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600 ps Molecular dynamics reveals stable substructures and flexible hinge points in cAMP dependent protein kinase
Author(s) -
Tsigelny Igor,
Greenberg Jerry P.,
Cox Sarah,
Nichols William L.,
Taylor Susan S.,
Ten Eyck Lynn F.
Publication year - 1999
Publication title -
biopolymers
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.556
H-Index - 125
eISSN - 1097-0282
pISSN - 0006-3525
DOI - 10.1002/(sici)1097-0282(19991015)50:5<513::aid-bip5>3.0.co;2-i
Subject(s) - dihedral angle , molecular dynamics , chemistry , hydrogen bond , crystallography , protein subunit , protein dynamics , dynamics (music) , maxima and minima , protein structure , helix (gastropod) , hinge , physics , molecule , computational chemistry , biochemistry , biology , gene , ecology , classical mechanics , snail , mathematical analysis , mathematics , organic chemistry , acoustics
Molecular dynamics simulations of the catalytic subunit of cAMP dependent protein kinase (cAPK) have been performed in an aqueous environment. The relations among the protein hydrogen‐bonding network, secondary structural elements, and the internal motions of rigid domains were examined. The values of fluctuations of protein dihedral angles during dynamics show quite distinct maxima in the regions of loops and minima in the regions of α‐helices and β‐strands. Analyses of conformation snapshots throughout the run show stable subdomains and indicate that these rigid domains are constrained during the dynamics by a stable network of hydrogen bonds. The most stable subdomain during the dynamics was in the small lobe including part of the carboxy‐terminal tail. The most significant flexible region was the highly conserved glycine‐rich loop between β strands 1 and 2 in the small lobe. Many of the main chain dihedral angle changes measured in a comparison of the crystallographic structures of “open” and “closed” conformations of cAPK correspond to the highly flexible residues found during dynamics. © 1999 John Wiley & Sons, Inc. Biopoly 50: 513–524, 1999