Two-dimensional NMR and all-atom molecular dynamics of cytochrome P450 CYP119 reveal hidden conformational substates

J Biol Chem. 2010 Mar 26;285(13):9594-9603. doi: 10.1074/jbc.M109.087593. Epub 2010 Jan 22.

Abstract

Cytochrome P450 enzymes are versatile catalysts involved in a wide variety of biological processes from hormonal regulation and antibiotic synthesis to drug metabolism. A hallmark of their versatility is their promiscuous nature, allowing them to recognize a wide variety of chemically diverse substrates. However, the molecular details of this promiscuity have remained elusive. Here, we have utilized two-dimensional heteronuclear single quantum coherence NMR spectroscopy to examine a series of mutants site-specific labeled with the unnatural amino acid, [(13)C]p-methoxyphenylalanine, in conjunction with all-atom molecular dynamics simulations to examine substrate and inhibitor binding to CYP119, a P450 from Sulfolobus acidocaldarius. The results suggest that tight binding hydrophobic ligands tend to lock the enzyme into a single conformational substate, whereas weak binding low affinity ligands bind loosely in the active site, resulting in a distribution of localized conformers. Furthermore, the molecular dynamics simulations suggest that the ligand-free enzyme samples ligand-bound conformations of the enzyme and, therefore, that ligand binding may proceed largely through a process of conformational selection rather than induced fit.

Publication types

  • Research Support, N.I.H., Extramural

MeSH terms

  • Archaeal Proteins / chemistry*
  • Binding Sites
  • Catalysis
  • Catalytic Domain
  • Crystallography, X-Ray / methods
  • Cytochrome P-450 Enzyme System / chemistry*
  • Lauric Acids / chemistry
  • Ligands
  • Magnetic Resonance Spectroscopy / methods*
  • Methyltyrosines / chemistry
  • Models, Molecular
  • Mutation
  • Protein Conformation
  • Spectrophotometry / methods
  • Sulfolobus acidocaldarius / enzymology*

Substances

  • Archaeal Proteins
  • Lauric Acids
  • Ligands
  • Methyltyrosines
  • lauric acid
  • O-methyltyrosine
  • Cytochrome P-450 Enzyme System
  • CYP119 protein, Sulfolobus solfataricus