Quantum Chemical Studies of Intermediates and Reaction Pathways in Selected Enzymes and Catalytic Synthetic Systems

Noodleman, Louis; Lovell, Timothy; Han, Weiwei; Li, Jian; Himo, Fahmi

doi:10.1021/cr020625a

Cited by 353 publications

(303 citation statements)

References 396 publications

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“…A number of reviews of enzyme kinetics are available, with emphasis on one or more aspects. 1,7,8,[11][12][13][14]18,[23][24][25][26][27][28][29][30][31][32][33][34][35][36][37][38][39][40][41][42]44,46,48,49,63,84,94,95,124,143,144,179,[232][233][234][235][236] In this section, we provide a few remarks about the most relevant previous reviews.…”

Section: Previous Reviewsmentioning

confidence: 99%

Multidimensional Tunneling, Recrossing, and the Transmission Coefficient for Enzymatic Reactions

2006

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Section: Previous Reviewsmentioning

confidence: 99%

Multidimensional Tunneling, Recrossing, and the Transmission Coefficient for Enzymatic Reactions

2006

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“…This methodology provides an accurate description of geometry and electronic environment in the TS, and has been used extensively in studies of enzyme catalysis 13. We computed a QM model of the TS for RhoA based on the 1ow3 structure by substituting the MgF 3 − core by a trigonal planar PO 3 − moiety with starting P−O bonds 1.71 Å.…”

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confidence: 99%

¹⁹F NMR and DFT Analysis Reveal Structural and Electronic Transition State Features for RhoA‐Catalyzed GTP Hydrolysis

et al. 2016

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Molecular details for RhoA/GAP catalysis of the hydrolysis of GTP to GDP are poorly understood. We use 19F NMR chemical shifts in the MgF3 − transition state analogue (TSA) complex as a spectroscopic reporter to indicate electron distribution for the γ‐PO3 − oxygens in the corresponding TS, implying that oxygen coordinated to Mg has the greatest electron density. This was validated by QM calculations giving a picture of the electronic properties of the transition state (TS) for nucleophilic attack of water on the γ‐PO3 − group based on the structure of a RhoA/GAP‐GDP‐MgF3 − TSA complex. The TS model displays a network of 20 hydrogen bonds, including the GAP Arg85′ side chain, but neither phosphate torsional strain nor general base catalysis is evident. The nucleophilic water occupies a reactive location different from that in multiple ground state complexes, arising from reorientation of the Gln‐63 carboxamide by Arg85′ to preclude direct hydrogen bonding from water to the target γ‐PO3 − group.

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“…FeMoco consists of fused [Mo-3Fe-3S] and [4Fe-3S] subcubanes that are bridged by three additional sulfides and share a central 6 -light atom of unknown identity (see Fig. 1) (6)(7)(8). At the cluster termini, FeMoco is externally coordinated by two protein residues and an organic homocitrate entity.…”

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Structural insights into a protein-bound iron-molybdenum cofactor precursor

Corbett

Fay

et al. 2006

Proc. Natl. Acad. Sci. U.S.A.

101

106

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The iron-molybdenum cofactor (FeMoco) of the nitrogenase MoFe protein is a highly complex metallocluster that provides the catalytically essential site for biological nitrogen fixation. FeMoco is assembled outside the MoFe protein in a stepwise process requiring several components, including NifB-co, an iron-and sulfurcontaining FeMoco precursor, and NifEN, an intermediary assembly protein on which NifB-co is presumably converted to FeMoco. Through the comparison of Azotobacter vinelandii strains expressing the NifEN protein in the presence or absence of the nifB gene, the structure of a NifEN-bound FeMoco precursor has been analyzed by x-ray absorption spectroscopy. The results provide physical evidence to support a mechanism for FeMoco biosynthesis. The NifEN-bound precursor is found to be a molybdenum-free analog of FeMoco and not one of the more commonly suggested cluster types based on a standard [4Fe-4S] architecture. A facile scheme by which FeMoco and alternative, non-molybdenum-containing nitrogenase cofactors are constructed from this common precursor is presented that has important implications for the biosynthesis and biomimetic chemical synthesis of FeMoco.biosynthesis ͉ extended x-ray absorption fine structure ͉ nitrogenase ͉ x-ray absorption spectroscopy

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Quantum Chemical Studies of Intermediates and Reaction Pathways in Selected Enzymes and Catalytic Synthetic Systems

Cited by 353 publications

References 396 publications

Multidimensional Tunneling, Recrossing, and the Transmission Coefficient for Enzymatic Reactions

Multidimensional Tunneling, Recrossing, and the Transmission Coefficient for Enzymatic Reactions

¹⁹F NMR and DFT Analysis Reveal Structural and Electronic Transition State Features for RhoA‐Catalyzed GTP Hydrolysis

Structural insights into a protein-bound iron-molybdenum cofactor precursor

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Quantum Chemical Studies of Intermediates and Reaction Pathways in Selected Enzymes and Catalytic Synthetic Systems

Cited by 353 publications

References 396 publications

Multidimensional Tunneling, Recrossing, and the Transmission Coefficient for Enzymatic Reactions

Multidimensional Tunneling, Recrossing, and the Transmission Coefficient for Enzymatic Reactions

19F NMR and DFT Analysis Reveal Structural and Electronic Transition State Features for RhoA‐Catalyzed GTP Hydrolysis

Structural insights into a protein-bound iron-molybdenum cofactor precursor

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¹⁹F NMR and DFT Analysis Reveal Structural and Electronic Transition State Features for RhoA‐Catalyzed GTP Hydrolysis