Predicting common protein mechanisms by the light of evolution

描述（由申请人提供）：某些关键的细胞成分，我们称之为“常见蛋白质”，在生命的主要部门中高度保守，属于功能上分化为许多分层排列的亚组的大量蛋白质类别。因此，这些蛋白质中的每一种都表现出重复的结构和/或机制主题的变化。这些包括，例如，AAA+ ATP酶，P-环GTP酶和蛋白激酶，由于它们的生物医学意义，它们是我们初步研究的重点。AAA+ ATP酶与遗传性痉挛性截瘫和神经系统疾病扭转性肌张力障碍、Zellweger综合征、新生儿肾上腺脑白质营养不良和婴儿Refsum病相关。GT3 Ras在癌症中起关键作用，蛋白激酶是重要的癌症和糖尿病药物靶点。结构生物学的一个主要目标是在活细胞的背景下以原子细节来理解蛋白质机制。尽管在确定蛋白质结构方面取得了显着进展，但是，潜在的蛋白质机制的许多方面仍然不清楚。确定这些机制是一项艰巨的任务，需要许多精心挑选的假设和实验来整理。然而，这些假设并不是在概念真空中形成的，而是基于从初步观察中获得的线索。在进化过程中对蛋白质施加的功能限制是这方面的潜在信息来源，因为这些限制是由于并因此反映了潜在的机制。此外，由于自然选择在其原生环境中对生物体的基因组序列施加了这些限制，因此这些信息缺乏有时与体外实验系统或体内细胞培养相关的人为偏见，并且可能揭示由于当前实验方法的固有局限性而被忽视的功能关键特征。因此，这个项目的广泛，长期的目标是表征常见蛋白质的功能限制，从而提供线索，其潜在的机制，以帮助实验设计。在过去的十年中，我们已经开发和应用了严格的统计程序来表征跨相关蛋白质亚组和相关蛋白质亚组内的序列保守的复杂模式。利用这些方法和其他方法，该项目将实现以下具体目标：（i）检测和非常精确地比对来自几种常见蛋白质类别的尽可能多的序列，（ii）通过比对的统计分析来鉴定、分类和量化作用于这些蛋白质的功能约束，（iii）鉴定与这些约束相关的结构和化学特征，（iv）类似地分析与这些蛋白质在功能上相互作用的蛋白质。并在此基础上提出分子机制。

DESCRIPTION (provided by applicant): Certain key cellular constituents, which we term "common proteins", are highly conserved across the major divisions of life and belong to vast protein classes that have functionally diverged into many hierarchically arranged subgroups. Thus each of these proteins manifests variations on recurring structural and/or mechanistic themes. These include, for example, AAA+ ATPases, P-loop GTPases and protein kinases, which were the focus of our preliminary studies due to their biomedical significance. AAA+ ATPases are associated with hereditary spastic paraplegia and the neurologic disorders torsin dystonia, Zellweger syndrome, neonatal adrenoleukodystrophy, and infantile Refsum disease. The GTPase Ras plays a key role in cancer, and protein kinases are important cancer and diabetes drug targets. A major goal of structural biology is to understand protein mechanisms in atomic-detail within the context of the living cell. Despite remarkable progress in determining protein structures, however, many aspects of underlying protein mechanisms remain unclear. Determining these mechanisms is a daunting task that will require many carefully chosen hypotheses and experiments to sort out. Such hypotheses are not formulated in a conceptual vacuum, however, but rather are based on clues obtained from preliminary observations. The functional constraints imposed on proteins during evolution are a potential source of information in this regard, inasmuch as these are due to and thus reflect underlying mechanisms. Moreover, because natural selection imposes these constraints on the genomic sequences of living organisms within their native environments, such information lacks the artifactual biases sometimes associated with in vitro experimental systems or with in vivo cell cultures and may reveal functionally critical features that have been overlooked due to the inherent limitations of current experimental methods. Thus the broad, long-range goal of this project is to characterize the functional constraints imposed on common proteins and to thereby provide clues to their underlying mechanisms as an aid to experimental design. Over the past decade we have developed and applied statistically rigorous procedures for characterizing complex patterns of sequence conservation across and within subgroups of related proteins. Using these and other approaches this project will accomplish the following specific aims: (i) Detect and very accurately align as many sequences as possible from several common protein classes, (ii) Identify, categorize and quantify the functional constraints acting on these proteins through statistical analysis of the alignments, (iii) Identify structural and chemical features associated with these constraints, (iv) Similarly analyze proteins that functionally interact with these proteins. And (v) propose molecular mechanisms based on these analyses.