Conformational profile of bombesin assessed using different computational protocols

Abstract

The present work involves the study of the conformational profile of bombesin using different computational procedures used to explore the configurational space based on molecular dynamics simulations. Specifically, the present study describes the effect of using Berendsen's versus Langevin's thermostat and on the other hand, the use of the multicanonical replica exchange molecular dynamics as compared to standard molecular dynamics. In these simulations the solvent was modeled using the Onufriev, Bashford and Case implementation of Generalized Born procedure. The detailed computational analysis agrees well with the aggregated information previously reported in the NMR study of the peptide in a mixture of trifluoroethanol/water. Present results show a clear preference for the peptide to attain a helical structure on the segment 6–14, with a tendency to adopt a α-helix at the C-terminus aligning the aromatic residues Trp 8 and His 12 together with Gln 7, known to be important for peptide mediated activation. Finally, the three methodologies used in the present work yield similar structural results, although a detailed analysis reveals biases that need to be considered when performing this kind of studies.