Enzyme polarization of substrates of dihydrofolate reductase by different theoretical methods

Stephen P. Greatbanks, Jill E. Gready, Ajay C. Limaye, Alistair P. Rendell

Research output: Contribution to journalArticle

25 Citations (Scopus)

Abstract

We have investigated the importance of polarization by the enzyme dihydrofolate reductase (DHFR) on its substrates, folate and dihydrofolate, using a series of quantum mechanical (QM) techniques (Hartree-Fock (HF), Moller-Plesset second-order perturbation theory (MP2), local density approximation (LDA) and generalized gradient approximation (GGA) density functional theory (DFT) calculations) in which the bulk enzyme is included in the calculations as point charges. Polarization, in terms of both charges on components (residues) of the folate and dihydrofolate molecules and changes in the electron density, particularly of the pterin ring of the substrates, and the implications for the catalytic reduction are discussed. Significant differences in polarization behavior are observed for the different theoretical methods employed. The consequences of this, particularly for choosing an appropriate model for quantum mechanical/molecular mechanical (QM/MM) calculations, are pointed out. The HF and MP2 QM methods show small polarizations (~0.04 electrons) of the pterin ring but quite large polarizations with both LDA and GGA DFT methods (0.3-0.5 electrons). This large difference in polarization for both folate and dihydrofolate arises as a result of substantial differences between the charge distributions for the gas-phase DFT and HF calculations, specifically the charges on the dianionic glutamate side chain. Some recent literature reports of incorrect representation of anionic systems by DFT methods are noted. The DFT results are similar to the previously reported LDA DFT results of Bajorath et al. predicting a large polarization of the pterin ring of folate (Proteins 9:217- 224,1991) and dihydrofolate (PNAS 88:6423-6426, 1991) of ~0.5-0.6 electrons.

Original languageEnglish
Pages (from-to)157-165
Number of pages9
JournalPROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS
Volume37
Issue number2
Publication statusPublished - 1 Nov 1999
Externally publishedYes

Keywords

  • Atomic charges
  • Density functional methods
  • Dihydrofolate
  • Electron density differences
  • Enzyme mechanism
  • Folate
  • NADPH
  • Quantum chemical methods
  • Reductase
  • Substrate polarization

Fingerprint Dive into the research topics of 'Enzyme polarization of substrates of dihydrofolate reductase by different theoretical methods'. Together they form a unique fingerprint.

  • Cite this