Computational Studies of Early Stage Cell Entry Events by Non-enveloped Viruses

描述(由申请人提供)：我目前是密歇根大学化学和生物物理系的博士后研究员。我是通过国家科学基金会的生物学博士后奖学金获得资助的。我最初的博士后研究重点是病毒衣壳的机械方面。我开发了一个理论框架和多尺度计算方法，允许第一原理计算病毒衣壳的弹性性质。我对了解病毒衣壳的弹性特性感兴趣，这既是为了加强纳米技术设计工作，也是为了了解与病毒生命周期事件相关的衣壳的形态变化。到目前为止，我已经对几种病毒系统进行了模拟，包括田菁花叶病毒、豌豆褪绿斑驳病毒、HK97、乙肝病毒和诺沃克病毒。这项工作在解释原子力显微镜对病毒的纳米压痕研究方面产生了影响。我还对拉萨病毒进行了一项研究，准确地预测了衣壳相关Z蛋白的结构及其与几种宿主蛋白的相互作用。预测的结构得到了随后的实验研究的证实。 我正在进行的项目主要集中在香港97的成熟过渡上。我一直在以一种多尺度的方法探索这个系统，其中我使用粗略的建模方法来模拟整个衣壳，并构建了一种可能性，使系统能够在短时间尺度上过渡。我特别感兴趣的是观察对称破缺是否发生在结构成熟转变期间。我还在使用全原子模型进行研究，以准确预测与成熟转变相关的自由能，并检测自由能表面作为pH的函数的变化。虽然到目前为止，我的背景主要是生物系统的机械性能，但我正在利用剩余的博士后时间专注于更多与生物化学/生物医学相关的问题。我已经开始探索一个关于抗体-靶标结合自由能的合作项目。与我的合作者，海军研究实验室的刘金尼博士(见支持信)，我们计划通过计算预测单域抗体-靶标复合体突变的相对结合自由能，并通过实验设计突变并测试预测。我对参与抗体研究的兴趣是，我最终想探索病毒与抗体的相互作用，并尝试 了解免疫系统如何对病毒做出反应，以及为什么许多病毒能够逃脱免疫系统的检测。 拟议的项目旨在了解与非包膜病毒进入细胞有关的事件。触发无包膜病毒发生构象变化的常见线索是pH变化和受体结合。我选择研究这两种现象的模型系统。脊髓灰质炎病毒的结构特征很好，包括与脊髓灰质炎病毒受体复杂的结构。受体结合事件诱导构象变化到脱涂层立即，该结构也存在。我将进行研究，以了解与受体结合相关的自由能。我还将研究在没有受体和存在受体的情况下向去涂层中间体的转变。我还将研究衣壳的结构和动力学是如何通过受体结合而改变的，特别是识别孔道开放模式，它可以从衣壳内部释放膜活性多肽。鸡舍病毒(FHV)也具有良好的结构特征，与脊髓灰质炎病毒有许多共同的特征，包括膜活性多肽的外化，但构象变化是由低pH环境引起的。我将进行研究，通过进行PKA计算来确定可能导致构象变化的残基。我将与斯克里普斯的杰克·约翰逊教授密切合作，为FHV膜活性多肽的释放构建模型路径(见支持信)。对于这些逃逸路径，我将计算自由能景观如何受pH变化的影响。本项目提出的工作旨在为进一步研究病毒感染奠定基础。我希望通过研究病毒-膜相互作用和基因组释放的机制来继续这项工作。我还希望我的实验室能有一个专注于免疫系统对病毒入侵反应的组件。II还与阿姆斯特丹VU大学的Gijs Woite教授持续合作，他的实验室在病毒上进行AFM纳米压痕实验。他的博士后WoutRoos博士可能很快就会开始一个初级教员的职位，在那里他和我将在病毒与细胞相互作用的机制方面进行合作(参见 支持函)。 我的目标是在美国一家主要研究机构获得化学工程、生物(医学)工程或生物物理系的教职。该实验室的重点将是病毒生命周期和感染的计算和理论研究。我的动机是了解驱动生物系统的物理机制，并做出可以为实验提供信息并导致人类健康益处的发现。无包膜病毒早期细胞进入事件的计算研究。

DESCRIPTION (provided by applicant): I am currently a postdoctoral fellow at the University of Michigan in the departments of Chemistry and Biophysics. I am supported through a National Science Foundation postdoctoral fellowship in biology. My initial postdoctoral research was focused on mechanical aspects of virus capsids. I developed a theoretical framework and multiscale computational methodology, which allows for first-principle calculation of viral capsid elastic properties. My interest in understanding elastic properties of viral capsids is both to enhance nanotechnology design efforts but also to understand morphological changes in capsids related to virus life cycle events. I have conducted simulations of several virus systems so far, including Sesbania mosaic virus, cowpea chlorotic mottle virus, HK97, hepatitis B virus, and Norwalk virus. This work has been impactful in interpreting AFM nanoindentation studies on viruses. I also conducted a study on Lassa virus in which I accurately predicted the structure of the capsid associated Z-protein and its interactions with several host proteins. The predicted structures where confirmed by a subsequent experimental study. My ongoing projects are primarily focused on the maturation transition of HK97. I have been exploring this system in a multiscale approach in which I am using coarse modeling methods to simulate the entire capsid and have constructed a potential to allow the system to transition on a short time scale. I am particularly interested in observing if symmetry breaking occurs during the structural maturation transition. I am also undertaking studies using all-atom models to accurately predict the free energy associated with the maturation transition and detect changes in the free energy surface as a function of pH. While my background to date has been primarily in mechanical properties of biological systems, I am using my remaining time as a postdoc to focus on more biochemically/biomedically relevant problems. I have begun exploring a collaborative project on antibody-target binding free energies. With my collaborator, Dr. Jinny Liu at the Naval Research Labs (see Support Letter), we plan to computationally predict relative binding free energies of mutants of single-domain antibodies-target complexes and experimentally engineer the mutations and test the predictions. My interest in getting involved in antibody research is that I eventually would like to explore virus-antibody interactions and try to understand how the immune system responds to viruses and why many viruses are able to escape detection from the immune system. The proposed project is aimed at understanding events associated with non-enveloped virus entry into cells. The common cues that trigger non-enveloped viruses to undergo conformational changes are pH changes and receptor binding. I have chosen to study a model system for both of these phenomena. Poliovirus is structurally well characterized including a structure in complex with the poliovirus receptor. The receptor binding events induces a conformational change to an uncoating immediate for which there is also a structure. I will conduct studies to understand the free energy associated with receptor binding. I will also study the transition to the uncoating intermediate both in the absence and presence of the receptor. I will also examine how the structure and dynamics of the capsid are altered by receptor binding with particular interest in indentifying pore opening modes, which can release a membrane active peptide from the capsid interior. Flock House virus (FHV) is also structurally well characterized and shares many common features with poliovirus, including the externalization of a membrane active peptide, but the conformational changes are induced by a low pH environment. I will conduct studies to indentify residues that could be responsible for the conformational changes by performing pKa calculations. I will construct model pathways for the release of the membrane active peptide of FHV in close collaboration with Prof. Jack Johnson at Scripps (see Support Letter). For these escape pathways I will compute how the free energy landscape is affected by pH alterations. The work proposed in this project is intended to lay a foundation for further studies on virus infection. I hope to continue this work by examining virus-membrane interactions and the mechanisms of genome release. I also hope to have a component of my lab that will focus on the immune system response to virus invasion. II also have an ongoing collaboration with Prof. Gijs Wuite at VU University Amsterdam, where his lab performs AFM nanoindentation experiments on viruses. His postdoc Dr. Wouter Roos is likely to begin a junior faculty position soon, where he and I will collaborate on mechanics of virus-cell interactions (see Support Letter). It is my goal to obtain a faculty position in a chemical engineering, bio(medical) engineering or biophysics department at a major research institute in the US. The focus of the lab will be on computational and theoretical studies of virus life cycles and infection. I am motivated to understand the physical mechanisms that drive biological systems and make discoveries that can inform experiments and lead to human health benefits. Computational Studies of Early Stage Cell Entry Events by Non-enveloped Viruses.