EFFECTS OF DIFFERENT CONTINUUM DIELECTRIC MODELS IN A MOLECULAR-DYNAMICS AND ENERGY MINIMIZATION STUDY OF THE ANTIGENIC LOOP OF FOOT-AND-MOUTH-DISEASE VIRUS

This study presents the influence of the dielectric constant on the fi nal structure of the major antigenic loop of the FMDV serotype C. Mini mizations have been performed on the nine-residue peptide Ac-TASARGDLA -NHMe, using two expressions for the dielectric constant: a distance-i ndependent (epsilon = kappa), and a distance-dependent (epsilon = kapp a()r) forms, and for kappa values from 1 to 10. In addition, kappa=40 and 80 has Asia been considered for the constant expression of the di electrics. The calculations suggest, for both expressions of the diele ctrics. that for the sequence under study a value of K in the range of 2-6 performs an adequate treatment of the electrostatic interactions. Finally, molecular dynamic simulations at 298 K calculated with an ef fective 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-r ay diffraction studies.