Dynamic modelling of a helical peptide in solution using NMR data: Multiple conformations and multi-spin effects |
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Authors: | Johan Kemmink Ruud M. Scheek |
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Affiliation: | (1) European Molecular Biology Laboratory, Meyerhofstrasse 1, D-69012 Heidelberg, Germany;(2) The Groningen Biomolecular Science and Biotechnology Institute, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands |
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Abstract: | Summary Nuclear Overhauser effect (NOE) measurements on molecules in solution provide information about only the ensemble-averaged properties of these molecules. An algorithm is presented that uses a list of NOEs to produce an ensemble of molecules that on average agrees with these NOEs, taking into account the effect of surrounding spins on the buildup of each NOE (spin diffusion). A simplified molecular dynamics simulation on several copies of the molecule in parallel is restrained by forces that are derived directly from differences between calculated and measured NOEs. The algorithm is tested on experimental NOE data of a helical peptide derived from bovine pancreatic trypsin inhibitor. |
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Keywords: | Molecular dynamics Ensemble dynamics Peptide conformation NOE Spin diffusion Bovine pancreatic trypsin inhibitor (BPTI) |
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