Electronic polarization is important in stabilizing the native structures of proteins

Chang G. Ji, John Zhang

Research output: Contribution to journalArticle

Abstract

Quantum mechanical computations of proteins based on the molecular fragment approach have been carried out, and polarized protein-specific charges have been derived to provide accurate electrostatic interactions for a benchmark set of proteins. Our study shows that, under the polarized protein-specific force field, the native structure indeed corresponds to the lowest-energy conformation for these proteins. In contrast, when a standard mean-field force field such as AMBER is used, the energies of many decoy structures of proteins could be lower than those of the native structures. Furthermore, MD simulations were carried out and verified that the native structures of these proteins not only are statically more stable but are also dynamically more stable under the polarized protein-specific force field. The present results, together with several recent studies, provide strong evidence that protein polarization is critical to stabilizing the native structures of proteins.

Original languageEnglish (US)
Pages (from-to)16059-16064
Number of pages6
JournalJournal of Physical Chemistry B
Volume113
Issue number49
DOIs
StatePublished - Dec 10 2009

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Polarization
proteins
Proteins
polarization
electronics
field theory (physics)
decoys
Coulomb interactions
Conformations
fragments
electrostatics
energy
simulation
interactions

ASJC Scopus subject areas

  • Physical and Theoretical Chemistry
  • Materials Chemistry
  • Surfaces, Coatings and Films

Cite this

Electronic polarization is important in stabilizing the native structures of proteins. / Ji, Chang G.; Zhang, John.

In: Journal of Physical Chemistry B, Vol. 113, No. 49, 10.12.2009, p. 16059-16064.

Research output: Contribution to journalArticle

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