Effects of different continium 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 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.
Vega
M C
MC
Department d'Enginyeria Quimica, Escola Tecnica Superior d'Enginyers Industrials de Barcelona, Universitat Politècnica de Catalunya, Spain.
Alemán
C
C
Alhambra
C
C
Perez
J J
JJ
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
D000956:Antigens, Viral; D036022:Capsid Proteins; D009842:Oligopeptides; C442501:VP1 protein, Foot-and-mouth disease virus