Activation energy of catalysis-related domain motion in E. coli adenylate kinase

Yury E. Shapiro, Eva Meirovitch

Research output: Contribution to journalArticlepeer-review

39 Scopus citations

Abstract

Adenylate kinase from E. coli (AKeco), folded into domains CORE, AMPbd, and LID, catalyzes the reaction AMP + ATP ↔ 2ADP. Previous X-ray crystallography and optical solution methods showed that the domains AMPbd and LID, and the conserved P-loop, execute large-amplitude catalysis-related motions. We used 15N NMR spin relaxation methods to find that the simplified model-free (MF) analysis does not, whereas our general Slowly Relaxing Local Structure analysis does, detect catalytic domain motion. SRLS set for the first time the correlation time for domain motion at τL. = 8.2 ns, to be compared with τm = 15.1 ns for global tumbling. These results were obtained at 303 K. Herein we conduct a temperature-dependent investigation of τL and τm in the range of 288-310 K. We found that the activation energy for global tumbling is Ea = 16.9 ± 0.5 kJ/mol, the hydrodynamic volume of hydrated AKeco is 65.6 ± 2.1 nm3, its radius is 2.50 ± 0.03 nm, and the number of hydration layers is 1.77. The average τL value decreases from 11 ns at 288 K to 4 ns at 310 K, with activation energies of 29.7 ± 3.3, 32.1 ± 4.3, and 30.4 ± 4.3 kJ/mol for the domains AMPbd and LID, and the catalytic P-loop, respectively. These values are two-to-three times smaller than typical activation energies of enzymatic reactions. Hence kinase catalysis appears not to be controlled by domain motion in the ligand-free enzyme. However, the latter process clearly facilitates important mechanical aspects such as steric recognition and capturing of the AMP and ATP substrates, their proper positioning for phosphorylation, and the release of the ADP product.

Original languageEnglish
Pages (from-to)11519-11524
Number of pages6
JournalJournal of Physical Chemistry B
Volume110
Issue number23
DOIs
StatePublished - 15 Jun 2006

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