Publications

2013

Hamilton TL, Peters JW, Skidmore ML, Boyd ES.”Molecular evidence for an active endogenous microbiome beneath glacial ice”. ISME J. 2013 Mar 14.

[Epub ahead of print]

Mulder DW, Ratzloff MW, Shepard EM, Byer AS, Noone SM, Peters JW, Broderick JB, King PW. “EPR and FTIR Analysis on the Mechanism of H2 Activation by [FeFe]-Hydrogenase HydA1 from Chlamydomonas reinhardtii”. J Am Chem Soc. 2013 Apr 11. [Epub ahead of print]

Mitra D, George SJ, Guo Y, Kamali S, Keable S, Peters JW, Pelmenschikov V, Case DA, Cramer SP. "Characterization of [4Fe-4S] Cluster Vibrations and Structure in Nitrogenase Fe Protein at Three Oxidation Levels via Combined NRVS, EXAFS, and DFT Analyses" J Am Chem Soc. 2013 Feb 11. [Epub ahead of print]

Meuser JE, Baxter BK, Spear JR, Peters JW, Posewitz MC, Boyd ES. "Contrasting Patterns of Community Assembly in the Stratified Water Column of Great Salt Lake, Utah" Microb Ecol. 2013 Jan 25. [Epub ahead of print]

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2011-2012

T.L. Hamilton, K. Vogl, D.A. Bryant, E.S. Boyd, J.W. Peters, “Environmental constraints defining the distribution, composition, and evolution of chlorophototrophs in thermal features of Yellowstone National Park,” Geobiology 10(3):236-49 (2012)

Joshi N, Shepard EM, Byer AS, Swanson KD, Broderick JB, Peters JW. "Iron-sulfur cluster coordination in the [FeFe]-hydrogenase H cluster biosynthetic factor HydF" , FEBS Lett.Oct 4. pii: S0014-5793(12)00736-3. doi: 10.1016/j.febslet.2012.09.028. Epub ahead of print (2012)

Duffus BR, Hamilton TL, Shepard EM, Boyd ES, Peters JW, Broderick JB. Radical AdoMet enzymes in complex metal cluster biosynthesis. Biochim Biophys Acta. 1824(11):1254-63 (2012)

Schut GJ, Boyd ES, Peters JW, Adams MW. The modular respiratory complexes involved in hydrogen and sulfur metabolism by heterotrophic hyperthermophilic archaea and their evolutionary implications. FEMS Microbiol Rev. Jun 19. doi: 10.1111/j.1574-6976.2012.00346.x. Epub ahead of print (2012)

Peters JW, Broderick JB. Emerging paradigms for complex iron-sulfur cofactor assembly and insertion. Annu Rev Biochem. 81:429-50 (2012)

Boyd ES, Fecteau KM, Havig JR, Shock EL, Peters JW. Modeling the habitat range of phototrophs in yellowstone national park: toward the development of a comprehensive fitness landscape. Front Microbiol. 3:221 (2012)

Zadvornyy OA, Lucon JE, Gerlach R, Zorin NA, Douglas T, Elgren TE, Peters JW. Photo-induced H2 production by [NiFe]-hydrogenase from T. roseopersicina covalently linked to a Ru(II) photosensitizer. J Inorg Biochem. 106(1):151-5 (2012)

Kofoed MA, Wampler DA, Pandey AS, Peters JW, Ensign SA. Roles of the redox-active disulfide and histidine residues forming a catalytic dyad in reactions catalyzed by 2-ketopropyl coenzyme M oxidoreductase/carboxylase. J Bacteriol. 193(18):4904-13 (2011)

Cornish AJ, Gärtner K, Yang H, Peters JW, Hegg EL. Mechanism of proton transfer in [FeFe]-hydrogenase from Clostridium pasteurianum. J Biol Chem. 286(44):38341-7 (2011)

T.L. Hamilton, K. Vogl, D.A. Bryant, E.S. Boyd, and J.W. Peters “Environmental constraints defining the distribution, composition, and evolution of chlorophototrophs in thermal features of Yellowstone National Park” Geobiology – Submitted (2011)

Hamilton TL, Jacobson M, Ludwig M, Boyd ES, Bryant DA, Dean DR, Peters JW. Differential accumulation of nif structural gene mRNA in Azotobacter vinelandii. J Bacteriol. 193(17):4534-6 (2011)

Hamilton TL, Ludwig M, Dixon R, Boyd ES, Dos Santos PC, Setubal JC, Bryant DA, Dean DR, Peters JW. Transcriptional profiling of nitrogen fixation in Azotobacter vinelandii. J Bacteriol. 193(17):4477-86 (2011)

Mulder DW, Shepard EM, Meuser JE, Joshi N, King PW, Posewitz MC, Broderick JB, Peters JW. Insights into [FeFe]-hydrogenase structure, mechanism, and maturation. Structure 19(8):1038-52 (2011)

Boyd ES, Lange RK, Mitchell AC, Havig JR, Hamilton TL, Lafrenière MJ, Shock EL, Peters JW, Skidmore M. Diversity, abundance, and potential activity of nitrifying and nitrate-reducing microbial assemblages in a subglacial ecosystem. Appl Environ Microbiol. 77(14):4778-87 (2011)

Meuser JE, Boyd ES, Ananyev G, Karns D, Radakovits R, Narayana Murthy UM, Ghirardi ML, Dismukes GC, Peters JW, Posewitz MC. Evolutionary significance of an algal gene encoding an [FeFe]-hydrogenase with F-domain homology and hydrogenase activity in Chlorella variabilis NC64A. Planta 234(4):829-43 (2011)

E.S. Boyd, A.D. Anbar, S. Miller, T.L. Hamilton, M. Lavin, and J.W. Peters “A late methanogen origin for molybdenum-dependent nitrogenase” Geobiology 9:221-232 (2011) – highlighted in Science as Editor’s Choice

Hamilton TL, Lange RK, Boyd ES, Peters JW. Biological nitrogen fixation in acidic high-temperature geothermal springs in Yellowstone National Park, Wyoming. Environ Microbiol. 13(8):2204-15 (2011)

Pandey AS, Mulder DW, Ensign SA, Peters JW. Structural basis for carbon dioxide binding by 2-ketopropyl coenzyme M oxidoreductase/carboxylase. FEBS Lett. 585(3):459-64 (2011)

E.M. Shepard, E.S. Boyd, J.B. Broderick, and J.W. Peters “Biosynthesis of complex iron-sulfur enzymes” Curr. Opin. Struct. Biol. 15:319-327 (2011)

J.W. Peters, L.M. Rubio “Biochemistry of Mo-nitrogenase” in The Molecular Basis of the Nitrogen Cycle (ed. J. Moir) Horizon Scientific Press In press (2011)

D.W. Mulder and J.W. Peters “Nucleotide-dependent conformational change and complex interactions in nitrogenase” in Methods in Nitrogen Fixation (ed. by M.W. Ribbe) Springer/Humana Press In press (2011)

Mulder DW, Peters JW. Small angle x-ray scattering spectroscopy. Methods Mol

Biol. 766:177-189 (2011)

Boyd ES, Hamilton TL, Peters JW. An alternative path for the evolution of biological nitrogen fixation. Front Microbiol. 2:205 (2011)

J.W. Peters, E.S. Boyd, S. D’Adamo, D.W. Mulder, J. Therien, and M.C. Posewitz “Hydrogenases, nitrogenases, anoxia, and H2 production in water-oxidizing phototrophs” in Algae for Biofuels and Energy(ed.M.A. Borowitzka) Springer/Humana Press In press (2011)

Hamilton TL, Boyd ES, Peters JW. Environmental constraints underpin the distribution and phylogenetic diversity of nifH in the Yellowstone geothermal complex. Microb Ecol. 2011 61(4):860-70 (2011)

K.D. Swanson, B.R. Duffus, T.E. Beard, J.W. Peters, and J.B. Broderick “Cyanide and carbon monoxide ligand formation in hydrogenase biosynthesis” Epub ahead of print DOI: 10.1002/ejic.201001056 (2011) – included inside cover art.

J.M. Boyd, J.A. Endrizzi, T.L. Hamilton, D.M. Downs, and J.W. Peters “FAD binding by ApbE protein from Salmonella enterica: a new class of flavoproteins” J. Bacteriol. 193:887-895 (2011)

D.W. Mulder, A.S. Pandey, S.A. Ensign, and J.W. Peters “Carbon dioxide binding and redox dependent substrate activation at the active site of 2-ketopropyl coenzyme M oxidoreductase/carboxylase” FEBS Lett. 585:459-464 (2011)

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2009-2010

I.I. Brown, D.A. Bryant, D. Casamatta, K.L. Thomas-Keprta, S.A. Sarkisova, G. Shen, J.E. Graham, E.S. Boyd, J.W. Peters, D.H. Garrison, and D.S. McKay “Polyphasic characterization of a thermotolerant siderophilic filamentous cyanobacterium that produces intracellular iron deposits” Appl. Environ. Microbiol. 76:6664-6672 (2010)

D.A. Sliwa, A.M. Krishnakumar, J.W. Peters, and S.A. Ensign “Molecular basis for enantioselectivity in the (R)- and (S) hydroxypropylthioethanesulfonate dehydrogenases, a unique pair of stereoselective short-chain dehydrogenases/reductases involved in aliphatic epoxide carboxylation” Biochemistry 49:248-251 (2010)

Zadvornyy, O; Barrows, AM; Zorin, NA; Peters, JW; Elgren, TE. High level of hydrogen production activity achieved for hydrogenase encapsulated in sol–gel material doped with carbon nanotubes. ***J. Mater. Chem.*, 2010; 20**: 1065–1067.

Shepard, EM; Duffus, BR; George, SJ; McGlynn, SE; Challand, MR; Swanson, KD; Roach, PL; Cramer, SP; Peters, JW; Broderick, JB. [FeFe]-Hydrogenase Maturation: HydG-Catalyzed Synthesis of Carbon Monoxide. J. Am. Chem. Soc. 2010; 132: 9247-9249.

Boyd, ES; Hamilton, TL; Spear, JR; Lavin, M; Peters, JW. [FeFe]-hydrogenase in Yellowstone National Park: evidence for dispersal limitation and phylogenetic niche conservatism. ISME J. 2010; 4: 1485-1495.

Shepard, EM; McGlynn, SE; Bueling, AL; Grady-Smith, CS; George, SJ; Winslow, MA; Cramer, SP; Peters, JW; Broderick, JB. Synthesis of the 2Fe subcluster of the [FeFe]-hydrogenase H cluster on the HydF scaffold. Proc. Natl. Acad. Sci. USA 2010; 107: 10448-10453.

Mulder, DW; Boyd, ES; Sarma, R; Lange, RK; Endrizzi, JA; Broderick, JB; Peters, JW. Stepwise [FeFe]-hydrogenase H-cluster assembly revealed in the structure of HydA(DeltaEFG). Nature 2010; 465: 248-251.

Sliwa, DA; Krishnakumar, AM; Peters, JW; Ensign, SA. Molecular basis for enantioselectivity in the (R)- and (S)-hydroxypropylthioethanesulfonate dehydrogenases, a unique pair of stereoselective short-chain dehydrogenases/reductases involved in aliphatic epoxide carboxylation. Biochemistry 2010; 49: 3487-3498.

Soboh, B; Boyd, ES; Zhao, D; Peters, JW; Rubio, LM. Substrate specificity and evolutionary implications of a NifDK enzyme carrying NifB-co at its active site. FEBS Lett. 2010; 584: 1487-1492.

Driesener, RC; Challand, MR; McGlynn, SE; Shepard, EM; Boyd, ES; Broderick, JB; Peters, JW; Roach, PL. [FeFe]-hydrogenase cyanide ligands derived from S-adenosylmethionine-dependent cleavage of tyrosine. Angew. Chem. Int. Ed. Engl. 2010; 49: 1687-1690.

Sarma, R; Barney, BM; Keable, S; Dean, DR; Seefeldt, LC; Peters, JW. Insights into substrate binding at FeMo-cofactor in nitrogenase from the structure of an alpha-70(Ile) MoFe protein variant. J. Inorg. Biochem. 2010; 104: 385-389.

Zadvornyy, OA; Allen, M; Brumfield, SK; Varpness, Z; Boyd, ES; Zorin, NA; Serebriakova, L; Douglas, T; Peters, JW. Hydrogen enhances nickel tolerance in the purple sulfur bacterium Thiocapsa roseopersicina. Environ. Sci. Technol. 2010; 44: 834-840.

McGlynn, SE; Boyd, ES; Shepard, EM; Lange, RK; Gerlach, R; Broderick, JB; Peters, JW. Identification and characterization of a novel member of the radical AdoMet enzyme superfamily and implications for the biosynthesis of the Hmd hydrogenase active site cofactor. J. Bacteriol. 2010; 192: 595-598.

Beer, LL; Boyd, ES; Peters, JW; Posewitz, MC. Engineering algae for biohydroen and biofuel production. Curr. Opin. Biotechnol. 2009; 20: 264-271.

Mulder, DW; Ortillo, DO; Gardenghi, DJ; Naumov, AV; Ruebush, SS; Szilagyi, RK; Huynh B; Broderick, JB; Peters, JW. Activation of HydA^∆EFG requires a preformed [4Fe-4S] cluster. Biochemistry 2009; 48: 6240-6248.

Boyd, ES; Spear, JR; Peters, JW. [FeFe] hydrogenase genetic diversity provides insight into molecular adaption in a saline microbial mat community. Appl. Environ. Microbiol. 2009; 75: 4620-4623.

Mcglynn, SE; Mulder, DW; Shepard, SE; Broderick, JB; Peters, JW. Hydrogenase cluster biosynthesis: organometallic chemisty nature's way. Dalton Trans. 2009; 4274-4285.

Peters, JW. Carbon monoxide and cyanide lignads in the active site of [FeFe]-hydrogeanse. In Metal ions in life sciences. Sigel, A; Sigel, H; Sigel, RKO; Eds. RSC Pub: 2009; 6, 179-218.

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2006-2008

Sarma, R; Barney, BM; Hamilton, TL; Jones, A; Seefeldt, LC; Peters, JW. Crystal structure of the L protein of Rhodobacter sphaeroides light-independent protochlorophyllide reductase with MgADP bound: a homologue of the nitrogenase Fe protein. Biochemistry 2008; 47: 13004-13015.

Krishnakumar, AM; Sliwa, D; Endrizzi, JA; Boyd, ES; Ensign, SA; Peters, JW. Getting a handle on the role of coenzyme M in alkene metabolism. Microbiol. Mol. Biol. Rev.; 72: 445-456.

Posewitz, MC; Mulder, DW; Peters, JW. New Frontiers in Hydrogenase Structure and Biosynthesis. Current Chemical Biology 2008; 2: 178-199.

McGlynn, SE; Shepard, EM; Winslow, MA; Naumov, AV; Duschene, KS; Posewitz, MC; Broderick, WE; Broderick, WE; Broderick, JB; Peters, JW. HydF as a scaffold protein in [FeFe] hydrogenase H-cluster biosynthesis. FEBS Lett. 2008; 582: 2183-2187.

Pandey, AS; Harris, TV; Giles, LJ; Peters, JW; Szilagyi, RK. Dithiomethylether as a ligand in the hydrogenase h-cluster. J. Am. Chem. Soc. 2008; 130: 4533-4540.

Sarma R; Mulder, DW; Brecht, E; Szilagy, RK; Seefeldt, LC; Tsuruta, H; Peters, JW. Probing the MgATP-bound conformation of the nitrogenase Fe protein by solution small-angle X-ray scattering. Biochemistry 2007; 46: 14058-14066.

Peters, JW; Bothner, B; Kelly, S. Unfolding the mystery of protein stability. Yellowstone Sci 2007.

McGlynn, SE; Ruebush, SS; Naumov, A; Nagy, LE; Dubini, A; King, PW; Broderick, JB; Posewitz, MC; Peters, JW. In vitro activation of [FeFe] hydrogenase: new insights into hydrogenase maturation. J. Biol. Inorg. Chem. 2007; 12: 443-447.

Sen, S; Peters, JW. The thermal adaptation of the nitrogenase Fe protein from thermophilic Methanobacter thermoautotrophicus. Proteins 2006; 62: 450-460.

Peters, JW; Szilagyi, RK; Naumov, A; Douglas, T,. A radical solution for the biosynthesis of the H-cluster of hydrogenase. FEBS Lett. 2006; 580: 363-367.

Pandey, AS; Nocek, B; Clark, DD; Ensign, SA; Peters, JW. Mechanistic implications of the structure of the mixed-disulfide intermediate of the disulfide oxidoreductase, 2-ketopropyl-coenzyme M oxidoreductase/carboxylase. Biochemistry 2006; 45: 113-120.

Steunou, AS; Bhaya, D; Bateson, MM; Melendrez, MC; Ward, DM; Brecht, E; Peters, JW; Kuhl, M; Grossman, AR. In situ analysis of nitrogen fixation and metabolic switching in unicellular thermophilic cyanobacteria inhabiting hot spring microbial mats. Proc. Natl. Acad. Sci. USA 2006; 103: 2398-2403.

Peters, JW; Szilagyi, RK. Exploring new frontiers of nitrogenase structure and mechanism. Curr. Opin. Chem. Biol. 2006; 10: 101-108.

Sen, S; Krishnakumar, A; McClead, J; Johnson, MK; Seefeldt, LC; Szilagyi, RK;

Peters, JW. Insights into the role of nucleotide-dependent conformational change in nitrogenase catalysis: Structural characterization of the nitrogenase Fe protein Leu127 deletion variant with bound MgATP. J. Inorg. Biochem. 2006; 100: 1041-1052.

Krishnakumar, AM; Nocek, BP; Clark, DD; Ensign, SA; Peters, JW. Structural basis for stereoselectivity in the (R)- and (S)-hydroxypropylthioethanesulfonate dehydrogenases. Biochemistry 2006; 45: 8831-8840.

Schwab, DE; Tard, C; Brecht, E; Peters, JW; Pickett, CJ; Szilagyi, RK. On the electronic structure of the hydrogenase H-cluster. Chem. Commun. 2006: 3696-3698.

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2004-2005

Sen, S; Peters, JW. The role of MgATP in nitrogenase catalysis In Proceedings of the 14th International Nitrogen Fixation Congress, 2005.

Copik, AJ; Nocek, BP; Swierczek, SI; Ruebush, S; Jang, SB; Meng, L; D'Souza V, M; Peters, JW; Bennett, B; Holz, RC. EPR and X-ray crystallographic characterization of the product-bound form of the MnII-loaded methionyl aminopeptidase from Pyrococcus furiosus. Biochemistry 2005; 44: 121-129.

Girbal, L; von Abendroth, G; Winkler, M; Benton, PM; Meynial-Salles, I; Croux, C; Peters, JW; Happe, T; Soucaille, P. Homologous and heterologous overexpression in Clostridium acetobutylicum and characterization of purified clostridial and algal Fe-only hydrogenases with high specific activities. Appl. Environ. Microbiol. 2005; 71: 2777-27781.

Elgren, TE; Zadvorny, OA; Brecht, E; Douglas, T; Zorin, NA; Maroney, MJ; Peters, JW. Immobilization of active hydrogenases by encapsulation in polymeric porous gels. Nano Lett. 2005; 5: 2085-2087.

Varpness, Z; Peters, JW; Young, M; Douglas, T. Biomimetic synthesis of a H2 catalyst using a protein cage architecture. Nano Lett. 2005; 5: 2306-2309.

Benton, PMC; Peters, JW. Nitrogenase structures. In Nitrogen Fixation, Smith, B. E.; Richards, R., Eds. Kluwer: 2004; pp 77-96.

Nocek, B; Boyd, J; Ensign, SA; Peters, JW. Crystallization and preliminary X-ray analysis of an acetone carboxylase from Xanthobacter autotrophicus strain Py2. Acta Crystallogr. D. Biol. Crystallogr. 2004; 60: 385-387.

Sen, S; Igarashi, R; Smith, A; Johnson, MK; Seefeldt, LC; Peters, JW. A

conformational mimic of the MgATP-bound "on state" of the nitrogenase iron protein. Biochemistry 2004; 43: 1787-1797.

Jang, SB; Jeong, MS; Seefeldt, LC; Peters, JW. Structural and biochemical implications of single amino acid substitutions in the nucleotide-dependent switch regions of the nitrogenase Fe protein from Azotobacter vinelandii. J. Biol. Inorg. Chem. 2004; 9: 1028-1033.

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2002-2003

Swierczek, K; Peters, JW; Hengge, AC. A convenient synthesis of phosphonothioic acids. Tetrahedron 2003; 59: 595-599.

Drennan, CL; Peters, JW. Surprising cofactors in metalloenzymes. Curr. Opin. Struct. Biol. 2003; 13: 220-226.

Swierczek, K; Pandey, AS; Peters, JW; Hengge, AC. A comparison of phosphonothioic acids with phosphonic acids as phosphatase inhibitors. J. Med. Chem. 2003; 46: 3703-3708.

Benton, PMC; Peters, JW. Nitrogenase structures. In Nitrogen Fixation at the Millenium, Leigh, G. L., Ed. Elsevier: 2002.

Peters, JW. A trio of transition metals in anaerobic CO2 fixation. Science 2002; 298: 552-553.

Chen, Z; Lemon, BJ; Huang, S; Swartz, DJ; Peters, JW; Bagley, KA. Infrared studies of the CO-inhibited form of the Fe-only hydrogenase from Clostridium pasteurianum I: examination of its light sensitivity at cryogenic temperatures. Biochemistry 2002; 41: 2036-2043.

Nocek, B; Clark, DD; Ensign, SA; Peters, JW. Crystallization and preliminary X-ray analysis of an R-2-hydroxypropyl-coenzyme M dehydrogenase. Acta Crystallogr. D. Biol. Crystallogr. 2002; 58: 1470-1473.

Nocek, B; Jang, SB; Jeong, MS; Clark, DD; Ensign, SA; Peters, JW. Structural basis for CO2 fixation by a novel member of the disulfide oxidoreductase family of enzymes, 2-ketopropyl-coenzyme M oxidoreductase/carboxylase. Biochemistry 2002; 41: 12907-12913.

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2000-2001

Lemon, BJ; Peters, JW. Fe-only hydrogenases. In Handbook of Metalloproteins, Messerschmidt, A.; Huber, R.; Poulos, T.; Weighardt, K., Eds. 2001

pp 738-750.

Chiu, H; Peters, JW; Lanzilotta, WN; Ryle, MJ; Seefeldt, LC; Howard, JB; Rees, DC. MgATP-Bound and nucleotide-free structures of a nitrogenase protein complex between the Leu 127 Delta-Fe-protein and the MoFe-protein. Biochemistry 2001; 40: 641-650.

Jang, SB; Jeong, MS; Clark, DD; Ensign, SA; Peters, JW. Crystallization and preliminary X-ray analysis of a NADPH 2-ketopropyl-coenzyme M oxidoreductase/carboxylase. Acta Crystallogr. D. Biol. Crystallogr. 2001; 57: 445-447.

Sorlie, M; Christiansen, J; Lemon, BJ; Peters, JW; Dean, DR; Hales, BJ. Mechanistic features and structure of the nitrogenase alpha-Gln195 MoFe protein. Biochemistry 2001; 40: 1540-1549.

Jang, SB; Seefeldt, LC; Peters, JW. Modulating the midpoint potential of the [4Fe-4S] cluster of the nitrogenase Fe protein. Biochemistry 2000; 39: 641-648.

Nicolet, Y; Lemon, BJ; Fontecilla-Camps, JC; Peters, JW. A novel FeS cluster in Fe-only hydrogenases. Trends Biochem. Sci. 2000; 25: 138-143.

Bennett, B; Lemon, BJ; Peters, JW. Reversible carbon monoxide binding and inhibition at the active site of the Fe-only hydrogenase. Biochemistry 2000; 39: 7455-7460.

Jang, SB; Seefeldt, LC; Peters, JW. Insights into nucleotide signal transduction in nitrogenase: structure of an iron protein with MgADP bound. Biochemistry 2000; 39: 14745-14752.

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1996-1999

Peters, JW; Bellamy, HD. Extension of Fe MAD phases in the structure determination of a multiple [FeS] cluster containing hydrogenase. J. Appl. Crystallogr. 1999; 32: 1180-1182.

Lemon, BJ; Peters, JW. Binding of exogenously added carbon monoxide at the active site of the iron-only hydrogenase (CpI) from Clostridium pasteurianum. Biochemistry 1999; 38: 12969-12973.

Peters, JW. Structure and mechanism of iron-only hydrogenases. Curr. Opin. Struct. Biol. 1999; 9: 670-676.

Peters, JW; Lanzilotta, WN; Lemon, BJ; Seefeldt, LC. X-ray crystal structure of the Fe-only hydrogenase (CpI) from Clostridium pasteurianum to 1.8 angstrom resolution. Science 1998; 282: 1853-1858.

Peters, JW; Stowell, MH; Soltis, SM; Finnegan, MG; Johnson, MK; Rees, DC. Redox-dependent structural changes in the nitrogenase P-cluster. Biochemistry 1997; 36: 1181-1187.

Peters, JW. A brief overview of nitrogenase structure and function. Life Support and Biosphere Science 1996; 3: 175-181.

Stowell, MHB; Soltis, SM; Kisker, C; Peters, JW; Schindelin, H; Rees, DC; Cascio, D; Beamer, L; Hart, PJ; Wiener, MC; Whitby, FG. A simple device for studying macromolecular crystals under moderate gas pressures (0.1-10 MPa). J. Appl. Crystallogr. 1996; 29: 608-613.

Peters, JW; Stowell, MH; Rees, DC. A leucine-rich repeat variant with a novel repetitive protein structural motif. Nat. Struct. Biol. 1996; 3: 991-994.

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1991-1995

Peters, JW; Fisher, K; Dean, DR. Nitrogenase structure and function: a biochemical-genetic perspective. Annu. Rev. Microbiol 1995; 49: 335-366.

Peters, JW; Fisher, K; Newton, WE; Dean, DR. Involvement of the P cluster in intramolecular electron transfer within the nitrogenase MoFe protein. J. Biol. Chem. 1995; 270: 27007-27013.

Peters, JW; Fisher, K; Dean, DR. Identification of a nitrogenase protein-protein interaction site defined by residues 59 through 67 within the Azotobacter vinelandii Fe protein. J. Biol. Chem. 1994; 269: 28076-28083.

Raybuck, SA; Ramer, SE; Abbanat, DR; Peters, JW; Ormejohnson, WH; Ferry, JG; Walsh, CT. Demonstration of carbon-carbon bond-cleavage of acetyl coenzyme-a by using isotopic exchange catalyzed by the Co dehydrogenase complex from acetate-grown methanosarcina-thermophila. J. Bacteriol. 1991; 173: 929-932.

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Projects

Publications

2013

Hamilton TL, Peters JW, Skidmore ML, Boyd ES.”Molecular evidence for an active endogenous microbiome beneath glacial ice”. ISME J. 2013 Mar 14.

[Epub ahead of print]

Mulder DW, Ratzloff MW, Shepard EM, Byer AS, Noone SM, Peters JW, Broderick JB, King PW. “EPR and FTIR Analysis on the Mechanism of H2 Activation by [FeFe]-Hydrogenase HydA1 from Chlamydomonas reinhardtii”. J Am Chem Soc. 2013 Apr 11. [Epub ahead of print]

Meuser JE, Baxter BK, Spear JR, Peters JW, Posewitz MC, Boyd ES. "Contrasting Patterns of Community Assembly in the Stratified Water Column of Great Salt Lake, Utah" Microb Ecol. 2013 Jan 25. [Epub ahead of print]

2011-2012

T.L. Hamilton, K. Vogl, D.A. Bryant, E.S. Boyd, J.W. Peters, “Environmental constraints defining the distribution, composition, and evolution of chlorophototrophs in thermal features of Yellowstone National Park,” Geobiology 10(3):236-49 (2012)

Joshi N, Shepard EM, Byer AS, Swanson KD, Broderick JB, Peters JW. "Iron-sulfur cluster coordination in the [FeFe]-hydrogenase H cluster biosynthetic factor HydF" , FEBS Lett.Oct 4. pii: S0014-5793(12)00736-3. doi: 10.1016/j.febslet.2012.09.028. Epub ahead of print (2012)

Duffus BR, Hamilton TL, Shepard EM, Boyd ES, Peters JW, Broderick JB. Radical AdoMet enzymes in complex metal cluster biosynthesis. Biochim Biophys Acta. 1824(11):1254-63 (2012)

Schut GJ, Boyd ES, Peters JW, Adams MW. The modular respiratory complexes involved in hydrogen and sulfur metabolism by heterotrophic hyperthermophilic archaea and their evolutionary implications. FEMS Microbiol Rev. Jun 19. doi: 10.1111/j.1574-6976.2012.00346.x. Epub ahead of print (2012)

Peters JW, Broderick JB. Emerging paradigms for complex iron-sulfur cofactor assembly and insertion. Annu Rev Biochem. 81:429-50 (2012)

Boyd ES, Fecteau KM, Havig JR, Shock EL, Peters JW. Modeling the habitat range of phototrophs in yellowstone national park: toward the development of a comprehensive fitness landscape. Front Microbiol. 3:221 (2012)

Zadvornyy OA, Lucon JE, Gerlach R, Zorin NA, Douglas T, Elgren TE, Peters JW. Photo-induced H2 production by [NiFe]-hydrogenase from T. roseopersicina covalently linked to a Ru(II) photosensitizer. J Inorg Biochem. 106(1):151-5 (2012)

Kofoed MA, Wampler DA, Pandey AS, Peters JW, Ensign SA. Roles of the redox-active disulfide and histidine residues forming a catalytic dyad in reactions catalyzed by 2-ketopropyl coenzyme M oxidoreductase/carboxylase. J Bacteriol. 193(18):4904-13 (2011)

Cornish AJ, Gärtner K, Yang H, Peters JW, Hegg EL. Mechanism of proton transfer in [FeFe]-hydrogenase from Clostridium pasteurianum. J Biol Chem. 286(44):38341-7 (2011)

T.L. Hamilton, K. Vogl, D.A. Bryant, E.S. Boyd, and J.W. Peters “Environmental constraints defining the distribution, composition, and evolution of chlorophototrophs in thermal features of Yellowstone National Park” Geobiology – Submitted (2011)

Hamilton TL, Jacobson M, Ludwig M, Boyd ES, Bryant DA, Dean DR, Peters JW. Differential accumulation of nif structural gene mRNA in Azotobacter vinelandii. J Bacteriol. 193(17):4534-6 (2011)

Hamilton TL, Ludwig M, Dixon R, Boyd ES, Dos Santos PC, Setubal JC, Bryant DA, Dean DR, Peters JW. Transcriptional profiling of nitrogen fixation in Azotobacter vinelandii. J Bacteriol. 193(17):4477-86 (2011)

Mulder DW, Shepard EM, Meuser JE, Joshi N, King PW, Posewitz MC, Broderick JB, Peters JW. Insights into [FeFe]-hydrogenase structure, mechanism, and maturation. Structure 19(8):1038-52 (2011)

Boyd ES, Lange RK, Mitchell AC, Havig JR, Hamilton TL, Lafrenière MJ, Shock EL, Peters JW, Skidmore M. Diversity, abundance, and potential activity of nitrifying and nitrate-reducing microbial assemblages in a subglacial ecosystem. Appl Environ Microbiol. 77(14):4778-87 (2011)

E.S. Boyd, A.D. Anbar, S. Miller, T.L. Hamilton, M. Lavin, and J.W. Peters “A late methanogen origin for molybdenum-dependent nitrogenase” Geobiology 9:221-232 (2011) – highlighted in Science as Editor’s Choice

Hamilton TL, Lange RK, Boyd ES, Peters JW. Biological nitrogen fixation in acidic high-temperature geothermal springs in Yellowstone National Park, Wyoming. Environ Microbiol. 13(8):2204-15 (2011)

Pandey AS, Mulder DW, Ensign SA, Peters JW. Structural basis for carbon dioxide binding by 2-ketopropyl coenzyme M oxidoreductase/carboxylase. FEBS Lett. 585(3):459-64 (2011)

E.M. Shepard, E.S. Boyd, J.B. Broderick, and J.W. Peters “Biosynthesis of complex iron-sulfur enzymes” Curr. Opin. Struct. Biol. 15:319-327 (2011)

J.W. Peters, L.M. Rubio “Biochemistry of Mo-nitrogenase” in The Molecular Basis of the Nitrogen Cycle (ed. J. Moir) Horizon Scientific Press In press (2011)

D.W. Mulder and J.W. Peters “Nucleotide-dependent conformational change and complex interactions in nitrogenase” in Methods in Nitrogen Fixation (ed. by M.W. Ribbe) Springer/Humana Press In press (2011)

Mulder DW, Peters JW. Small angle x-ray scattering spectroscopy. Methods Mol

Biol. 766:177-189 (2011)

Boyd ES, Hamilton TL, Peters JW. An alternative path for the evolution of biological nitrogen fixation. Front Microbiol. 2:205 (2011)

J.W. Peters, E.S. Boyd, S. D’Adamo, D.W. Mulder, J. Therien, and M.C. Posewitz “Hydrogenases, nitrogenases, anoxia, and H2 production in water-oxidizing phototrophs” in Algae for Biofuels and Energy(ed.M.A. Borowitzka) Springer/Humana Press In press (2011)

Hamilton TL, Boyd ES, Peters JW. Environmental constraints underpin the distribution and phylogenetic diversity of nifH in the Yellowstone geothermal complex. Microb Ecol. 2011 61(4):860-70 (2011)

K.D. Swanson, B.R. Duffus, T.E. Beard, J.W. Peters, and J.B. Broderick “Cyanide and carbon monoxide ligand formation in hydrogenase biosynthesis” Epub ahead of print DOI: 10.1002/ejic.201001056 (2011) – included inside cover art.

J.M. Boyd, J.A. Endrizzi, T.L. Hamilton, D.M. Downs, and J.W. Peters “FAD binding by ApbE protein from Salmonella enterica: a new class of flavoproteins” J. Bacteriol. 193:887-895 (2011)

D.W. Mulder, A.S. Pandey, S.A. Ensign, and J.W. Peters “Carbon dioxide binding and redox dependent substrate activation at the active site of 2-ketopropyl coenzyme M oxidoreductase/carboxylase” FEBS Lett. 585:459-464 (2011)

2009-2010

Zadvornyy, O; Barrows, AM; Zorin, NA; Peters, JW; Elgren, TE. High level of hydrogen production activity achieved for hydrogenase encapsulated in sol–gel material doped with carbon nanotubes. J. Mater. Chem., 2010; 20: 1065–1067.

Shepard, EM; Duffus, BR; George, SJ; McGlynn, SE; Challand, MR; Swanson, KD; Roach, PL; Cramer, SP; Peters, JW; Broderick, JB. [FeFe]-Hydrogenase Maturation: HydG-Catalyzed Synthesis of Carbon Monoxide. J. Am. Chem. Soc. 2010; 132: 9247-9249.

Boyd, ES; Hamilton, TL; Spear, JR; Lavin, M; Peters, JW. [FeFe]-hydrogenase in Yellowstone National Park: evidence for dispersal limitation and phylogenetic niche conservatism. ISME J. 2010; 4: 1485-1495.

Shepard, EM; McGlynn, SE; Bueling, AL; Grady-Smith, CS; George, SJ; Winslow, MA; Cramer, SP; Peters, JW; Broderick, JB. Synthesis of the 2Fe subcluster of the [FeFe]-hydrogenase H cluster on the HydF scaffold. Proc. Natl. Acad. Sci. USA 2010; 107: 10448-10453.

Mulder, DW; Boyd, ES; Sarma, R; Lange, RK; Endrizzi, JA; Broderick, JB; Peters, JW. Stepwise [FeFe]-hydrogenase H-cluster assembly revealed in the structure of HydA(DeltaEFG). Nature 2010; 465: 248-251.

Soboh, B; Boyd, ES; Zhao, D; Peters, JW; Rubio, LM. Substrate specificity and evolutionary implications of a NifDK enzyme carrying NifB-co at its active site. FEBS Lett. 2010; 584: 1487-1492.

Driesener, RC; Challand, MR; McGlynn, SE; Shepard, EM; Boyd, ES; Broderick, JB; Peters, JW; Roach, PL. [FeFe]-hydrogenase cyanide ligands derived from S-adenosylmethionine-dependent cleavage of tyrosine. Angew. Chem. Int. Ed. Engl. 2010; 49: 1687-1690.

Sarma, R; Barney, BM; Keable, S; Dean, DR; Seefeldt, LC; Peters, JW. Insights into substrate binding at FeMo-cofactor in nitrogenase from the structure of an alpha-70(Ile) MoFe protein variant. J. Inorg. Biochem. 2010; 104: 385-389.

Zadvornyy, OA; Allen, M; Brumfield, SK; Varpness, Z; Boyd, ES; Zorin, NA; Serebriakova, L; Douglas, T; Peters, JW. Hydrogen enhances nickel tolerance in the purple sulfur bacterium Thiocapsa roseopersicina. Environ. Sci. Technol. 2010; 44: 834-840.

McGlynn, SE; Boyd, ES; Shepard, EM; Lange, RK; Gerlach, R; Broderick, JB; Peters, JW. Identification and characterization of a novel member of the radical AdoMet enzyme superfamily and implications for the biosynthesis of the Hmd hydrogenase active site cofactor. J. Bacteriol. 2010; 192: 595-598.

Beer, LL; Boyd, ES; Peters, JW; Posewitz, MC. Engineering algae for biohydroen and biofuel production. Curr. Opin. Biotechnol. 2009; 20: 264-271.

Mulder, DW; Ortillo, DO; Gardenghi, DJ; Naumov, AV; Ruebush, SS; Szilagyi, RK; Huynh B; Broderick, JB; Peters, JW. Activation of HydA∆EFG requires a preformed [4Fe-4S] cluster. Biochemistry 2009; 48: 6240-6248.

Boyd, ES; Spear, JR; Peters, JW. [FeFe] hydrogenase genetic diversity provides insight into molecular adaption in a saline microbial mat community. Appl. Environ. Microbiol. 2009; 75: 4620-4623.

Mcglynn, SE; Mulder, DW; Shepard, SE; Broderick, JB; Peters, JW. Hydrogenase cluster biosynthesis: organometallic chemisty nature's way. Dalton Trans. 2009; 4274-4285.

Peters, JW. Carbon monoxide and cyanide lignads in the active site of [FeFe]-hydrogeanse. In Metal ions in life sciences. Sigel, A; Sigel, H; Sigel, RKO; Eds. RSC Pub: 2009; 6, 179-218.

2006-2008

Sarma, R; Barney, BM; Hamilton, TL; Jones, A; Seefeldt, LC; Peters, JW. Crystal structure of the L protein of Rhodobacter sphaeroides light-independent protochlorophyllide reductase with MgADP bound: a homologue of the nitrogenase Fe protein. Biochemistry 2008; 47: 13004-13015.

Krishnakumar, AM; Sliwa, D; Endrizzi, JA; Boyd, ES; Ensign, SA; Peters, JW. Getting a handle on the role of coenzyme M in alkene metabolism. Microbiol. Mol. Biol. Rev.; 72: 445-456.

Posewitz, MC; Mulder, DW; Peters, JW. New Frontiers in Hydrogenase Structure and Biosynthesis. Current Chemical Biology 2008; 2: 178-199.

McGlynn, SE; Shepard, EM; Winslow, MA; Naumov, AV; Duschene, KS; Posewitz, MC; Broderick, WE; Broderick, WE; Broderick, JB; Peters, JW. HydF as a scaffold protein in [FeFe] hydrogenase H-cluster biosynthesis. FEBS Lett. 2008; 582: 2183-2187.

Pandey, AS; Harris, TV; Giles, LJ; Peters, JW; Szilagyi, RK. Dithiomethylether as a ligand in the hydrogenase h-cluster. J. Am. Chem. Soc. 2008; 130: 4533-4540.

Sarma R; Mulder, DW; Brecht, E; Szilagy, RK; Seefeldt, LC; Tsuruta, H; Peters, JW. Probing the MgATP-bound conformation of the nitrogenase Fe protein by solution small-angle X-ray scattering. Biochemistry 2007; 46: 14058-14066.

Peters, JW; Bothner, B; Kelly, S. Unfolding the mystery of protein stability. Yellowstone Sci 2007.

McGlynn, SE; Ruebush, SS; Naumov, A; Nagy, LE; Dubini, A; King, PW; Broderick, JB; Posewitz, MC; Peters, JW. In vitro activation of [FeFe] hydrogenase: new insights into hydrogenase maturation. J. Biol. Inorg. Chem. 2007; 12: 443-447.

Sen, S; Peters, JW. The thermal adaptation of the nitrogenase Fe protein from thermophilic Methanobacter thermoautotrophicus. Proteins 2006; 62: 450-460.

Peters, JW; Szilagyi, RK; Naumov, A; Douglas, T,. A radical solution for the biosynthesis of the H-cluster of hydrogenase. FEBS Lett. 2006; 580: 363-367.

Pandey, AS; Nocek, B; Clark, DD; Ensign, SA; Peters, JW. Mechanistic implications of the structure of the mixed-disulfide intermediate of the disulfide oxidoreductase, 2-ketopropyl-coenzyme M oxidoreductase/carboxylase. Biochemistry 2006; 45: 113-120.

Steunou, AS; Bhaya, D; Bateson, MM; Melendrez, MC; Ward, DM; Brecht, E; Peters, JW; Kuhl, M; Grossman, AR. In situ analysis of nitrogen fixation and metabolic switching in unicellular thermophilic cyanobacteria inhabiting hot spring microbial mats. Proc. Natl. Acad. Sci. USA 2006; 103: 2398-2403.

Peters, JW; Szilagyi, RK. Exploring new frontiers of nitrogenase structure and mechanism. Curr. Opin. Chem. Biol. 2006; 10: 101-108.

Sen, S; Krishnakumar, A; McClead, J; Johnson, MK; Seefeldt, LC; Szilagyi, RK;

Peters, JW. Insights into the role of nucleotide-dependent conformational change in nitrogenase catalysis: Structural characterization of the nitrogenase Fe protein Leu127 deletion variant with bound MgATP. J. Inorg. Biochem. 2006; 100: 1041-1052.

Krishnakumar, AM; Nocek, BP; Clark, DD; Ensign, SA; Peters, JW. Structural basis for stereoselectivity in the (R)- and (S)-hydroxypropylthioethanesulfonate dehydrogenases. Biochemistry 2006; 45: 8831-8840.

Schwab, DE; Tard, C; Brecht, E; Peters, JW; Pickett, CJ; Szilagyi, RK. On the electronic structure of the hydrogenase H-cluster. Chem. Commun. 2006: 3696-3698.

2004-2005

Sen, S; Peters, JW. The role of MgATP in nitrogenase catalysis In Proceedings of the 14th International Nitrogen Fixation Congress, 2005.

Copik, AJ; Nocek, BP; Swierczek, SI; Ruebush, S; Jang, SB; Meng, L; D'Souza V, M; Peters, JW; Bennett, B; Holz, RC. EPR and X-ray crystallographic characterization of the product-bound form of the MnII-loaded methionyl aminopeptidase from Pyrococcus furiosus. Biochemistry 2005; 44: 121-129.

Elgren, TE; Zadvorny, OA; Brecht, E; Douglas, T; Zorin, NA; Maroney, MJ; Peters, JW. Immobilization of active hydrogenases by encapsulation in polymeric porous gels. Nano Lett. 2005; 5: 2085-2087.

Varpness, Z; Peters, JW; Young, M; Douglas, T. Biomimetic synthesis of a H2 catalyst using a protein cage architecture. Nano Lett. 2005; 5: 2306-2309.

Benton, PMC; Peters, JW. Nitrogenase structures. In Nitrogen Fixation, Smith, B. E.; Richards, R., Eds. Kluwer: 2004; pp 77-96.

Nocek, B; Boyd, J; Ensign, SA; Peters, JW. Crystallization and preliminary X-ray analysis of an acetone carboxylase from Xanthobacter autotrophicus strain Py2. Acta Crystallogr. D. Biol. Crystallogr. 2004; 60: 385-387.

Sen, S; Igarashi, R; Smith, A; Johnson, MK; Seefeldt, LC; Peters, JW. A

conformational mimic of the MgATP-bound "on state" of the nitrogenase iron protein. Biochemistry 2004; 43: 1787-1797.

Jang, SB; Jeong, MS; Seefeldt, LC; Peters, JW. Structural and biochemical implications of single amino acid substitutions in the nucleotide-dependent switch regions of the nitrogenase Fe protein from Azotobacter vinelandii. J. Biol. Inorg. Chem. 2004; 9: 1028-1033.

Zadvornyy, O; Barrows, AM; Zorin, NA; Peters, JW; Elgren, TE. High level of hydrogen production activity achieved for hydrogenase encapsulated in sol–gel material doped with carbon nanotubes. ***J. Mater. Chem.*, 2010; 20**: 1065–1067.

Mulder, DW; Ortillo, DO; Gardenghi, DJ; Naumov, AV; Ruebush, SS; Szilagyi, RK; Huynh B; Broderick, JB; Peters, JW. Activation of HydA^∆EFG requires a preformed [4Fe-4S] cluster. Biochemistry 2009; 48: 6240-6248.