ANTIBODY STRUCTURE AND CATALYSIS BY DESIGN

这项提议的广泛、长期的目标是开发技术 用于对抗体结构进行建模，从而能够预测 影响AN结合和潜在催化活性的突变 抗体，并将促进我们对功能和 酶催化所必需的空间关系。技术 由这笔赠款开发的将加强抗体的生物医学用途 作为治疗剂和诊断工具，并将有助于创造新的 抗体的用途，如高度特异的蛋白酶或其他催化 用于未知酶的反应的试剂。抗体模型 将基于对数据库的分析和表征 可用的结晶学抗体结构。酶催化部位 将检查共享特征，以开发将 被用作模板来创建或改进抗体中的催化部位。 这些建模技术的发展将受到结果的推动 在史蒂夫教授的实验室里进行的诱变实验 本科维奇介绍了催化抗体NPN43C9。具体目标是：1) 通过连续分析完善NPN43C9抗体的现行模型 我们的抗体结构数据库，蛋白质结构分析，以及 计算技术；2)开发工具以确定 任何一组残基的多个结构之间的序列同源性 结构相似性可以与序列同源性相关联；3) 开发和测试确定循环的正确几何形状的方法 在互补判定域和真几何中 可变区重链和轻链的关系，两个因素 确定抗原结合口袋的大小和形状；4) 使用我们的抗体结构数据库来计算结构 每个氨基酸残基的可变性，并结合这一点 将信息输入模型，便于建模；5)预测 特定残基在抗原和底物结合中的作用， NPN43C9模型的催化作用和抗体结构，并提示 特定突变以检验这些假说；6)确定 构成催化剂的重要几何和环境因素 酶中的基序，并将这些基序用作设计的模板 抗体催化部位。发展假说的迭代过程 从模型出发，通过突变对假设进行实验验证，以及 将实验结果应用于进一步的技术开发 抗体结构分析、构建催化模体和提纯 NPN43C9抗体模型将提供强大的跨学科 了解抗体结构和酶催化作用的方法 一般抗体和特异性催化抗体的发展。

The broad, long-term objective of this proposal is to develop techniques for modeling antibody structures that will allow the prediction of mutations affecting the binding and potential catalytic activity of an antibody, and will advance our understanding of the functional and spatial relationships necessary for enzyme catalysis. Techniques developed by this grant will enhance the biomedical uses for antibodies as therapeutic agents and as diagnostic tools, and will help create new uses for antibodies such as highly specific proteases or other catalytic reagents for reactions for which no enzyme is known. Antibody models will be based on analysis and characterization of the database of available crystallographic antibody structures. Enzyme catalytic sites will be examined for shared characteristics to develop motifs that will be used as templates to create or improve catalytic sites in antibodies. Development of these modeling techniques will be driven by the results of mutagenesis experiments performed in the laboratory of Prof. Steve Benkovic on the catalytic antibody NPN43C9. The Specific aims are 1) to refine the current model of the NPN43C9 antibody by continued analysis of our antibody structural database, analysis of protein structures, and computational techniques; 2) to develop tools for the determination of sequence homology among multiple structures for any set of residues so that structural similarity can be correlated with sequence homology; 3) to develop and test methods for determining the proper geometry for loops in the complementarity determining regions and the proper geometric relationship between variable region heavy and light chains, both factors that determine the size and shape of the antigen binding pocket; 4) to use our antibody structural database to calculate the structural variability of each amino acid residue and to incorporate this information into the model to facilitate model building; 5) to predict the role of specific residues in antigen and substrate binding, catalysis, and antibody structure from the NPN43C9 model and to suggest specific mutations to test these hypotheses; 6) to determine the important geometric and environmental factors that make up catalytic motifs in enzymes, and to use these motifs as templates in the design of antibody catalytic sites. The iterative process of developing hypotheses from the model, testing the hypotheses experimentally by mutagenesis, and applying the experimental results to further development of techniques of antibody structural analysis, building catalytic motifs, and refining the NPN43C9 antibody model will provide a powerful interdisciplinary approach for understanding antibody structure and enzyme catalysis in general and catalytic antibody development in specific.