CAREER: Atomistic Simulations of Enzymatic Modulation of Long-Timescale Biomolecular Switches

亚细胞信号过程一般涉及生物分子之间的识别和瞬时相互作用以及构象的转换。这些信令过程有时会在非常长的时间尺度(几秒到几分钟)内发生。为了让开关信号在生物上相关的时间尺度(毫秒)发生，大自然提供了酶来催化和提高这些过程的速度。计算生物物理学中的主要挑战之一是在原子细节上描述超出微秒时间尺度的生物分子事件。该项目利用原理调查者(PI)开发的加速分子动力学模拟方法来获取长时间尺度的事件，并完全模拟肽基脯氨酰顺-反式异构酶(PPIase)的酶机理。PPIase是一类普遍存在的酶，在许多重要的信号通路中催化其蛋白质底物上的Pro基肽键缓慢的顺式-反式转换。这个职业计划的目标是研究生物分子顺式-反式开关的构象转变，包括依赖于磷酸化的顺式-反式开关，以及与之相关的PPIase的机制作用。实验已经提供了关于PPIase的丰富的结构洞察力和动力学信息，但它们还不能在原子水平上提供机制的完整图景。用目前的实验技术很难实现这种水平的直接观测。因此，更好地理解某些亚细胞过程所需的PPIase的作用机制一直难以捉摸，也存在争议。这一职业项目将在基础研究和科学培训方面产生广泛的影响。通过解开生物分子开关机制和伴随的蛋白质动力学的原子细节，将在物理化学水平上更好地理解分子机器的内部工作原理。在更高的层面上，这无疑将阐明细胞信号是如何在正常和异常条件下发生的。此外，从这个项目中获得的知识将使PI能够做出可检验的假设，并提出特定的问题，然后可以通过实验解决这些问题。更重要的是，该项目为吸引和培养下一代科学家提供了绝佳的机会。计算化学跨越许多学科，包括化学、生物、物理、数学和计算机科学，因此，为吸引学生进入科学领域提供了一个极好的工具。计算化学在教学中的一个优势是，对原本看起来抽象的概念的动态原子和分子描述可以被理解。除了培训本科生和研究生外，该项目还将使PI能够让高中生在安全的环境中接触科学研究，并通过佐治亚州立大学成熟的Bio-Bus推广计划接触到高中生和中学生。这一外展计划将有助于提高学龄儿童的科学素养，并为更多的受众提供机会，特别是在科学和工程领域少数族裔代表不足的学区。

Sub-cellular signaling processes generally involve recognition and transient interactions between biomolecules and switching of conformations. These signaling processes, at times, occur over very long timescales (seconds to minutes). For the on-off signaling to take place at biologically relevant timescales (milliseconds), nature has provided enzymes to catalyze and increase the rates of these processes. One of the major challenges in computational biophysics is describing, at the atomistic detail, biomolecular events that are beyond the microsecond timescale. This project takes advantage of an accelerated molecular dynamics simulation method developed by the principle investigator (PI) to access long timescale events and fully model the enzymatic mechanism of peptidyl prolyl cis-trans isomerases (PPIases). PPIases are a class of ubiquitous enzymes that catalyze the notoriously slow cis-trans switching of the prolyl peptide bond of their protein substrates in many important signaling pathways. The goal of this CAREER project is to investigate the conformational transitions of cis-trans biomolecular switches, including the phosphorylation dependent cis-trans switches, and the associated mechanistic role of PPIases. Experiments have provided wealth of structural insights and kinetic information on PPIases, but they have not been able to provide a complete picture of the mechanism at the atomistic level. Direct observations at this level are hard to achieve with current experimental techniques. As a result, the mechanism of action of PPIases that is required for better understanding of certain sub-cellular processes has been elusive and controversial.This CAREER project will have broad impacts in fundamental research as well as scientific training. By unraveling the atomistic details of biomolecular switching mechanisms and the accompanying protein dynamics, a better understanding of the inner workings of molecular machines at the physicochemical level will be achieved. And at a higher level, this will undoubtedly illuminate how cellular signaling takes place under normal and aberrant conditions. Also, the knowledge gained from this project will allow the PI to make testable hypotheses and to ask specific questions that can then be addressed experimentally. More importantly, this project provides an excellent opportunity to attract and train the next generation of scientists. Computational chemistry cuts across many disciplines, including chemistry, biology, physics, mathematics, and computer science, and therefore, provides an excellent tool for attracting students into the sciences. An advantage of computational chemistry in teaching is the fact that dynamic atomistic and molecular descriptions of concepts that would otherwise seem abstract can be made understandable. In addition to training undergraduate and graduate students, this project will allow the PI to expose high school students to scientific research in a safe environment and reach out to high school and middle school students through a well-established Bio-Bus outreach program at Georgia State University. This outreach program will help to raise scientific literacy amongst school-aged children and provide access to a larger audience, especially those in school districts with underrepresented minorities in science and engineering.