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Mapping the Substrate Recognition Pathway in Cytochrome P450.

Navjeet Ahalawat1, Jagannath Mondal1

  • 1Tata Institute of Fundamental Research, Center for Interdisciplinary Sciences , Hyderabad 500107 , India.

Journal of the American Chemical Society
|November 28, 2018
PubMed
Summary
This summary is machine-generated.

Cytochrome P450 enzymes utilize a single, dominant pathway for substrate access, involving substrate-induced structural changes rather than large protein openings. This clarifies how substrates reach the catalytic center in these vital metalloenzymes.

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Area of Science:

  • Biochemistry
  • Enzymology
  • Structural Biology

Background:

  • Cytochrome P450s are crucial metalloenzymes for drug metabolism and detoxification.
  • The mechanism of substrate access to their active site remains unclear, especially given closed crystal structures.

Purpose of the Study:

  • To investigate if conformational heterogeneity in Cytochrome P450 leads to varied substrate access pathways.
  • To elucidate the mechanism of substrate entry into the catalytic center of Cytochrome P450.

Main Methods:

  • Atomistic molecular dynamics simulations (multi-microsecond).
  • Analysis of spontaneous substrate association with P450cam.
  • Markov state modeling and free-energy analysis.

Main Results:

  • Substrate recognition in P450cam occurs via a single, well-defined dominant pathway.
  • Substrate binding involves a key surface channel and substrate-induced side-chain displacements.
  • Catalytic center access does not require large-scale protein opening.

Conclusions:

  • Cytochrome P450 substrate recognition is driven by substrate-induced structural rearrangements.
  • A comprehensive model for substrate access in Cytochrome P450 is established, reconciling previous findings.