Accurate Calculation of Electric Fields Inside Enzymes

X. Wang, X. He, J. Z.H. Zhang

Research output: Chapter in Book/Report/Conference proceedingChapter

Abstract

The specific electric field generated by a protease at its active site is considered as an important source of the catalytic power. Accurate calculation of electric field at the active site of an enzyme has both fundamental and practical importance. Measuring site-specific changes of electric field at internal sites of proteins due to, eg, mutation, has been realized by using molecular probes with C[dbnd]O or C[tbnd]N groups in the context of vibrational Stark effect. However, theoretical prediction of change in electric field inside a protein based on a conventional force field, such as AMBER or OPLS, is often inadequate. For such calculation, quantum chemical approach or quantum-based polarizable or polarized force field is highly preferable. Compared with the result from conventional force field, significant improvement is found in predicting experimentally measured mutation-induced electric field change using quantum-based methods, indicating that quantum effect such as polarization plays an important role in accurate description of electric field inside proteins. In comparison, the best theoretical prediction comes from fully quantum mechanical calculation in which both polarization and inter-residue charge transfer effects are included for accurate prediction of electrostatics in proteins.

Original languageEnglish (US)
Title of host publicationComputational Approaches for Studying Enzyme Mechanism Part B
PublisherAcademic Press Inc.
Pages45-72
Number of pages28
DOIs
StatePublished - 2016

Publication series

NameMethods in Enzymology
Volume578
ISSN (Print)0076-6879
ISSN (Electronic)1557-7988

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Keywords

  • Charge transfer effect
  • Electric field
  • Molecular fragmentation
  • Polarization effect
  • Stark shift

ASJC Scopus subject areas

  • Biochemistry
  • Molecular Biology

Cite this

Wang, X., He, X., & Zhang, J. Z. H. (2016). Accurate Calculation of Electric Fields Inside Enzymes. In Computational Approaches for Studying Enzyme Mechanism Part B (pp. 45-72). (Methods in Enzymology; Vol. 578). Academic Press Inc.. https://doi.org/10.1016/bs.mie.2016.05.043