Molecular dynamics simulation of highly charged proteins: Comparison of the particle-particle particle-mesh and reaction field methods for the calculation of electrostatic interactions

Raimundo Gargallo, Philippe H. Hünenberger, Francesc X. Avilés, Baldomero Oliva

Research output: Contribution to journalArticleResearchpeer-review

35 Citations (Scopus)

Abstract

Molecular dynamics (MD) simulations of the activation domain of porcine procarboxypeptidase B (ADBp) were performed to examine the effect of using the particle-particle particle-mesh (P3M) or the reaction field (RF) method for calculating electrostatic interactions in simulations of highly charged proteins. Several structural, thermodynamic, and dynamic observables were derived from the MD trajectories, including estimated entropies and solvation free energies and essential dynamics (ED). The P3M method leads to slightly higher atomic positional fluctuations and deviations from the crystallographic structure, along with somewhat lower values of the total energy and solvation free energy. However, the ED analysis of the system leads to nearly identical results for both simulations. Because of the strong similarity between the results, both methods appear well suited for the simulation of highly charged globular proteins in explicit solvent. However, the lower computational demand of the RF method in the present implementation represents a clear advantage over the P3M method.
Original languageEnglish
Pages (from-to)2161-2172
JournalProtein Science
Volume12
Issue number10
DOIs
Publication statusPublished - 1 Oct 2003

Keywords

  • Electrostatics
  • Entropy
  • Essential dynamics
  • Molecular dynamics
  • Procarboxypeptidase B
  • Solvation

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