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Proton Relay Network in P450cam is Formed Upon Docking of its Redox Partner Putidaredoxin (Pdx)

preprint
submitted on 28.01.2019, 17:02 and posted on 29.01.2019, 15:54 by Ilke Ugur Marion, Prasanna Chandrasekhar
Cytochromes P450 are versatile heme-based enzymes responsible for vital life processes. Of these, P450cam (substrate camphor) has been most studied. Despite this, precise mechanisms of the key O-O cleavage step remain elusive to date; effects observed in various enzyme mutants remain unexplained. We have carried out extended (up to 1000 ns) MM-MD and follow-on QM/MM computations, both on the well-studied FeOO state and, for the first time, on Cpd(0). Our simulations include (all camphor-bound) : (1) WT (wild type), FeOO state. (2) WT, Cpd(0). (3) Pdx-docked-WT, FeOO state. (4) Pdx-docked WT, Cpd(0). (5) Pdx-docked T252A mutant, Cpd(0). Among our key findings, for the first time to our knowledge: (1) Effect of Pdx docking goes far beyond that indicated in prior studies: it leads to specific alterations in secondary structure that create the crucial proton relay network. (2) The specific proton relay networks we identify are FeOO(H)---T252---nH2O---D251 in WT and FeOO(H)---nH2O---D251 in T252A mutant; both occur with Pdx docking. (3) Direct interaction of D251 with -FeOOH is, respectively, rare/frequent in WT/T252A mutant. (4) T252 is in the proton relay network. (5) Positioning of camphor is crucial: when camphor is part of H-bonding network, coupling is facilitated.

Funding

Ashwin-Ushas Corporation

History

Email Address of Submitting Author

chandra.p2@ashwin-ushas.com

Institution

Ashwin-Ushas Corporation

Country

USA

ORCID For Submitting Author

0000-0002-4495-4936

Declaration of Conflict of Interest

No conflict of interest

Version Notes

DRAFT2 2019-01-28

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