This Article Full Text Full Text (PDF) All Versions of this Article: biophysj.106.093195v1 92/5/1709    most recent Alert me when this article is cited Alert me if a correction is posted Services Similar articles in this journal Similar articles in PubMed Alert me to new issues of the journal Download to citation manager Citing Articles Citing Articles via HighWire Citing Articles via Google Scholar Google Scholar Articles by Balog, E. Articles by Fidy, J. Search for Related Content PubMed PubMed Citation Articles by Balog, E. Articles by Fidy, J.

The Influence of Interdomain Interactions on the Intradomain Motions in Yeast Phosphoglycerate Kinase: A Molecular Dynamics Study

Erika Balog ^*, Monique Laberge ^*  and Judit Fidy ^*

^* Department of Biophysics and Radiation Biology and Research Group for Membrane Biology of the Hungarian Academy of Sciences, Faculty of Medicine, Semmelweis University, Budapest, Hungary; and Department of Biochemistry and Biophysics and Johnson Research Foundation, University of Pennsylvania Medical Center, Philadelphia, Pennsylvania 19104-6059

Correspondence: Address reprint requests to Judit Fidy, Dept. of Biophysics and Radiation Biology, Faculty of Medicine, Semmelweis University, PO Box 263, H-1444 Budapest, Hungary. Tel.: 36-1-267-6261; Fax: 36-1-266-6656; E-mail: judit{at}puskin.sote.hu.

A 3-ns molecular dynamics simulation in explicit solvent was performed to examine the inter- and intradomain motions of the two-domain enzyme yeast phosphoglycerate kinase without the presence of substrates. To elucidate contributions from individual domains, simulations were carried out on the complete enzyme as well as on each isolated domain. The enzyme is known to undergo a hinge-bending type of motion as it cycles from an open to a closed conformation to allow the phosphoryl transfer occur. Analysis of the correlation of atomic movements during the simulations confirms hinge bending in the nanosecond timescale: the two domains of the complete enzyme exhibit rigid body motions anticorrelated with respect to each other. The correlation of the intradomain motions of both domains converges, yielding a distinct correlation map in the enzyme. In the isolated domain simulations—in which interdomain interactions cannot occur—the correlation of domain motions no longer converges and shows a very small correlation during the same simulation time. This result points to the importance of interdomain contacts in the overall dynamics of the protein. The secondary structure elements responsible for interdomain contacts are also discussed.

This article has been cited by other articles:

				M. Laberge and T. Yonetani Molecular Dynamics Simulations of Hemoglobin A in Different States and Bound to DPG: Effector-Linked Perturbation of Tertiary Conformations and HbA Concerted Dynamics Biophys. J., April 1, 2008; 94(7): 2737 - 2751. [Abstract] [Full Text] [PDF]