title: 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.
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.
authors: CABin division, DST Ramanujan Fellow, Indian Agricultural Statistics Research Institute, PUSA campus, New Delhi-110012, India. gajula@iasri.res.in
authors: M N V
authors: MN
authors: Prasad Gajula
authors: K P
authors: KP
authors: Vogel
authors: Anil
authors: A
authors: Rai
authors: Franziska
authors: F
authors: Dietrich
authors: H J
authors: HJ
authors: Steinhoff
mesh_terms: D003198:Computer Simulation; D004578:Electron Spin Resonance Spectroscopy; D056004:Molecular Dynamics Simulation; D011487:Protein Conformation; D013113:Spin Labels; D016596:Vinculin / Q000737:chemistry*
chemical_list: D013113:Spin Labels; D016596:Vinculin