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Energetic and entropic contributions to the interactions between like‐charged groups in cationic peptides: A molecular dynamics simulation study
Author(s) -
Villarreal Marcos,
Montich Guillermo
Publication year - 2002
Publication title -
protein science
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 3.353
H-Index - 175
eISSN - 1469-896X
pISSN - 0961-8368
DOI - 10.1110/ps.0203002
Subject(s) - molecular dynamics , chemistry , counterion , van der waals force , peptide , chemical physics , potential of mean force , cationic polymerization , lysine , static electricity , alanine , computational chemistry , amino acid , crystallography , ion , molecule , physics , organic chemistry , biochemistry , quantum mechanics
Abstract The interaction between like‐charged amino acid residues has been proposed to stabilize the folded state of peptides and proteins, and to modulate the substrate binding and the action mechanism of enzymes. We have used an alanine‐ and lysine‐based peptide as a model system to study the interaction between like charges, and we have performed a 16‐nsec molecular dynamics simulation in solution. The calculated potential of mean force for the approach of the lysine's Nζ atoms showed a minimum at a distance of 0.7 nm, in agreement with the separation probabilities obtained from analysis of protein crystal structures. The analysis of the individual energy components showed that the solvent polarization pays for the approach of the like charges and that the van der Waals energies do not contribute significantly. The entropic contributions have been divided in conformational and desolvation terms. Both terms favor the formation of the charge pair. A 10‐fold increase in counterion concentration was observed—with respect to its bulk concentration—next to the peptide charges, which helps to stabilize the peptide charges at a close distance.