The use of NMR chemical shifts to analyse the MD trajectories: simulation of bovine p
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.
Related Articles 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. J Pept Sci. 2003 Jul;9(7):450-60 Authors: Busetta B, Picard P, Precigoux G 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. PMID: 12916642 [PubMed - indexed for MEDLINE] Source: PubMed |
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