The use of NMR chemical shifts to analyse the MD trajectories: simulation of bovine pancreatic trypsin inhibitor dynamics in water as a test case for solvent influences
✍ Scribed by Bernard Busetta; Philippe Picard; Gilles Precigoux
- Publisher
- John Wiley and Sons
- Year
- 2003
- Tongue
- English
- Weight
- 136 KB
- Volume
- 9
- Category
- Article
- ISSN
- 1075-2617
- DOI
- 10.1002/psc.466
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✦ Synopsis
Abstract
In this paper the NMR secondary chemical shifts, that are estimated from a set of 3D‐structures, are compared with the observed ones to appraise the behaviour of a known x‐ray diffraction structure (of the bovine pancreatic trypsin inhibitor protein) when various molecular dynamics are applied. The results of a 200 ps molecular dynamics under various conditions are analysed and different ways to modify the molecular dynamics are considered. With the purpose of avoiding the time‐consuming explicit representation of the solvent (water) molecules, an attempt was made to understand the role of the solvent and to develop an implicit representation, which may be refined. A simulation of hydrophobic effects in an aqueous environment is also proposed which seems to provide a better approximation of the observed solution structure of the protein. Copyright © 2003 European Peptide Society and John Wiley & Sons, Ltd.