title: 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 Trp8 and His12 together with Gln7, 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.
authors.affiliation: Department of Chemistry, Durban University of Technology, Steve Biko Campus, P.O. Box 1334, Durban 4000, South Africa.
authors.forename: Parul
authors.initials: P
authors.lastname: Sharma
authors.forename: Parvesh
authors.initials: P
authors.lastname: Singh
authors.forename: Krishna
authors.initials: K
authors.lastname: Bisetty
authors.forename: Francesc J
authors.initials: FJ
authors.lastname: Corcho
authors.forename: Juan J
authors.initials: JJ
authors.lastname: Perez
mesh_terms: D020816:Amino Acid Motifs; D001839:Bombesin / Q000737:chemistry*; D006639:Histidine / Q000737:chemistry; D006860:Hydrogen Bonding; D009682:Magnetic Resonance Spectroscopy; D056004:Molecular Dynamics Simulation; D013997:Time Factors; D014364:Tryptophan / Q000737:chemistry
chemical_list: D006639:Histidine; D014364:Tryptophan; D001839:Bombesin