DC Field | Value | Language |
dc.contributor.author | Beier, Christian | |
dc.contributor.author | Steinhoff, Heinz-Jurgen | |
dc.date.accessioned | 2021-12-23T16:00:50Z | - |
dc.date.available | 2021-12-23T16:00:50Z | - |
dc.date.issued | 2006 | |
dc.identifier.issn | 00063495 | |
dc.identifier.uri | https://osnascholar.ub.uni-osnabrueck.de/handle/unios/4613 | - |
dc.description.abstract | Electron paramagnetic resonance (EPR) spectroscopy using site-directed spin-labeling is an appropriate technique to analyze the structure and dynamics of flexible protein regions as well as protein-protein interactions under native conditions. The analysis of a set of protein mutants with consecutive spin-label positions leads to the identification of secondary and tertiary structure elements. In the first place, continuous-wave EPR spectra reflect the motional freedom of the spin-label specifically linked to a desired site within the protein. EPR spectra calculations based on molecular dynamics ( MD) and stochastic dynamics simulations facilitate verification or refinement of predicted computer-aided models of local protein conformations. The presented spectra simulation algorithm implies a specialized in vacuo MD simulation at 600 K with additional restrictions to sample the entire accessible space of the bound spin-label without large temporal effort. It is shown that the distribution of spin-label orientations obtained from such MD simulations at 600 K agrees well with the extrapolated motion behavior during a long timescale MD at 300 K with explicit water. The following potential-dependent stochastic dynamics simulation combines the MD data about the site-specific orientation probabilities of the spin-label with a realistic rotational diffusion coefficient yielding a set of trajectories, each more than 700 ns long, essential to calculate the EPR spectrum. Analyses of a structural model of the loop between helices E and F of bacteriorhodopsin are illustrated to demonstrate the applicability and potentials of the reported simulation approach. Furthermore, effects on the motional freedom of bound spin-labels induced by solubilization of bacteriorhodopsin with Triton X-100 are examined. | |
dc.language.iso | en | |
dc.publisher | CELL PRESS | |
dc.relation.ispartof | BIOPHYSICAL JOURNAL | |
dc.subject | ANGSTROM RESOLUTION | |
dc.subject | BACTERIORHODOPSIN | |
dc.subject | Biophysics | |
dc.subject | BROWNIAN DYNAMICS | |
dc.subject | CRYSTAL-STRUCTURE | |
dc.subject | EPR-SPECTROSCOPY | |
dc.subject | NITROXIDE SIDE-CHAINS | |
dc.subject | PROTEIN DYNAMICS | |
dc.subject | PROTON TRANSLOCATION | |
dc.subject | SPIN LABEL | |
dc.subject | T4 LYSOZYME | |
dc.title | A structure-based simulation approach for electron paramagnetic resonance spectra using molecular and stochastic dynamics simulations | |
dc.type | journal article | |
dc.identifier.doi | 10.1529/biophysj.105.080051 | |
dc.identifier.isi | ISI:000240368700026 | |
dc.description.volume | 91 | |
dc.description.issue | 7 | |
dc.description.startpage | 2647 | |
dc.description.endpage | 2664 | |
dc.contributor.orcid | 0000-0002-5888-0157 | |
dc.contributor.researcherid | H-3791-2014 | |
dc.identifier.eissn | 15420086 | |
dc.publisher.place | 50 HAMPSHIRE ST, FLOOR 5, CAMBRIDGE, MA 02139 USA | |
dcterms.isPartOf.abbreviation | Biophys. J. | |
dcterms.oaStatus | Green Published, Bronze | |
crisitem.author.dept | FB 04 - Physik | - |
crisitem.author.deptid | fb04 | - |
crisitem.author.parentorg | Universität Osnabrück | - |
crisitem.author.netid | StHe633 | - |