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

在骆驼(骆驼、羊驼、双峰驼)中，在这些动物中发现的抗体的一个子集是独特的，因为抗原结合部位只有3个环，因此可变区由表示为VHH的单个结构域组成(这与传统抗体的更大的两个结构域、6个环可变区形成对比)。因此，VHH代表了自然界中产生的最小的此类结构。该项目的目标是开发一个分子模拟框架，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的关系的基本问题。特别是，它旨在(1)阐明VHH中典型结构和非规范结构出现的关键残基和相互作用，以及(2)阐明环灵活性和正则结构与非正则结构对抗原位点(表位)结合亲和力的功能相关性。这种工程抗体在医学、分离和催化等领域的新应用中具有重要意义。阐明抗体活性部位的结构和动力学，以及小抗体如何与配体和蛋白质结合是理解其生物学功能的关键。因此，这项工作也有望补充使用核磁共振和X射线晶体分析来确定生物分子结构的科学家的工作。所提出的建模工作与世界上几个研究VHH系统结构的研究小组所进行的实验工作是协同进行的。这项工作将促进与康奈尔大学的一位同事的合作，他对抗体和VHH的表位映射研究感兴趣。主要的教育成果将是在两年的时间里培训一名博士生，他们将在介于生物、物理和计算建模之间的不断增长的界面领域获得宝贵的工作经验。此外，预计在两个常规学期期间，将至少有一名康奈尔大学本科生研究员参与该项目。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。这项研究的结果将至少用于两节课：一门新的分子模拟课程和一门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.