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 在具有原子细节的天然条件下蛋白质折叠的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，一种增强的模拟方法，自引导的分子/langevin动力学（SGMD/SGLD）方法是发展分子系统中系统运动的发展。这种方法能够解决慢速事件，例如结晶，肽折叠和分子捕获。它使我们能够直接访问可逆的蛋白质折叠事件。 由于错误折叠和聚集的途径，细胞中的蛋白质折叠并不总是自发的。伴侣蛋白分子通过壮观的ATP驱动的结合和释放底物蛋白来防止这种脱路反应并促进蛋白质折叠。 蛋白质折叠在密闭环境中。 粗粒状的兰格文动力学用于检查局限于​​碳纳米管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），确定螺旋螺旋的稳定性。得出的结果与聚合物理论一致。随着λ强度的增加，序列的依赖性很强。对于两亲性序列，螺旋稳定性随λ的增加而增加，而对于多酰胺，状态图是λ和D的复杂函数。减小纳米管内衬的疏水贴片的大小，它们模拟了核糖体隧道的化学异质性，从而增加了核心隧道的异质性。我们的结果为解释核糖体隧道中肽的结构形成和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。 在结合或释放配体时，许多参与细胞信号转导的蛋白质在非活性和活性构象之间切换。 氮调节蛋白C（NTRC）的这些构象之间的切换是细菌氮代谢的关键步骤之一。 NTRC的活性和非活动形式的结构最近通过NMR光谱确定。 NTRC通过天冬氨酸的活性位点的磷酸化变得活跃。我们已经使用了多个SGLD仿真来研究NTRC的活性和非活动构象的动力学。 用有限差的POISSON-BOLTZMANN方法对PKA值的计算表明，磷酸化可以改变接近活性位点的残留物的PKA值，而SGLD模拟表明磷酸化结合了与此磷酸化相结合的，他可以稳定活性形式结构的结构。此外，模拟表明，调节螺旋可以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。 内部组和蛋白质动力学之间的电离之间的耦合。 蛋白质内部组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，进而可以改变可电离基团的PKA值。为了研究蛋白质如何响应内部组的电离，我们对葡萄球菌核酸酶（SN）的变体进行了一系列SGLD模拟，其中将可电离基团埋在蛋白质核心中。 这项工作是与约翰·霍普金斯大学（Johns Hopkins University）的贝特兰·加西亚·莫雷诺（Bertrand Garcia-Moreno）教授合作进行的，后者在实验上描述了大量SN的变体。模拟表明，该蛋白质可以通过大规模重组主链来应对内部组的充电。他们还建议这样的充电事件可以触发这些内部组的水合增加。这项研究强调了内部组PKA值的困难：对水合模式变化以及可能大规模构象重排的同时描述。 使用Langevin网络模型（LNM）探索肌球蛋白II效率。 开发了Langevin网络模型，并用于研究扇贝肌球蛋白II的功率效率。 该蛋白质的先前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，以创建一种使用相对较少的计算机时间来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的动力和后动力中风结构，以及鸡溶菌酶和4珠测试系统。 Rotne-prager张量用于对所有系统作用溶剂摩擦。 通过将Langevin模式与无摩擦ENM模式进行比较，这项研究表明，与肌球蛋白结构的其他模式相比，临界功率中风模式相对不受摩擦的影响。 该结果可以用作研究肌球蛋白II的结构效率的第一步。 硼酸的结构和反应机制。 与查尔斯·W·博克（费城大学），托尼·D·詹姆斯（托尼·D·詹姆斯（Tony D. Bortezomib（以前称为PS-341，并以Velcade的销售）是一种新型的S26蛋白酶体的甲状腺抗甲酸抑制剂，该蛋白酶体最近批准了FDA用于治疗复发性多发性骨髓瘤患者的治疗，该疾病是对常规疗法难治性的疾病。在几项关于硼酸的LCB研究（BAS）的研究中，进行了从头静止的计算：BA单体和二聚体的结构表征；描述了硼键的性质（特别是有效的，氢和多重键合）；阐明了溶液相中的原始和氧化硼碳酸化机制。这些结果提供了对硼化学的急需洞察力，这将有助于指导未来的QM/MM对硼酸抑制蛋白酶体的研究，这些蛋白酶体在癌症治疗中表现出很大的希望。 研究连接肽对胰岛素稳定性的六个残基的影响。 胰岛素是调节血糖水平的51个残基二聚体（链A 21残基和B 30残基）。最近，一项研究134显示了胰岛素的稳定性提高，其中使用六个残基肽（GGGPRR）将B链的C端连接到A链的N末端。 NMR实验表明，产生的单链胰岛素类似物（SCI-57）在具有相似结合亲和力的野生型胰岛素上提高了稳定性。观察到较少波动的更精致的结构，但是连接肽的作用的程度尚不清楚。我们在显式溶剂中使用了分子动力学模拟来研究这种连接肽对使用CHARMM的胰岛素的影响。在各种温度（300K，325K，340K和350K）下模拟了SCI-57及其两个链类似物（2CA）。这两个连锁店都保持其本地构型为30万，没有明显的违反NOE。与SCI-57相比，2CA在末端残基上显示出更多的波动。在升高的温度下，Sci-57仍然保持其构象，其中2CA开始失去其二级结构元素。对于增强的采样，也正在执行SGLD模拟，显示出与两个系统的高温模拟中所见相似的趋势。链条和连接肽之间的特定相互作用仍在研究中。 该项目对治疗设计有影响。