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John Peters' lab Personnel

Oleg A. Zadvornyy

Senior Research Scientist,

Lab manager

 

Washington State University
Institute of Biological Chemistry
237 Clark Hall
Pullman, WA 99164

Tel: 509-335-9837

 

E-mail: oleg.zadvornyy@wsu.edu

 

Research Interests

 

I came to Prof. John Peters’ lab at Montana State University in 2005 to study hydrogenases from phototrophic bacteria. My research focuses on the structural and biochemical characterization of variety of enzymes involved in nitrogen (nitrogenases), hydrogen (hydrogenases) and carbon (bifurcation enzymes, enzymes of methanogenesis and propylene metabolism) enzymes of metabolisms. In the lab we are using anaerobic techniques for expression, purification and crystallization oxygen sensitive enzymes, containing different metal co-factors. I have been studding hydrogenases from phototrophic bacteria and their role in the detoxification of metal ions in bacterial cells. The area of my research expended to characterization of hydrogenases encapsulated in silica gel materials and development of photo hydrogen producing catalysts, photosensitizers and sensor systems based on hydrogenases and nitrogenase. Recently I have been working on structural characterization of LmrR as a scaffold protein for different applications.

Structural Characterization of the Nitrogenase MoFe Protein

 

The biological reduction of dinitrogen to ammonia is catalyzed by the complex metalloenzyme nitrogenase. Structures of the nitrogenase component proteins, Fe protein and MoFe protein, and the stabilized complexes these component proteins, have been determined, providing a foundation for a number of fundamental aspects of the complicated catalytic mechanism. The reduction of dinitrogen to ammonia is a complex process that involves the binding of N2 followed by reduction with multiple electrons and protons. Electron transfer into nitrogenase is typically constrained to the unique electron donor, the Fe protein.

Substrate acetylene trapped near the active site

 

We have crystallized and solved 1.7 Å crystal structure of the α-96Arg→Gln variant of the MoFe protein in the presence of the substrate acetylene. Computational analysis supports favorable binding of acetylene in the position revealed in crystallographic work at the active site of the α-96Arg→Gln variant of the MoFe protein.

 

Differences at the acetylene binding site in the α-96Arg-→Gln variant and native MoFe proteins. The differences in the positions of the α-70Val, α-98Asn, α-96Arg, and α-96Gln involved in the acetylene binding at the active site of the α-96Arg→Gln variant (in green) and native (3U7Q [21], in magenta) MoFe proteins are shown. Acetylene is modeled into the Fo-Fc electron density map (contoured to 4.0 σ, blue mesh) near the FeMo-co. The amino acids of MoFe protein and homocitrate (HCA) are shown in sticks, FeMo-co is shown in balls and sticks. The water molecule involved in the interaction between α-98Asn and α-96Gln is shown as a green ball, other water molecules are shown in red exes.

Structural characterization of the P1+ intermediate state of the P-cluster of nitrogenase

 

Our previous work has revealed that the P-cluster undergoes redox dependent structural changes and that the transition from the all-ferrous resting (PN) state to the two electron oxidized P2+ state is accompanied by protein serince hydroxyl and backbone amide ligation to Fe. In this work, the MoFe protein was poised at defined potentials with redox mediators in an electrochemical cell, and the three distinct structural states of the P-cluster (P2+, P1+, and PN) were characterized by X-ray crystallography and confirmed by computational analysis. These analyses revealed that the three oxidation states differ in coordination implicating that the P1+ state retains the serine hydroxyl coordination but lacks the backbone amide coordination observed in the P2+ states. These results provide a complete picture of the redox-dependent ligand rearrangements of the three P-cluster redox states.

Structural representations of the P2+, P1+ and PN  redox states of the P cluster, highlighting differences in ligation.

 

Structural characterization of bifurcating enzymes

 

Recently a new type of enzyme system was described to regulate the redox pools of Fd, NAD(H) and NADP(H) in anaerobes, which lack the canonical transhydrogenases. The redox pools in some anaerobes are balanced by a bifurcating enzyme called NADH-dependent ferredoxin NADP oxidoreductase (Nfn). This was first reported in Clostridium kluyveri and catalyzes the production of NADPH coupled to the simultaneous oxidation of NADH and reduced Fd. This enzyme carried out flavin-based electron bifurcation, a fundamental mechanism of biological energy conservation. In anaerobes, Nfn is directly involved in shuttling electrons between the three main redox carriers in anaerobes, Fd, NADH and NADPH. In our laboratory we are working on NfnI and NfnII from Pyrococcus furiosus in collaboration with Prof. Mike Adams group from University of Georgia.

 

Crystals of Nfn I from P. furiosus

 

Structural characterization of hydrogenases from phototrophic bacteria

We have been working on the structural characterization of hydrogenase from the purple sulfur bacteria Thiocapsa roseopersicina.  This hydrogenase is a heterodimer consist of large and small subunits with molecular weights of 64 and 34 kD. The hydrogenase from T. roseopersicina is highly stable during storage under aerobic conditions with a half-life at 4° C of more than two months. It is highly thermal stable as well and remains active up to temperatures of 80°C.  The hydrogenase from T. roseopersicina with high activity and stability is promising as a hydrogen-activating catalyst for development of fuel cells and hydrogen sensors based on direct bioelectrocatalysis.

Transmission electron microscopy data of the hydrogenase from T. roseopersicina indicated that it is organized in complicated super molecular complexes consisting of 6 αβ-dimer units. Together with Professor L. Tang from the University of Kansas, performing cryoreconstruction experiments, we found that the super molecular complex consists of 2 agglomerated rings composed of three heterodimers (6 heterodimers total) (Figure 1).

Metal detoxification and nano particles formation by microorganisms and their hydrogenases

A common microbial strategy for detoxifying metals involves redox transformation which often results in metal precipitation and/or immobilization. The focus of our research is the influence of ionic nickel [Ni(II)] on growth of the purple sulfur bacterium,Thiocapsa roseopersicina.  The results show that Ni(II) in the bulk medium at micromolar concentrations results in growth inhibition; specifically, an increase in the lag phase of growth, a decrease in the specific growth rate, and a decrease in total protein concentration when compared to growth controls containing no added Ni(II).  The inhibitory effects of Ni(II) on the growth of T. roseopersicina could be partially overcome by the addition of hydrogen (H2) gas.  However, the inhibitory effects of Ni(II) on the growth of T. roseopersicina were not alleviated by H2 in a strain containing deletions in all hydrogenase-encoding genes.  Transmission electron micrographs of wild-type T. roseopersicinagrown in the presence of Ni(II) and H2 revealed a significantly greater number of dense nanoparticulates associated with the cells when compared to wild-type cells grown in the absence of H2and hydrogenase-mutant strains grown in the presence of H2.  X-ray diffraction and vibrating sample magnetometry of the dense nanoparticles indicated the presence of zero-valent Ni, suggesting Ni(II) reduction (Figure 2).

Purified T. roseopersicina hyn-encoded hydrogenase catalyzed the formation of zero valent Ni particles in vitro, suggesting a role for this hydrogenase in Ni(II) reduction in vivo (Figure 3).  Collectively, these results suggest a link between H2metabolism, Ni(II) tolerance, and Ni(II) reduction in T. roseopersicina. We have been Currently, collaborating with the Pushchino group (Russia) we have been working on purification as well as spectroscopic, and structural characterization of a hox encoded [NiFe]-hydrogenase from Chloroflexus aurantiacus.

Encapsulation of hydrogenases in sol-gel material doped with carbon nanotubes

 

Much attention has been directed towards developing hydrogen fuel technology in order to realize the tremendous potential hydrogen gas has as a clean, renewable, and reliable fuel source.  The enzyme hydrogenase can catalyze the production of hydrogen from protons and electrons. We have demonstrated that silica-derived gels can be used to stabilize hydrogenases.  We have been investigating the conditions for encapsulation to promote significantly enhanced levels of activities by doping gels with multi-walled carbon nanotubes, polyethylene glycol and methyl viologen (Scheme 1).  Optimization of these dopants results in hydrogen production levels comparable to those observed for the enzyme in solution.  Encapsulation of active hydrogenases in solid materials is a promising advancement towards their use in hydrogen producing catalytic materials applications.

Development of light harvesting hydrogen producing catalyst stable to oxygen based on hydrogenases and photosensitizer

 

The exposed surfaces of the protein-based H2 producing catalyst systems (both the hydrogenase and synthetic protein cage systems) provide a rich template for covalent attachment of light harvesting antennae systems including either molecular, colloidal, or solid surfaces. The overall goal of this research is to maximize the light harvesting capacity of each self-assembled protein-based catalyst for optimized and directed electron transfer to the protein catalyst.  For the hydrogenases, covalent attachment is not simple since the ability to heterologously express the enzymes of interest in a manner that allows the purification of large amounts of homogenous preparations of enzyme is not straightforward.  We have therefore been using a two pronged approach involving pilot work targeted at providing a preliminary analysis of the effects of coupling model light harvesting complexes to both [NiFe]- and [FeFe]-hydrogenases that are the targets of our studies and in parallel improving the means to express hydrogenase enzymes and engineer modification sites in an informed manner.
Our intitial studies on covalent attachment has been using the [NiFe]-hydrogenase from Thiocapsa roseopersicina as a model system because it is highly stable in comparison with other [NiFe]-hydrogenases.  In our pilot work, the enhanced stability of this enzyme allows it to retain a signficantly larger percentage of activity that other [NiFe]-hydrogenase or [FeFe]-hydrogenases upon labeling.  The photocatalytic ruthenium complex ([Ru(bpy)2(5-NH2phen)]2+) (Ru(II)-complex) has been covalently attached to stable [NiFe]- hydrogenase from T. roseopersicina using 1-ethyl-3-(3-dimethylaminopropyl carbodiimide (EDC) which links amino groups of the complex to exposed carboxyl groups of the hydrogenase.  We have optimized the conditions for the light depended hydrogen production by the covalently modified protein with the Ru(II) complex (Figure 4). We have been able to show that labeled T. roseopersicina hydrogenase retains ~50% of its activity after labeling and highest activities are observed at pH 5.0 under a nitrogen atmosphere and irradiated by 150,000 Lux light.  So far we were unable to demonstrate light dependent reaction by labeled hydrogenase without an electron carrier; however we have found that attachment of the Ru(II) complex to the hydrogenase greatly enhances light dependent hydrogenase activity (22 times) over that of the equivalent Ru(II) complex concentrations in solution.

Education

1998-2004
Ph.D. in Biochemistry, Institute of Basic Biological Problems of the Russian Academy of Sciences, Pushchino, Moscow Region, Russian Federation.
Ph.D. thesis: “Redox interaction of hydrogenase from phototrophic bacteria with metals” (2004)
1996-1998
M.Sc. in Biochemistry, Pushchino State University, Pushchino, Moscow Region, Russian Federation.
M.Sc. thesis: “Effect of various light conditions on the PAL (phenilalanine ammonia lyase) activity in pea and arabidopsis leafs.” (1998)
1991-1996
M.Sc. in Plant physiology, Leo Tolstoy’s Tula State Teachers Training University, Tula,
M.Sc.: “Influence of chromium salts and UV-light on the habitus of wheat and leguminous plants.” (1996)Research Experience

Research Experience

2016 – present
Senior Research Scientist,  Prof. John Peters’ lab

Institute of Biological Chemistry, Washington State University, Pullman, WA

2005-2016
Research Scientist, Postdoctoral Researcher
Department of Chemistry and Biochemistry, Montana State University, Bozeman, MT.

1998-2005
Research Fellow
Laboratory of Biochemistry and Biotechnology of Phototrophic Microorganisms of the Institute of Basic Biological Problems of the Russian Academy of Sciences, Pushchino, Moscow Region, Russian Federation.

Dr. Nikolay Zorin’s Lab
Study the structure and crystallization hydrogenase from phototrophic bacteria, purification hydrogenases from different bacteria.
Structural characterization of MoFe protein of nitrogenise with amino acid substitutions in the active site to understand a catalytic mechanism of nitrogenise.
Study properties and stability of hydrogenases encapsulated in silica gel.
Investigation the transformation of metal ions by hydrogenases and bacteria.
Prof. Ivan Gogotov’s Lab
hydrogen metabolism in photosynthetic bacteria and cyanobacteria;
reduction and oxidation metals by oxidoreductase;
investigation of enzyme properties;
hydrogen enzyme electrode
1996-1998
Junior Researcher
Laboratory of regulation of plant growth and photosynthesis of the Institute of Basic Biological Problems of the Russian Academy of Sciences, Pushchino, Moscow Region, Russian Federation.

Dr. Evgeny Muzafarov’s Lab
Purification and properties of PAL (phenilalanine ammonia lyase); effect of light condition on PAL activity.

Publications

 

  1. Peters JW, Beratan DN, Bothner B, Dyer RB, Harwood CS, Heiden ZM, Hille R, Jones AK, King PW, Lu Y, Lubner CE, Minteer SD, Mulder DW, Raugei S, Schut GJ, Seefeldt LC, Tokmina-Lukaszewska M, Zadvornyy OA, Zhang P, Adams MW. A new era for electron bifurcation. Curr Opin Chem Biol. 2018 Aug 1;47:32-38. doi: 10.1016/j.cbpa.2018.07.026. [Epub ahead of print] Review. PubMed PMID: 30077080
  1. Keable SM, Zadvornyy OA, Johnson LE, Ginovska B3 Rasmussen AJ4 Danyal K, Eilers BJ, Prussia GA, LeVan AX, Raugei S, Seefeldt LC, Peters JW. Structural characterization of the P1+ intermediate state of the P-cluster of nitrogenase. (2018) J Biol Chem. 2018 May 2. pii: jbc.RA118.002435. doi: 10.1074/jbc.RA118.002435
  1. Keable SM, Vertemara J, Zadvornyy OA, Eilers BJ, Danyal K, Rasmussen AJ, De Gioia L, Zampella G, Seefeldt LC, Peters JW. Structural characterization of the nitrogenase molybdenum-iron protein with the substrate acetylene trapped near the active site. (2018) J Inorg Biochem. 180:129-134. doi: 10.1016/j.jinorgbio.2017.12.008. Epub 2017 Dec 13
  1. Artz JH, Zadvornyy OA, Mulder DW, King PW, Peters JW. (2017) Structural Characterization of Poised States in the Oxygen Sensitive Hydrogenases and Nitrogenases. Methods Enzymol. 595:213-259. doi: 10.1016/bs.mie.2017.07.005. Epub 2017 Aug 21
  1. Nguyen DMN, Schut GJ, Zadvornyy OA, Tokmina-Lukaszewska M, Poudel S, Lipscomb GL, Adams LA, Dinsmore JT, Nixon WJ, Boyd ES, Bothner B, Peters JW, Adams MWW. (2017) Two functionally distinct NADP+-dependent ferredoxin oxidoreductases maintain the primary redox balance of Pyrococcus furiosus. J Biol Chem. 292(35):14603-14616. doi: 10.1074/jbc.M117.794172. Epub 2017 Jul 13
  1. Artz JH, Mulder DW, Ratzloff MW, Lubner CE, Zadvornyy OA, LeVan AX, Williams SG, Adams MWW, Jones AK, King PW, Peters JW. (2017) Reduction Potentials of [FeFe]-Hydrogenase Accessory Iron-Sulfur Clusters Provide Insights into the Energetics of Proton Reduction Catalysis. J Am Chem Soc. 139(28):9544-9550. doi: 10.1021/jacs.7b02099. Epub 2017 Jul 6
  1. Carolyn E. Lubner, David P. Jennings, David W. Mulder, Gerrit J. Schut, Oleg A. Zadvornyy, John Hoben, Monika Tokmina-Lukaszewska, Luke Berry, Diep Nguyen, Gina L. Lipscomb, Brian Bothner, Anne K. Jones, Anne-Frances Miller, Paul W. King, Michael W.W. Adams, and John W. Peters (2017) Mechanism of Energy Conservation by Electron Bifurcation, Nat Chem Biol. (6):655-659. doi: 10.1038/nchembio.2348. Epub 2017 Apr 10
  1. Schut GJ, Zadvornyy O, Wu CH, Peters JW, Boyd ES, Adams MW. (2016) The role of geochemistry and energetics in the evolution of modern respiratory complexes from a proton-reducing ancestor. Biochim Biophys Acta. Jul;1857(7):958-70
  1. Artz JH, White SN, Zadvornyy OA, Fugate CJ, Hicks D, Gauss GH, Posewitz MC, Boyd ES, Peters JW. (2015) Biochemical and Structural Properties of a Thermostable Mercuric Ion Reductase from Metallosphaera sedula. Front Bioeng Biotechnol. Jul 13;3:97. doi: 10.3389/fbioe.2015.00097. eCollection 2015. PubMed PMID: 26217660; PubMed Central PMCID: PMC4500099
  1. Zadvornyy OA, Boyd ES, Posewitz MC, Zorin NA, Peters JW. Biochemical and Structural Characterization of Enolase from Chloroflexus aurantiacus: Evidence for a Thermophilic Origin. Front Bioeng Biotechnol. 2015 Jun 1;3:74. doi: 10.3389/fbioe.2015.00074. eCollection 2015. PubMed PMID: 26082925; PubMed Central PMCID: PMC4450660
  1. Danyal K, Rasmussen AJ, Keable SM, Inglet BS, Shaw S, Zadvornyy OA, Duval S, Dean DR, Raugei S, Peters JW, Seefeldt LC. (2015) Fe protein-independent substrate reduction by nitrogenase MoFe protein variants. Biochemistry. 54(15):2456-62. doi: 10.1021/acs.biochem.5b00140. Epub 2015 Apr 7. PubMed PMID: 25831270
  1. Swanson KD, Ratzloff MW, Mulder DW, Artz JH, Ghose S, Hoffman A, White S, Zadvornyy OA, Broderick JB, Bothner B, King PW, Peters JW. (2015) [FeFe]-hydrogenase oxygen inactivation is initiated at the H cluster 2Fe subcluster. J Am Chem Soc. Feb 11;137(5):1809-16. doi: 10.1021/ja510169s. Epub 2015 Jan 29. PubMed PMID: 25579778
  1. Therien JB, Zadvornyy OA, Posewitz MC, Bryant DA, Peters JW. Growth of Chlamydomonas reinhardtii in acetate-free medium when co-cultured with alginate-encapsulated, acetate-producing strains of Synechococcus sp. PCC 7002. Biotechnol Biofuels. 2014 Oct 18;7(1):154. doi: 10.1186/s13068-014-0154-2. eCollection 2014. PubMed PMID: 25364380; PubMed Central PMCID: PMC4216383
  1. Cohen AE, Soltis SM, González A, Aguila L, Alonso-Mori R, Barnes CO, Baxter EL, Brehmer W, Brewster AS, Brunger AT, Calero G, Chang JF, Chollet M, Ehrensberger P, Eriksson TL, Feng Y, Hattne J, Hedman B, Hollenbeck M, Holton JM, Keable S, Kobilka BK, Kovaleva EG, Kruse AC, Lemke HT, Lin G, Lyubimov AY, Manglik A, Mathews II, McPhillips SE, Nelson S, Peters JW, Sauter NK, Smith CA, Song J, Stevenson HP, Tsai Y, Uervirojnangkoorn M, Vinetsky V, Wakatsuki S, Weis WI, Zadvornyy OA, Zeldin OB, Zhu D, Hodgson KO. (2014) Goniometer-based femtosecond crystallography with X-ray free electron lasers. Proc Natl Acad Sci U S A. 111(48):17122-7. doi: 10.1073/pnas.1418733111. Epub Oct 31. PubMed PMID: 25362050; PubMed Central PMCID: PMC4260607
  1. Oleg A. Zadvornyy, Janice E. Lucon, Robin Gerlach, Nikolay A. Zorin, Trevor Douglas, Timothy E. Elgren , John W. Peters. (2012) Photo-induced H2 production by [NiFe]-hydrogenase from T. roseopersicina covalently linked to a Ru(II) photosensitizer. J. Inorg. Biochem. 106(1), 151-155.(http://www.sciencedirect.com/science/article/pii/S0162013411002686)
  1. Gogotov I.N., Zadvornyy O.A., Zorin N.A., Serebriakova L.T. Bacterial hydrogenases. In Phototrophic microorganisms. Edit Galchenko B.F. Moscow:Max-Press, 2010, v. 15, pp 260-289 (Russian)
  1. Oleg A. Zadvorny, Amy M. Barrows, Nikolay A. Zorin, John W. Peters and Timothy E. Elgren. (2010) High level of hydrogen production activity achieved for hydrogenase encapsulated in sol–gel material doped with carbon nanotubes. J. Mater. Chem., 20, 1065–1067. (http://www.rsc.org/Publishing/Journals/JM/article.asp?doi=b922296k)
  1. Oleg A. Zadvornyy, Mark Allen, Susan K. Brumfield, Zack Varpness, Eric S. Boyd, Nikolay A. Zorin, Larisa Serebriakova, Trevor Douglas, and John W. Peters. (2010) Hydrogen enhances nickel tolerance in the purple sulfur bacterium Thiocapsa roseopersicina. Environ. Scien. Thechnol., 44, 834-840. (http://pubs.acs.org/doi/abs/10.1021/es901580n)
  1. Zadvorny O.A., Zorin N.A., Gogotov I.N. (2006) Transformation of metals and metal ions by hydrogenases from phototrophic bacteria. Archives of Microbiology, Jan; 184 (5), 279-285. (http://www.ncbi.nlm.nih.gov/pubmed/16283252)
  1. Elgren T.E., Zadvorny O.A., Brecht E., Douglas T., Zorin N.A., Maroney M.J., Peters J.W. (2005) Immobilization of active hydrogenases by encapsulation in polymeric porous gels. Nano letters, 5 (10), 2085. (http://www.ncbi.nlm.nih.gov/pubmed/16218742)
  1. Zadvorny O.A., Zorin N.A., Gogotov I.N. and Gorlenko V.M. (2004) Properties of stable hydrogenase from the purple sulfur bacterium Lamprobacter modestohalophilus. Biochemistry (Mosc). Feb; 69 (2), 164-9.( http://www.ncbi.nlm.nih.gov/pubmed/15000682)
  1. Morozov S.V., Karyakina E.E., Zadvorny O.A., Zorin N.A., Varfolomeev S.D., Karyakin A.A. (2002) Bioelectrocatalysis by T. roseopersicina hydrogenase immobilised on different carbon supports. Russian Journal of Electrochemistry, 38 (1), 97-102
  1. Zorin N.A., Gogotov I.N., Zadvorny O.A. (2002) Redox reaction of bacterial hydrogenase with metals and metal ions. Microelements in Medicine, 3 (2), 66-68. (Russian)
  1. Zadvorny O.A., Zorin N.A., Gogotov I.N. (2000) The effect of metal ions on hydrogenase of purple sulphur bacterium Thiocapsa roseopersicina. Biochemistry (Mosc) 65 (11), 1287-1291. (http://www.ncbi.nlm.nih.gov/pubmed/11112845)
  1. Gogotov I.N., Zorin N.A., Zadvorny O.A. (1999) Accumulation and extraction of metals by phototrophic microorganisms. In Environment and Soils: selective lectures of VIII-IX Russian Schools., Moscow: Politex, pp. 238-251 (Russian)