1
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Lewis NM, Kisgeropoulos EC, Lubner CE, Fixen KR. Characterization of ferredoxins involved in electron transfer pathways for nitrogen fixation implicates differences in electronic structure in tuning 2[4Fe4S] Fd activity. J Inorg Biochem 2024; 254:112521. [PMID: 38471286 DOI: 10.1016/j.jinorgbio.2024.112521] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2023] [Revised: 03/03/2024] [Accepted: 03/05/2024] [Indexed: 03/14/2024]
Abstract
Ferredoxins (Fds) are small proteins which shuttle electrons to pathways like biological nitrogen fixation. Physical properties tune the reactivity of Fds with different pathways, but knowledge on how these properties can be manipulated to engineer new electron transfer pathways is lacking. Recently, we showed that an evolved strain of Rhodopseudomonas palustris uses a new electron transfer pathway for nitrogen fixation. This pathway involves a variant of the primary Fd of nitrogen fixation in R. palustris, Fer1, in which threonine at position 11 is substituted for isoleucine (Fer1T11I). To understand why this substitution in Fer1 enables more efficient electron transfer, we used in vivo and in vitro methods to characterize Fer1 and Fer1T11I. Electrochemical characterization revealed both Fer1 and Fer1T11I have similar redox transitions (-480 mV and - 550 mV), indicating the reduction potential was unaffected despite the proximity of T11 to an iron‑sulfur (FeS) cluster of Fer1. Additionally, disruption of hydrogen bonding around an FeS cluster in Fer1 by substituting threonine with alanine (T11A) or valine (T11V) did not increase nitrogenase activity, indicating that disruption of hydrogen bonding does not explain the difference in activity observed for Fer1T11I. Electron paramagnetic resonance spectroscopy studies revealed key differences in the electronic structure of Fer1 and Fer1T11I, which indicate changes to the high spin states and/or spin-spin coupling between the FeS clusters of Fer1. Our data implicates these electronic structure differences in facilitating electron flow and sets a foundation for further investigations to understand the connection between these properties and intermolecular electron transfer.
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Affiliation(s)
- Nathan M Lewis
- Department of Plant and Microbial Biology and the Biotechnology Institute, University of Minnesota, Minneapolis, MN, United States of America
| | | | - Carolyn E Lubner
- National Renewable Energy Laboratory, Golden, CO, United States of America.
| | - Kathryn R Fixen
- Department of Plant and Microbial Biology and the Biotechnology Institute, University of Minnesota, Minneapolis, MN, United States of America.
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2
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Warmack RA, Maggiolo AO, Orta A, Wenke BB, Howard JB, Rees DC. Structural consequences of turnover-induced homocitrate loss in nitrogenase. Nat Commun 2023; 14:1091. [PMID: 36841829 PMCID: PMC9968304 DOI: 10.1038/s41467-023-36636-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2022] [Accepted: 02/09/2023] [Indexed: 02/26/2023] Open
Abstract
Nitrogenase catalyzes the ATP-dependent reduction of dinitrogen to ammonia during the process of biological nitrogen fixation that is essential for sustaining life. The active site FeMo-cofactor contains a [7Fe:1Mo:9S:1C] metallocluster coordinated with an R-homocitrate (HCA) molecule. Here, we establish through single particle cryoEM and chemical analysis of two forms of the Azotobacter vinelandii MoFe-protein - a high pH turnover inactivated species and a ∆NifV variant that cannot synthesize HCA - that loss of HCA is coupled to α-subunit domain and FeMo-cofactor disordering, and formation of a histidine coordination site. We further find a population of the ∆NifV variant complexed to an endogenous protein identified through structural and proteomic approaches as the uncharacterized protein NafT. Recognition by endogenous NafT demonstrates the physiological relevance of the HCA-compromised form, perhaps for cofactor insertion or repair. Our results point towards a dynamic active site in which HCA plays a role in enabling nitrogenase catalysis by facilitating activation of the FeMo-cofactor from a relatively stable form to a state capable of reducing dinitrogen under ambient conditions.
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Affiliation(s)
- Rebeccah A Warmack
- Division of Chemistry and Chemical Engineering 147-75, California Institute of Technology, Pasadena, CA, 91125, USA.
| | - Ailiena O Maggiolo
- Division of Chemistry and Chemical Engineering 147-75, California Institute of Technology, Pasadena, CA, 91125, USA
| | - Andres Orta
- Biochemistry and Molecular Biophysics Graduate Program, California Institute of Technology, Pasadena, CA, 91125, USA
| | - Belinda B Wenke
- Division of Chemistry and Chemical Engineering 147-75, California Institute of Technology, Pasadena, CA, 91125, USA
| | - James B Howard
- Department of Biochemistry, University of Minnesota, Minneapolis, MN, 55455, USA
| | - Douglas C Rees
- Division of Chemistry and Chemical Engineering 147-75, California Institute of Technology, Pasadena, CA, 91125, USA.
- Howard Hughes Medical Institute, California Institute of Technology, Pasadena, CA, USA.
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3
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Threatt SD, Rees DC. Biological nitrogen fixation in theory, practice, and reality: a perspective on the molybdenum nitrogenase system. FEBS Lett 2023; 597:45-58. [PMID: 36344435 PMCID: PMC10100503 DOI: 10.1002/1873-3468.14534] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2022] [Revised: 10/30/2022] [Accepted: 10/31/2022] [Indexed: 11/09/2022]
Abstract
Nitrogenase is the sole enzyme responsible for the ATP-dependent conversion of atmospheric dinitrogen into the bioavailable form of ammonia (NH3 ), making this protein essential for the maintenance of the nitrogen cycle and thus life itself. Despite the widespread use of the Haber-Bosch process to industrially produce NH3 , biological nitrogen fixation still accounts for half of the bioavailable nitrogen on Earth. An important feature of nitrogenase is that it operates under physiological conditions, where the equilibrium strongly favours ammonia production. This biological, multielectron reduction is a complex catalytic reaction that has perplexed scientists for decades. In this review, we explore the current understanding of the molybdenum nitrogenase system based on experimental and computational research, as well as the limitations of the crystallographic, spectroscopic, and computational techniques employed. Finally, essential outstanding questions regarding the nitrogenase system will be highlighted alongside suggestions for future experimental and computational work to elucidate this essential yet elusive process.
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Affiliation(s)
- Stephanie D Threatt
- Division of Chemistry and Chemical Engineering, Howard Hughes Medical Institute, California Institute of Technology, Pasadena, CA, USA
| | - Douglas C Rees
- Division of Chemistry and Chemical Engineering, Howard Hughes Medical Institute, California Institute of Technology, Pasadena, CA, USA
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4
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Dance I. Calculating the chemical mechanism of nitrogenase: new working hypotheses. Dalton Trans 2022; 51:12717-12728. [PMID: 35946501 DOI: 10.1039/d2dt01920e] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The enzyme nitrogenase converts N2 to NH3 with stoichiometry N2 + 8H+ + 8e- → 2NH3 + H2. The mechanism is chemically complex with multiple steps that must be consistent with much accumulated experimental information, including exchange of H2 and N2 and the N2-dependent hydrogenation of D2 to HD. Previous investigations have developed a collection of working hypotheses that guide ongoing density functional investigations of mechanistic steps and sequences. These include (i) hypotheses about the serial provision of protons and their conversion to H atoms bonded to S and Fe atoms of the FeMo-co catalytic site, (ii) the migration of H atoms over the surface of FeMo-co, (iii) the roles of His195, (iv) identification of three protein channels, one for the ingress of N2, a separate pathway for the passage of exogenous H2 (D2) and product H2 (HD), and a hydrophilic pathway for egress of product NH3. Two additional working hypotheses are described in this paper. N2 passing along the N2 channel approaches and binds end-on to the exo coordination position of Fe2, with favourable energetics when FeMo-co is pre-hydrogenated. This exo-Fe2-N2 is apparently not reduced but has a promotional role by expanding the reaction zone. A second N2 can enter via the N2 ingress channel and bind at the endo-Fe6 position, where it is surrounded by H atom donors suitable for the N2 → NH3 conversion. It is proposed that this endo-Fe6 position is also the binding site for H2 (generated or exogenous), accounting for the competitive inhibition of N2 reduction by H2. The HD reaction occurs at the endo-Fe6 site, promoted by N2 at the exo-Fe2 site. The second hypothesis concerns the most stable electronic states of FeMo-co with ligands bound at Fe2 and Fe6, and provides a protocol for management of electronic states in mechanism calculations.
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Affiliation(s)
- Ian Dance
- School of Chemistry, UNSW Sydney, NSW 2051, Australia.
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5
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Dance I. Structures and reaction dynamics of N 2 and H 2 binding at FeMo-co, the active site of nitrogenase. Dalton Trans 2021; 50:18212-18237. [PMID: 34860237 DOI: 10.1039/d1dt03548g] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
The chemical reactions occurring at the Fe7MoS9C(homocitrate) cluster, FeMo-co, the active site of the enzyme nitrogenase (N2 → NH3), are enigmatic. Experimental information collected over a long period reveals aspects of the roles of N2 and H2, each with more than one type of reactivity. This paper reports investigations of the binding of H2 and N2 at intact FeMo-co, using density functional simulations of a large 486 atom relevant portion of the protein, resulting in 27 new structures containing H2 and/or N2 bound at the exo and endo coordination sites of the participating Fe atoms, Fe2 and Fe6. Binding energies and transition states for association/dissociation are determined, and trajectories for the approach, binding and separation of H2/N2 are described, including diffusion of these small molecules through proximal protein. Influences of surrounding amino acids are identified. FeMo-co deforms geometrically when binding H2 or N2, and a procedure for calculating the energy cost involved, the adaptation energy, is introduced here. Adaptation energies, which range from 7 to 36 kcal mol-1 for the reported structures, are influenced by the protonation state of the His195 side chain. Seven N2 structures and three H2 structures have negative binding free energies, which include the estimated entropy penalties for binding of N2, H2 from proximal protein. These favoured structures have N2 bound end-on at exo-Fe2, exo-Fe6 and endo-Fe2 positions of FeMo-co, and H2 bound at the endo-Fe2 position. Various postulated structures with N2 bridging Fe2 and Fe6 revert to end-on-N2 at endo positions. The structures are also assessed via the calculated potential energy barriers for association and dissociation. Barriers to the binding of H2 range from 1 to 20 kcal mol-1 and barriers to dissociation of H2 range from 3 to 18 kcal mol-1. Barriers to the binding of N2, in either side-on or end-on mode, range from 2 to 18 kcal mol-1, while dissociation of bound N2 encounters barriers of 3 to 8 kcal mol-1 for side-on bonding and 7 to 18 kcal mol-1 for end-on bonding. These results allow formulation of mechanisms for the H2/N2 exchange reaction, and three feasible mechanisms for associative exchange and three for dissociative exchange are identified. Consistent electronic structures and potential energy surfaces are maintained throughout. Changes in the spin populations of Fe2 and Fe6 connected with cluster deformation and with metal-ligand bond formation are identified.
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Affiliation(s)
- Ian Dance
- School of Chemistry, UNSW Sydney, NSW 2051, Australia.
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6
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Banerjee R, Lipscomb JD. Small-Molecule Tunnels in Metalloenzymes Viewed as Extensions of the Active Site. Acc Chem Res 2021; 54:2185-2195. [PMID: 33886257 DOI: 10.1021/acs.accounts.1c00058] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Rigorous substrate selectivity is a hallmark of enzyme catalysis. This selectivity is generally ascribed to a thermodynamically favorable process of substrate binding to the enzyme active site based upon complementary physiochemical characteristics, which allows both acquisition and orientation. However, this chemical selectivity is more difficult to rationalize for diminutive molecules that possess too narrow a range of physical characteristics to allow either precise positioning or discrimination between a substrate and an inhibitor. Foremost among these small molecules are dissolved gases such as H2, N2, O2, CO, CO2, NO, N2O, NH3, and CH4 so often encountered in metalloenzyme catalysis. Nevertheless, metalloenzymes have evolved to metabolize these small-molecule substrates with high selectivity and efficiency.The soluble methane monooxygenase enzyme (sMMO) acts upon two of these small molecules, O2 and CH4, to generate methanol as part of the C1 metabolic pathway of methanotrophic organisms. sMMO is capable of oxidizing many alternative hydrocarbon substrates. Remarkably, however, it will preferentially oxidize methane, the substrate with the fewest discriminating physical characteristics and the strongest C-H bond. Early studies led us to broadly attribute this specificity to the formation of a "molecular sieve" in which a methane- and oxygen-sized tunnel provides a size-selective route from bulk solvent to the completely buried sMMO active site. Indeed, recent cryogenic and serial femtosecond ambient temperature crystallographic studies have revealed such a route in sMMO. A detailed study of the sMMO tunnel considered here in the context of small-molecule tunnels identified in other metalloenzymes reveals three discrete characteristics that contribute to substrate selectivity and positioning beyond that which can be provided by the active site itself. Moreover, the dynamic nature of many tunnels allows an exquisite coordination of substrate binding and reaction phases of the catalytic cycle. Here we differentiate between the highly selective molecular tunnel, which allows only the one-dimensional transit of small molecules, and the larger, less-selective channels found in typical enzymes. Methods are described to identify and characterize tunnels as well as to differentiate them from channels. In metalloenzymes which metabolize dissolved gases, we posit that the contribution of tunnels is so great that they should be considered to be extensions of the active site itself. A full understanding of catalysis by these enzymes requires an appreciation of the roles played by tunnels. Such an understanding will also facilitate the use of the enzymes or their synthetic mimics in industrial or pharmaceutical applications.
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Affiliation(s)
- Rahul Banerjee
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, Minnesota 55391, United States
| | - John D. Lipscomb
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, Minnesota 55391, United States
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7
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Affiliation(s)
- Oliver Einsle
- Institute for Biochemistry, Albert-Ludwigs-University Freiburg, 79104 Freiburg, Germany
| | - Douglas C. Rees
- Division of Chemistry and Chemical Engineering, Howard Hughes Medical Institute, California Institute of Technology, Pasadena California 91125, United States
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8
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Dance I. Computational Investigations of the Chemical Mechanism of the Enzyme Nitrogenase. Chembiochem 2020; 21:1671-1709. [DOI: 10.1002/cbic.201900636] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2019] [Indexed: 12/15/2022]
Affiliation(s)
- Ian Dance
- School of Chemistry UNSW Sydney Sydney 2052 Australia
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9
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Survey of the Geometric and Electronic Structures of the Key Hydrogenated Forms of FeMo-co, the Active Site of the Enzyme Nitrogenase: Principles of the Mechanistically Significant Coordination Chemistry. INORGANICS 2019. [DOI: 10.3390/inorganics7010008] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
The enzyme nitrogenase naturally hydrogenates N2 to NH3, achieved through the accumulation of H atoms on FeMo-co, the Fe7MoS9C(homocitrate) cluster that is the catalytically active site. Four intermediates, E1H1, E2H2, E3H3, and E4H4, carry these hydrogen atoms. I report density functional calculations of the numerous possibilities for the geometric and electronic structures of these poly-hydrogenated forms of FeMo-co. This survey involves more than 100 structures, including those with bound H2, and assesses their relative energies and most likely electronic states. Twelve locations for bound H atoms in the active domain of FeMo-co, including Fe–H–Fe and Fe–H–S bridges, are studied. A significant result is that transverse Fe–H–Fe bridges (transverse to the pseudo-threefold axis of FeMo-co and shared with triply-bridging S) are not possible geometrically unless the S is hydrogenated to become doubly-bridging. The favourable Fe–H–Fe bridges are shared with doubly-bridging S. ENDOR data for an E4H4 intermediate trapped at low temperature, and interpretations in terms of the geometrical and electronic structure of E4H4, are assessed in conjunction with the calculated possibilities. The results reported here yield a set of 24 principles for the mechanistically significant coordination chemistry of H and H2 on FeMo-co, in the stages prior to N2 binding.
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10
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Dance I. How feasible is the reversible S-dissociation mechanism for the activation of FeMo-co, the catalytic site of nitrogenase? Dalton Trans 2019; 48:1251-1262. [PMID: 30607401 DOI: 10.1039/c8dt04531c] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
The active site of the enzyme nitrogenase (N2→ NH3) is a Fe7MoS9C cluster that contains three doubly-bridging μ-S atoms around a central belt. A vanadium nitrogenase variant has a slightly different cluster, containing two μ-S atoms. Recent crystal structures have revealed substitution of one μ-S (S2B, bridging Fe2 and Fe6), by CO in Mo-nitrogenase and an uncertain light atom in V-nitrogenase. These systems retained catalytic activity, and were able to recover the lost μ-S atom. Electron density attributed to the dissociated S is displaced by 7 Å in the crystal structure of the non-standard V-protein. The hypothesis arising from these observations is that the chemical mechanism of nitrogenase involves reversible dissociation of S2B, leaving Fe2 and Fe6 seriously under-coordinated and reactive in trapping N2 and binding reaction intermediates. Accumulated experimental evidence points to the Fe2-S2B-Fe6 domain as the centre of catalytic hydrogenation of N2. Using DFT simulations of a large model (>488 atoms) containing all relevant surrounding protein residues, I have investigated the chemical steps that could allow dissociation of S2B. The participation of H atoms is crucial, as is involvement of the nearby side chain of His195 that can function as proton donor to S2B and hydrogen-bonding supporter of displaced S2B. A significant result is that after ingress and binding of N2 at Fe2 the breaking of the Fe2-S2B bond can be strongly exergonic with negligible kinetic barrier. Subsequent extension of the Fe6-S2B bond and dissociation as H2S (or SH-) is endergonic by 20-25 kcal mol-1, partly because the separating H2S is restricted by surrounding amino-acids. I present a number of reaction sequences and energy landscapes, and derive thirteen chemical principles relevant to the postulated S-dissociation mechanism. A key conclusion is that unhooking of S2BH or S2BH2 from Fe2 is favourable, likely, and propitious for subsequent H transfer to bound N2 or reaction intermediates. The space between Fe2 and Fe6 supports two bridging ligands, and another H atom on Fe6 can move without kinetic barrier to occupy the bridging position vacated by S2B.
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Affiliation(s)
- Ian Dance
- School of Chemistry, UNSW Sydney, Sydney 2000, Australia.
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11
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Dance I. What is the role of the isolated small water pool near FeMo‐co, the active site of nitrogenase? FEBS J 2018; 285:2972-2986. [DOI: 10.1111/febs.14519] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2018] [Revised: 05/02/2018] [Accepted: 05/22/2018] [Indexed: 01/14/2023]
Affiliation(s)
- Ian Dance
- School of Chemistry UNSW Sydney NSW Australia
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12
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Dance I. Evaluations of the accuracies of DMol3 density functionals for calculations of experimental binding enthalpies of N2, CO, H2, C2H2 at catalytic metal sites. MOLECULAR SIMULATION 2017. [DOI: 10.1080/08927022.2017.1413711] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Affiliation(s)
- Ian Dance
- School of Chemistry, UNSW Sydney, Sydney, Australia
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13
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Morrison CN, Spatzal T, Rees DC. Reversible Protonated Resting State of the Nitrogenase Active Site. J Am Chem Soc 2017; 139:10856-10862. [PMID: 28692802 PMCID: PMC5553094 DOI: 10.1021/jacs.7b05695] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
![]()
Protonated states of the nitrogenase
active site are mechanistically
significant since substrate reduction is invariably accompanied by
proton uptake. We report the low pH characterization by X-ray crystallography
and EPR spectroscopy of the nitrogenase molybdenum iron (MoFe) proteins
from two phylogenetically distinct nitrogenases (Azotobacter
vinelandii, Av, and Clostridium pasteurianum, Cp) at pHs between 4.5 and 8. X-ray data at pHs of 4.5–6
reveal the repositioning of side chains along one side of the FeMo-cofactor,
and the corresponding EPR data shows a new S = 3/2
spin system with spectral features similar to a state previously observed
during catalytic turnover. The structural changes suggest that FeMo-cofactor
belt sulfurs S3A or S5A are potential protonation sites. Notably,
the observed structural and electronic low pH changes are correlated
and reversible. The detailed structural rearrangements differ between
the two MoFe proteins, which may reflect differences in potential
protonation sites at the active site among nitrogenase species. These
observations emphasize the benefits of investigating multiple nitrogenase
species. Our experimental data suggest that reversible protonation
of the resting state is likely occurring, and we term this state “E0H+”, following the Lowe–Thorneley
naming scheme.
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Affiliation(s)
- Christine N Morrison
- Division of Chemistry and Chemical Engineering and ‡Howard Hughes Medical Institute, California Institute of Technology , Pasadena, California 91125, United States
| | - Thomas Spatzal
- Division of Chemistry and Chemical Engineering and ‡Howard Hughes Medical Institute, California Institute of Technology , Pasadena, California 91125, United States
| | - Douglas C Rees
- Division of Chemistry and Chemical Engineering and ‡Howard Hughes Medical Institute, California Institute of Technology , Pasadena, California 91125, United States
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14
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Zhao L, Rathnayake UM, Dewage SW, Wood WN, Veltri AJ, Cisneros GA, Hendrickson TL. Characterization of tunnel mutants reveals a catalytic step in ammonia delivery by an aminoacyl-tRNA amidotransferase. FEBS Lett 2016; 590:3122-32. [DOI: 10.1002/1873-3468.12347] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2016] [Revised: 07/27/2016] [Accepted: 07/28/2016] [Indexed: 11/07/2022]
Affiliation(s)
- Liangjun Zhao
- Department of Chemistry; Wayne State University; Detroit MI USA
| | | | | | - Whitney N. Wood
- Department of Chemistry; Wayne State University; Detroit MI USA
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15
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Baral B, Teixeira da Silva JA, Izaguirre-Mayoral ML. Early signaling, synthesis, transport and metabolism of ureides. JOURNAL OF PLANT PHYSIOLOGY 2016; 193:97-109. [PMID: 26967003 DOI: 10.1016/j.jplph.2016.01.013] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/13/2015] [Revised: 12/04/2015] [Accepted: 01/11/2016] [Indexed: 05/26/2023]
Abstract
The symbiosis between α nitrogen (N2)-fixing Proteobacteria (family Rhizobiaceae) and legumes belonging to the Fabaceae (a single phylogenetic group comprising three subfamilies: Caesalpinioideae, Mimosoideae and Papilionoideae) results in the formation of a novel root structure called a nodule, where atmospheric N2 is fixed into NH3(+). In the determinate type of nodules harbored by Rhizobium-nodulated Fabaceae species, newly synthesized NH3(+) is finally converted into allantoin (C4H6N4O3) and allantoic acid (C4H8N4O4) (ureides) through complex pathways involving at least 20 different enzymes that act synchronously in two types of nodule cells with contrasting ultrastructure, including the tree nodule cell organelles. Newly synthesized ureides are loaded into the network of nodule-root xylem vessels and transported to aerial organs by the transpirational water current. Once inside the leaves, ureides undergo an enzymatically driven reverse process to yield NH4(+) that is used for growth. This supports the role of ureides as key nitrogen (N)-compounds for the growth and yield of legumes nodulated by Rhizobium that grow in soils with a low N content. Thus, a concrete understanding of the mechanisms underlying ureide biogenesis and catabolism in legumes may help agrobiologists to achieve greater agricultural discoveries. In this review we focus on the transmembranal and transorganellar symplastic and apoplastic movement of N-precursors within the nodules, as well as on the occurrence, localization and properties of enzymes and genes involved in the biogenesis and catabolism of ureides. The synthesis and transport of ureides are not unique events in Rhizobium-nodulated N2-fixing legumes. Thus, a brief description of the synthesis and catabolism of ureides in non-legumes was included for comparison. The establishment of the symbiosis, nodule organogenesis and the plant's control of nodule number, synthesis and translocation of ureides via feed-back inhibition mechanisms are also reviewed.
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Affiliation(s)
- Bikash Baral
- Faculty of Agriculture and Forestry, University of Helsinki, P.O. Box 27, Latokartanonkaari 7, FIN-00014 Helsinki, Finland.
| | | | - Maria Luisa Izaguirre-Mayoral
- Biological Nitrogen Fixation Laboratory, Chemistry Department, Faculty of Science, Tshwane University of Technology, Private Bag X680, Pretoria 0001, South Africa.
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16
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Gee LB, Leontyev I, Stuchebrukhov A, Scott AD, Pelmenschikov V, Cramer SP. Docking and migration of carbon monoxide in nitrogenase: the case for gated pockets from infrared spectroscopy and molecular dynamics. Biochemistry 2015; 54:3314-9. [PMID: 25919807 DOI: 10.1021/acs.biochem.5b00216] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Evidence of a CO docking site near the FeMo cofactor in nitrogenase has been obtained by Fourier transform infrared spectroscopy-monitored low-temperature photolysis. We investigated the possible migration paths for CO from this docking site using molecular dynamics calculations. The simulations support the notion of a gas channel with multiple internal pockets from the active site to the protein exterior. Travel between pockets is gated by the motion of protein residues. Implications for the mechanism of nitrogenase reactions with CO and N2 are discussed.
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Affiliation(s)
- Leland B Gee
- †Department of Chemistry, University of California, Davis, California 95616, United States
| | - Igor Leontyev
- §InterX Inc., Berkeley, California 94710, United States
| | - Alexei Stuchebrukhov
- †Department of Chemistry, University of California, Davis, California 95616, United States
| | - Aubrey D Scott
- †Department of Chemistry, University of California, Davis, California 95616, United States
| | | | - Stephen P Cramer
- †Department of Chemistry, University of California, Davis, California 95616, United States.,‡Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
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17
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Hussein HA, Borrel A, Geneix C, Petitjean M, Regad L, Camproux AC. PockDrug-Server: a new web server for predicting pocket druggability on holo and apo proteins. Nucleic Acids Res 2015; 43:W436-42. [PMID: 25956651 PMCID: PMC4489252 DOI: 10.1093/nar/gkv462] [Citation(s) in RCA: 107] [Impact Index Per Article: 11.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2015] [Accepted: 04/27/2015] [Indexed: 12/21/2022] Open
Abstract
Predicting protein pocket's ability to bind drug-like molecules with high affinity, i.e. druggability, is of major interest in the target identification phase of drug discovery. Therefore, pocket druggability investigations represent a key step of compound clinical progression projects. Currently computational druggability prediction models are attached to one unique pocket estimation method despite pocket estimation uncertainties. In this paper, we propose ‘PockDrug-Server’ to predict pocket druggability, efficient on both (i) estimated pockets guided by the ligand proximity (extracted by proximity to a ligand from a holo protein structure) and (ii) estimated pockets based solely on protein structure information (based on amino atoms that form the surface of potential binding cavities). PockDrug-Server provides consistent druggability results using different pocket estimation methods. It is robust with respect to pocket boundary and estimation uncertainties, thus efficient using apo pockets that are challenging to estimate. It clearly distinguishes druggable from less druggable pockets using different estimation methods and outperformed recent druggability models for apo pockets. It can be carried out from one or a set of apo/holo proteins using different pocket estimation methods proposed by our web server or from any pocket previously estimated by the user. PockDrug-Server is publicly available at: http://pockdrug.rpbs.univ-paris-diderot.fr.
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Affiliation(s)
- Hiba Abi Hussein
- INSERM, UMRS-973, MTi, Université Paris Diderot, 35 Rue Hélène Brion, 75205 Paris Cedex 13, case courier 7113, Paris, France Université Paris Diderot, Sorbonne Paris Cité, UMRS-973, MTi, Paris, France
| | - Alexandre Borrel
- INSERM, UMRS-973, MTi, Université Paris Diderot, 35 Rue Hélène Brion, 75205 Paris Cedex 13, case courier 7113, Paris, France Université Paris Diderot, Sorbonne Paris Cité, UMRS-973, MTi, Paris, France Division of Pharmaceutical Chemistry, Faculty of pharmacy, University of Helsinki, Viikinkaari 9 (P.O. Box 56) FI-00014, Finland
| | - Colette Geneix
- INSERM, UMRS-973, MTi, Université Paris Diderot, 35 Rue Hélène Brion, 75205 Paris Cedex 13, case courier 7113, Paris, France Université Paris Diderot, Sorbonne Paris Cité, UMRS-973, MTi, Paris, France
| | - Michel Petitjean
- INSERM, UMRS-973, MTi, Université Paris Diderot, 35 Rue Hélène Brion, 75205 Paris Cedex 13, case courier 7113, Paris, France Université Paris Diderot, Sorbonne Paris Cité, UMRS-973, MTi, Paris, France
| | - Leslie Regad
- INSERM, UMRS-973, MTi, Université Paris Diderot, 35 Rue Hélène Brion, 75205 Paris Cedex 13, case courier 7113, Paris, France Université Paris Diderot, Sorbonne Paris Cité, UMRS-973, MTi, Paris, France
| | - Anne-Claude Camproux
- INSERM, UMRS-973, MTi, Université Paris Diderot, 35 Rue Hélène Brion, 75205 Paris Cedex 13, case courier 7113, Paris, France Université Paris Diderot, Sorbonne Paris Cité, UMRS-973, MTi, Paris, France
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18
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Borrel A, Regad L, Xhaard H, Petitjean M, Camproux AC. PockDrug: A Model for Predicting Pocket Druggability That Overcomes Pocket Estimation Uncertainties. J Chem Inf Model 2015; 55:882-95. [PMID: 25835082 DOI: 10.1021/ci5006004] [Citation(s) in RCA: 70] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
Predicting protein druggability is a key interest in the target identification phase of drug discovery. Here, we assess the pocket estimation methods' influence on druggability predictions by comparing statistical models constructed from pockets estimated using different pocket estimation methods: a proximity of either 4 or 5.5 Å to a cocrystallized ligand or DoGSite and fpocket estimation methods. We developed PockDrug, a robust pocket druggability model that copes with uncertainties in pocket boundaries. It is based on a linear discriminant analysis from a pool of 52 descriptors combined with a selection of the most stable and efficient models using different pocket estimation methods. PockDrug retains the best combinations of three pocket properties which impact druggability: geometry, hydrophobicity, and aromaticity. It results in an average accuracy of 87.9% ± 4.7% using a test set and exhibits higher accuracy (∼5-10%) than previous studies that used an identical apo set. In conclusion, this study confirms the influence of pocket estimation on pocket druggability prediction and proposes PockDrug as a new model that overcomes pocket estimation variability.
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Affiliation(s)
- Alexandre Borrel
- †INSERM, UMRS-973, MTi, Paris, France.,‡University Paris Diderot, Sorbonne Paris Cité, UMRS-973, MTi, Paris, France.,§University of Helsinki, Division of Pharmaceutical Chemistry, Faculty of Pharmacy, Helsinki, Finland
| | - Leslie Regad
- †INSERM, UMRS-973, MTi, Paris, France.,‡University Paris Diderot, Sorbonne Paris Cité, UMRS-973, MTi, Paris, France
| | - Henri Xhaard
- §University of Helsinki, Division of Pharmaceutical Chemistry, Faculty of Pharmacy, Helsinki, Finland
| | - Michel Petitjean
- †INSERM, UMRS-973, MTi, Paris, France.,‡University Paris Diderot, Sorbonne Paris Cité, UMRS-973, MTi, Paris, France
| | - Anne-Claude Camproux
- †INSERM, UMRS-973, MTi, Paris, France.,‡University Paris Diderot, Sorbonne Paris Cité, UMRS-973, MTi, Paris, France
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19
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Morrison CN, Hoy JA, Zhang L, Einsle O, Rees DC. Substrate pathways in the nitrogenase MoFe protein by experimental identification of small molecule binding sites. Biochemistry 2015; 54:2052-60. [PMID: 25710326 PMCID: PMC4590346 DOI: 10.1021/bi501313k] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
![]()
In
the nitrogenase molybdenum-iron (MoFe) protein, we have identified
five potential substrate access pathways from the protein surface
to the FeMo-cofactor (the active site) or the P-cluster using experimental
structures of Xe pressurized into MoFe protein crystals from Azotobacter vinelandii and Clostridium pasteurianum. Additionally, all published structures of the MoFe protein, including
those from Klebsiella pneumoniae, were analyzed for
the presence of nonwater, small molecules bound to the protein interior.
Each pathway is based on identification of plausible routes from buried
small molecule binding sites to both the protein surface and a metallocluster.
Of these five pathways, two have been previously suggested as substrate
access pathways. While the small molecule binding sites are not conserved
among the three species of MoFe protein, residues lining the pathways
are generally conserved, indicating that the proposed pathways may
be accessible in all three species. These observations imply that
there is unlikely a unique pathway utilized for substrate access from
the protein surface to the active site; however, there may be preferred
pathways such as those described here.
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Affiliation(s)
- Christine N Morrison
- †Division of Chemistry and Chemical Engineering, California Institute of Technology 114-96, Pasadena, California 91125, United States
| | - Julie A Hoy
- †Division of Chemistry and Chemical Engineering, California Institute of Technology 114-96, Pasadena, California 91125, United States
| | - Limei Zhang
- †Division of Chemistry and Chemical Engineering, California Institute of Technology 114-96, Pasadena, California 91125, United States
| | - Oliver Einsle
- ‡Institut für Biochemie and BIOSS Centre for Biological Signaling Studies, Albert-Ludwigs-Universität Freiburg, 79104 Freiburg, Germany
| | - Douglas C Rees
- †Division of Chemistry and Chemical Engineering, California Institute of Technology 114-96, Pasadena, California 91125, United States.,§Howard Hughes Medical Institute, California Institute of Technology, Pasadena, California 91125, United States
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20
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Kingsley LJ, Lill MA. Substrate tunnels in enzymes: structure-function relationships and computational methodology. Proteins 2015; 83:599-611. [PMID: 25663659 DOI: 10.1002/prot.24772] [Citation(s) in RCA: 99] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2014] [Revised: 01/08/2015] [Accepted: 01/14/2015] [Indexed: 12/14/2022]
Abstract
In enzymes, the active site is the location where incoming substrates are chemically converted to products. In some enzymes, this site is deeply buried within the core of the protein, and, in order to access the active site, substrates must pass through the body of the protein via a tunnel. In many systems, these tunnels act as filters and have been found to influence both substrate specificity and catalytic mechanism. Identifying and understanding how these tunnels exert such control has been of growing interest over the past several years because of implications in fields such as protein engineering and drug design. This growing interest has spurred the development of several computational methods to identify and analyze tunnels and how ligands migrate through these tunnels. The goal of this review is to outline how tunnels influence substrate specificity and catalytic efficiency in enzymes with buried active sites and to provide a brief summary of the computational tools used to identify and evaluate these tunnels.
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Affiliation(s)
- Laura J Kingsley
- Department of Medicinal Chemistry and Molecular Pharmacology, College of Pharmacy, Purdue University, West Lafayette, Indiana
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21
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Wang Y, Li H, Shi Y. Evidence for hydrogen-bonded ammonia wire influencing the ESMPT process of the 7-hydroxy-4-methylcoumarin·(NH3)3 cluster. NEW J CHEM 2015. [DOI: 10.1039/c5nj01079a] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The different types of excited-state hydrogen-bonded dynamics mechanisms orderly provide two driving forces for the excited-state multiple proton transfer (ESMPT) reaction of the 7H4MC·(NH3)3 cluster.
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Affiliation(s)
- Ye Wang
- Institute of Atomic and Molecular Physics
- Jilin University
- Changchun 130012
- China
| | - Hui Li
- Institute of Atomic and Molecular Physics
- Jilin University
- Changchun 130012
- China
| | - Ying Shi
- Institute of Atomic and Molecular Physics
- Jilin University
- Changchun 130012
- China
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22
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Dance I. The pathway for serial proton supply to the active site of nitrogenase: enhanced density functional modeling of the Grotthuss mechanism. Dalton Trans 2015; 44:18167-86. [DOI: 10.1039/c5dt03223g] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Proton translocation along a chain of eight waters to the active site of nitrogenase is described in detail, using density functional simulations with a 269 atom system that includes surrounding amino acids.
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Affiliation(s)
- Ian Dance
- School of Chemistry
- UNSW Australia
- Sydney 2052
- Australia
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23
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Dance I. Misconception of reductive elimination of H2, in the context of the mechanism of nitrogenase. Dalton Trans 2015; 44:9027-37. [DOI: 10.1039/c5dt00771b] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Calculated atom partial charges reveal misconceptions of reductive elimination of H2.
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Affiliation(s)
- Ian Dance
- School of Chemistry
- University of New South Wales
- Sydney 2052
- Australia
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24
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Smith D, Danyal K, Raugei S, Seefeldt LC. Substrate channel in nitrogenase revealed by a molecular dynamics approach. Biochemistry 2014; 53:2278-85. [PMID: 24654842 DOI: 10.1021/bi401313j] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Mo-dependent nitrogenase catalyzes the biological reduction of N2 to two NH3 molecules at FeMo-cofactor buried deep inside the MoFe protein. Access of substrates, such as N2, to the active site is likely restricted by the surrounding protein, requiring substrate channels that lead from the surface to the active site. Earlier studies on crystallographic structures of the MoFe protein have suggested three putative substrate channels. Here, we have utilized submicrosecond atomistic molecular dynamics simulations to allow the nitrogenase MoFe protein to explore its conformational space in an aqueous solution at physiological ionic strength, revealing a putative substrate channel. The viability of this observed channel was tested by examining the free energy of passage of N2 from the surface through the channel to FeMo-cofactor, resulting in the discovery of a very low energy barrier. These studies point to a viable substrate channel in nitrogenase that appears during thermal motions of the protein in an aqueous environment and that approaches a face of FeMo-cofactor earlier implicated in substrate binding.
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Affiliation(s)
- Dayle Smith
- Pacific Northwestern National Laboratory , Richland, Washington 99352, United States
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