Abstract
The effect of polypeptides having different charge on the activity of Thiocapsa roseopersicina HydSL hydrogenase was studied. Strong inhibition was shown for poly-L-lysine bearing positive charge. The inhibition was reversible and competitive to methyl viologen, an electron acceptor, in the reaction of hydrogen oxidation catalyzed by the hydrogenase. Peptides carrying less positive charge had weaker inhibiting effect, while neutral and negatively charged peptides did not inhibit the hydrogenase. Molecular docking of poly-L-lysine to T. roseopersicina hydrogenase showed strong affinity of this polypeptide to the acceptor-binding site of the enzyme. The calculated binding constant is close to the experimentally measured value (K i = 2.1 μM).
Similar content being viewed by others
References
Gogotov, I. N., Zadvorny, O. A., Zorin, N. A., and Serebryakova, L. T. (2010) Bacterial hydrogenases, in Proc. Winogradsky Institute of Microbiology, issue 15: Photosynthetic Microorganisms (Galchenko, V. F., ed.) [in Russian], MAKS Press, Moscow, pp. 260–289.
Vignais, P., and Billoud, B. (2007) Occurrence, classification, and biological function of hydrogenases: an overview, Chem. Rev., 107, 4206–4272.
Yagi, T., and Higuchi, Y. (2013) Studies on hydrogenase, Proc. Jpn. Acad. Ser. B, Phys. Biol. Sci., 89, 16–33.
Armstrong, F., and Albracht, S. (2005) [NiFe]-hydrogenases: spectroscopic and electrochemical definition of reactions and intermediates, Phil. Trans. R. Soc., 363, 937–954.
Voronin, O. G., Konischeva, E. V., Zorin, N. A., Fedotenkov, F. A., Karyakina, E. E., Karpachova, G. P., Orlov, A. V., Kiseleva, S. G., and Karyakin, A. A. (2013) Modification of the electrode surface with analogues of hydrogenase substrates for highly active fuel bioelectrocatalysts development, Nano-Microsystems Techn., 5, 15–19.
Abdullatypov, A. V., and Tsygankov, A. A. (2013) Homology modeling of the spatial structure of HydSL hydrogenase from purple sulfur bacterium Thiocapsa roseopersicina BBS, Comput. Res. Model. (Moscow), 5, 737–747.
Noda, K., Zorin, N. A., Nakamura, C., Miyake, M., Gogotov, I. N., Asada, Y., Akutsu, H., and Miyake, J. (1998) Langmuir-Blodgett film of hydrogenase for electrochemical hydrogen production, Thin Solid Films, 327–329, 639–642.
Bogorov, L. V. (1974) The properties of Thiocapsa roseopersicina, strain BBS, isolated from an estuary of the White Sea, Mikrobiologiya, 43, 326–333.
Zadvorny, O. A., Zorin, N. A., and Gogotov, I. N. (2000) Influence of metal ions on hydrogenase from the purple sulfur bacterium Thiocapsa roseopersicina, Biochemistry (Moscow), 65, 1287–1291.
Sherman, M. B., Orlova, E. V., Zorin, N. A., Smirnova, E. A., Kuranova, I. P., and Gogotov, I. N. (1987) The structure of hydrogenase microcrystals from Thiocaspa roseopersicina, Doklady Akad. Nauk SSSR, 295, 509–512.
Gogotov, I. N., Zorin, N. A., and Kondratieva, E. N. (1976) Purification and properties of Thiocapsa roseopersicina hydrogenase, Biokhimiya, 41, 836–842.
Thorneley, R. N. F. (1974) A convenient electrochemical preparation of reduced methyl viologen and a kinetic study of the reaction with oxygen using an anaerobic stoppedflow apparatus, Biochim. Biophys. Acta, 333, 487–496.
Trott, O., and Olson, A. J. (2010) AutoDock Vina: improving the speed and accuracy of docking with a new scoring function, efficient optimization, and multithreading, J. Comput. Chem., 31, 455–461.
Krieger, E., Dunbrack, R. L., Jr., Hooft, R. W., and Krieger, B. (2012) Assignment of protonation states in proteins and ligands: combining pK a prediction with hydrogen bonding network optimization, Methods Mol. Biol., 819, 405–421.
Sanner, F. (1999) Python: a programming language for software integration and development, J. Mol. Graphics Model., 17, 57–61.
Krasnov, K. S., Vorobyov, N. K., Godnev, I. N., Vasilieva, V. N., Vasiliev, V. P., Kiseleva, V. L., Belonogov, K. N., and Gostikin, V. N. (2001) Physical Chemistry (Krasnov, K. S., ed.) [in Russian], Vol. 1, Vysshaya Shkola, Moscow.
Zadvorny, O. A., Zorin, N. A., and Gogotov, I. N. (2006) Transformation of metals and metal ions by hydrogenases from phototrophic bacteria, Arch. Microbiol., 184, 279–285.
Kondratieva, E. N., and Gogotov, I. N. (1981) Molecular Hydrogen in Microbial Metabolism [in Russian], Nauka, Moscow.
Guermuer, Y. (1999) Improved performance in protein secondary structure prediction by inhomogeneous score combination, Bioinformatics, 15, 413–421.
Combet, C., Blanchet, C., Geourjon, C., and Deleage, G. (2000) NPS: network protein sequence analysis, Trends Biochem. Sci., 25, 147–150.
Matias, P. M., Soares, C. M., Saraiva, L. M., Coelho, R., Morais, J., Le Gall, J., and Carrondo, M. A. (2001) [NiFe] hydrogenase from Desulfovibrio desulfuricans ATCC 27774: gene sequencing, three-dimensional structure determination and refinement at 1.8 Å and modeling studies of its interaction with the tetraheme cytochrome c 3, J. Biol. Inorg. Chem., 6, 63–81.
Author information
Authors and Affiliations
Corresponding author
Additional information
Published in Russian in Biokhimiya, 2014, Vol. 79, No. 8, pp. 1009–1014.
Originally published in Biochemistry (Moscow) On-Line Papers in Press, as Manuscript BM14-084, July 13, 2014.
Rights and permissions
About this article
Cite this article
Abdullatypov, A.V., Zorin, N.A. & Tsygankov, A.A. Interaction of HydSL hydrogenase from the purple sulfur bacterium Thiocapsa roseopersicina BBS with methyl viologen and positively charged polypeptides. Biochemistry Moscow 79, 805–811 (2014). https://doi.org/10.1134/S0006297914080082
Received:
Revised:
Published:
Issue Date:
DOI: https://doi.org/10.1134/S0006297914080082