Moving toward an accurate molecular dynamics force field for intrinsically disordered proteins

该项目的目标是提高分子动力学（MD）模拟的准确性，以研究内在无序蛋白质（IDP）的结构和动力学。 胞内无序蛋白（IDP）约占真核细胞（比细菌更复杂的生物体的细胞）中蛋白质的三分之一，并参与许多重要的细胞过程，但正如其名称所暗示的那样，它们的结构并不明确。 在这个项目中，研究人员将开发力场，描述原子如何相互作用的物理定律，可用于MD模拟中的IDP。 这项工作将有助于了解国内流离失所者如何为生活机制作出贡献。新的MD力场参数将公开提供，以便其他人可以在模拟中使用它们。 跨学科研究将由三名研究生进行，他们将收集医学博士，生物物理学，物理和有机化学以及各种光谱技术的专业知识。该项目将促进教授实验室之间的国际合作。Urbanc（PI）和Schweitzer-Stenner（Co-PI）在费城德雷克塞尔大学和Harald Schwalbe在法兰克福/德国的约翰沃尔夫冈歌德大学。PI和Co-PI将在德雷克塞尔大学组织关于MD模拟未折叠肽的夏季研讨会，并将努力吸引学生和教师参加这次活动，目标是来自邻近机构的代表性不足的少数民族。研究成果将通过年度Kaczmarczik日活动，提供在物理和化学部门在德雷克塞尔大学进行的研究演示给公众，主要是来自当地费城地区的高中生的特点。对未折叠肽的实验研究表明，对于水中的大多数氨基酸残基，骨架二面角被限制在Ramachandran图中对应于聚脯氨酸II（pPII）和β链的两个主要区域。在所有氨基酸中，丙氨酸显示出最高的pPII倾向，这在常规使用基于丙氨酸的短肽作为参考系统的分子动力学（MD）力场开发的背景下是重要的。目前的MD力场始终无法再现在体外观察到的基于丙氨酸的短肽的高pPII含量。PI和合作者已经获得了水中GxG（G-甘氨酸，x-除Q，G，P和W外的所有氨基酸）肽中大多数天然存在的客体残基x的多个实验数据，这使他们能够独特地确定残基特异性内在构象系综。该提案将利用这一综合实验数据集来测试现有MD力场和水模型在水中再现GxG肽中客体残基x的构象倾向的能力（目标1）;导出现有MD力场的新参数化，AMBER ff 99 SB，并将其与最能捕捉GxG肽中客体残基x的内在构象倾向的水模型联合收割机结合，以获得新的力场AMBER ff 99 SB EXP-GxG（Aim 2）;并对所得的AMBER ff 99 SB EXP-GxG力场进行系统的五步评估，以测试其向较长的未折叠肽的可转移性及其捕获蛋白质折叠和蛋白质自组装成可溶性蛋白质寡聚体的能力（目的3）。MD力场发展的这些进展将改善对IDP的MD模拟的预测。该奖项由细胞和分子生物科学部的分子生物物理学小组和化学部的化学理论、模型和计算方法项目共同资助。该奖项反映了NSF的法定使命，并通过使用基金会的知识价值和更广泛的影响审查标准进行评估，被认为值得支持。

The goal of this project is to improve the accuracy of molecular dynamics (MD) simulations for studying the structure and dynamics of intrinsically disordered proteins (IDPs). Intrinsically disordered proteins (IDPs) make up about a third of the proteins found in eukaryotic cells (cells of more complex organisms than bacteria), and are involved in many essential cellular processes, but as their name implies, their structures are not well defined. In this project, the investigators will develop force fields, the physics based laws that describe how atoms interact with each other, that can be used for IDPs in MD simulations. This work will contribute to understanding how IDPs contribute to the machinery of life. New MD force field parameters will be made publicly available such that others can use them in their simulations. The interdisciplinary research will carried out by three graduate students who will gather expertise in MD, biophysics, physical and organic chemistry, and a variety of spectroscopic techniques. The project will foster an international collaboration among the laboratories of Profs. Urbanc (PI) and Schweitzer-Stenner (Co-PI) at Drexel University in Philadelphia and Harald Schwalbe at the Johann Wolfgang Goethe University in Frankfurt/Germany. PI and Co-PI will organize summer workshops on MD simulations of unfolded peptides at Drexel University and an effort will be made to attract students and faculty targeting underrepresented minorities from neighboring institutions to attend this event. The research outcomes will be featured through the annual Kaczmarczik Day event, which offers demonstrations of research conducted at the Physics and Chemistry Departments at Drexel University to the general public, mostly high school students from the local Philadelphia area. Experimental research on unfolded peptides demonstrate that for most amino acid residues in water the backbone dihedral angles are restricted to two predominant regions in Ramachandran plot corresponding to polyproline II (pPII) and beta-strand. Of all amino acids, alanine shows the highest pPII propensity, which is important in the context of molecular dynamics (MD) force field development that routinely uses alanine-based short peptides as reference systems. Current MD force fields consistently fail to reproduce the high pPII content of alanine-based short peptides observed in vitro. The PIs and collaborators have acquired multiple experimental data for most naturally occurring guest residue x in GxG (G-glycine, x-all amino acids other than Q, G, P and W) peptides in water, which allowed them to uniquely determine residue-specific intrinsic conformational ensembles. This proposal will utilize this comprehensive set of experimental data to test the existing MD force fields and water models with respect to their ability to reproduce the conformational propensities of guest residues x in GxG peptides in water (Aim 1); derive a new parameterization of the existing MD force field, AMBER ff99SB, and combine it with the water model that best captures the intrinsic conformational propensities of guest residues x in GxG peptides to obtain the new force field AMBER ff99SB EXP-GxG (Aim 2); and conduct a systematic five-step assessment of the resulting AMBER ff99SB EXP-GxG force field that will test its transferability to longer unfolded peptides and its ability to capture protein folding and protein self-assembly into soluble protein oligomers (Aim 3). These advances in MD force field development will improve predictions of MD simulations of IDPs. This award is jointly funded by the Molecular Biophysics Cluster of the Division of Cellular and Molecular Biosciences and the Chemical Theory, Models and Computational Methods Program in the Chemistry Division.This award reflects NSF's statutory mission and has been deemed worthy of support through evaluation using the Foundation's intellectual merit and broader impacts review criteria.