ANTIBODY STRUCTURE AND CATALYSIS BY DESIGN

这项建议的广泛和长期目标是发展技术， 用于模拟抗体结构， 突变影响的结合和潜在的催化活性， 抗体，并将推进我们对功能和 酶催化所必需的空间关系。 技术 这项资助开发的抗体将增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 抗体如高度特异性蛋白酶或其它催化剂的用途 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， 可用的晶体抗体结构。 酶催化位点 将被检查的共同特点，以发展图案， 可用作模板以产生或改善抗体中的催化位点。 这些建模技术的发展将由结果驱动 在史蒂夫教授的实验室里进行的诱变实验 Benkovic对催化抗体NPN 43 C9的研究。 具体目标是：（1） 通过继续分析完善NPN 43 C9抗体的当前模型 我们的抗体结构数据库，分析蛋白质结构， 计算技术; 2）开发用于确定 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; 3） 开发和测试确定环路正确几何形状的方法 在互补决定区和适当的几何 可变区重链和轻链之间的关系，两个因素 其决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，并将其并入 信息纳入模型，以促进模型的建立; 5）预测 特异性残基在抗原和底物结合中的作用， 催化，和抗体结构从NPN 43 C9模型，并建议 具体突变来测试这些假设; 6）以确定 构成催化剂的重要几何和环境因素 基序的酶，并使用这些基序作为模板的设计， 抗体催化位点。 发展假设的迭代过程 从模型中，通过诱变实验测试假设，以及 将实验结果应用于技术的进一步发展 抗体结构分析，构建催化基序， NPN 43 C9抗体模型将提供一个强大的跨学科 了解抗体结构和酶催化的方法 一般和催化抗体发展的具体。

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.