Journal
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
Volume 114, Issue 6, Pages E931-E940Publisher
NATL ACAD SCIENCES
DOI: 10.1073/pnas.1620667114
Keywords
allostery; community maps; protein kinases; catalytic cycle; protein dynamics
Categories
Funding
- Public Health Service/NIH Grant [GM100310]
- NIH [GM034921]
- National Center for Multiscale Modeling of Biological System from the NIH [P41GM103712-S1]
- Pittsburgh Supercomputing Center (PSC)
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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-a-vis the wild-type protein to study the perturbations in its dynamic profile such that it interferes with transfer of the.-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.
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