MOLECULAR DYNAMICS SIMULATIONS FOR PROTEIN AGGREGATION

这个子项目是许多研究子项目中利用 资源由NIH/NCRR资助的中心拨款提供。子项目和 调查员(PI)可能从NIH的另一个来源获得了主要资金， 并因此可以在其他清晰的条目中表示。列出的机构是 该中心不一定是调查人员的机构。 错误折叠的蛋白质往往会形成称为淀粉样纤维的有序聚集体，这些纤维与20多种病理疾病有关，包括阿尔茨海默氏症和帕金森氏症等疾病。人们相信，至少在阿尔茨海默病的情况下，形成纤维的非纤维中间体是有毒的物种。由于这些非刚性结构的构象和瞬变性质的快速波动，很难获得对这些非纤维中间体的结构和动力学的实验洞察。该项目的目标是使用分子动力学模拟来了解触发A-β淀粉样纤维形成的早期事件。我们小组以前的工作(1)已经证实，多肽间疏水和静电相互作用的形成在这些纤维中广泛存在的β-片状结构的形成中是至关重要的。也有人认为(2)分子内盐桥的形成，防止两个不成对的电荷埋藏在蛋白质的低介电内部，对A-β淀粉样蛋白的形成至关重要。对我们小组中的一个单体A-β蛋白进行的模拟(3)表明，需要显式溶剂模拟，模拟池中明确包括水分子来解释盐桥形成的机制。另一项关于Abeta肽低聚物短链的研究(4)表明，这些蛋白质聚集的可能机制是停靠锁定机制，其中单体链与预先形成的聚集体的初始对接是快速的，然后在锁定阶段，对接的单体缓慢重排。为了最终确定A-β蛋白中肽内盐桥的形成机制和A-β蛋白非纤维中间体的形成机制，我们需要对蛋白质的低聚物进行显式溶剂模拟。由于水分子被明确地添加到模拟中，并且模拟的时间尺度是几微秒，因此这些模拟的计算要求太高，不能在小型计算机集群上执行。利用国家超级计算应用中心现有的计算资源，利用NAMD分子动力学模拟软件包，可以在并行机上高效地进行大分子模拟，上述模拟是可行的。使用先前的分配从abeta蛋白的二聚体模拟中获得的初步数据表明，除了单体结构的巨大变化外，分子内盐桥和β折叠在二聚体模拟中比单体模拟略微更稳定。实验(2)表明具有稳定的分子内盐桥和β-折叠的结构加速了abeta蛋白的聚集。为了最终确定这些结果，并得出分子内盐桥形成的可信机制，我们需要模拟abeta蛋白的三聚体和四聚体。因此，我们要求更新我们的建议，并从NCSA资源中获得额外的计算时间。参考文献：(1)Klimov，D.K.；Thirumalai，D.Structure 2003，11,295-307。(2)Sciarretta，K.L等人，生物化学，2005年，44,6003。(3)Tarus，B.；Straub，J.E.；Thirumalai，D.J.Am化学。SoC。2006年(印刷版)。(4)Nguyen，P.H.；Li，M.S.；Stock，G.；Straub，J.E.；Thirumalai，D.Proc.娜塔莉。阿卡德。SCI。美国2006,104,111-116。

This subproject is one of many research subprojects utilizing the resources provided by a Center grant funded by NIH/NCRR. The subproject and investigator (PI) may have received primary funding from another NIH source, and thus could be represented in other CRISP entries. The institution listed is for the Center, which is not necessarily the institution for the investigator. Misfolded proteins tend to form ordered aggregates called amyloid fibrils and these fibrils are linked to more than twenty pathological diseases including diseases like Alzheimers and Parkinsons. It is believed, atleast in the case of Alzheimers disease that non-fibrillar intermediates in the formation of fibrils are the toxic species. Experimental insight into the structure and kinetics of these non-fibrillar intermediates is hard to get due to the rapid fluctuations in the conformations and transient nature of these non-rigid structures. The goal of the project is to use molecular dynamics simulations to understand the early events which trigger the formation of the A-beta amyloid fibrils. Previous work(1) from our group has already established that the formation of interpeptide hydrophobic and electrostatic interactions are crucial in the formation of the beta sheet structures which are widely present in these fibrils. It is also believed(2) that an intramolecular salt bridge formation which prevents the burial of two unpaired charges in the low dielectric interior of the protein is crucial to the formation of the A-beta amyloid. The simulations(3) performed on a monomeric A-beta protein in our group reveal that explicit solvent simulations, with water molecules explicitly included in the simulation cell are required to explain the mechanisms of the salt bridge formation. Another study(4) on short strands of the Abeta peptide oligomers has shown that the possible mechanism of aggregation of these proteins is a dock-lock mechanism where the initial docking of a monomer strand to a preformed aggregate is rapid and then in the lock phase, the docked monomer slowly rearranges. To establish conclusively the mechanism of intra peptide salt bridge formation in A-beta protein and the mechanism for the formation of non-fibrillar intermediates of A-beta proteins we need to perform explicit solvent simulations with oligomers of proteins. Since water molecules are explicitly added to the simulation and the time scale of simulation is a few micro seconds, these simulations are computationally too demanding to be performed on small computer clusters. With the computational resources available at National Center for Supercomputing Applications and using NAMD molecular dynamics simulation package which is well suited to efficiently run macromolecular simulations on parallel machines the above mentioned simulations are feasible. Preliminary data obtained from the dimer simulations of the abeta protein using the previous allocation shows that in addition to the huge change in the structure of the monomers, the intramolecular salt bridge and beta sheet are marginally more stable in the dimer simulations compared to the monomer simulations. Experiments(2) show that structures with stable intramolecular salt bridge and beta sheet accelerate the aggregation of the abeta protein. To establish these results conclusively and to arrive at a plausible mechanism for the formation of intramolecular salt bridge we need to simulate trimers and tetramers of the abeta protein. So we request to renew our proposal and grant additional computational time from the NCSA resources. References: (1) Klimov, D.K.; Thirumalai, D. Structure 2003, 11, 295-307. (2) Sciarretta, K.L, et al., Biochemistry 2005, 44, 6003. (3) Tarus, B.; Straub, J.E.; Thirumalai, D. J. Am. Chem. Soc. 2006 (inprint). (4) Nguyen, P.H.; Li, M.S.; Stock, G.; Straub, J.E.; Thirumalai, D. Proc. Natl. Acad. Sci. USA 2006, 104, 111-116.