A novel view of domain flexibility in E-coli adenylate kinase based on structural mode-coupling 15N NMR relaxation

Adenylate kinase from Escherichia coli (AKeco), consisting of a single 23.6 kDa polypeptide chain folded into domains CORE, AMPbd and LID, catalyzes the reaction AMP + ATP --> 2ADP. In the ligand-free enzyme the domains AMPbd and LID execute large-amplitude movements controlling substrate binding and product release during catalysis. Domain flexibility is investigated herein with the slowly relaxing local structure (SRLS) model for N-15 relaxation. SRLS accounts rigorously for coupling between the global and local N-H motions through a local ordering potential exerted by the protein structure at the N-H bond. The latter reorients with respect to its protein surroundings, which reorient on the slower time scale associated with the global protein tumbling. AKeco diffuses globally with correlation time tau(m) = 15.1 ns, while locally two different dynamic cases prevail. The domain CORE features ordering about the equilibrium N-H bond orientation with order parameters, S-2, of 0.8-0.9 and local motional correlation times, tau, mainly between 5-130 ps. This represents a conventional rigid protein structure with rapid small-amplitude N-H fluctuations. The domains AMPbd and LID feature small parallel (Z(M)) ordering of S (2) = 0.2-0.5 which can be reinterpreted as high perpendicular (Y-M) ordering. M denotes the local ordering/local diffusion frame. Local motion about Z(M) is given by tau(parallel to) approximate to 5 ps and local motion of the effective Z(M) axis about Y-M by tau(perpendicular to) = 6-11 ns. Z(M) is tilted at approximately 20degrees from the N-H bond. The orientation of the Y-M axis may be considered parallel to the C-i -1(alpha)-C-i(alpha) axis. The tau(perpendicular to) mode reflects collective nanosecond peptide-plane;lotions, interpretable as domain motion. A powerful new model of protein flexibility/domain motion has been established. Conformational exchange (R-ex) processes accompany the tau(perpendicular to), mode. The SRLS analysis is compared with the conventional model-free analysis. (C) 2002 Academic Press.