Role of electrostatics in the structure, energy, and dynamics of biomolecules

A model study of N-methylalanylacetamide

Bernard Pettitt, Martin Karplus

Research output: Contribution to journalArticle

56 Citations (Scopus)

Abstract

The contribution of electrostatic interactions to a range of structural, energetic, and dynamic properties of the alanine dipeptide is examined. An empirical energy function is employed to represent the dipeptide, and the partial atomic charges are varied from zero to values used in standard models for amino acids and proteins. It is demonstrated that, although there are large differences in the absolute energy of models with different charges, the relative energies of the various dipeptide conformers are less sensitive to the charges. The minimum energy structures of the conformers are only weakly dependent on the charges. A normal mode analysis shows that only a few modes are sensitive to the charges and that thermodynamic quantities, which represent sums over the modes, are essentially the same for all the models. Comparison of the harmonic dynamics results with those from an ensemble of molecular dynamics trajectories reveals that the electrostatic contributions to the potential surface introduce anharmonic effects.

Original languageEnglish (US)
Pages (from-to)1166-1173
Number of pages8
JournalJournal of the American Chemical Society
Volume107
Issue number5
StatePublished - 1985
Externally publishedYes

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Dipeptides
Biomolecules
Static Electricity
Electrostatics
Surface potential
Molecular Dynamics Simulation
Coulomb interactions
Thermodynamics
Alanine
Molecular dynamics
Amino acids
Trajectories
Proteins
Amino Acids

ASJC Scopus subject areas

  • Chemistry(all)

Cite this

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abstract = "The contribution of electrostatic interactions to a range of structural, energetic, and dynamic properties of the alanine dipeptide is examined. An empirical energy function is employed to represent the dipeptide, and the partial atomic charges are varied from zero to values used in standard models for amino acids and proteins. It is demonstrated that, although there are large differences in the absolute energy of models with different charges, the relative energies of the various dipeptide conformers are less sensitive to the charges. The minimum energy structures of the conformers are only weakly dependent on the charges. A normal mode analysis shows that only a few modes are sensitive to the charges and that thermodynamic quantities, which represent sums over the modes, are essentially the same for all the models. Comparison of the harmonic dynamics results with those from an ensemble of molecular dynamics trajectories reveals that the electrostatic contributions to the potential surface introduce anharmonic effects.",
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