Dynamics of dehaloperoxidase-hemoglobin A derived from NMR relaxation spectroscopy and molecular dynamics simulation

• Published in: Journal of inorganic biochemistry Vol. 181; pp. 65 - 73
• Main Authors: Zhao, Jing, Xue, Mengjun, Gudanis, Dorota, Gracz, Hanna, Findenegg, Gerhard H., Gdaniec, Zofia, Franzen, Stefan
• Format: Journal Article
• Language: English
• Published: United States Elsevier Inc 01-04-2018
• Subjects: Model-free analysis; Multifunctional-enzyme; Peroxidase; Peroxygenase; Protein dynamics; 2,4,6-TBP; Multifunctional-enzyme; 2,4,6-TCP; NMR; Peroxygenase; MD; Peroxidase; Protein dynamics; Model-free analysis; HSQC; DHP A; 4-BP
• ISSN: 0162-0134; 1873-3344
• DOI: 10.1016/j.jinorgbio.2018.01.006

Dehaloperoxidase-hemoglobin is the first hemoglobin identified with biologically-relevant oxidative functions, which include peroxidase, peroxygenase and oxidase activities. Herein we report a study of the protein backbone dynamics of DHP using heteronuclear NMR relaxation methods and molecular dynamics (MD) simulations to address the role of protein dynamics in switching from one function to another. The results show that DHP's backbone helical regions and turns have average order parameters of S2 = 0.87 ± 0.03 and S2 = 0.76 ± 0.08, respectively. Furthermore, DHP is primarily a monomer in solution based on the overall tumbling correlation time τm is 9.49 ± 1.65 ns calculated using the prolate diffusion tensor model in the program relax. A number of amino acid residues have significant Rex using the Lipari-Szabo model-free formalism. These include Lys3, Ile6, Leu13, Gln18, Arg32, Ser48, Met49, Thr56, Phe60, Arg69, Thr71 Cys73, Ala77, Asn81, Gly95, Arg109, Phe115, Leu127 and Met136, which may experience slow conformational motions on the microseconds-milliseconds time scale according to the model. Caution should be used when the model contains >4 fitting parameters. The program caver3.0 was used to identify tunnels inside DHP obtained from MD simulation snapshots that are consistent with the importance of the Xe binding site, which is located at the central intersection of the tunnels. These tunnels provide diffusion pathways for small ligands such as O2, H2O and H2O2 to enter the distal pocket independently of the trajectory of substrates and inhibitors, both of which are aromatic molecules.
Dehaloperoxidase-hemoglobin secondary protein structure is color mapped with dynamic information of protein backbone obtained from NMR relaxation experiments using the model-free analysis. The tunnel structure revealed by MD simulations shows diffusion pathways between distal pocket and exterior solvent environment. [Display omitted]
•Helical regions of the globin are quite rigid, while turns are flexible.•Amino acids in the D and E helices of the distal pocket show relatively high chemical exchange.•The crystallographic dimer interface exhibits relatively high chemical exchange.•Two dominant tunnels intersect at the main Xe binding site behind the distal pocket.•Methionines are disproportionately represented among residues with high chemical exchange.