Domain flexibility in ligand-free and inhibitor-bound Escherichia coli adenylate kinase based on a mode-coupling analysis of 15N spin relaxation

Adenylate kinase from Escherichia coli (AKeco), consisting of a 23.6-kDa polypeptide chain folded into domains CORE, AMPbd, and LID catalyzes the reaction AMP + ATP <----> 2ADP. The domains AMPbd and LID execute large-amplitude movements during catalysis. Backbone dynamics of ligand-free and AP(5)A-inhibitor-bound AKeco is studied with slowly relaxing local structure (SRLS) N-15 relaxation, an approach particularly suited when the global (tau(m)) and the local (tau) motions are likely to be coupled. For AKeco tau(m) = 15.1 ns, whereas for AKeco*AP(5)A tau(m) = 11.6 ns. The CORE domain of AKeco features an average squared order parameter, , of 0.84 and correlation times tau(f) = 5-130 ps. Most of the AKeco*AP(5)A backbone features = 0.90 and tau(f) = 33-193 ps. These data are indicative of relative rigidity. Domains AMPbd and LID of AKeco, and loops beta(1)/alpha(1), alpha(2)/alpha(3), alpha(4)/beta(3), alpha(5)/beta(4) and beta(8)/alpha(7) of AKeco*AP(5)A, feature a novel type of protein flexibility consisting of nanosecond peptide plane reorientation about the C-i-1(alpha)-C-i(alpha) axis, with correlation time tau(perpendicular to) = 5.6-11.3 ns. The other microdynamic parameters underlying this dynamic model include S-2 = 0.13-0.5, tau(\\), on the ps time scale, and a diffusion tilt beta(MD) ranging from 12 to 21degrees. For the ligand-free enzyme the tau(perpendicular to) mode was shown to represent segmental domain motion, accompanied by conformational exchange contributions R-ex less than or equal to 4.4 s(-1). Loop alpha(4)/beta(3) and alpha(5)/beta(4) dynamics in AKeco*AP(5)A is related to the energetic counter-balancing of substrate binding effect apparently driving kinase catalysis. The other flexible AKeco*AP(5)A loops may relate to domain motion toward product release.