From Genomic Sequences to Protein Structure and Function

描述（由申请人提供）：本项目旨在解决基因组序列、蛋白质结构和功能之间关系的基本问题。该项目的当前阶段主要集中在“假设的”细菌蛋白质的结构研究上。现在，我们将讨论高等真核生物基因组规模研究中最令人惊讶的结果之一：在过去两年中，已经清楚地表明，超过30%的人类基因至少以一种选择性剪接形式表达。我们的论文是，选择性剪接代表了在高级真核生物中产生功能多样性的一种根本不同的机制，但其效用受到维持结构完整性的限制。一方面，外显子的重用具有类似于软件模块重用的优点——保留了公共子功能。另一方面，蛋白质的亚结构本身并不是模块化的——外显子的随机组合很少会产生可行的折叠结构。我们的目标是深入探索这两个原则之间的相互作用——什么样的结构变化可以被容纳，什么样的功能多样性的结果？除了提供对选择性剪接、结构和功能之间关系的理解之外，这项研究还将阐明蛋白质进化的各个方面——在什么情况下，亚结构可以重组以产生修饰的折叠？什么样的构象变化伴随着这样的重组？帧移位会导致折叠的，完全不同的结构吗？最后，许多疾病与选择性剪接有关。相应的结构通常在结构上是不可活的，还是形成具有病理功能的替代结构？

DESCRIPTION (provided by applicant): This program project addresses fundamental questions concerning the relationship between genome sequence, protein structure, and function. The present period of the project has focused on structural studies of 'hypothetical' proteins from bacteria. We will now address one of the most surprising outcomes from genome scale studies of higher Eukaryotes: in the last two years it has become clear that in excess of 30% of human genes are expressed in at least one alternatively spliced form. Our thesis is that alternative splicing represents a fundamentally different mechanism for the generation of functional diversity in higher Eukaryotes, but that its utility is moderated by the constraints of maintaining structural integrity. On the one hand, reuse of exons has advantages similar to the reuse of software modules - common sub-function is preserved. On the other, protein substructures are not inherently modular - random combinations of exons would only very rarely lead to viable, folded structures. We aim to thoroughly explore the interplay between these two principles - what kinds of structural change can be accommodated, and what kinds of functional diversity result? In addition to providing an understanding of the relationship between alternative splicing, structure and function, the study will illuminate aspects of protein evolution - under what circumstances can substructures be recombined to generate modified folds? What kinds of conformational change accompany such recombination? Do frame shifts result in folded, completely different structures? Finally, many diseases are associated with alternative splicing. Are the corresponding structures usually non-viable structurally, or do they form alternative structures with pathological functions? To answer these questions, we will determine and analyze a series of carefully chosen structures (50 to 100 over 5 years). Proteins for study will be chosen on the basis of three considerations: likely impact of the splice forms on protein structure, functional role of the splicing, and relevance to disease.