Abstract
In this report, the main contributions of FMN were employed in the reductive cleavage reaction of AzrC protein (as a member of azoreductase family). Molecular dynamics simulations of three models in the presence and absence of FMN and ligand were performed to gather information about the dynamic nature of active site residues of AzrC. Combination of pairwise decomposition and alanine scanning calculations provides critical information about the FMN binding sites. The MD results analyzed by alanine scanning method revealed the high negative scores for N 10 (A) A, N 12 (A) A, S 17 (A) A and Y 151 (A) A mutations, which were in agreement with pairwise decomposition analyses. Hydrogen bond analyses indicated that these residues play critical roles in establishing appropriate hydrogen bonds between AzrC and FMN. Negative energy results for nonpolar residues such as W 103 (A), M 102 (A) and F 105 (A) and binding free energy analyses of three complexes indicate that the VDW interactions could be regarded as some favorable contribution in FMN and AzrC protein and confirmed the critical role of FMN in ligand binding (35.84 %), in addition to its catalytic function. This information could be used for future experimental investigations.
Similar content being viewed by others
References
V. Brissos, N. Gonçalves, E.P. Melo, L.O. Martins, Improving kinetic or thermodynamic stability of an azoreductase by directed evolution. PLoS ONE 9, e87209 (2014)
D.A. Case, T.E. Cheatham, T. Darden, H. Gohlke, R. Luo, K.M. Merz, A. Onufriev, C. Simmerling, B. Wang, R.J. Woods, The Amber biomolecular simulation programs. J. Comput. Chem. 26, 1668–1688 (2005)
K.C. Chen, J.Y. Wu, D.J. Liou, S.C.J. Hwang, Decolorization of the textile dyes by newly isolated bacterial strains. J. Biotechnol. 101, 57–68 (2003)
T. Darden, D. York, L. Pedersen, Particle mesh Ewald: an N· log (N) method for Ewald sums in large systems. J. Chem. Phys. 98, 10089–10092 (1993)
A.B. dos Santos, F.J. Cervantes, J.B. van Lier, Review paper on current technologies for decolourisation of textile wastewaters: perspectives for anaerobic biotechnology. Bioresour. Technol. 98, 2369–2385 (2007)
H. Gohlke, C. Kiel, D.A. Case, Insights into protein–protein binding by binding free energy calculation and free energy decomposition for the Ras–Raf and Ras–RalGDS complexes. J. Mol. Biol. 330, 891–913 (2003)
V. Hornak, R. Abel, A. Okur, B. Strockbine, A. Roitberg, C. Simmerling, Comparison of multiple Amber force fields and development of improved protein backbone parameters. Proteins 65, 712–725 (2006)
W. Humphrey, A. Dalke, K. Schulten, VMD: visual molecular dynamics. J. Mol. Graph. 14, 33–38 (1996)
A. Jakalian, D.B. Jack, C.I. Bayly, Fast, efficient generation of high-quality atomic charges. AM1-BCC model: II. Parameterization and validation. J. Comput. Chem. 23, 1623–1641 (2002)
W.L. Jorgensen, J. Chandrasekhar, J.D. Madura, R.W. Impey, M.L. Klein, Comparison of simple potential functions for simulating liquid water. J. Chem. Phys. 79, 926–935 (1983)
W. Kabsch, C. Sander, Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical features. Biopolymers 22, 2577–2637 (1983)
Y.M. Kolekar, P.D. Konde, V.L. Markad, S.V. Kulkarni, A.U. Chaudhari, K.M. Kodam, Effective bioremoval and detoxification of textile dye mixture by Alishewanella sp. KMK6. Appl. Microbiol. Biotechnol. 97, 881–889 (2013)
P.A. Kollman, I. Massova, C. Reyes, B. Kuhn, S. Huo, L. Chong, M. Lee, T. Lee, Y. Duan, W. Wang, O. Donini, P. Cieplak, J. Srinivasan, D.A. Case, T.E. Cheatham 3rd, Calculating structures and free energies of complex molecules: combining molecular mechanics and continuum models. Acc. Chem. Res. 33, 889–897 (2000)
J. Kongsted, U. Ryde, An improved method to predict the entropy term with the MM/PBSA approach. J. Comput. Aided Mol. Des. 23, 63–71 (2009)
G. Lamm, A. Szabo, Langevin modes of macromolecules. J. Chem. Phys. 85, 7334–7348 (1986)
L. Li, V.N. Uversky, A.K. Dunker, S.O. Meroueh, A computational investigation of allostery in the catabolite activator protein. J. Am. Chem. Soc. 129, 15668–15676 (2007)
Z.J. Liu, H. Chen, N. Shaw, S.L. Hopper, L. Chen, S. Chen, C.E. Cerniglia, B.C. Wang, Crystal structure of an aerobic FMN-dependent azoreductase (AzoA) from Enterococcus faecalis. Arch. Biochem. Biophys. 463, 68–77 (2007)
I. Massova, P.A. Kollman, Computational alanine scanning to probe protein-protein interactions: a novel approach to evaluate binding free energies. J. Am. Chem. Soc. 121, 8133–8143 (1999)
K. Matsumoto, Y. Mukai, D. Ogata, F. Shozui, J.M. Nduko, S. Taguchi, T. Ooi, Characterization of thermostable FMN-dependent NADH azoreductase from the moderate thermophile Geobacillus stearothermophilus. Appl. Microbiol. Biotechnol. 86, 1431–1438 (2010)
G.M. Morris, D.S. Goodsell, R. Huey, A.J. Olson, Distributed automated docking of flexible ligands to proteins: parallel applications of AutoDock 2.4. J. Comput. Aided Mol. Des. 10, 293–304 (1996)
D. Ogata, T. Ooi, T. Fujiwara, S. Taguchi, I. Tanaka, M. Yao, Crystallization and preliminary X-ray studies of azoreductases from Bacillus sp. B29. Acta Crystallogr., Sect. F: Struct. Biol. Cryst. Commun. 66, 503–505 (2010)
T. Ooi, T. Shibata, R. Sato, H. Ohno, S. Kinoshita, T.L. Thuoc, S. Taguchi, An azoreductase, aerobic NADH-dependent flavoprotein discovered from Bacillus sp.: functional expression and enzymatic characterization. Appl. Microbiol. Biotechnol. 75, 377–386 (2007)
D.A. Pearlman, D.A. Case, J.W. Caldwell, W.S. Ross, T.E. Cheatham III, S. DeBolt, D. Ferguson, G. Seibel, P. Kollman, AMBER, a package of computer programs for applying molecular mechanics, normal mode analysis, molecular dynamics and free energy calculations to simulate the structural and energetic properties of molecules. Comput. Phys. Commun. 91, 1–41 (1995)
J.N. Roberts, R. Singh, J.C. Grigg, M.E. Murphy, T.D. Bugg, L.D. Eltis, Characterization of dye-decolorizing peroxidases from Rhodococcus jostii RHA1. Biochemistry 50, 5108–5119 (2011)
T. Robinson, G. McMullan, R. Marchant, P. Nigam, Remediation of dyes in textile effluent: a critical review on current treatment technologies with a proposed alternative. Bioresour. Technol. 77, 247–255 (2001)
A. Ryan, C.J. Wang, N. Laurieri, I. Westwood, E. Sim, Reaction mechanism of azoreductases suggests convergent evolution with quinone oxidoreductases. Protein Cell 1, 780–790 (2010)
J.P. Ryckaert, G. Ciccotti, H.J. Berendsen, Numerical integration of the cartesian equations of motion of a system with constraints: molecular dynamics of-alkanes. J. Comput. Phys. 23, 327–341 (1977)
S. Mahmood, A. Khalid, M. Arshad, T. Mahmood, D.E. Crowley, Bacterial decolorization and degradation of azo dyes: a review. Crit. Rev. Biotechnol. 42, 138–157 (2011)
I. Stoica, S.K. Sadiq, P.V. Coveney, Rapid and accurate prediction of binding free energies for saquinavir-bound HIV-1 proteases. J. Am. Chem. Soc. 130, 2639–2648 (2008)
J. Wang, W. Wang, P.A. Kollman, D.A. Case, Automatic atom type and bond type perception in molecular mechanical calculations. J. Mol. Graph. Model. 25, 247–260 (2006)
J. Wang, R.M. Wolf, J.W. Caldwell, P.A. Kollman, D.A. Case, Development and testing of a general amber force field. J. Comput. Chem. 25, 1157–1174 (2004)
J. Yu, D. Ogata, Z. Gai, S. Taguchi, I. Tanaka, T. Ooi, M. Yao, Structures of AzrA and of AzrC complexed with substrate or inhibitor: insight into substrate specificity and catalytic mechanism. Acta Crystallogr. D Biol. Crystallogr. 70, 553–564 (2014)
V. Zoete, O. Michielin, Comparison between computational alanine scanning and per-residue binding free energy decomposition for protein–protein association using MM-GBSA: application to the TCR-p-MHC complex. Proteins 67, 1026–1047 (2007)
Author information
Authors and Affiliations
Corresponding author
Additional information
Fariba Dehghanian and Maryam Kay are contributed equally to this work.
Electronic supplementary material
Below is the link to the electronic supplementary material.
Rights and permissions
About this article
Cite this article
Dehghanian, F., Haghshenas, H., Kay, M. et al. A molecular dynamics investigation on the interaction properties of AzrC and its cofactor. J IRAN CHEM SOC 13, 2143–2153 (2016). https://doi.org/10.1007/s13738-016-0932-9
Received:
Accepted:
Published:
Issue Date:
DOI: https://doi.org/10.1007/s13738-016-0932-9