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

BMC Genomics

Research

MNV Prasad Gajula¹  Anil Rai¹  HJ Steinhoff²  KP Vogel²  Franziska Dietrich³ 

[1] CABin division, DST Ramanujan Fellow, Indian Agricultural Statistics Research Institute, PUSA campus, 110012, New Delhi, India;Department of Physics, University of Osnabrueck, Barbara strasse-7, D49076, Osnabrueck, Germany;IZKF Leipzig, Faculty of Medicine, University of Leipzig, Liebigstr. 21, D-04103, Leipzig, Germany;

关键词: Electron Paramagnetic Resonance;    Molecular Dynamic Simulation;    Electron Paramagnetic Resonance Spectrum;    Nitroxide;    Spin Label;   

DOI  :  10.1186/1471-2164-14-S2-S4

来源: Springer

【 摘 要 】

BackgroundInvestigation 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.MethodsVinculin 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.ResultsThe 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.ConclusionsThe 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.

【 授权许可】

CC BY   
© Prasad Gajula et al.; licensee BioMed Central Ltd. 2013