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Jiang H, Ryde U. Thermodynamically Favourable States in the Reaction of Nitrogenase without Dissociation of any Sulfide Ligand. Chemistry 2022; 28:e202103933. [PMID: 35006641 PMCID: PMC9305431 DOI: 10.1002/chem.202103933] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2021] [Indexed: 12/16/2022]
Abstract
We have used combined quantum mechanical and molecular mechanical (QM/MM) calculations to study the reaction mechanism of nitrogenase, assuming that none of the sulfide ligands dissociates. To avoid the problem that there is no consensus regarding the structure and protonation of the E4 state, we start from a state where N2 is bound to the cluster and is protonated to N2H2, after dissociation of H2. We show that the reaction follows an alternating mechanism with HNNH (possibly protonated to HNNH2) and H2NNH2 as intermediates and the two NH3 products dissociate at the E7 and E8 levels. For all intermediates, coordination to Fe6 is preferred, but for the E4 and E8 intermediates, binding to Fe2 is competitive. For the E4, E5 and E7 intermediates we find that the substrate may abstract a proton from the hydroxy group of the homocitrate ligand of the FeMo cluster, thereby forming HNNH2, H2NNH2 and NH3 intermediates. This may explain why homocitrate is a mandatory component of nitrogenase. All steps in the suggested reaction mechanism are thermodynamically favourable compared to protonation of the nearby His‐195 group and in all cases, protonation of the NE2 atom of the latter group is preferred.
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Affiliation(s)
- Hao Jiang
- Department of Theoretical Chemistry, Lund University Chemical Centre, P. O. Box 124, 221 00, Lund, Sweden
| | - Ulf Ryde
- Department of Theoretical Chemistry, Lund University Chemical Centre, P. O. Box 124, 221 00, Lund, Sweden
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2
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Nicolet Y, Cherrier MV, Amara P. Radical SAM Enzymes and Metallocofactor Assembly: A Structural Point of View. ACS BIO & MED CHEM AU 2022; 2:36-52. [PMID: 37102176 PMCID: PMC10114646 DOI: 10.1021/acsbiomedchemau.1c00044] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
This Review focuses on the structure-function relationship of radical S-adenosyl-l-methionine (SAM) enzymes involved in the assembly of metallocofactors corresponding to the active sites of [FeFe]-hydrogenase and nitrogenase [MoFe]-protein. It does not claim to correspond to an extensive review on the assembly machineries of these enzyme active sites, for which many good reviews are already available, but instead deals with the contribution of structural data to the understanding of their chemical mechanism (Buren et al. Chem. Rev.2020, 142 ( (25), ) 11006-11012; Britt et al. Chem. Sci.2020, 11 ( (38), ), 10313-10323). Hence, we will present the history and current knowledge about the radical SAM maturases HydE, HydG, and NifB as well as what, in our opinion, should be done in the near future to overcome the existing barriers in our understanding of this fascinating chemistry that intertwine organic radicals and organometallic complexes.
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Affiliation(s)
- Yvain Nicolet
- Univ. Grenoble Alpes, CEA, CNRS, IBS, Metalloproteins Unit, F-38000 Grenoble, France
| | - Mickael V. Cherrier
- Univ. Grenoble Alpes, CEA, CNRS, IBS, Metalloproteins Unit, F-38000 Grenoble, France
| | - Patricia Amara
- Univ. Grenoble Alpes, CEA, CNRS, IBS, Metalloproteins Unit, F-38000 Grenoble, France
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3
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Yu H, Zhang Q, Xu J, Wang X, Luo L. Assessment of density functional theory in studying on the transition states of a Diiron-mediated N N bond cleavage reaction. COMPUT THEOR CHEM 2021. [DOI: 10.1016/j.comptc.2021.113418] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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4
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Cao L, Ryde U. Putative reaction mechanism of nitrogenase after dissociation of a sulfide ligand. J Catal 2020. [DOI: 10.1016/j.jcat.2020.08.028] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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5
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Cao L, Ryde U. N 2H 2 binding to the nitrogenase FeMo cluster studied by QM/MM methods. J Biol Inorg Chem 2020; 25:521-540. [PMID: 32266560 PMCID: PMC7186253 DOI: 10.1007/s00775-020-01780-5] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2019] [Accepted: 03/25/2020] [Indexed: 12/15/2022]
Abstract
We have made a systematic combined quantum mechanical and molecular mechanical (QM/MM) investigation of possible structures of the N2 bound state of nitrogenase. We assume that N2 is immediately protonated to a N2H2 state, thereby avoiding the problem of determining the position of the protons in the cluster. We have systematically studied both end-on and side-on structures, as well as both HNNH and NNH2 states. Our results indicate that the binding of N2H2 is determined more by interactions and steric clashes with the surrounding protein than by the intrinsic preferences of the ligand and the cluster. The best binding mode with both the TPSS and B3LYP density-functional theory methods has trans-HNNH terminally bound to Fe2. It is stabilised by stacking of the substrate with His-195 and Ser-278. However, several other structures come rather close in energy (within 3-35 kJ/mol) at least in some calculations: The corresponding cis-HNNH structure terminally bound to Fe2 is second best with B3LYP. A structure with HNNH2 terminally bound to Fe6 is second most stable with TPSS (where the third proton is transferred to the substrate from the homocitrate ligand). Structures with trans-HNNH, bound to Fe4 or Fe6, or cis-HNNH bound to Fe6 are also rather stable. Finally, with the TPSS functional, a structure with cis-HNNH side-on binding to the Fe3-Fe4-Fe5-Fe7 face of the cluster is also rather low in energy, but all side-on structures are strongly disfavoured by the B3LYP method.
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Affiliation(s)
- Lili Cao
- Department of Theoretical Chemistry, Chemical Centre, Lund University, P. O. Box 124, 221 00, Lund, Sweden
| | - Ulf Ryde
- Department of Theoretical Chemistry, Chemical Centre, Lund University, P. O. Box 124, 221 00, Lund, Sweden.
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6
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Abstract
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Nitrogenase
is the only enzyme that can cleave the strong triple
bond in N2. The active site contains a complicated MoFe7S9C cluster. It is believed that it needs to accept
four protons and electrons, forming the E4 state, before
it can bind N2. However, there is no consensus on the atomic
structure of the E4 state. Experimental studies indicate
that it should contain two hydride ions bridging two pairs of Fe ions,
and it has been suggested that both hydride ions as well as the two
protons bind on the same face of the cluster. On the other hand, density
functional theory (DFT) studies have indicated that it is energetically
more favorable with either three hydride ions or with a triply protonated
carbide ion, depending on the DFT functional. We have performed a
systematic combined quantum mechanical and molecular mechanical (QM/MM)
study of possible E4 states with two bridging hydride ions.
Our calculations suggest that the most favorable structure has hydride
ions bridging the Fe2/6 and Fe3/7 ion pairs. In fact, such structures
are 14 kJ/mol more stable than structures with three hydride ions,
showing that pure DFT functionals give energetically most favorable
structures in agreement with experiments. An important reason for
this finding is that we have identified a new type of broken-symmetry
state that involves only two Fe ions with minority spin, in contrast
to the previously studied states with three Fe ions with minority
spin. The energetically best structures have the two hydride ions
on different faces of the FeMo cluster, whereas better agreement with
ENDOR data is obtained if they are on the same face; such structures
are only 6–22 kJ/mol less stable.
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Affiliation(s)
- Lili Cao
- Department of Theoretical Chemistry, Lund University, Chemical Centre, P.O. Box 124, SE-221 00 Lund, Sweden
| | - Ulf Ryde
- Department of Theoretical Chemistry, Lund University, Chemical Centre, P.O. Box 124, SE-221 00 Lund, Sweden
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7
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Cao L, Ryde U. Extremely large differences in DFT energies for nitrogenase models. Phys Chem Chem Phys 2019; 21:2480-2488. [PMID: 30652711 DOI: 10.1039/c8cp06930a] [Citation(s) in RCA: 50] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Nitrogenase is the only enzyme that can cleave the triple bond in N2, making nitrogen avaiable for other organisms. It contains a complicated MoFe7S9C(homocitrate) cluster in its active site. Many computational studies with density-functional theory (DFT) of the nitrogenase enzyme have been presented, but they do not show any consensus - they do not even agree where the first four protons should be added, forming the central intermediate E4. We show that the prime reason for this is that different DFT methods give relative energies that differ by almost 600 kJ mol-1 for different protonation states. This is 4-30 times more than what is observed for other systems. The reason for this is that in some structures, the hydrogens bind to sulfide or carbide ions as protons, whereas in other structures they bind to the metals as hydride ions, changing the oxidation state of the metals, as well as the Fe-C, Fe-S and Fe-Fe distances. The energies correlate with the amount of Hartree-Fock exchange in the method, indicating a variation in the amount of static correlation in the structures. It is currently unclear which DFT method gives the best results for nitrogenase. We show that non-hybrid DFT functionals and TPSSh give the most accurate structures of the resting active site, whereas B3LYP and PBE0 give the best H2 dissociation energies. However, no DFT method indicates that a structure of E4 with two bridging hydride ions is lowest in energy, as spectroscopic experiments indicate.
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Affiliation(s)
- Lili Cao
- Department of Theoretical Chemistry, Lund University, P. O. Box 124, SE-221 00 Lund, Sweden.
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8
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Liu J, Lai J, Qi L, Liu X, Zhang L, Li Y. Theoretical Study on the Catalytic Oxidation of
p
‐Iodophenol by Horseradish Peroxidase in a Chemiluminescent System. ChemistrySelect 2018. [DOI: 10.1002/slct.201802123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Jian Liu
- School of Control Science and EngineeringShandong University 17923 Jingshi Road, Jinan, Shandong, P.R. China
| | - Jiahui Lai
- School of Control Science and EngineeringShandong University 17923 Jingshi Road, Jinan, Shandong, P.R. China
| | - Liguo Qi
- Taian City Central Hospital 29 Longtan Road, Taian Shandong, P.R. China
| | - Xiumei Liu
- School of Pharmaceutical SciencesShandong University 44 Wenhua West Road Jinan, Shandong, P.R. China
| | - Lili Zhang
- School of Mechanical and Automotive EngineeringQilu University of Technology 3501 Daxue Road, Jinan Shandong, P.R. China
| | - Yibin Li
- School of Control Science and EngineeringShandong University 17923 Jingshi Road, Jinan, Shandong, P.R. China
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9
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Cao L, Caldararu O, Ryde U. Protonation and Reduction of the FeMo Cluster in Nitrogenase Studied by Quantum Mechanics/Molecular Mechanics (QM/MM) Calculations. J Chem Theory Comput 2018; 14:6653-6678. [DOI: 10.1021/acs.jctc.8b00778] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Lili Cao
- Department of Theoretical Chemistry, Lund University, Chemical Centre, P.O. Box 124, SE-221 00 Lund, Sweden
| | - Octav Caldararu
- Department of Theoretical Chemistry, Lund University, Chemical Centre, P.O. Box 124, SE-221 00 Lund, Sweden
| | - Ulf Ryde
- Department of Theoretical Chemistry, Lund University, Chemical Centre, P.O. Box 124, SE-221 00 Lund, Sweden
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10
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Benediktsson B, Bjornsson R. QM/MM Study of the Nitrogenase MoFe Protein Resting State: Broken-Symmetry States, Protonation States, and QM Region Convergence in the FeMoco Active Site. Inorg Chem 2017; 56:13417-13429. [DOI: 10.1021/acs.inorgchem.7b02158] [Citation(s) in RCA: 57] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Bardi Benediktsson
- Science Institute, University of Iceland, Dunhagi 3, 107 Reykjavik, Iceland
| | - Ragnar Bjornsson
- Science Institute, University of Iceland, Dunhagi 3, 107 Reykjavik, Iceland
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11
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Cao L, Caldararu O, Ryde U. Protonation States of Homocitrate and Nearby Residues in Nitrogenase Studied by Computational Methods and Quantum Refinement. J Phys Chem B 2017; 121:8242-8262. [DOI: 10.1021/acs.jpcb.7b02714] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Lili Cao
- Department of Theoretical
Chemistry, Lund University, Chemical Centre, P.O. Box 124, SE-221 00 Lund, Sweden
| | - Octav Caldararu
- Department of Theoretical
Chemistry, Lund University, Chemical Centre, P.O. Box 124, SE-221 00 Lund, Sweden
| | - Ulf Ryde
- Department of Theoretical
Chemistry, Lund University, Chemical Centre, P.O. Box 124, SE-221 00 Lund, Sweden
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12
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McKee ML. A New Nitrogenase Mechanism Using a CFe8S9 Model: Does H2 Elimination Activate the Complex to N2 Addition to the Central Carbon Atom? J Phys Chem A 2016; 120:754-64. [PMID: 26821350 DOI: 10.1021/acs.jpca.5b10384] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
A truncated model of the FeMo cofactor is used to explore a new mechanism for the conversion of N2 to NH3 by the nitrogenase enzyme. After four initial protonation/reduction steps, the H4CFe8S9 cluster has two hydrogen atoms attached to sulfur, one hydrogen bridging two iron centers and one hydrogen bonded to carbon. The loss of the CH and FeHFe hydrogens as molecular hydrogen activates the cluster to addition of N2 to the carbon center. This unique step takes place at a nearly planar four-coordinate carbon center and leads to an intermediate with a significantly weakened N-N bond. A hydrogen attached to a sulfur atom is then transferred to the distal nitrogen atom. Additional prontonation/reduction steps are modeled by adding a hydrogen atom to sulfur and locating the transition states for transfer to nitrogen. The first NH3 is lost in a thermal neutral step, while the second step is endothermic. The loss of H2 activates the complex by reducing the barrier for N2 addition by 3.5 kcal/mol. Since this is the most difficult step in the mechanism, reducing the barrier for this step justifies the "extra expense" of H2 production.
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Affiliation(s)
- Michael L McKee
- Department of Chemistry and Biochemistry, Auburn University , Auburn, Alabama 36849, United States
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13
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Wiig JA, Lee CC, Hu Y, Ribbe MW. Tracing the interstitial carbide of the nitrogenase cofactor during substrate turnover. J Am Chem Soc 2013; 135:4982-3. [PMID: 23514429 DOI: 10.1021/ja401698d] [Citation(s) in RCA: 55] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The fate of the interstitial atom of the nitrogenase cofactor during substrate turnover has remained a topic of interest since the discovery of this atom more than a decade ago. In this study, we labeled the interstitial carbide atom with (14)C and (13)C isotopes and traced the fate of the isotope under turnover conditions. Our results show that the interstitial carbide cannot be exchanged upon turnover, nor can it be used as a substrate and incorporated into the products. These observations point to a role of the interstitial carbide in stabilizing the cofactor structure, although a function of this atom in indirectly modulating the reactivity of the cofactor or directly interacting with the substrate cannot be excluded.
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Affiliation(s)
- Jared A Wiig
- Department of Molecular Biology and Biochemistry, University of California, Irvine , California 92697-3900, United States
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14
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Abstract
Molecular dynamics simulations of biomolecules have matured into powerful tools of structural biology. In addition to the commonly used empirical force field potentials, quantum mechanical descriptions are gaining popularity for structure optimization and dynamic simulations of peptides and proteins. In this chapter, we introduce methodological developments such as the QM/MM framework and linear-scaling QM that make efficient calculations on large biomolecules possible. We identify the most common scenarios in which quantum descriptions of peptides and proteins are employed, such as structural refinement, force field development, treatment of unusual residues, and predicting spectroscopic and exited state properties. The benefits and shortcomings of QM potentials, in comparison to classical force fields, are discussed, with special emphasis on the sampling problems of protein conformational space. Finally, recent examples of QM/MM calculations in light-sensitive membrane proteins illustrate typical applications of the reviewed methods.
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Affiliation(s)
- Thomas Steinbrecher
- Institute of Physical Chemistry, Karlsruhe Institute of Technology, Karlsruhe, Germany
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15
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16
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Luo Y, Li Y, Yu H, Zhao J, Chen Y, Hou Z, Qu J. DFT Studies on the Reduction of Dinitrogen to Ammonia by a Thiolate-Bridged Diiron Complex as a Nitrogenase Mimic. Organometallics 2011. [DOI: 10.1021/om200950q] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Yi Luo
- State Key Laboratory of Fine
Chemicals, School of Pharmaceutical
Science and Technology, Dalian University of Technology, Dalian 116024, People's Republic of China
| | - Yang Li
- State Key Laboratory of Fine
Chemicals, School of Pharmaceutical
Science and Technology, Dalian University of Technology, Dalian 116024, People's Republic of China
| | - Hang Yu
- State Key Laboratory of Fine
Chemicals, School of Pharmaceutical
Science and Technology, Dalian University of Technology, Dalian 116024, People's Republic of China
| | - Jinfeng Zhao
- State Key Laboratory of Fine
Chemicals, School of Pharmaceutical
Science and Technology, Dalian University of Technology, Dalian 116024, People's Republic of China
| | - Yanhui Chen
- State Key Laboratory of Fine
Chemicals, School of Pharmaceutical
Science and Technology, Dalian University of Technology, Dalian 116024, People's Republic of China
| | - Zhaomin Hou
- State Key Laboratory of Fine
Chemicals, School of Pharmaceutical
Science and Technology, Dalian University of Technology, Dalian 116024, People's Republic of China
- Organometallic Chemistry Laboratory, RIKEN Advanced Science Institute, 2-1 Hirosawa, Wako,
Saitama 351-0198, Japan
| | - Jingping Qu
- State Key Laboratory of Fine
Chemicals, School of Pharmaceutical
Science and Technology, Dalian University of Technology, Dalian 116024, People's Republic of China
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18
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Gerlach DL, Lehnert N. Fischer-Tropsch chemistry at room temperature? Angew Chem Int Ed Engl 2011; 50:7984-6. [PMID: 21761528 DOI: 10.1002/anie.201102979] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2011] [Indexed: 11/06/2022]
Abstract
The unique catalytic activity of vanadium nitrogenase suggests a new direction for the direct production of biofuels from CO with either synthetic catalysts or nitrogenase-containing bacteria. The reduction of CO by V nitrogenase to light hydrocarbons shows striking similarities to the established Fischer-Tropsch process; however, the enzyme does not use H(2) directly for this reaction. ADP=adenosine diphosphate, ATP= adenosine triphosphate.
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Affiliation(s)
- Deidra L Gerlach
- Department of Chemistry, University of Michigan, Ann Arbor, 48109, USA
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20
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Harris TV, Szilagyi RK. Nitrogenase structure and function relationships by density functional theory. Methods Mol Biol 2011; 766:267-291. [PMID: 21833874 DOI: 10.1007/978-1-61779-194-9_18] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
Modern density functional theory has tremendous potential with matching popularity in metalloenzymology to reveal the unseen atomic and molecular details of structural data, spectroscopic measurements, and biochemical experiments by providing insights into unobservable structures and states, while also offering theoretical justifications for observed trends and differences. An often untapped potential of this theoretical approach is to bring together diverse experimental structural and reactivity information and allow for these to be critically evaluated at the same level. This is particularly applicable for the tantalizingly complex problem of the structure and molecular mechanism of biological nitrogen fixation. In this chapter we provide a review with extensive practical details of the compilation and evaluation of experimental data for an unbiased and systematic density functional theory analysis that can lead to remarkable new insights about the structure-function relationships of the iron-sulfur clusters of nitrogenase.
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Affiliation(s)
- Travis V Harris
- Department of Chemistry and Biochemistry, Astrobiology Biogeochemistry Research Center, Montana State University, Bozeman, MT 59717, USA.
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21
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Dance I. Electronic Dimensions of FeMo-co, the Active Site of Nitrogenase, and Its Catalytic Intermediates. Inorg Chem 2010; 50:178-92. [DOI: 10.1021/ic1015884] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Affiliation(s)
- Ian Dance
- School of Chemistry, University of New South Wales, Sydney 2052, Australia
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22
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Xie H, Cao Z. Enzymatic Reduction of Nitrate to Nitrite: Insight from Density Functional Calculations. Organometallics 2009. [DOI: 10.1021/om9008197] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Affiliation(s)
- Hujun Xie
- Department of Applied Chemistry, School of Food Science and Biotechnology, Zhejiang Gongshang University, Hangzhou 310035, People's Republic of China
| | - Zexing Cao
- Department of Chemistry and State Key Laboratory of Physical Chemistry of Solid Surfaces, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, People's Republic of China
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