Backbone dynamics of Escherichia coli adenylate kinase at the extreme stages of the catalytic cycle studied by 15N NMR relaxation

Yury E. Shapiro, Michael A. Sinev, Elena V. Sineva, Vitali Tugarinov, Eva Meirovitch

Research output: Contribution to journalArticlepeer-review

48 Scopus citations

Abstract

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. Domains LID and AMPbd execute large-scale movements during catalysis. Backbone dynamics of ligand-free and AP5A-inhibitor-bound AKeco were studied comparatively with 15N NMR relaxation methods. Overall diffusion with correlation times of 15.05 (11.42) ns and anisotropy D(parallel)/D(perp) = 1.25 (1.10), and fast internal motions with correlation times up to 100 ps (50 ps), were determined for AKeco (AKeco*AP5A). Fast internal motions affect 93% of the AKeco sites, with pronounced preference for domains AMPbd and LID, and 47% of the AKeco*AP5A sites, with limited variability along the chain. The mean squared generalized order parameters, (S2), of secondary structure elements and loops are affected by ligand binding differentially and in a domain- specific manner. Nanosecond motions predominate within AMPbd. Prominent exchange contributions, associated in particular with residue G10 of the nucleotide-binding P-loop motif, are interpreted to reflect hydrogen-bond dynamics at the inhibitor-binding site. The hypothesis of energetic counter balancing of substrate binding based on crystallographic data is strongly supported by the solution NMR results. Correlations between backbone dynamics and domain displacement are established.

Original languageEnglish (US)
Pages (from-to)6634-6644
Number of pages11
JournalBiochemistry
Volume39
Issue number22
DOIs
StatePublished - Jun 6 2000

All Science Journal Classification (ASJC) codes

  • Biochemistry

Fingerprint Dive into the research topics of 'Backbone dynamics of Escherichia coli adenylate kinase at the extreme stages of the catalytic cycle studied by <sup>15</sup>N NMR relaxation'. Together they form a unique fingerprint.

Cite this