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This article is part of the supplement: Selected articles from ISCB-Asia 2012

Open Access Research

How far in-silico computing meets real experiments. A study on the structure and dynamics of spin labeled vinculin tail protein by molecular dynamics simulations and EPR spectroscopy

MNV Prasad Gajula1*, KP Vogel2, Anil Rai1, Franziska Dietrich3 and HJ Steinhoff2

Author affiliations

1 CABin division, DST Ramanujan Fellow, Indian Agricultural Statistics Research Institute, PUSA campus, New Delhi-110012, India

2 Department of Physics, University of Osnabrueck, Barbara strasse-7, D49076-Osnabrueck, Germany

3 IZKF Leipzig, Faculty of Medicine, University of Leipzig, Liebigstr. 21, D-04103 Leipzig, Germany

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Citation and License

BMC Genomics 2013, 14(Suppl 2):S4  doi:10.1186/1471-2164-14-S2-S4

Published: 15 February 2013

Abstract

Background

Investigation of conformational changes in a protein is a prerequisite to understand its biological function. To explore these conformational changes in proteins we developed a strategy with the combination of molecular dynamics (MD) simulations and electron paramagnetic resonance (EPR) spectroscopy. The major goal of this work is to investigate how far computer simulations can meet the experiments.

Methods

Vinculin tail protein is chosen as a model system as conformational changes within the vinculin protein are believed to be important for its biological function at the sites of cell adhesion. MD simulations were performed on vinculin tail protein both in water and in vacuo environments. EPR experimental data is compared with those of the simulated data for corresponding spin label positions.

Results

The calculated EPR spectra from MD simulations trajectories of selected spin labelled positions are comparable to experimental EPR spectra. The results show that the information contained in the spin label mobility provides a powerful means of mapping protein folds and their conformational changes.

Conclusions

The results suggest the localization of dynamic and flexible regions of the vinculin tail protein. This study shows MD simulations can be used as a complementary tool to interpret experimental EPR data.