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    Keywords: PEPTIDE ; SIMULATIONS ; SPECTRA ; Germany ; PROTEINS ; DYNAMICS ; SIMULATION ; PARAMETERS ; VACCINE ; KINETICS ; ALPHA-HELIX ; CD4-BINDING DOMAIN ; CONFORMATIONAL SWITCH ; EXPLICIT SOLVENT WATER ; GP120 ; IMMUNOGENIC PEPTIDE ; molecular dynamics simulation,peptide,convergence ; MOLECULAR-DYNAMICS SIMULATION ; TRIFLUOROETHANOL
    Abstract: To examine the conformational properties in aqueous solution of a 15-residue peptide that is a potential pharmacophore for AIDS vaccine development, molecular dynamics simulations were performed in water starting from structures determined experimentally in three different organic solvents. Convergence characteristics of the simulation are examined in Cartesian and conformational spaces. In addition, novel analysis tools are employed including a multidimensional scaling method to represent the distance between trajectory frames. As these methods are based on a variety of physical parameters, they provide a useful cross-check on the structural convergence. Theoretical two-dimensional (2D) H-1-NMR spectra are also generated. These are superficially quite different in appearance, demonstrating that backbone similarities difficult to identify by visual inspection of 2D NMR data can be revealed using the methods described here. (C) 2003 Wiley Periodicals, Inc
    Type of Publication: Journal article published
    PubMed ID: 14517902
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