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Proton relay network in P450cam formed upon docking of putidaredoxin
Author(s) -
Ugur Ilke,
Chandrasekhar Prasanna
Publication year - 2020
Publication title -
proteins: structure, function, and bioinformatics
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 1.699
H-Index - 191
eISSN - 1097-0134
pISSN - 0887-3585
DOI - 10.1002/prot.25835
Subject(s) - chemistry , docking (animal) , stereochemistry , protonation , mutant , heme , hydrogen bond , redox , camphor , molecular dynamics , enzyme , crystallography , computational chemistry , biochemistry , molecule , ion , organic chemistry , medicine , nursing , gene
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 partly elusive to date; effects observed in various enzyme mutants remain partly unexplained. We have carried out extended (to 1000 ns) MM‐MD and follow‐on quantum mechanics/molecular mechanics computations, both on the well‐studied FeOO state and on Cpd(0) (compound 0). Our simulations include (all camphor‐bound) : (a) WT (wild type), FeOO state. (b) WT, Cpd(0). (c) Pdx (Putidaredoxin, redox partner of P450)‐docked‐WT, FeOO state. (d) Pdx‐docked WT, Cpd(0). (e) Pdx‐docked T252A mutant, Cpd(0). Among our key findings: (a) Effect of Pdx docking appears to go far beyond that indicated in prior studies: it leads to specific alterations in secondary structure that create the crucial proton relay network. (b) Specific proton relay networks we identify are: FeOO(H)⋯T252⋯nH 2 O⋯D251 in WT ; FeOO(H)⋯nH 2 O⋯D251 in T252A mutant ; both occur with Pdx docking. (c) Direct interaction of D251 with –FeOOH is, respectively, rare/frequent in WT/T252A mutant. (d) In WT, T252 is in the proton relay network. (e) Positioning of camphor appears significant: when camphor is part of H‐bonding network, second protonation appears to be facilitated.