Convergence in peptide folding simulation: multiple trajectories of a potential AIDS pharmacophore
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Updated: Aug 30, 2026

Assessment of Immunologically Relevant Dynamic Tertiary Structural Features of the HIV-1 V3 Loop Crown R2 Sequence by ab initio Folding
Published on: September 15, 2010
Dan Mihailescu1, Jennifer Reed, Jeremy C Smith
1Interdisciplinary Center for Scientific Computing, IWR, Heidelberg University, Im Neuenheimer Feld 368, D-69120 Heidelberg, Germany.
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) 1H-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.
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