Predicting mutation-induced stark shifts in the active site of a protein with a polarized force field

Xianwei Wang, Xiao He, John Z.H. Zhang

Research output: Contribution to journalArticle

Abstract

The electric field inside a protein has a significant effect on the protein structure, function, and dynamics. Recent experimental developments have offered a direct approach to measure the electric field by utilizing a nitrile-containing inhibitor as a probe that can deliver a unique vibration to the specific site of interest in the protein. The observed frequency shift of the nitrile stretching vibration exhibits a linear dependence on the electric field at the nitrile site, thus providing a direct measurement of the relative electric field. In the present work, molecular dynamics simulations were carried out to compute the electric field shift in human aldose reductase (hALR2) using a polarized protein-specific charge (PPC) model derived from fragment-based quantum-chemistry calculations in implicit solvent. Calculated changes of electric field in the active site of hALR2 between the wild type and mutants were directly compared with measured vibrational frequency shifts (Stark shifts). Our study demonstrates that the Stark shifts calculated using the PPC model are in much better agreement with the experimental data than widely used nonpolarizable force fields, indicating that the electronic polarization effect is important for the accurate prediction of changes in the electric field inside proteins.

Original languageEnglish (US)
Pages (from-to)6015-6023
Number of pages9
JournalJournal of Physical Chemistry A
Volume117
Issue number29
DOIs
StatePublished - Jul 25 2013

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ASJC Scopus subject areas

  • Physical and Theoretical Chemistry

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