The Sampling of Conformational Dynamics in Ambient-Temperature Crystal Structures of Arginine Kinase.
Arginine kinase provides a model for functional dynamics, studied through crystallography, enzymology, and nuclear magnetic resonance. Structures are now solved, at ambient temperature, for the transition state analog (TSA) complex. Analysis of quasi-rigid sub-domain displacements show that differences between the two TSA structures average about 5% of changes between substrate-free and TSA forms, and they are nearly co-linear. Small backbone hinge rotations map to sites that also flex on substrate binding. Anisotropic atomic displacement parameters (ADPs) are refined using rigid-body TLS constraints. Consistency between crystal forms shows that they reflect intrinsic molecular properties more than crystal lattice effects. In many regions, the favored directions of thermal/static displacement are appreciably correlated with movements on substrate binding. Correlation between ADPs and larger substrate-associated movements implies that the latter approximately follow paths of low-energy intrinsic motions.
Department of Math/Science, Concordia University, Portland, OR 97211, USA.
Michael H
MH
Godsey
Department Biochemistry and Molecular Biology, School of Medicine, Oregon Health & Science University, Portland, OR 97239, USA.
Omar
O
Davulcu
Molecular Biology Consortium, Lawrence Berkeley Natl. Lab., Berkeley, CA 94720, USA.
Jay C
JC
Nix
Department of Biochemistry, University of Utah School of Medicine, Salt Lake City, UT 8412, USA.
Jack J
JJ
Skalicky
Department of Chemistry and Biochemistry, Ohio State University, Columbus, OH 43210, USA.
Rafael P
RP
Brüschweiler
Department Biochemistry and Molecular Biology, School of Medicine, Oregon Health & Science University, Portland, OR 97239, USA. Electronic address: chapmami@ohsu.edu.
Michael S
MS
Chapman
D000818:Animals; D016880:Anisotropy; D001122:Arginine Kinase / Q000737:chemistry*; D018360:Crystallography, X-Ray; D006737:Horseshoe Crabs / Q000737:chemistry / Q000201:enzymology*; D008958:Models, Molecular; D011485:Protein Binding; D017433:Protein Structure, Secondary; D017434:Protein Structure, Tertiary; D013696:Temperature
D001122:Arginine Kinase
ADP; ambient; anisotropic; change; conformational; crystal; dynamics; induced-fit; protein; selection; temperature