title: A Threshold-Minimization Scheme for Exploring the Energy Landscape of Biomolecules: Application to a Cyclic Peptide and a Disaccharide.
abstract: We present a scheme, called the threshold-minimization method, for globally exploring the energy landscapes of small systems of biomolecular interest where typical exploration moves always require a certain degree of subsequent structural relaxation in order to be efficient, e.g., systems containing small or large circular carbon chains such as cyclic peptides or carbohydrates. We show that using this threshold-minimization method we can not only reproduce the global minimum and relevant local minima but also overcome energetic barriers associated with different types of isomerism for the example of a cyclic peptide, cyclo-(Gly)4. We then apply the new method to the disaccharide α-d-glucopyranose-1-2-β-d-fructofuranose, report energetically preferred configurations and barriers to boat-chair isomerization in the glucopyranosyl ring, and discuss the energy landscape.
authors.affiliation: School of Chemistry, University of Birmingham , Edgbaston, Birmingham B15 2TT, United Kingdom.
authors.forename: Sridhar
authors.initials: S
authors.lastname: Neelamraju
authors.affiliation: School of Chemistry, University of Birmingham , Edgbaston, Birmingham B15 2TT, United Kingdom.
authors.forename: Roy L
authors.initials: RL
authors.lastname: Johnston
authors.affiliation: Max Planck Institute for Solid State Research , Heisenbergstrasse 1, D-70569 Stuttgart, Germany.
authors.forename: J Christian
authors.initials: JC
authors.lastname: Schön
mesh_terms: D004187:Disaccharides / Q000737:chemistry* / Q000378:metabolism; D009010:Monte Carlo Method; D010456:Peptides, Cyclic / Q000737:chemistry* / Q000378:metabolism; D011487:Protein Conformation
chemical_list: D004187:Disaccharides; D010456:Peptides, Cyclic