Effect of the reaction field electrostatic term on the molecular dynamics simulation of the activation domain of procarboxypeptidase B.
Molecular dynamics simulations of the activation domain of porcine procarboxypeptidase B (ADBp) were performed in order to examine the effects of the inclusion of a reaction field (RF) term into the calculation of electrostatics forces for highly charged proteins. Two simulations were performed with the GROMOS96 package, studying the influence of counterions on the final results. Comparison with previous results without the inclusion of the RF term (Martí-Renom, M.A., Mas,J.M., Oliva,B., Querol,E. and Avilés,F.X., Protein Engng, 1998, 11, 101-110) shows that the structure is well maintained when the RF term is included. Moreover, the analysis of the trajectories shows that simulations of solvated highly-charged proteins are sensitive to the presence of counterions, the secondary structures being more stable when their charges are neutralized.
Gargallo
R
R
Departament de Quimica Analítica, Universitat de Barcelona, Martí i Franqués, 1-11, 08028, Barcelona, Spain.
Oliva
B
B
Querol
E
E
Avilés
F X
FX
D000595:Amino Acid Sequence; D000818:Animals; D043424:Carboxypeptidase B; D002268:Carboxypeptidases / Q000737:chemistry* / Q000378:metabolism*; D003198:Computer Simulation; D004789:Enzyme Activation; D004792:Enzyme Precursors / Q000737:chemistry* / Q000378:metabolism*; D006860:Hydrogen Bonding; D008958:Models, Molecular; D008969:Molecular Sequence Data; D011487:Protein Conformation; D055672:Static Electricity; D013552:Swine
D004792:Enzyme Precursors; D002268:Carboxypeptidases; D043424:Carboxypeptidase B