Dresden 2011 – wissenschaftliches Programm
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MO: Fachverband Molekülphysik
MO 1: Biomolecules
MO 1.4: Vortrag
Montag, 14. März 2011, 11:15–11:30, TOE 317
Coarse graining protein motion: FIRST/FRODA and normal modes of motion. Can theory meet experiment? — •J Emilio Jimenez-Roldan1,2, Stephen A Wells1, Robert B Freedman2, and Rudolf A Röemer1 — 1Dept. Physics, Centre for Scientific Computing, University of Warwick, Coventry, CV4 7AL U.K. — 2Life Sciences, Coventry, University of Warwick, CV4 7AL, U.K.
We explore the conformational change of Protein Disulphide Isomerase using Rigid Cluster Decomposition constraints and Normal Modes of Motion. Our simulations show that the active sites of the protein are able to move within a range over 40 Angstroms for one of the directions of motion. In order to test these results we carry out polyactylamide gel electrophoresis experiments using cross-linkers of different lengths that bind to the active sites to identify the minimum length between the active sites. Our simulations are based on first, the coarse graining model criteria defined by FIRST software which is able to identify flexible and constrainted regions, and second, on Normal Modes of Motion which map out the directions of motion for a given network. Using the FRODA module, together with the coarse graining constrains given by FIRST and Normal Modes of Motion we identify large scale conformational changes at low computational cost.