Proton relay network in P450cam formed upon docking of putidaredoxin

Ugur I., Chandrasekhar P.

PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS, vol.88, no.4, pp.558-572, 2020 (SCI-Expanded) identifier identifier identifier

  • Publication Type: Article / Article
  • Volume: 88 Issue: 4
  • Publication Date: 2020
  • Doi Number: 10.1002/prot.25835
  • Journal Name: PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS
  • Journal Indexes: Science Citation Index Expanded (SCI-EXPANDED), Scopus, Agricultural & Environmental Science Database, BIOSIS, Biotechnology Research Abstracts, CAB Abstracts, EMBASE, Food Science & Technology Abstracts, INSPEC, MEDLINE, Veterinary Science Database
  • Page Numbers: pp.558-572
  • Keywords: cytochrome P450, water channel, proton transport, putidaredoxin, molecular dynamics, QM, MM, QUANTUM MECHANICS/MOLECULAR MECHANICS, COMPOUND-I FORMATION, CYTOCHROME P450CAM, ACTIVE-SITE, CRYSTAL-STRUCTURE, CATALYTIC CYCLE, CONFORMATIONAL STATE, MOLECULAR-DYNAMICS, STRUCTURAL-CHANGES, OXYGEN ACTIVATION
  • Middle East Technical University Affiliated: No

Abstract

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 OO 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)MIDLINE HORIZONTAL ELLIPSIST252MIDLINE HORIZONTAL ELLIPSISnH2OMIDLINE HORIZONTAL ELLIPSISD251 in WT; FeOO(H)MIDLINE HORIZONTAL ELLIPSISnH2OMIDLINE HORIZONTAL ELLIPSISD251 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.