Ahuja Lalima G, Kornev Alexandr P, McClendon Christopher L, Veglia Gianluigi, Taylor Susan S
Department of Pharmacology, University of California, San Diego, La Jolla, CA 92093.
Cardiovascular and Metabolic Diseases, Medicinal Chemistry, Pfizer Biomedical Institute, Pfizer, Inc., Cambridge, MA 02139.
Proc Natl Acad Sci U S A. 2017 Feb 7;114(6):E931-E940. doi: 10.1073/pnas.1620667114. Epub 2017 Jan 23.
The expertise of protein kinases lies in their dynamic structure, wherein they are able to modulate cellular signaling by their phosphotransferase activity. Only a few hundreds of protein kinases regulate key processes in human cells, and protein kinases play a pivotal role in health and disease. The present study dwells on understanding the working of the protein kinase-molecular switch as an allosteric network of "communities" composed of congruently dynamic residues that make up the protein kinase core. Girvan-Newman algorithm-based community maps of the kinase domain of cAMP-dependent protein kinase A allow for a molecular explanation for the role of protein conformational entropy in its catalytic cycle. The community map of a mutant, Y204A, is analyzed vis-à-vis the wild-type protein to study the perturbations in its dynamic profile such that it interferes with transfer of the γ-phosphate to a protein substrate. Conventional biochemical measurements are used to ascertain the effect of these dynamic perturbations on the kinetic profiles of both proteins. These studies pave the way for understanding how mutations far from the kinase active site can alter its dynamic properties and catalytic function even when major structural perturbations are not obvious from static crystal structures.
蛋白激酶的专长在于其动态结构，在这种结构中，它们能够通过磷酸转移酶活性调节细胞信号传导。只有几百种蛋白激酶调节人类细胞中的关键过程，并且蛋白激酶在健康和疾病中起着关键作用。本研究致力于理解蛋白激酶分子开关作为由构成蛋白激酶核心的动态一致的残基组成的“群落”的变构网络的工作方式。基于Girvan-Newman算法的环磷酸腺苷依赖性蛋白激酶A激酶结构域的群落图谱为蛋白构象熵在其催化循环中的作用提供了分子解释。分析突变体Y204A相对于野生型蛋白的群落图谱，以研究其动态谱中的扰动，从而干扰γ-磷酸向蛋白底物的转移。使用传统的生化测量来确定这些动态扰动对两种蛋白动力学谱的影响。这些研究为理解即使从静态晶体结构中看不出明显的主要结构扰动时，远离激酶活性位点的突变如何改变其动态性质和催化功能铺平了道路。
