Molecular Dynamics Simulations Of Biological Macromolecules

生物大分子的分子动力学模拟

• 批准号: 8939759
• 负责人: Bernard R Brooks
• 金额: $ 49.06万
• 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/8939759
• 关键词: ATP Hydrolysis; Address; Affect; Affinity; Agitation; Amino Acids; Atlases; Basal Ganglia; Basic Science; Behavior; Binding; Bioinformatics; Biological; Biophysics; C-terminal; Ca(2+)-Transporting ATPase; Calcium ion; Cell physiology; Cells; Cereals; Collaborations; Complex; Computational Biology; Computing Methodologies; Cyclic AMP; Cyclic Nucleotides; Cytoplasm; Data Set; Development; Disease; Electron Microscopy; Electrons; Enzymes; Event; Family; Filtration; Frequencies; Galactosidase; Gene Expression Microarray Analysis; Goals; Human Genetics; Image Analysis; Integral Membrane Protein; Ion Channel; Kidney Diseases; Kidney Failure; Kinesin; Laboratories; Ligands; Measurement; Meiosis; Membrane; Methods; Microscopic; Microtubules; Mitosis; Modeling; Molecular; Molecular Biology; Molecular Conformation; Molecular Models; Motion; Motor; Movement; Muscle; Muscle Cells; Mutate; N Domain; NPHS2 protein; National Heart, Lung, and Blood Institute; Nerve; Nucleotides; Pathway interactions; Pharmaceutical Preparations; Phosphorylation; Phosphorylation Site; Play; Process; Protein Dephosphorylation; Proteins; Proteinuria; Protons; Publishing; Quantum Mechanics; Research; Research Project Grants; Resolution; Reticulum; Role; SERCA1; Sampling; Sarcoplasmic Reticulum; Science; Scientist; Self Perception; Signal Transduction; Sinoatrial Node; Site; Solutions; Spinal Ganglia; Structure; Structure-Activity Relationship; Synapses; System; Techniques; Testing; Threonine; Time; Trefoil Motif; United States National Institutes of Health; Walking; Water; Work; X-Ray Crystallography; base; biophysical properties; computer studies; conformational conversion; design; dimer; evaluation/testing; in vivo; insight; interest; macromolecule; models and simulation; molecular dynamics; molecular mechanics; molecular modeling; novel; podocyte; polarized cell; polypeptide; programs; simulation; slit diaphragm; small molecule; tandem mass spectrometry; theories; tool

Several diverse projects are being pursued. These are the major ones pursued during the past year. Coarse-grained and all-atom molecular dynamics of an ion channel Hyperpolarization-activated cyclic nucleotide-gated 2 (HCN2) ion channels are expressed in the sinoatrial node, dorsal root ganglia and the basal ganglia. They play fundamental roles in electric signaling in nerve, muscle and synapse, but their function and gating mechanism are not completely understood. The overall goal of the project is to gain insight into the mechanism of the HCN2 channel activation upon binding of cyclic adenosine monophosphate (cAMP) to its intracellular C-terminal. Many mechanisms have been proposed for the opening motion propagation in the channel, but they do not completely explain the entire channel behavior. A novel theory states that upon cAMP binding, a part of the HCN2 C-terminal, called the C-helix, stabilizes its secondary structure and moves towards the binding pocket to make contacts with cAMP. Its movement is correlated with the opening conformational change of the channel pore. This theory is being tested using a novel computational method, the self-guided Langevin dynamics (SGLD), which employs guided forces to enhance the low-frequency motion and accelerate the protein conformational search. Starting from the holo state structure and using the distances from tmFRET measurements as constrains, the protein is guided into its apo state. The simulations enable sampling of conformations along this transition, giving insight into the occurring structural changes and ultimately into the HCN2 gating mechanism. Coarse-grained simulations of HCN2 bring information about the folding pathway and additional insight into the stability of the protein with and without ligand. Computational study of the β-galactosidase This work is a collaboration with a cryo-EM laboratory within the NIH. It was sparked by their publishing of a solution structure at 3.2 resolution of β-galactosidase, one of the most used enzymes in molecular biology. Its long sequence (1024 aminoacids) and the fact that it forms a tetramer in order to function, make it an ideal system to apply SGLD and Coarse-grained modeling. This study will add robustness to the cryo-EM technique by comparing the structure and dynamics of the solution cryo-EM structure and the previously published X-ray crystallography structures. 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.

正在追求几个不同的项目。这些是过去一年中追求的主要措施。 离子通道的粗粒和全原子分子动力学 超极化激活的循环核苷酸门控2（HCN2）离子通道在正弦节点，背根神经节和基底神经节中表达。它们在神经，肌肉和突触中的电信号传导中扮演着基本角色，但尚未完全了解它们的功能和门控机制。该项目的总体目标是深入了解循环腺苷一磷酸（CAMP）与其细胞内C末端的结合后HCN2通道激活的机理。已经提出了许多用于通道中开放运动传播的机制，但它们并不能完全解释整个通道行为。一种新颖的理论指出，在CAMP结合后，HCN2 C末端的一部分称为C螺旋，稳定其二级结构，并朝着结合口袋移动以与CAMP接触。它的运动与通道孔的开放构象变化相关。该理论正在使用一种新型计算方法，即自引导的Langevin Dynamics（SGLD），该方法采用引导力来增强低频运动并加速蛋白质构象搜索。从Holo状态结构开始，并使用TMFret测量的距离作为约束，该蛋白质被引导到其APO状态。这些模拟能够沿着这种过渡进行构象的采样，从而深入了解发生的结构变化，并最终进入HCN2门控机制。 HCN2的粗粒细粒模拟带来了有关折叠途径的信息，并提供了对蛋白质稳定性和没有配体的稳定性的更多见解。 β-半乳糖苷酶的计算研究 这项工作是与NIH内的冷冻EM实验室的合作。它是通过在3.2分辨率的β-半乳糖苷酶（分子生物学中最常用的酶之一）的3.2分辨率下发布的溶液结构引起的。它的长序列（1024个氨基酸）以及为了发挥功能而形成四聚体的事实，使其成为应用SGLD和粗粒建模的理想系统。这项研究将通过比较溶液冷冻结构的结构和动力学和先前发表的X射线晶体学结构来增加差异EM技术的鲁棒性。 钙ATPase构象通过自引导的Langevin Dynamics模拟 肌质网（SR）CA2+-ATPase（SERCA1A）将钙离子从细胞质转运到网状钙并放松肌肉细胞。 已经确定了各种结合状态中SERCA1的许多晶体结构，这些结构提供了对整个膜转运Ca2+机理的见解。 分子建模和仿真研究也致力于理解这一重要过程。 SERCA1A是一种整体膜蛋白。 它包括一个994个氨基酸残基的单多肽链。 从晶体结构可以清楚地看出，SERCA具有10个螺旋跨膜结构域（M），一个执行器结构域（A），核苷酸结合结构域（N）和磷酸化结构域（P）。 Ca2+传输周期从ATP通过Ca2+依赖性磷酸化的Ca2e1开始，导致Ca2e1p高能中间体形成。 CA2E1P转移到Ca2e2p，该Ca2e2p释放到SR的管腔中并导致E2P状态。去磷酸化后，E2P转移到E2状态并关闭腔门。 通过热搅拌，E2通过将质子释放到细胞质中来转移到E1。 E1具有高Ca2+亲和力，并与Ca2+结合以形成Ca2e1。 要了解运输机制，希望在构象转变过程中研究动态过程。 自引导的Langevin Dynamics（SGLD）是一种模拟方法，能够研究具有较大构象变化的事件。 SERCA在不同结合状态下的SGLD模拟产生构象状态之间的构象转变。 已经确定了E1.2CA2+和E2.p状态的新构象，在E2状态下，晶体结构是首选构象。 在微管上行走的驱动蛋白的原子机制 驱动蛋白是属于细胞骨架运动蛋白类别的蛋白质。驱动蛋白将ATP水解的能量转化为沿着微管的垫脚运动，该运动支持几种重要的细胞功能，包括有丝分裂，减数分裂和细胞货物的运输。由于动力素是一种基本蛋白质，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。 与低分辨率电子显微镜图像结合使用，进行了自引导的Langevin动力学模拟，以研究水中驱动蛋白运动结构域的分子运动和构象变化，并与微管结合。 SGLD使模拟能够达到构象变化所需的时间尺度，以了解ATP结合和与微管相互作用的作用。 分析肾小球磷光蛋白酶 肾脏过滤屏障的疾病是终末期肾衰竭的主要原因。大多数疾病会影响足细胞，偏振细胞，这些细胞通过独特的细胞连接复合物（缝隙diaphragm）连接。足细胞需要紧密控制的信号传导以保持其完整性，活力和功能。在这里，我们提供了体内磷酸化的，肾小球表达的蛋白质的地图集，包括基于无偏见的串联质谱方法，该基因产物鉴定出了足细胞特异性基因产物。我们发现了2,449种磷酸化的蛋白质，对应于4,171个鉴定出高浓度的磷酸化残基，并对该数据集进行了系统的生物信息学分析。在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，几个位点靠近已知的残基被人类遗传形式的蛋白尿形式突变。在缝隙diaphragm蛋白质蛋白苏氨酸-234（T234）上发现的一个地点位于Podocin二聚体的界面上，两种T234残基在小于10埃埃斯特罗姆的T234残基之间都有距离。我们表明，磷酸化对二聚体的形成进行严格调节，这可能代表了大型含有蛋白质的大型pHB域家族的一般原理。