MOLECULAR DYNAMICS SIMULATIONS FOR PROTEIN AGGREGATION

这个子项目是许多研究子项目中的一个 由NIH/NCRR资助的中心赠款提供的资源。子项目和 研究者（PI）可能从另一个NIH来源获得了主要资金， 因此可在其他CRISP条目中表示。所列机构为 研究中心，而研究中心不一定是研究者所在的机构。 错误折叠的蛋白质倾向于形成有序的聚集体，称为淀粉样纤维，这些纤维与二十多种病理疾病有关，包括阿尔茨海默病和帕金森病等疾病。据信，至少在阿尔茨海默病的情况下，原纤维形成中的非原纤维中间体是有毒物质。由于这些非刚性结构的构象和瞬态性质的快速波动，很难获得对这些非纤维状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淀粉样蛋白原纤维形成的早期事件。我们小组先前的工作（1）已经确定，肽间疏水和静电相互作用的形成在这些原纤维中广泛存在的β折叠结构的形成中是至关重要的。还认为（2）防止两个不成对电荷在蛋白质的低介电内部中掩埋的分子内盐桥形成对于A-β淀粉样蛋白的形成是至关重要的。我们小组对单体A-β蛋白进行的模拟（3）表明，需要明确的溶剂模拟，其中水分子明确包含在模拟单元中，以解释盐桥形成的机制。对Abeta肽寡聚体短链的另一项研究（4）表明，这些蛋白质聚集的可能机制是对接锁定机制，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蛋白中肽内盐桥形成的机制和A-β蛋白的非纤维中间体形成的机制，我们需要用蛋白质的寡聚体进行明确的溶剂模拟。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，因此这些模拟在计算上要求太高，无法在小型计算机集群上执行。利用国家超级计算应用中心的计算资源，并使用NAMD分子动力学模拟软件包，该软件包非常适合在并行机上有效地运行大分子模拟，上述模拟是可行的。使用先前的分配从abeta蛋白的二聚体模拟获得的初步数据显示，除了单体结构的巨大变化之外，与单体模拟相比，在二聚体模拟中分子内盐桥和β折叠略微更稳定。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，并得出一个合理的分子内盐桥形成的机制，我们需要模拟三聚体和四聚体的abeta蛋白。因此，我们请求更新我们的提案，并从NCSA资源中提供额外的计算时间。参考文献：（1）Klimov，D.K.; Thirumalai，D.结构2003，11，295-307。(2)Sciffetta，K.L等人，生物化学2005，44，6003. (3)Tarus，B.; Straub，J.E.; Thirumalai，D. J. Am. Chem. Soc. 2006（印本）。(4)Nguyen，P.H.; Li，M.S.; Stock，G.; Straub，J.E.; Thirumalai，D. Proc. Natl. Acad. Sci. USA 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.