Modelling the dynamics of an antigenic peptide using NMR relaxation data

Abstract

The internal dynamics of a cyclic peptide which was designed to mimic an antigenic loop of the haemagglutinin, is studied through heteronuclear relaxation along the 13C alpha-1H alpha vectors and through homonuclear relaxation along the 1H alpha-1HN and 1H beta-1H beta' vectors. Order parameters are extracted from the longitudinal and cross-relaxation data. Molecular dynamics simulations are performed and the order parameters are calculated in different ways from the trajectories. The simulation, which is performed in vacuo, gives smaller order parameters (vector motions of larger amplitude) than the experimental results. However, the general features of the experimental order parameters are reproduced by the molecular dynamics simulation. The flexibility of the molecule can then be investigated from the results of the molecular dynamics. It shows that the mobility observed through the order parameters is due to motions in flanking regions, remote from the observed vectors.