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Title: The energy landscape of adenylate kinase during catalysis

Abstract

Kinases perform phosphoryl-transfer reactions in milliseconds; without enzymes, these reactions would take about 8,000 years under physiological conditions. Despite extensive studies, a comprehensive understanding of kinase energy landscapes, including both chemical and conformational steps, is lacking. In this paper, we scrutinize the microscopic steps in the catalytic cycle of adenylate kinase, through a combination of NMR measurements during catalysis, pre-steady-state kinetics, molecular-dynamics simulations and crystallography of active complexes. We find that the Mg 2+ cofactor activates two distinct molecular events: phosphoryl transfer (>10 5-fold) and lid opening (10 3-fold). In contrast, mutation of an essential active site arginine decelerates phosphoryl transfer 10 3-fold without substantially affecting lid opening. Finally, our results highlight the importance of the entire energy landscape in catalysis and suggest that adenylate kinases have evolved to activate key processes simultaneously by precise placement of a single, charged and very abundant cofactor in a preorganized active site.

Authors:
 [1];  [1];  [1];  [1];  [1];  [1];  [1];  [1];  [1];  [1];  [2];  [3];  [1]
  1. Brandeis Univ., Waltham, MA (United States). Dept. of Biochemistry. Howard Hughes Medical Inst.
  2. Univ. of California, Berkeley, CA (United States)
  3. Brandeis Univ., Waltham, MA (United States). Dept. of Physics
Publication Date:
Research Org.:
Brandeis Univ., Waltham, MA (United States)
Sponsoring Org.:
USDOE Office of Science (SC), Basic Energy Sciences (BES) (SC-22); National Inst. of Health (NIH) (United States); Damon Runyon Cancer Research Foundation (United States)
Contributing Org.:
Univ. of California, Berkeley, CA (United States)
OSTI Identifier:
1182309
Grant/Contract Number:  
FG02-05ER15699; RO1-GM100966; DRG-2114-12
Resource Type:
Journal Article: Accepted Manuscript
Journal Name:
Nature Structural & Molecular Biology
Additional Journal Information:
Journal Volume: 22; Journal Issue: 2; Journal ID: ISSN 1545-9993
Publisher:
Nature Publishing Group
Country of Publication:
United States
Language:
ENGLISH
Subject:
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CHEMISTRY; Enzyme mechanisms; Kinases; Solution-state NMR; X-ray crystallography

Citation Formats

Kerns, S. Jordan, Agafonov, Roman V., Cho, Young-Jin, Pontiggia, Francesco, Otten, Renee, Pachov, Dimitar V., Kutter, Steffen, Phung, Lien A., Murphy, Padraig N., Thai, Vu, Alber, Tom, Hagan, Michael F., and Kern, Dorothee. The energy landscape of adenylate kinase during catalysis. United States: N. p., 2015. Web. doi:10.1038/nsmb.2941.
Kerns, S. Jordan, Agafonov, Roman V., Cho, Young-Jin, Pontiggia, Francesco, Otten, Renee, Pachov, Dimitar V., Kutter, Steffen, Phung, Lien A., Murphy, Padraig N., Thai, Vu, Alber, Tom, Hagan, Michael F., & Kern, Dorothee. The energy landscape of adenylate kinase during catalysis. United States. doi:10.1038/nsmb.2941.
Kerns, S. Jordan, Agafonov, Roman V., Cho, Young-Jin, Pontiggia, Francesco, Otten, Renee, Pachov, Dimitar V., Kutter, Steffen, Phung, Lien A., Murphy, Padraig N., Thai, Vu, Alber, Tom, Hagan, Michael F., and Kern, Dorothee. Mon . "The energy landscape of adenylate kinase during catalysis". United States. doi:10.1038/nsmb.2941. https://www.osti.gov/servlets/purl/1182309.
@article{osti_1182309,
title = {The energy landscape of adenylate kinase during catalysis},
author = {Kerns, S. Jordan and Agafonov, Roman V. and Cho, Young-Jin and Pontiggia, Francesco and Otten, Renee and Pachov, Dimitar V. and Kutter, Steffen and Phung, Lien A. and Murphy, Padraig N. and Thai, Vu and Alber, Tom and Hagan, Michael F. and Kern, Dorothee},
abstractNote = {Kinases perform phosphoryl-transfer reactions in milliseconds; without enzymes, these reactions would take about 8,000 years under physiological conditions. Despite extensive studies, a comprehensive understanding of kinase energy landscapes, including both chemical and conformational steps, is lacking. In this paper, we scrutinize the microscopic steps in the catalytic cycle of adenylate kinase, through a combination of NMR measurements during catalysis, pre-steady-state kinetics, molecular-dynamics simulations and crystallography of active complexes. We find that the Mg2+ cofactor activates two distinct molecular events: phosphoryl transfer (>105-fold) and lid opening (103-fold). In contrast, mutation of an essential active site arginine decelerates phosphoryl transfer 103-fold without substantially affecting lid opening. Finally, our results highlight the importance of the entire energy landscape in catalysis and suggest that adenylate kinases have evolved to activate key processes simultaneously by precise placement of a single, charged and very abundant cofactor in a preorganized active site.},
doi = {10.1038/nsmb.2941},
journal = {Nature Structural & Molecular Biology},
number = 2,
volume = 22,
place = {United States},
year = {Mon Jan 12 00:00:00 EST 2015},
month = {Mon Jan 12 00:00:00 EST 2015}
}

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