Berlin 2012 – scientific programme
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BP: Fachverband Biologische Physik
BP 15: Proteins II
BP 15.5: Talk
Wednesday, March 28, 2012, 16:15–16:30, H 1058
Dielectric Relaxation Spectroscopy of Ubiquitin by Poisson-Boltzmann-Monte Carlo Studies — •Stephan Kramer1, Bartosz Kohnke1, and Reiner Kree2 — 1Institut f. Numerische u. Angewandte Mathematik, Universität Göttingen, Lotzestrasse 16-18, D-37083 Göttingen — 2Institut f. Theoretische Physik, Universität Göttingen, Friedrich-Hundt-Platz 1, D-37077 Göttingen
To reliably predict the function of ubiquitin it is necessary to know its conformational dynamics on all relevant time-scales. Due to its omnipresence in a multitude of key regulatory processes like molecular recognition or signal transduction these time-scales span from nano- to microseconds. Not all of them are accessible by NMR relaxation dispersion techniques which so far have been the standard way to measure conformational sampling. Only recently [1] dielectric relaxation spectroscopy (DRS) was introduced as further means to measure internal dynamics beyond the temporal resolution NMR is capable of. To get further insight into the measurement process we want to simulate DRS on a single molecule level using standard Monte Carlo techniques for the intramolecular motion. The properties of the ionic solvent and its interaction with the protein are assesed by solving the corresponding Poisson-Boltzmann equation by multigrid methods. For comparison with DRS experiments we compute dielectric loss spectra from the bulk dielectric moment to assess the the interconversion of different comformations of ubiquitin.
[1] David Ban et al. Kinetics of Conformational Sampling in Ubiquitin, Angew. Chem. Int. Ed. 2011, 50, 11437-11440