Modulation of functionally significant conformational equilibria in adenylate kinase by high concentrations of trimethylamine oxide attributed to volume exclusion

Sureshbabu Nagarajan; Dan Amir; Asaf Grupi; David P. Goldenberg; Allen P. Minton; Elisha Haas

doi:10.1016/j.bpj.2011.03.065

Modulation of functionally significant conformational equilibria in adenylate kinase by high concentrations of trimethylamine oxide attributed to volume exclusion

Sureshbabu Nagarajan, Dan Amir, Asaf Grupi, David P. Goldenberg, Allen P. Minton, Elisha Haas

The Mina and Everard Goodman Faculty of Life Sciences - at Bar-Ilan University

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Abstract

The effect of an inert small molecule osmolyte, trimethyl amine N-oxide (TMAO), upon the conformational equilibria of Escherichia coli adenylate kinase was studied using time-resolved FRET. The relative populations of open and closed clefts between the LID and the CORE domains were measured as functions of the concentrations of the substrate ATP over the concentration range 0-18 mM and TMAO over the concentration range 0-4 M. A model was constructed according to which the enzyme exists in equilibrium among four conformational states, corresponding to combinations of open and closed conformations of the LID-CORE and AMP-CORE clefts. ATP is assumed to bind only to those conformations with the closed LID-CORE cleft, and TMAO is assumed to be differentially excluded as a hard spherical particle from each of the four conformations in accordance with calculations based upon x-ray crystallographic structures. This model was found to describe quantitatively the dependence of the fraction of the closed LID-CORE cleft upon the concentrations of both ATP and TMAO over the entire range of concentrations with just five undetermined parameters.

Original language	English
Pages (from-to)	2991-2999
Number of pages	9
Journal	Biophysical Journal
Volume	100
Issue number	12
DOIs	https://doi.org/10.1016/j.bpj.2011.03.065
State	Published - 22 Jun 2011

Bibliographical note

Funding Information:
This work was supported by research and equipment grants from the Israel Science Foundation (ISF 1102/06), the United States-Israel Binational foundation (BSF 2005270), the U.S. National Science Foundation (MCB-0749464), by the Marie Curie Transfer of Knowledge grant from the European Union (29936), and by the Damadian Center for Magnetic Resonance Research, Bar-Ilan University. A.P.M.'s research is supported by the Intramural Research Division of the National Institute of Diabetes and Digestive and Kidney Diseases.

Funding

This work was supported by research and equipment grants from the Israel Science Foundation (ISF 1102/06), the United States-Israel Binational foundation (BSF 2005270), the U.S. National Science Foundation (MCB-0749464), by the Marie Curie Transfer of Knowledge grant from the European Union (29936), and by the Damadian Center for Magnetic Resonance Research, Bar-Ilan University. A.P.M.'s research is supported by the Intramural Research Division of the National Institute of Diabetes and Digestive and Kidney Diseases.

Funders	Funder number
Damadian Center for Magnetic Resonance Research
National Science Foundation	MCB-0749464
National Institute of Diabetes and Digestive and Kidney Diseases
European Commission	29936
United States-Israel Binational Science Foundation	BSF 2005270
Bar-Ilan University
Israel Science Foundation	ISF 1102/06

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title = "Modulation of functionally significant conformational equilibria in adenylate kinase by high concentrations of trimethylamine oxide attributed to volume exclusion",

abstract = "The effect of an inert small molecule osmolyte, trimethyl amine N-oxide (TMAO), upon the conformational equilibria of Escherichia coli adenylate kinase was studied using time-resolved FRET. The relative populations of open and closed clefts between the LID and the CORE domains were measured as functions of the concentrations of the substrate ATP over the concentration range 0-18 mM and TMAO over the concentration range 0-4 M. A model was constructed according to which the enzyme exists in equilibrium among four conformational states, corresponding to combinations of open and closed conformations of the LID-CORE and AMP-CORE clefts. ATP is assumed to bind only to those conformations with the closed LID-CORE cleft, and TMAO is assumed to be differentially excluded as a hard spherical particle from each of the four conformations in accordance with calculations based upon x-ray crystallographic structures. This model was found to describe quantitatively the dependence of the fraction of the closed LID-CORE cleft upon the concentrations of both ATP and TMAO over the entire range of concentrations with just five undetermined parameters.",

author = "Sureshbabu Nagarajan and Dan Amir and Asaf Grupi and Goldenberg, {David P.} and Minton, {Allen P.} and Elisha Haas",

note = "Funding Information: This work was supported by research and equipment grants from the Israel Science Foundation (ISF 1102/06), the United States-Israel Binational foundation (BSF 2005270), the U.S. National Science Foundation (MCB-0749464), by the Marie Curie Transfer of Knowledge grant from the European Union (29936), and by the Damadian Center for Magnetic Resonance Research, Bar-Ilan University. A.P.M.'s research is supported by the Intramural Research Division of the National Institute of Diabetes and Digestive and Kidney Diseases. ",

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N2 - The effect of an inert small molecule osmolyte, trimethyl amine N-oxide (TMAO), upon the conformational equilibria of Escherichia coli adenylate kinase was studied using time-resolved FRET. The relative populations of open and closed clefts between the LID and the CORE domains were measured as functions of the concentrations of the substrate ATP over the concentration range 0-18 mM and TMAO over the concentration range 0-4 M. A model was constructed according to which the enzyme exists in equilibrium among four conformational states, corresponding to combinations of open and closed conformations of the LID-CORE and AMP-CORE clefts. ATP is assumed to bind only to those conformations with the closed LID-CORE cleft, and TMAO is assumed to be differentially excluded as a hard spherical particle from each of the four conformations in accordance with calculations based upon x-ray crystallographic structures. This model was found to describe quantitatively the dependence of the fraction of the closed LID-CORE cleft upon the concentrations of both ATP and TMAO over the entire range of concentrations with just five undetermined parameters.

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Modulation of functionally significant conformational equilibria in adenylate kinase by high concentrations of trimethylamine oxide attributed to volume exclusion

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