Molecular Dynamics Simulations Of Biological Macromolecules

生物大分子的分子动力学模拟

• 批准号: 9157313
• 负责人: Bernard R Brooks
• 金额: $ 45.04万
• 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/9157313
• 关键词: ATP Hydrolysis; Address; Affect; Affinity; Agitation; Amino Acids; Amyloid; Area; Atlases; Basic Science; Behavior; Binding; Bioinformatics; Biological; Biophysics; Ca(2+)-Transporting ATPase; Calcium ion; Cell physiology; Cells; Cereals; Collaborations; Comparative Study; Complex; Computational Biology; Computing Methodologies; Cyclic AMP; Cyclic Nucleotides; Cytoplasm; Cytoplasmic Tail; Data Set; Development; Disease; Disinhibition; Electron Microscopy; Electrons; Elements; Employee Strikes; Energy Transfer; Event; Family; Family suidae; Felis catus; Filtration; Galactosidase; Gene Expression Microarray Analysis; Human; Human Genetics; Image Analysis; Integral Membrane Protein; Ion Channel; Ions; Ireland; Kidney Diseases; Kidney Failure; Kinesin; Laboratories; Ligands; Meiosis; Membrane; Methods; Microscopic; Microscopy; Microtubules; Mitosis; Modeling; Molecular; Molecular Conformation; Molecular Models; Motion; Motor; Movement; Muscle; Muscle Cells; Mutate; Mutation; N Domain; NPHS2 protein; National Heart, Lung, and Blood Institute; National Institute of Diabetes and Digestive and Kidney Diseases; Nerve; Non-Insulin-Dependent Diabetes Mellitus; Nucleotides; Peptides; Pharmaceutical Preparations; Phosphorylation; Phosphorylation Site; Play; Point Mutation; Process; Protein Dephosphorylation; Protein Dynamics; Proteins; Proteinuria; Protons; Publishing; Quantum Mechanics; Rattus; Relative (related person); Research; Research Project Grants; Resolution; Reticulum; Roentgen Rays; Role; SERCA1; Sarcoplasmic Reticulum; Science; Scientist; Self Perception; Shelter facility; Signal Transduction; Site; Solvents; Structure; Structure-Activity Relationship; Surface; Synapses; System; Techniques; Testing; Threonine; Time; Transition Elements; Translating; Trefoil Motif; Universities; Walking; Washington; Water; Work; X-Ray Crystallography; base; biophysical properties; college; computer studies; conformational conversion; cyclic-nucleotide gated ion channels; design; dimer; evaluation/testing; improved; in vivo; insight; interest; islet amyloid polypeptide; macromolecule; models and simulation; molecular dynamics; molecular mechanics; molecular modeling; monomer; podocyte; polarized cell; polypeptide; programs; protein function; simulation; slit diaphragm; small molecule; solid state nuclear magnetic resonance; tandem mass spectrometry; tool

Several diverse projects are being pursued. These are the major ones pursued during the past year. Calcium ATPase Conformational Transition through Self-Guided Langevin Dynamics Simulation The sarcoplasmic reticulum (SR) Ca2+-ATPase (SERCA1a) transport calcium ions from cytoplasm into the reticulum and relaxes the muscle cells. Many crystal structures of SERCA1 in various binding states have been determined, which provide insights into the mechanism of transport Ca2+ across the membrane. Molecular modeling and simulation studies are also devoted to the understanding of this important process. SERCA1a is an integral membrane protein. It comprises a single polypeptide chain of 994 amino acid residues. It is clear from the crystal structures that SERCA has a 10 helices trans-membrane domain (M), an actuator domain (A), a nucleotide binding domain (N), and a phosphorylation domain (P). The Ca2+ transport cycle starts with Ca2E1 through the Ca2+ dependent phosphorylation by ATP, leading to the formation of the Ca2E1P high-energy intermediate. Ca2E1P transits to Ca2E2P, which releases Ca2+ into the lumen of SR and leads to the E2P state. After dephosphorylation, E2P transits to E2 state and closes the luminal gate. Through thermo agitation, E2 transits to E1 by releasing protons into the cytoplasm. E1 has high Ca2+ affinity and binds with Ca2+ to form Ca2E1. To understand the transport mechanism, it is desirable to study the dynamic process during the conformation transition. Self-guided Langevin dynamics (SGLD) is a simulation method capable of studying events with large conformational change. SGLD simulations of SERCA at different binding states produce conformational transitions between conformational states. New conformations for E1.2Ca2+ and E2.P state have been identified and at E2 state the crystal structure is a preferred conformation. Atomic mechanism of the kinesin walking on microtubule Kinesin is a protein belonging to the class of Cytoskeletal motor proteins. 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. Analysis of the glomerular phosphoproteome Diseases of the kidney filtration barrier are a leading cause of endstage renal failure. Most disorders affect the podocytes, polarized cells that are connected by a unique cell junctional complex, the slit diaphragm. Podocytes require tightly controlled signaling to maintain their integrity, viability and function. Here we provide an atlas of in vivo phosphorylated, glomerulus-expressed proteins including podocyte-specific gene products identified in an unbiased tandem mass spectrometry-based approach. We discovered 2,449 phosphorylated proteins corresponding to 4,171 identified high-confident phosphorylated residues and performed a systematic bioinformatics analysis of this dataset. Among the 146 phosphorylation sites found on proteins abundantly expressed in podocytes, several sites resided close to residues known to be mutated in human genetic forms of proteinuria. One such site discovered on the slit diaphragm protein Podocin, threonine-234 (T234), resides at the interface of Podocin dimers with a distance between both T234 residues of less than 10 Angstrom. We show that phosphorylation critically regulates dimer formation and that this may represent a general principle for the assembly of the large family of PHB-domain containing proteins. 
Cyclic nucleotide modulation of structure and dynamics of a hyperpolarization-activated cyclic nucleotide-gated ion channel Hyperpolarization-activated cyclic nucleotide-gated 2 (HCN2) ion channels play a fundamental role in electric signaling in nerves, muscles, and synapses; however, their ligand gating mechanism is not well understood. There is little structural information on HCN2, as only its cytoplasmic domain in the holo form has been solved by X-ray crystallography. At the N-terminus, this structure contains the C-linker (helices A-F) and the cyclic nucleotide binding domain (CNBD), comprising of eight β-strands and helices A-C. cAMP modulates the HCN2 channel opening and it also promotes oligomerization. Through collaboration between experimental and computational methods, this study brings insight into the mechanism of cyclic adenosine monophosphate (cAMP) modulation of the HCN2 channel by exploring the monomer and tetramer dynamics in the apo and holo states. We performed all-atom, as well as coarse-grained (CG) molecular dynamics simulations. In the CNBD the distance between the C-helix and the β-roll in the binding pocket increases in the absence of cAMP. Our results corroborate recent transition metal ion Frster resonance energy transfer and double electron-electron resonance studies showing the outward movement of the C-helix in the absence of cAMP. The most striking dynamics observed in simulations of the apo monomer is the unfolding of the C-helix together with loss of contact between A and B helices in the C-linker, and the CNBD. In contrast, in the holo monomer, these contacts are retained, although the C-helix is unstable. In both the apo and the holo tetramer, the C-helix remains folded. We inferred that this is due to a reduced solvent accessible surface area, as the C-helix of a subunit is sheltered by the adjacent subunit. The folding/unfolding interplay of the C-helix translates into the vertical movement of the CNBD. As recently observed in MloK1, an analogous prokaryotic ion channel, this vertical displacement induces CNBD disinhibition, which promotes channel opening. This study is conducted in collaboration with Dr. R. Best (NIDDK) and Dr. W. Zagotta (University of Washington). Computational study of β-galactosidase With study is a collaborative project with the group of Dr. S. Subramaniam (NCI). Their cryo-electron (cryo-EM) microscopy work has recently produced a very high-resolution (2.2 ) for β-galactosidase, with promise to improve even further. Their technique is able to pin-point ions and water molecules interacting with the molecule. Our computational study focuses on the dynamic behavior of the resulting cryo-EM and that of previously-published X-ray structures. This comparative study provides insight into minuscule, albeit crucial, differences in structural aspects that could influence protein dynamics and function. Structure and dynamics of human islet amyloid polypeptide Islet amyloid polypeptide (IAPP, or amylin), is a 37-long peptide that is the main constituent of amyloid aggregates of type-II diabetes. Certain species acquire the disease, whereas others dont. Human (hIAPP) and cat IAPP have been shown to aggregate, but rat and pig do not. Starting from the solid-state NMR structure for hIAPP we perform single-point mutations towards the other species types and perform molecular dynamics simulations on the resulting structures. By analyzing the stability of each structure we infer the relative contributions of mutations on different structural elements, and establish which has a dominant modulating effect. This is a comprehensive study in collaboration with the group of Dr. N-V. Buchete (University College Dublin, Ireland).

几个不同的项目正在进行中。这些是过去一年中所追求的主要目标。 通过自引导朗之万动力学模拟实现钙 ATP 酶构象转变 肌浆网 (SR) Ca2+-ATP 酶 (SERCA1a) 将钙离子从细胞质转运到网织并放松肌肉细胞。 SERCA1 在各种结合状态下的许多晶体结构已被确定，这为了解 Ca2+ 跨膜转运机制提供了见解。 分子建模和模拟研究也致力于理解这一重要过程。 SERCA1a 是一种整合膜蛋白。 它包含 994 个氨基酸残基的单条多肽链。 从晶体结构可以清楚地看出，SERCA具有10个螺旋的跨膜结构域(M)、致动结构域(A)、核苷酸结合结构域(N)和磷酸化结构域(P)。 Ca2+ 运输循环从 Ca2E1 开始，通过 ATP 进行 Ca2+ 依赖性磷酸化，从而形成 Ca2E1P 高能中间体。 Ca2E1P转变为Ca2E2P，将Ca2+释放到SR管腔中并导致E2P状态。去磷酸化后，E2P 转变为 E2 态并关闭管腔门。 通过热搅拌，E2 通过将质子释放到细胞质中转变为 E1。 E1具有高Ca2+亲和力，与Ca2+结合形成Ca2E1。 为了了解运输机制，需要研究构象转变期间的动态过程。 自引导朗之万动力学（SGLD）是一种能够研究具有较大构象变化的事件的模拟方法。 SERCA 在不同结合状态下的 SGLD 模拟会产生构象状态之间的构象转变。 E1.2Ca2+ 和 E2.P 态的新构象已被识别，并且在 E2 态晶体结构是优选的构象。 驱动蛋白在微管上行走的原子机制 驱动蛋白是属于细胞骨架运动蛋白类的蛋白质。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。 肾小球磷酸蛋白质组分析 肾脏滤过屏障疾病是终末期肾衰竭的主要原因。大多数疾病都会影响足细胞，即通过独特的细胞连接复合物（狭缝隔膜）连接的极化细胞。足细胞需要严格控制的信号传导以维持其完整性、活力和功能。在这里，我们提供了体内磷酸化、肾小球表达的蛋白质的图谱，包括通过无偏串联质谱法鉴定的足细胞特异性基因产物。我们发现了 2,449 个磷酸化蛋白质，对应于 4,171 个已识别的高可信度磷酸化残基，并对这个数据集进行了系统的生物信息学分析。在足细胞中大量表达的蛋白质上发现的 146 个磷酸化位点中，有几个位点靠近已知在人类蛋白尿遗传形式中突变的残基。在狭缝隔膜蛋白 Podocin 上发现的一个这样的位点，苏氨酸-234 (T234)，位于 Podocin 二聚体的界面上，两个 T234 残基之间的距离小于 10 埃。我们证明磷酸化关键性地调节二聚体的形成，这可能代表了含有 PHB 结构域的蛋白质大家族组装的一般原则。 
超极化激活环核苷酸门控离子通道的结构和动力学的环核苷酸调节 超极化激活的环核苷酸门控 2 (HCN2) 离子通道在神经、肌肉和突触的电信号传导中发挥着重要作用；然而，它们的配体门控机制尚不清楚。 HCN2 的结构信息很少，因为 X 射线晶体学仅解析了其全息形式的细胞质结构域。在 N 末端，该结构包含 C 接头（螺旋 A-F）和环核苷酸结合结构域 (CNBD)，由八条 β 链和螺旋 A-C 组成。 cAMP 调节 HCN2 通道开放并促进寡聚化。通过实验和计算方法的合作，本研究通过探索 apo 和 Holo 态的单体和四聚体动力学，深入了解环磷酸腺苷 (cAMP) 调节 HCN2 通道的机制。我们进行了全原子以及粗粒度 (CG) 分子动力学模拟。在 CNBD 中，在没有 cAMP 的情况下，结合袋中的 C 螺旋和 β 卷之间的距离会增加。我们的结果证实了最近的过渡金属离子 Frster 共振能量转移和双电子-电子共振研究，显示在没有 cAMP 的情况下 C 螺旋向外运动。在 apo 单体模拟中观察到的最引人注目的动态是 C 螺旋的展开以及 C 连接子中 A 和 B 螺旋与 CNBD 之间接触的丧失。相反，在全单体中，尽管 C 螺旋不稳定，但这些接触被保留。在 apo 和全息四聚体中，C 螺旋均保持折叠状态。我们推断这是由于溶剂可及表面积减少，因为亚基的​​ C 螺旋受到相邻亚基的遮挡。 C 螺旋的折叠/展开相互作用转化为 CNBD 的垂直运动。正如最近在 MloK1（一种类似的原核离子通道）中观察到的，这种垂直位移会诱导 CNBD 去抑制，从而促进通道开放。这项研究是与 R. Best 博士（NIDDK）和 W. Zagotta 博士（华盛顿大学）合作进行的。 β-半乳糖苷酶的计算研究 With Study 是与 S. Subramaniam 博士 (NCI) 团队的合作项目。他们的冷冻电子 (cryo-EM) 显微镜工作最近获得了非常高分辨率 (2.2) 的 β-半乳糖苷酶，并有望进一步提高。他们的技术能够精确定位与分子相互作用的离子和水分子。我们的计算研究重点是由此产生的冷冻电镜和先前发表的 X 射线结构的动态行为。这项比较研究提供了对可能影响蛋白质动力学和功能的结构方面微小但至关重要的差异的见解。 人胰岛淀粉样多肽的结构和动力学 胰岛淀粉样多肽（IAPP，或胰淀素）是一种 37 长的肽，是 II 型糖尿病淀粉样蛋白聚集体的主要成分。某些物种会感染这种疾病，而其他物种则不会。人类 (hIAPP) 和猫 IAPP 已被证明会聚集，但大鼠和猪则不会。从 hIAPP 的固态 NMR 结构开始，我们对其他物种类型进行单点突变，并对所得结构进行分子动力学模拟。通过分析每个结构的稳定性，我们推断突变对不同结构元件的相对贡献，并确定哪个具有主导调节作用。这是与 N-V 博士小​​组合作进行的一项综合研究。 Buchete（爱尔兰都柏林大学学院）。