In-Silico Study of the Structure and Dynamics of VHH Nanobodies

在骆驼类动物（大羊驼、羊驼、双峰骆驼）中，发现的一类抗体是独特的，它们的抗原结合位点只有3个环，因此可变区是由一个称为VHH的单结构域构成的（与传统抗体更大的两个结构域、6个环可变区形成对比）。因此，vhs代表了自然界中产生的最小的此类结构。本项目的目标是建立一个分子模型框架，以解决氨基酸序列与VHH结构域结合位点的结构和动力学行为之间关系的基本问题。特别是，它的目的是：(1)阐明vhs中典型（典型）和非典型结构出现的关键残基和相互作用；(2)阐明环灵活性和典型与非典型结构与抗原位点（表位）结合亲和力的功能相关性。这项工作有望帮助对抗体设计感兴趣的广泛的生物工程界。这种工程抗体在医学、分离和催化方面的新应用很重要。阐明抗体活性位点的结构和动力学以及小抗体结合配体和蛋白质的方式对了解其生物学功能至关重要。因此，这项工作也有望成为使用核磁共振和x射线晶体分析来确定生物分子结构的科学家的补充。所提出的建模工作与世界上几个研究小组在研究非复杂和复杂VHH系统结构方面所做的实验工作是协同的。这项工作将与康奈尔大学的一位同事合作，他对抗体和vhs的表位定位研究感兴趣。主要的教育成果将是在两年的时间里培养一名博士生，他将在生物学、物理学和计算建模之间日益增长的界面领域获得宝贵的工作经验。此外，预计至少有一名康奈尔大学本科生研究员将在两个常规学期中参与该项目。科学成果将通过专业会议和向当地高中提供教育软件的外联努力来传播。本研究结果将至少用于两门课程：一门新的分子模拟课程和高级热力学核心课程。

0933092EscobedoIntellectual merit In Camelids (Llamas, Alpacas, Bactrian Camels), a subset of antibodies found in these animals is unique in that the antigen-binding site has only 3 loops and the variable region is thus made by a single-domain denoted VHH (which contrasts with the larger two-domain, 6 loop variable region of conventional antibodies). VHHs thus represent the smallest such structure produced in nature. The goal of this project is to develop a molecular modeling framework to address fundamental questions on the relationship between aminoacid sequence and the structural and dynamical behavior of the binding site of VHH domains. In particular, it is intended to (1) elucidate the key residues and interactions that underlie the appearance of canonical (typical) and non-canonical structures in VHHs and (2) to elucidate the functional relevance of loop flexibility and canonical vs. non-canonical structures on the binding affinity to antigen sites (epitopes).Broader impactsThis work is expected to help the broad bioengineering community interested in the design of antibodies. Such engineered antibodies are important for novel applications in medicine, separations, and catalysis. Elucidating the structure and dynamics of the active site of antibodies and the way how small antibodies bind ligands and proteins is of key importance to understand their biological function. This work is thus also expected to be complementary to that of scientists who use NMR and x-ray crystal analyses to determine biomolecular structure. The proposed modeling work is synergistic with the experimental work performed by several research groups in the world who have been studying the structure of uncomplexed and complexed VHH systems. This work will gear up a collaboration with a colleague at Cornell who is interested in epitope-mapping studies for antibodies and VHHs. The main educational outcome will be the training of a Ph.D. student during two years, who will get valuable experience working in the growing interfacial area that lies between biology, physics, and computational modeling. In addition, it is expected that at least one Cornell undergraduate researcher will be associated with the project during two regular Semesters. Scientific results will be disseminated through professional meetings and an outreach effort to provide educational software to the local high school. Results from this investigation will be used in at least two classes: a new molecular simulations course and the advanced thermodynamics core course.