CAREER: Molecular Simulation Methods to Probe RNA Dynamics, Thermodynamics, and Interfacial Interactions

摘要-Vasstih-1554558核糖核酸(RNA)分子不是被动的信息载体，而是具有多种化学和物理性质的分子，可用于治疗、合成生物学、材料、生物传感和工程应用。所有这些应用的基础是动力学，它包括大量的模式，跨越巨大的时空尺度，并与内在结构特征(例如碱基配对)和一些外部因素(例如配体结合)有关。虽然RNA等生物分子的平衡波动是固有的，但大规模的构象转变在生物分子识别等界面过程中发挥着主导作用。这样的动力学性质被编码在生物分子的物理自由能景观中，对其进行稳健的采样可以提供关于RNA分子功能构象系综的关键热力学和动力学信息。PI计划观察小RNA分子的构象动力学和界面相互作用，以使它们能够用于上述应用。所提出的研究主要涉及两个问题：(1)什么物理变量对RNA分子的局部和全局构象转变负责？以及(2)这些构象转变如何促进RNA与一组不同的配体(小分子、短肽和球状蛋白)的界面相互作用？为了全面了解动力学和相互作用，建模和模拟工作将与光谱(核磁共振)和成像(电子冷冻显微镜)数据相结合。了解生物分子如何经历大规模结构变化以获得功能的细节是一个悬而未决的问题。众所周知，生物分子是灵活的，了解它们的动力学可以帮助我们深入了解它们的功能。然而，表征这种动态运动是具有挑战性的，因为没有一种单一的计算或实验技术可以解决所有时空尺度上的运动。建议的计算方法使用减少的一组坐标中的物理自由能景观(同时保持所有原子表示)，而不是所有自由度。计算和实验技术的结合可以建立在广泛的时间和长度尺度上研究这些动力学的新方法。教育计划将把分子理论、数值算法和可视化工具带给广泛的STEM学生和教育工作者。它可以影响和满足下一代科学标准，并扩大对工程学和生物物理学的参与，方法是开展一项更广泛的教育活动，通过举办关于免费软件工具的讲习班，将“视觉空间”思维作为一项关键技能传授给学生，并通过培训广泛的STEM人群(学生、教师和教职员工)进一步开发和传播这种工具。这些学生将前往参加地区和国家会议，并将通过与印度旗舰工程学校的合作，接触到国际指导和跨文化体验。

Abstract - Vashisth - 1554558Ribonucleic acid (RNA) molecules are not passive information carriers but molecules with versatile chemical and physical properties that can be exploited for therapeutic, synthetic biology, materials, bio-sensing, and engineering applications. Underlying all these applications are the dynamics which encompass a large number of modes, span vast spatiotemporal scales, and are connected to the intrinsic structural features (e.g. base-pairing) and some extrinsic factors (e.g. ligand binding). While equilibrium fluctuations in biomolecules such as RNA are inherent, it is the large-scale conformational transitions that play a dominant role in interfacial processes such as biomolecular recognition. Such dynamic properties are encoded in the physical free energy landscapes of biomolecules, the robust sampling of which can provide key thermodynamic and kinetic information on functional conformational ensembles of RNA molecules. The PI plans to look at conformational dynamics and interfacial interactions in small RNA molecules to enable their use for the above mentioned applications.The research proposed is broadly concerned with two questions: (1) What physical variables are responsible for local and global conformational transitions in RNA molecules? and (2) How do these conformational transitions facilitate interfacial interactions of RNA with a diverse group of ligands (small molecules, short peptides, and globular proteins)? To gain a holistic view of the dynamics and interactions, the modeling and simulation effort will be integrated with spectroscopic (nucleic magnetic resonance) and imaging (electron cryo-microscopy) data. Understanding the details of how biomolecules undergo large-scale structural changes to elicit function is an unsolved problem. It is known that biomolecules are flexible and understanding their dynamics may provide insights into their function. Though, it is challenging to characterize such dynamic motions because no single computational or experimental technique can resolve motions at all spatiotemporal scales. The proposed computational approaches use physical free-energy landscapes in a reduced set of coordinates (while maintaining the all atom representation) as opposed to all degrees-of-freedom. The combination of computational and experimental techniques could establish new approaches to study these dynamics at a wide spectrum of time and length scales.The educational plan will bring molecular theories, numerical algorithms, and visualization tools to a broad spectrum of STEM students and educators. It could impact and meet the Next Generation Science Standards and broaden participation in engineering and biophysics, through a broader educational initiative devoted to impart "visuospatial" thinking as a key skill via workshops on a freely-available software tool that will be further developed and disseminated via training of a wide spectrum of STEM population (students, teachers, and faculty). The students will travel to regional and national conferences, and will be exposed to international mentoring and multicultural experiences through partnerships with flagship engineering schools in India.