Computational Science and Engineering Division, Oak Ridge National Laboratory , Oak Ridge, Tennessee 37831, United States.
Acc Chem Res. 2014 Jan 21;47(1):149-56. doi: 10.1021/ar400084s. Epub 2013 Aug 29.
Functioning proteins do not remain fixed in a unique structure, but instead they sample a range of conformations facilitated by motions within the protein. Even in the native state, a protein exists as a collection of interconverting conformations driven by thermodynamic fluctuations. Motions on the fast time scale allow a protein to sample conformations in the nearby area of its conformational landscape, while motions on slower time scales give it access to conformations in distal areas of the landscape. Emerging evidence indicates that protein landscapes contain conformational substates with dynamic and structural features that support the designated function of the protein. Nuclear magnetic resonance (NMR) experiments provide information about conformational ensembles of proteins. X-ray crystallography allows researchers to identify the most populated states along the landscape, and computational simulations give atom-level information about the conformational substates of different proteins. This ability to characterize and obtain quantitative information about the conformational substates and the populations of proteins within them is allowing researchers to better understand the relationship between protein structure and dynamics and the mechanisms of protein function. In this Account, we discuss recent developments and challenges in the characterization of functionally relevant conformational populations and substates of proteins. In some enzymes, the sampling of functionally relevant conformational substates is connected to promoting the overall mechanism of catalysis. For example, the conformational landscape of the enzyme dihydrofolate reductase has multiple substates, which facilitate the binding and the release of the cofactor and substrate and catalyze the hydride transfer. For the enzyme cyclophilin A, computational simulations reveal that the long time scale conformational fluctuations enable the enzyme to access conformational substates that allow it to attain the transition state, therefore promoting the reaction mechanism. In the long term, this emerging view of proteins with conformational substates has broad implications for improving our understanding of enzymes, enzyme engineering, and better drug design. Researchers have already used photoactivation to modulate protein conformations as a strategy to develop a hypercatalytic enzyme. In addition, the alteration of the conformational substates through binding of ligands at locations other than the active site provides the basis for the design of new medicines through allosteric modulation.
有功能的蛋白质并非始终保持固定的独特结构，而是通过蛋白质内部的运动来不断探索各种构象。即使在天然状态下，蛋白质也是由热力学波动驱动的一系列构象转换体组成。快速运动可以使蛋白质在其构象景观的邻近区域探索构象，而较慢的运动则使蛋白质能够进入景观的远距离区域。新出现的证据表明，蛋白质景观包含具有动态和结构特征的构象亚基，这些亚基支持蛋白质的指定功能。核磁共振（NMR）实验提供了有关蛋白质构象总体的信息。X 射线晶体学使研究人员能够确定景观中最常出现的状态，而计算模拟则为不同蛋白质的构象亚基提供了原子水平的信息。这种能够对构象亚基及其内部蛋白质的构象群体进行特征描述并获取定量信息的能力，使研究人员能够更好地理解蛋白质结构与动力学之间的关系以及蛋白质功能的机制。在本综述中，我们讨论了蛋白质中功能相关构象群体和亚基的特征描述方面的最新进展和挑战。在某些酶中，功能相关构象亚基的探索与促进整体催化机制有关。例如，酶二氢叶酸还原酶的构象景观有多个亚基，这些亚基促进了辅助因子和底物的结合和释放，并催化了氢化物转移。对于酶亲环蛋白 A，计算模拟表明，长时间尺度的构象波动使酶能够进入构象亚基，从而使其达到过渡态，从而促进了反应机制。从长远来看，这种具有构象亚基的蛋白质的新观点对改善我们对酶、酶工程和更好的药物设计的理解具有广泛的意义。研究人员已经使用光激活来调节蛋白质构象，作为开发超催化酶的策略。此外，通过在活性部位以外的位置结合配体来改变构象亚基，为通过变构调节设计新药物提供了基础。
