HOME HELP FEEDBACK SUBSCRIPTIONS ARCHIVE SEARCH TABLE OF CONTENTS		QUICK SEARCH:   [advanced] Author: Keyword(s): Year:  Vol:  Page:

J. Biol. Chem., Vol. 281, Issue 33, 23792-23803, August 18, 2006

This Article Full Text Full Text (PDF) Supplemental Data All Versions of this Article: 281/33/23792    most recent M602870200v1 Submit a Letter to Editor Alert me when this article is cited Alert me when eLetters are posted Alert me if a correction is posted Citation Map Services Email this article to a friend Similar articles in this journal Similar articles in PubMed Alert me to new issues of the journal Download to citation manager Request Permissions Citing Articles Citing Articles via HighWire Citing Articles via Google Scholar Google Scholar Articles by Thompson, D. Articles by Simonson, T. Search for Related Content PubMed PubMed Citation Articles by Thompson, D. Articles by Simonson, T. Social Bookmarking                      What's this?

Molecular Dynamics Simulations Show That Bound Mg²⁺ Contributes to Amino Acid and Aminoacyl Adenylate Binding Specificity in Aspartyl-tRNA Synthetase through Long Range Electrostatic Interactions^*

Damien Thompson¹ and Thomas Simonson²

From the Laboratoire de Biochimie, CNRS, UMR7654, Department of Biology, Ecole Polytechnique, 91128 Palaiseau, France and Tyndall National Institute, University College Cork, Cork, Ireland

Molecular recognition between the aminoacyl-tRNA synthetase enzymes and their cognate amino acid ligands is essential for the faithful translation of the genetic code. In aspartyl-tRNA synthetase (AspRS), the co-substrate ATP binds preferentially with three associated Mg²⁺ cations in an unusual, bent geometry. The Mg²⁺ cations play a structural role and are thought to also participate catalytically in the enzyme reaction. Co-binding of the ATP· complex was shown recently to increase the Asp/Asn binding free energy difference, indicating that amino acid discrimination is substrate-assisted. Here, we used molecular dynamics free energy simulations and continuum electrostatic calculations to resolve two related questions. First, we showed that if one of the Mg²⁺ cations is removed, the Asp/Asn binding specificity is strongly reduced. Second, we computed the relative stabilities of the three-cation complex and the 2-cation complexes. We found that the 3-cation complex is overwhelmingly favored at ordinary magnesium concentrations, so that the protein is protected against the 2-cation state. In the homologous LysRS, the 3-cation complex was also strongly favored, but the third cation did not affect Lys binding. In tRNAbound AspRS, the single remaining Mg²⁺ cation strongly favored the Asp-adenylate substrate relative to Asn-adenylate. Thus, in addition to their structural and catalytic roles, the Mg²⁺ cations contribute to specificity in AspRS through long range electrostatic interactions with the Asp side chain in both the pre- and post-adenylation states.

Received for publication, March 27, 2006 , and in revised form, June 12, 2006.

^* The costs of publication of this article were defrayed in part by the payment of page charges. This article must therefore be hereby marked "advertisement" in accordance with 18 U.S.C. Section 1734 solely to indicate this fact.

The on-line version of this article (available at http://www.jbc.org) contains supplemental material including Fig. SM1 and Table SM1.

¹ Supported in part by an Egide postdoctoral fellowship.

² To whom correspondence should be addressed: Laboratoire de Biochimie (CNRS, UMR7654), Dept. of Biology, Ecole Polytechnique, 91128 Palaiseau, France. Tel.: 33-169-33-38-81; Fax: 33-169-33-30-13; E-mail: thomas.simonson{at}polytechnique.fr.

CiteULike    Complore    Connotea    Del.icio.us    Digg    Reddit    Technorati    What's this?

This article has been cited by other articles:

				D. Thompson, C. Lazennec, P. Plateau, and T. Simonson Ammonium Scanning in an Enzyme Active Site: THE CHIRAL SPECIFICITY OF ASPARTYL-tRNA SYNTHETASE J. Biol. Chem., October 19, 2007; 282(42): 30856 - 30868. [Abstract] [Full Text] [PDF]