title: Effects of different continium dielectric models in a molecular dynamics and energy minimization study of the antigenic loop of foot-and-mouth disease virus.
abstract: This study presents the influence of the dielectric constant on the final structure of the major antigenic loop of the FMDV serotype C. Minimizations have been performed on the nine-residue peptide Ac-TASARGDLA-NHMe, using two expressions for the dielectric constant: a distance-independent (epsilon = kappa), and a distance-dependent (epsilon = kappa *r) forms, and for kappa values from 1 to 10. In addition, kappa = 40 and 80 has also been considered for the constant expression of the dielectrics. The calculations suggest, for both expressions of the dielectrics, that for the sequence under study a value of kappa in the range of 2-6 performs an adequate treatment of the electrostatic interactions. Finally, molecular dynamic simulations at 298 K calculated with an effective dielectric constants of epsilon = 1*r and epsilon = 4*r are compared. The results indicated that a dielectric of epsilon = 4*r provides a peptide fluctuations which are in agreement with recent X-ray diffraction studies.
authors.affiliation: Department d'Enginyeria Quimica, Escola Tecnica Superior d'Enginyers Industrials de Barcelona, Universitat Politècnica de Catalunya, Spain.
authors.forename: M C
authors.initials: MC
authors.lastname: Vega
authors.forename: C
authors.initials: C
authors.lastname: Alemán
authors.forename: C
authors.initials: C
authors.lastname: Alhambra
authors.forename: J J
authors.initials: JJ
authors.lastname: Perez
mesh_terms: D000465:Algorithms; D000595:Amino Acid Sequence; D000956:Antigens, Viral / Q000737:chemistry*; D005537:Aphthovirus / Q000276:immunology*; D002213:Capsid / Q000737:chemistry*; D036022:Capsid Proteins; D003198:Computer Simulation; D004563:Electrochemistry; D006860:Hydrogen Bonding; D008969:Molecular Sequence Data; D009842:Oligopeptides / Q000737:chemistry*; D011487:Protein Conformation; D014961:X-Ray Diffraction
chemical_list: D000956:Antigens, Viral; D036022:Capsid Proteins; D009842:Oligopeptides; C442501:VP1 protein, Foot-and-mouth disease virus