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Cited by 14Protein Structure and DynamicsMetal-Catalyzed Oxygenation MechanismsPharmacogenetics and Drug Metabolism

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Reconciling conformational heterogeneity and substrate recognition in cytochrome P450

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Dandekar, Bhupendra R., Ahalawat, Navjeet, Mondal, Jagannath·2021·Biophysical Journal
DOI 10.1016/j.bpj.2021.02.040PMC PMC8204291

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Abstract

Cytochrome P450, the ubiquitous metalloenzyme involved in detoxification of foreign components, has remained one of the most popular systems for substrate-recognition process. However, despite being known for its high substrate specificity, the mechanistic basis of substrate-binding by archetypal system cytochrome P450cam has remained at odds with the contrasting reports of multiple diverse crystallographic structures of its substrate-free form. Here, we address this issue by elucidating the probability of mutual dynamical transition to the other crystallographic pose of cytochrome P450cam and vice versa via unbiased all-atom computer simulation. A robust Markov state model, constructed using adaptively sampled 84-μs-long molecular dynamics simulation trajectories, maps the broad and heterogenous P450cam conformational landscape into five key substates. In particular, the Markov state model identifies an intermediate-assisted dynamic equilibrium between a pair of conformations of P450cam, in which the substrate-recognition sites remain "closed" and "open," respectively. However, the estimate of a significantly higher stationary population of closed conformation, coupled with faster rate of open → closed transition than its reverse process, dictates that the net conformational equilibrium would be swayed in favor of "closed" conformation. Together, the investigation quantitatively infers that although a potential substrate of cytochrome P450cam would, in principle, explore a diverse array of conformations of substrate-free protein, it would mostly encounter a "closed" or solvent-occluded conformation and hence would follow an induced-fit-based recognition process. Overall, the work reconciles multiple precedent crystallographic, spectroscopic investigations and establishes how a statistical elucidation of conformational heterogeneity in protein would provide crucial insights in the mechanism of potential substrate-recognition process.

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Metadata

Authors
Dandekar, B. R., Ahalawat, N., & Mondal, J.
Affiliations
  • Tata Institute of Fundamental Research (IN)
  • Chaudhary Charan Singh Haryana Agricultural University (IN)
Corresponding author
Mondal, Jagannath
ORCID
Venue
Biophysical Journal
Publisher
Elsevier BV
Published
2021-05
Volume
120
Issue
9
Pages
1732-1745
ISSN
0006-3495 (ISSN-L)
DOI
10.1016/j.bpj.2021.02.040
PMC
PMC8204291
OpenAlex
W3134454869
Cited by
14
References
1
Citations by year
2026: 1 · 2025: 5 · 2024: 2 · 2023: 4 · 2022: 1 · 2021: 1
FWCI
0.63
Type
journal article
Language
en
Open access
Licence
Locations
  • Biophysical Journal (publishedVersion)
  • bioRxiv (Cold Spring Harbor Laboratory) (acceptedVersion, cc-by-nc-nd)
  • PubMed Central (publishedVersion)
  • PubMed (publishedVersion)
Funders
  • Tata Institute of Fundamental Research
  • Department of Science and Technology, Ministry of Science and Technology, India (CRG/2019/001219)
  • Department of Atomic Energy, Government of India (RTI 4007)
Topics
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Protein Structure and Dynamics
  • Physical Sciences › Chemistry › Inorganic Chemistry › Metal-Catalyzed Oxygenation Mechanisms
  • Life Sciences › Pharmacology, Toxicology and Pharmaceutics › Pharmacology › Pharmacogenetics and Drug Metabolism
Keywords
cytochrome P450cam, conformational heterogeneity, substrate recognition, induced fit, conformational equilibrium, Markov state models, protein dynamics, protein-ligand binding mechanism
MeSH terms
Cytochrome P-450 Enzyme System, Protein Binding, Protein Conformation, Substrate Specificity, Camphor 5-Monooxygenase

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