷酸化与该His的充电相结合可以稳定活性形式结构的整体。此外，模拟表明调节螺旋可能通过部分展开机制改变其构象。 该机制是细胞调节机制的核心。 内部基团电离与蛋白质动力学之间的耦合。 蛋白质内部基团的电离是生物系统能量转导的核心。 电离可以触发构象重排，从而改变可电离基团的 pKa 值。为了研究蛋白质如何响应内部基团的电离，我们对葡萄球菌核酸酶 (SN) 的变体进行了一系列 SGLD 模拟，其中可电离基团埋藏在蛋白质核心中。 这项工作是与约翰·霍普金斯大学的 Bertrand Garcia-Moreno 教授合作进行的，他通过实验鉴定了大量 SN 变体的特征。模拟表明，该蛋白质可以通过骨架的大规模重组来响应内部基团的充电。他们还表明，此类充电事件可能会引发这些内部基团的水合作用增加。这项研究强调了计算内部基团 pKa 值的困难：同时描述水合模式变化和可能的大规模构象重排的难度。 使用 Langevin 网络模型 (LNM) 探索肌球蛋白 II 效率。 开发朗之万网络模型并用于研究扇贝肌球蛋白 II 的动力冲程效率。 以前对该蛋白质的正常模式研究没有考虑溶剂摩擦对行为的影响。 Langevin 网络模型通过将弹性网络模型 (ENM) 与 Langevin 模式相结合来改进这些模型，创建一种使用相对少量的计算机时间计算模拟溶剂中蛋白质振动的方法。 这种新方法用于研究扇贝肌球蛋白 II 以及鸡溶菌酶和 4 珠测试系统的动力冲程前和动力冲程后的结构。 Rotne-Prager 张量用于影响所有系统的溶剂摩擦。 通过比较 Langevin 模式与无摩擦 ENM 模式，本研究表明，与肌球蛋白结构的其他模式相比，临界动力冲程模式相对不受摩擦的干扰。 该结果可作为检查肌球蛋白 II 结构效率的第一步。 硼酸的结构和反应机理。 与 Charles W. Bock（费城大学）、Tony D. James（英国巴斯大学）和 George D. Markham（福克斯蔡斯癌症中心）合作，研究了各种硼酸、硼酸和原硼酸的化学结构和反应机制。 Bortezomib（原名 PS-341，商品名 VELCADE）是一种新型的 S26 蛋白酶体二肽基硼酸抑制剂，最近被 FDA 批准用于治疗传统疗法难治的复发性多发性骨髓瘤患者。在多项关于硼酸 (BA) 的 LCB 研究中进行了从头算：BA 单体和二聚体的结构表征；描述了硼键的性质（特别是配位键、氢键和多重键）；并阐明了溶液相中的原始脱硼和氧化脱硼机制。这些结果为硼化学提供了急需的见解，将有助于指导未来硼酸抑制蛋白酶体的 QM/MM 研究，这些研究在癌症治疗中显示出巨大的前景。 研究六残基连接肽对胰岛素稳定性的影响。 胰岛素是一种 51 个残基的二聚体（A 链有 21 个残基，B 链有 30 个残基），可调节血糖水平。最近的一项研究134表明，使用六残基肽 (GGGPRR) 将 B 链的 C 末端连接到 A 链的 N 末端，从而提高了胰岛素的稳定性。 NMR 实验表明，所得单链胰岛素类似物 (SCI-57) 比具有相似结合亲和力的野生型胰岛素具有更高的稳定性。观察到了波动较小的更精细的结构，但连接肽的影响程度尚不清楚。我们在显式溶剂中进行分子动力学模拟，利用 CHARMM 研究这种连接肽对胰岛素的影响。 SCI-57 及其双链类似物 (2CA) 在不同温度（300K、325K、340K 和 350K）下进行模拟。两条链在 300K 时均保持其天然构象，没有明显的 NOE 违规。与 SCI-57 相比，2CA 在末端残基处显示出更多的波动。在高温下，SCI-57 仍保持其构象，其中 2CA 开始失去一些二级结构元素。为了增强采样，还执行了 SGLD 模拟，显示出与两个系统的高温模拟中看到的相似趋势。两条链和连接肽之间的特定相互作用仍在研究中。 该项目对治疗设计具有影响。