Enzyme active site interactions by Raman/FTIR, NMR, and Ab initio calculations

Research output: Chapter in Book/Report/Conference proceedingChapter

3 Citations (Scopus)

Abstract

Characterization of enzyme active site structure and interactions at high resolution is important for the understanding of the enzyme catalysis. Vibrational frequency and NMR chemical shift measurements of enzyme-bound ligands are often used for such purpose when X-ray structures are not available or when higher resolution active site structures are desired. This review is focused on how ab initio calculations may be integrated with vibrational and NMR chemical shift measurements to quantitatively determine high-resolution ligand structures (up to 0.001 Å for bond length and 0.01 Å for hydrogen bonding distance) and how interaction energies between bound ligand and its surroundings at the active site may be determined. Quantitative characterization of substrate ionic states, bond polarizations, tautomeric forms, conformational changes and its interactions with surroundings in enzyme complexes that mimic ground state or transition state can provide snapshots for visualizing the substrate structural evolution along enzyme-catalyzed reaction pathway. Our results have shown that the integration of spectroscopic studies with theoretical computation greatly enhances our ability to interpret experimental data and significantly increases the reliability of the theoretical analysis.

Original languageEnglish (US)
Title of host publicationAdvances in Protein Chemistry and Structural Biology
PublisherAcademic Press Inc.
Pages153-182
Number of pages30
Volume93
ISBN (Print)9780124165960
DOIs
StatePublished - 2013

Publication series

NameAdvances in Protein Chemistry and Structural Biology
Volume93
ISSN (Print)18761623

Fingerprint

Fourier Transform Infrared Spectroscopy
Catalytic Domain
Nuclear magnetic resonance
Enzymes
Chemical shift
Ligands
Bond length
Vibrational spectra
Substrates
Hydrogen Bonding
Electron transitions
Catalysis
Ground state
Hydrogen bonds
Theoretical Models
X-Rays
Polarization
X rays

Keywords

  • Bond polarization
  • Chemical shift calculations
  • Conformational change
  • Empirical correlations
  • Enzyme catalysis
  • Hydride transfer
  • Hydrogen bond
  • Ionic interaction
  • NMR spectroscopy
  • Phosphoryl transfer
  • Vibrational analysis
  • Vibrational spectroscopy

ASJC Scopus subject areas

  • Biochemistry
  • Structural Biology

Cite this

Deng, H. (2013). Enzyme active site interactions by Raman/FTIR, NMR, and Ab initio calculations. In Advances in Protein Chemistry and Structural Biology (Vol. 93, pp. 153-182). (Advances in Protein Chemistry and Structural Biology; Vol. 93). Academic Press Inc.. https://doi.org/10.1016/B978-0-12-416596-0.00005-1

Enzyme active site interactions by Raman/FTIR, NMR, and Ab initio calculations. / Deng, Hua.

Advances in Protein Chemistry and Structural Biology. Vol. 93 Academic Press Inc., 2013. p. 153-182 (Advances in Protein Chemistry and Structural Biology; Vol. 93).

Research output: Chapter in Book/Report/Conference proceedingChapter

Deng, H 2013, Enzyme active site interactions by Raman/FTIR, NMR, and Ab initio calculations. in Advances in Protein Chemistry and Structural Biology. vol. 93, Advances in Protein Chemistry and Structural Biology, vol. 93, Academic Press Inc., pp. 153-182. https://doi.org/10.1016/B978-0-12-416596-0.00005-1
Deng H. Enzyme active site interactions by Raman/FTIR, NMR, and Ab initio calculations. In Advances in Protein Chemistry and Structural Biology. Vol. 93. Academic Press Inc. 2013. p. 153-182. (Advances in Protein Chemistry and Structural Biology). https://doi.org/10.1016/B978-0-12-416596-0.00005-1
Deng, Hua. / Enzyme active site interactions by Raman/FTIR, NMR, and Ab initio calculations. Advances in Protein Chemistry and Structural Biology. Vol. 93 Academic Press Inc., 2013. pp. 153-182 (Advances in Protein Chemistry and Structural Biology).
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