Effect of the reaction field electrostatic term on the molecular dynamics simulation of the activation domain of procarboxypeptidase B

R. Gargallo, B. Oliva, E. Querol, F. X. Avilés

Research output: Contribution to journalArticleResearchpeer-review

10 Citations (Scopus)

Abstract

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 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.
Original languageEnglish
Pages (from-to)21-26
JournalProtein Engineering
Volume13
Issue number1
Publication statusPublished - 2 Mar 2000

Keywords

  • Electrostatics
  • Molecular dynamics
  • Procarboxypeptidase B
  • Reaction field
  • Salt effects

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