Interfacial and osmolyte-induced modulation of protein folding, assembly and adhesion

蛋白质是生命的基本组成部分，在我们的身体中发挥着多种功能，从保护我们免受感染的抗体到催化生化反应的酶。蛋白质的功能与蛋白质可以采用的构象（或形状）密切相关。该项目旨在开发新的计算工具来探测表面和溶液条件如何影响蛋白质的结构和功能。这些模拟将指导用于生物材料应用的新型蛋白质的设计，包括受生物启发的湿粘合剂和蛋白质支架。在这个项目的背景下开发的代码将免费提供。PI和她的团队正在积极开展拓展活动，包括针对五年级学生的化学项目，将在圣巴巴拉动物园展示的与湿粘合相关的动手模块的开发，以及让少数族裔高中学生参与暑期研究项目。这个项目的重点是内在无序肽，这是一类蛋白质，可以采取多种不同的构象，采用瞬态二级结构，并执行多种功能。由于缺乏天然褶皱，它们也容易自组装成从原纤维到凝聚的结构。在这个项目中，模型内在无序肽的结构、功能和组装将使用一系列模拟技术进行探索，从从头算分子动力学到粗粒度模型。该项目将实现三个具体目标。第一个目标将集中在对湿粘附的分子理解上，使用内在无序的贻贝足蛋白作为模型系统。PI将与生物粘附领域的领先实验小组密切合作，研究序列和表面组成如何影响粘附。这项研究将为开发一种新型的生物激发肽奠定基础，这种肽可以作为水下粘合剂。第二个目标是，PI将使用分子动力学模拟和Kirkwood-Buff溶液理论来确定渗透物氧化三甲胺抵消渗透物尿素的蛋白质变性作用的机制。在实验测量的基础上，开发并验证了TMAO/尿素相互作用的优化力场，并用于研究混合渗透液对内在无序肽聚集的影响。在第三个目标中，PI将开发新的混合动力学蒙特卡罗/分子动力学算法，将应用于纤维伸长的研究。该项目由分子和细胞生物科学部的分子生物物理集群和物理部的生命系统物理项目共同资助。

Proteins are fundamental building blocks of life, serving a multitude of functions in our body, from antibodies protecting us from infection, to enzymes catalyzing biochemical reactions. Protein function is intimately tied to the conformations (or shapes) that proteins can adopt. This project seeks to develop new computational tools to probe how surfaces and solution conditions affect protein structure and function. These simulations will guide the design of a new class of proteins for biomaterial applications, including biologically-inspired wet adhesives and protein scaffolds. Codes developed in the context of this project will be made freely available. The PI and her group are actively engaged in outreach activities, including a chemistry program geared at 5th grade students, the development of hands-on modules related to wet-adhesion that will be presented at the Santa Barbara zoo, and the involvement of underrepresented minority high school students in a summer research program.The focus of this project is on intrinsically disordered peptides, a class of proteins that can take on a multitude of disparate conformations, adopt transient secondary structures, and carry out multiple functions. With their lack of a native fold, they are also prone to self-assemble into structures ranging from fibrils to coacervates. In this project, the structure, function and assembly of model intrinsically disordered peptides will be probed using a hierarchy of simulations techniques, from ab initio molecular dynamics to coarse-grained models. The project will address three specific aims. The first aim will focus on a molecular understanding of wet adhesion, using the intrinsically disordered mussel-foot protein as a model system. Working closely with leading experimental groups in the field of biological adhesion, the PI will investigate how sequence and surface composition affect adhesion. This research will lay the groundwork for the development of a new class of biologically inspired peptides that can serve as underwater adhesives. In a second aim, the PI will use molecular dynamics simulations and the Kirkwood-Buff theory of solutions to determine the mechanism by which the osmolyte TMAO counteracts the protein denaturing effects of the osmolyte urea. An optimized force field for TMAO/urea interactions will be developed and validated based on experimental measurements, and used to study the effects of mixed osmolytes on the aggregation of intrinsically disordered peptides. In a third aim, the PI will develop novel hybrid kinetic Monte Carlo/Molecular Dynamics algorithms that will be applied to the study of fibril elongation.This project is jointly funded by the Molecular Biophysics Cluster in the Division of Molecular and Cellular Biosciences and the Physics of Living Systems Program in the Division of Physics.