600 ps Molecular Dynamics Reveals Stable Substructures and Flexible Hinge Points in cAMP Dependent Protein Kinase Igor Tsigelny 1 Jerry P. Greenberg 1,2 Sarah Cox 1 William L. Nichols 1 Susan S. Taylor 1 Lynn F. Ten Eyck 1,2 1 Department of Chemistry and Biochemistry, University of California at San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0654 2 San Diego Supercomputer Center, 10100 Hopkins Drive, La Jolla,CA 92093 Received 25 November 1998; accepted 12 April 1999 Abstract: 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 -helices and -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  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 Keywords: computer simulation; molecular dynamics; fluctuations in proteins; protein kinase INTRODUCTION The protein kinases represent a large family of enzymes. All perform the same reaction, namely the transfer of phosphate from ATP to a serine, threonine, or tyrosine residue of a protein substrate. These proteins are in- volved in cellular regulatory processes and play pivotal roles in diverse signal transduction pathways. Forty-nine Correspondence to: L. F. Ten Eyck Contract grant sponsor: NSF DBI 9616115 (L.T. and I.T.) and NIH/NCRR RR-08605 (J.P.G.) Biopolymers, Vol. 50, 513–524 (1999) © 1999 John Wiley & Sons, Inc. CCC 0006-3525/99/050513-12 513