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

无包膜病毒早期细胞进入事件的计算研究

• 批准号: 8281117
• 负责人: Eric Robert May
• 金额: $ 15.53万
• 依托单位: UNIVERSITY OF CONNECTICUT STORRS
• 依托单位国家: 美国
• 财政年份: 2013
• 资助国家: 美国
• 起止时间: 2013-02-06 至 2015-01-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/8281117
• 关键词: Address; Affect; Animals; Antibodies; Binding; Biological Models; Biology; Biophysics; C-terminal; Capsid; Capsid Proteins; Cells; Chemical Engineering; Chemistry; Collaborations; Complex; Computing Methodologies; Coxsackie Viruses; Cues; Detection; Echo Viruses; Engineering; Enterovirus; Environment; Event; Faculty; Fellowship; Foundations; Free Energy; Future; Genome; Goals; Health; Health Benefit; Hepatitis A Virus; Hepatitis B Virus; Housing; Human; Human Papillomavirus; Human poliovirus; Immune system; Infection; Invaded; Lassa virus; Lead; Letters; Life Cycle Stages; Mechanics; Medical; Membrane; Methodology; Methods; Michigan; Modeling; Mosaic Viruses; Mutation; N-terminal; Nanotechnology; Norwalk virus; Pathway interactions; Penetration; Peptides; Polioviruses; Positioning Attribute; Postdoctoral Fellow; Process; Property; Proteins; Reaction; Relative (related person); Research; Research Institute; Resolution; Rhinovirus; Risk; Sampling; Science; Shapes; Simulate; Staging; Structure; Surface; System; Techniques; Testing; Theoretical Studies; Therapeutic; Thermodynamics; Time; Translating; Universities; Viral; Virus; Virus Diseases; Virus Receptors; Virus-Cell Membrane Interaction; Work; arm; base; biological systems; computer studies; cowpea chlorotic mottle virus; design; interest; molecular dynamics; mutant; nanoindentation; particle; plasma protein Z; poliovirus receptor; public health relevance; receptor; receptor binding; research study; response; simulation

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.

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。我通过国家科学基金会生物学博士后奖学金获得支持。我最初的博士后研究集中在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，它允许病毒衣壳弹性特性的第一原理计算。我对理解病毒衣壳的弹性特性的兴趣是为了增强纳米技术的设计工作，也是为了理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、豇豆褪绿斑驳病毒、HK 97、B型肝炎病毒和诺瓦克病毒。这项工作在解释AFM对病毒的纳米压痕研究方面具有影响力。我还对拉沙病毒进行了一项研究，在这项研究中，我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。随后的实验研究证实了预测的结构。 我正在进行的项目主要集中在HK 97的成熟过渡上。我一直在多尺度方法中探索这个系统，其中我使用粗糙的建模方法来模拟整个衣壳，并构建了一个允许系统在短时间尺度上过渡的潜力。我特别感兴趣的是观察对称性破缺是否发生在结构成熟过渡期间。我还进行研究，使用全原子模型，以准确地预测与成熟过渡相关的自由能，并检测自由能表面的变化作为pH值的函数，而我的背景迄今为止一直主要是在生物系统的机械性能，我用我的剩余时间作为博士后专注于更多的生化/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Jinny Liu博士（见支持信），我们计划通过计算预测单结构域抗体-靶复合物突变体的相对结合自由能，并通过实验设计突变并测试预测。我参与抗体研究的兴趣在于，我最终想探索病毒与抗体的相互作用，并试图 了解免疫系统如何对病毒作出反应，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无包膜病毒进入细胞相关的事件。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。脊髓灰质炎病毒在结构上得到了很好的表征，包括与脊髓灰质炎病毒受体复合的结构。受体结合事件诱导构象变化为也存在结构的未包衣立即物。我将进行研究，以了解与受体结合相关的自由能。我还将研究在受体存在和不存在的情况下向未包被中间体的过渡。我还将研究如何通过受体结合来改变衣壳的结构和动力学，特别感兴趣的是识别开孔模式，其可以从衣壳内部释放膜活性肽。鸡群屋病毒（FHV）的结构特征也很好，与脊髓灰质炎病毒有许多共同特征，包括膜活性肽的外化，但构象变化是由低pH环境诱导的。本人将进行研究，通过pKa计算确定可能导致构象变化的残基。我将与Scripps的Jack约翰逊教授密切合作，构建FHV膜活性肽释放的模型途径（见支持信）。对于这些逃逸途径，我将计算自由能景观如何受到pH值变化的影响。本课题的研究工作为进一步研究病毒感染奠定了基础。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。我也希望我的实验室有一个部分，将重点放在免疫系统对病毒入侵的反应。II还与阿姆斯特丹自由大学的Gijs Wuite教授进行了持续的合作，他的实验室在病毒上进行AFM纳米压痕实验。他的博士后鲁什博士可能很快就会开始一个初级教师的职位，在那里他和我将合作研究病毒-细胞相互作用的机制（见 支持信）。 我的目标是在美国一家主要研究机构的化学工程、生物（医学）工程或生物物理学系获得一个教师职位。该实验室的重点将是对病毒生命周期和感染的计算和理论研究。我有动力去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带来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。