Polarizable force field for protein with charge response kernel

Miho Isegawa, Shigeki Kato

Research output: Contribution to journalArticle

11 Citations (Scopus)

Abstract

We present a molecular mechanical force field for polypeptides and proteins involving the electronic polarization effect described with the charge response kernel. All of the electrostatic parameters for 20 amino acids are obtained by ab initio electronic structure calculations and combined with the AMBER99 force field. The refittings of dihedral angle parameters in the torsional potentials are performed so as to reproduce the ab initio optimized geometries and relative energies for the conformers of dipeptides. The present force field is applied to molecular dynamics simulation calculations of the extended alanine tetra and cyclic pentapeptides in aqueous solution. The infrared spectra are calculated in order to analyze the charge polarization effect on the spectral profiles.

Original languageEnglish
Pages (from-to)2809-2821
Number of pages13
JournalJournal of Chemical Theory and Computation
Volume5
Issue number10
DOIs
Publication statusPublished - Oct 1 2009
Externally publishedYes

Fingerprint

field theory (physics)
Polarization
proteins
Proteins
Dipeptides
Polypeptides
Dihedral angle
Alanine
Electronic structure
Molecular dynamics
Amino acids
Electrostatics
polypeptides
alanine
polarization
Infrared radiation
Amino Acids
Peptides
amino acids
Geometry

All Science Journal Classification (ASJC) codes

  • Computer Science Applications
  • Physical and Theoretical Chemistry

Cite this

Polarizable force field for protein with charge response kernel. / Isegawa, Miho; Kato, Shigeki.

In: Journal of Chemical Theory and Computation, Vol. 5, No. 10, 01.10.2009, p. 2809-2821.

Research output: Contribution to journalArticle

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