Identifying cytochrome p450 functional networks and their allosteric regulatory elements

PLoS One. 2013 Dec 3;8(12):e81980. doi: 10.1371/journal.pone.0081980. eCollection 2013.


Cytochrome P450 (CYP) enzymes play key roles in drug metabolism and adverse drug-drug interactions. Despite tremendous efforts in the past decades, essential questions regarding the function and activity of CYPs remain unanswered. Here, we used a combination of sequence-based co-evolutionary analysis and structure-based anisotropic thermal diffusion (ATD) molecular dynamics simulations to detect allosteric networks of amino acid residues and characterize their biological and molecular functions. We investigated four CYP subfamilies (CYP1A, CYP2D, CYP2C, and CYP3A) that are involved in 90% of all metabolic drug transformations and identified four amino acid interaction networks associated with specific CYP functionalities, i.e., membrane binding, heme binding, catalytic activity, and dimerization. Interestingly, we did not detect any co-evolved substrate-binding network, suggesting that substrate recognition is specific for each subfamily. Analysis of the membrane binding networks revealed that different CYP proteins adopt different membrane-bound orientations, consistent with the differing substrate preference for each isoform. The catalytic networks were associated with conservation of catalytic function among CYP isoforms, whereas the dimerization network was specific to different CYP isoforms. We further applied low-temperature ATD simulations to verify proposed allosteric sites associated with the heme-binding network and their role in regulating metabolic fate. Our approach allowed for a broad characterization of CYP properties, such as membrane interactions, catalytic mechanisms, dimerization, and linking these to groups of residues that can serve as allosteric regulators. The presented combined co-evolutionary analysis and ATD simulation approach is also generally applicable to other biological systems where allostery plays a role.

MeSH terms

  • Allosteric Site*
  • Benzoflavones / metabolism
  • Benzoflavones / pharmacology
  • Biocatalysis
  • Cell Membrane / metabolism
  • Computational Biology / methods*
  • Cytochrome P-450 Enzyme System / chemistry*
  • Cytochrome P-450 Enzyme System / genetics
  • Cytochrome P-450 Enzyme System / metabolism*
  • Evolution, Molecular
  • Heme / metabolism
  • Molecular Dynamics Simulation*
  • Mutation
  • Oxazines / metabolism
  • Protein Conformation
  • Temperature


  • Benzoflavones
  • Oxazines
  • Heme
  • alpha-naphthoflavone
  • Cytochrome P-450 Enzyme System
  • nile red

Grant support

Funding of this research was provided by the U.S. Department of Defense Threat Reduction Agency Grant TMTI0004_09_BH_T. The opinions and assertions contained herein are the private views of the authors and are not to be construed as official or as reflecting the views of the US Army or the US Department of Defense. This paper has been approved for public release with unlimited distribution. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.