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

Yury E. Shapiro, Edith Kahana, Vitali Tugarinov, Zhichun Liang, Jack H. Freed, Eva Meirovitch

Research output: Contribution to journalArticlepeer-review

74 Scopus citations

Abstract

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 AP5A-inhibitor-bound AKeco is studied with slowly relaxing local structure (SRLS) 15N relaxation, an approach particularly suited when the global (m) and the local (m) motions are likely to be coupled. For AKeco m = 15.1 ns, whereas for AKeco*AP5A m = 11.6 ns. The CORE domain of AKeco features an average squared order parameter, 〈S2〉, of 0.84 and correlation times m = 5-130 ps. Most of the AKeco*AP5A backbone features 〈S2〉 = 0.90 and m = 33-193 ps. These data are indicative of relative rigidity. Domains AMPbd and LID of AKeco, and loops β1/α1, α2/α3, α4/β3, α5/β4, and β8/α7 of AKeco*AP5A, feature a novel type of protein flexibility consisting of nanosecond peptide plane reorientation Ci-1α - Ciα axis, with correlation time = 5.6-11.3 ns. The other microdynamic parameters underlying this dynamic model include S2 = 0.13-0.5, on the ps time scale, and a diffusion tilt βMD ranging from 12 to 21°. For the ligand-free enzyme the mode was shown to represent segmental domain motion, accompanied by conformational exchange contributions Rex ≤ 4.4 s-1. Loop α4/β3 and α5/β4 dynamics in AKeco*AP5A is related to the "energetic counter-balancing of substrate binding" effect apparently driving kinase catalysis. The other flexible AKeco*AP5A loops may relate to domain motion toward product release.

Original languageEnglish
Pages (from-to)6271-6281
Number of pages11
JournalBiochemistry
Volume41
Issue number20
DOIs
StatePublished - 21 May 2002

Fingerprint

Dive into the research topics of 'Domain flexibility in ligand-free and inhibitor-bound Escherichia coli adenylate kinase based on a mode-coupling analysis of 15N spin relaxation'. Together they form a unique fingerprint.

Cite this