Fluctuations and entropy in the energetics and function of protein complexes

描述（由申请人提供）：本提案的基本前提是蛋白质是动态实体，其内部运动是固有且大量构象熵的表达，构象熵的变化可以极大地影响蛋白质功能的能量学。下面我们将总结支持这些断言的最新结果。也许最简单的功能背景是配体与蛋白质的结合。因此，我们的一般假设是，蛋白质-配体相互作用的热力学可以通过蛋白质内部熵的变化来影响。虽然这一观点在文献中已经存在了一段时间，但直到最近，能够阐明这一观点的实验方法才变得可行。我们将测试蛋白质动力学（以及它所代表的熵）在蛋白质分子识别和更复杂的变构反应中的作用的一般性。前者将建立在现有的一系列例子的基础上，这些例子表明配体结合时构象熵变化的贡献与总体结合熵之间存在一般的大致线性关系。虽然这种关系不是必需的，但它的存在表明进化在优化蛋白质配体热力学中利用了构象熵。这个想法将使用最近校准的“熵计”进行定量探索，它依赖于构象熵的动态代理。内部蛋白质运动的综合测量将采用现已建立的溶液核磁共振弛豫方法进行。为了更充分地了解蛋白质基质内动力学的传播，将对蛋白质运动进行高压摄动研究，以阐明运动的耦合。最近其他人对分解代谢激活蛋白的研究表明，构象熵可能在蛋白质- dna识别中起着核心作用。因此，我们建议研究lac抑制因子中蛋白质- dna识别的结构和动态特性。lac抑制因子是原核生物遗传调控的范例。总的来说，这些研究将极大地扩展我们对蛋白质运动的本质及其在蛋白质功能能量学中所代表的构象熵的作用的认识。

DESCRIPTION (provided by applicant): The fundamental premise of this proposal is that proteins are dynamic entities, that their internal motion is an expression of an inherent and significant amount of conformational entropy and that changes in conformation entropy can greatly influence the energetics of protein function. Below we will summarize recent results that support these assertions. Perhaps the simplest functional context is the binding of a ligand by a protein. Thus our general hypothesis is that the thermodynamics of protein-ligand interactions can be influenced via changes in the protein internal entropy. Though this idea has been in the literature for some time it is only recently that the experimental methods that are capable of illuminating it have become available. We will test the generality of a role for protein dynamics (and the entropy it represents) in molecular recognition by proteins and in the more sophisticated allosteric response. The former will build upon an existing array of examples that indicate a general roughly linear relationship between the contributions of a change in conformational entropy upon ligand binding and the overall binding entropy. Though such a relationship is not required its existence suggests that evolution has exploited conformational entropy in the optimization of protein-ligand thermodynamics. This idea will be quantitatively explored using the recently calibrated "entropy meter" that relies on a dynamical proxy for conformational entropy. Comprehensive measurements of internal protein motion will be undertaken using the now well-established solution NMR relaxation methods. In an effort to more fully understand the propagation of dynamics within the protein matrix, a high-pressure perturbation study of protein motion will be carried out to illuminate coupling of motion. Recent work by others on the catabolite activator protein suggests that conformational entropy may play a central role in protein-DNA recognition. We therefore propose to examine the structural and dynamic properties underlying protein-DNA recognition in the lac repressor. The lac repressor is a paradigm for genetic regulation in prokaryotes. Overall these studies will greatly expand our appreciation of the nature of protein motion and the role of the conformational entropy that it represents in the energetics of protein function.