Computer simulation meets experiment: Molecular dynamics simulaitons of spin labeled proteins.

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Title: Computer simulation meets experiment: Molecular dynamics simulaitons of spin labeled proteins.
Authors: Gajula, M.N.V. Prasad
Thesis advisor: Prof. Dr. Heinz-Jürgen Steinhoff
Thesis referee: PD. Armen Mulkidjianian
Prof. Dr. Jochen Gemmer
Dr. Rainer Pankrath
Abstract: EPR spectroscopy of site-directed spin labeled proteins is extremely informative in the studies of protein dynamics; however, it is difficult to interpret the spectra in terms of the conformational dynamics in atomic detail.In the present work we aimed to investigate the site-specific structural dynamics of proteins by using MD simulations upon analyzing and interpreting the EPR data. The major goal of this work is to know how far the computer simulations can meet the experiments. As a first step, MD simulations are performed to identify the location and orientation of the tyrosine radical in the R2 subunit of ribonucleotide reductase. The MD results show that the tyrosine is moving away from the diiron center in its radical state. This data is in agreement with EPR results and suggests reorientation of the tyrosine radical when compared to its neutral state. In further studies, the behavior of a methanethiosulfonate spin label, R1, in various environments of the protein is characterized by using MD simulations. RMSD analysis and angle ß distributions of the nitroxide show that R1 in buried sites in a protein helix is significantly immobile and in surface exposed sites it is highly mobile. Analyses of MD data suggest that internal rotations of x4 and x5 dihedrals of R1 are dominant in the R1 dynamics.Our studies also show that interaction with the surrounding residues show significant influence on the dynamics of R1. MD simulations data of the vinculin tail protein, both in water and in vacuo, are compared to the experimental results for further analysis of 12 different R1 sites in various environments.In a study on the photosynthetic reaction center(RC),MD is used to identify the location of the R1 binding site (H156)and thereby exploring the conformational dynamics in the RC protein upon light activation. The distance between the primary quinone, QA, and H156R1 determined from MD is in reasonable agreement with that measured by EPR.
URL: https://repositorium.ub.uni-osnabrueck.de/handle/urn:nbn:de:gbv:700-2008041631
Subject Keywords: Molecular dynamics; EPR; MTSSL; Spin label; Tyrosine radical; Photosynthetic RC; Distance measurements
Issue Date: 18-Mar-2008
Type of publication: Dissertation oder Habilitation [doctoralThesis]
Appears in Collections:FB04 - E-Dissertationen

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