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The ability of charged Mg2+ to acidify H2O to form OH- proves critical for both proton transfers, where only the second occurs to the leaving group

Quantum chemical studies of intermediates and reaction pathways in selected enzymes and catalytic synthetic systems.

CHEMICAL REVIEWS, no. 2 (2004): 459-508

Cited by: 309|Views10
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Abstract

Department of Molecular Biology TPC-15, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, Johnson & Johnson Pharmaceutical Research and Development LLC, Welsh and McKean Roads, P.O. Box 776, Spring House, Pennsylvania 19477, and Theoretical Chemistry, Department of Biotechnology, Royal Institute of...More

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Introduction
  • At the University of Washington and at VU, Amsterdam, he developed a connection between density functional theory and the theory of broken symmetry, which he and collaborators applied to iron−sulfur clusters and proteins
  • His current research interests include electron-transfer and protontransfer energetics, reaction pathways in metalloenzymes, optical, Mossbauer, and ENDOR spectroscopy, magnetism in transition metal complexes, photochemistry, and click chemistry.
  • In both enzymatic and effective synthetic catalysts, the match between substrate and catalyst leads to both control and reactivity
Highlights
  • Louis Noodleman was born in Dayton, Ohio, (1950) grew up in Ohio and Virginia, and received his college education starting at Virginia Polytechnic Institute and at the Massachusetts Institute of Technology (MIT), B.S., in Physics, 1971, and Ph.D. in Materials Science, 1975, with K
  • An unusual example of versatility is observed in the enzymes galactose oxidase and cytochrome c oxidase, where tyrosine side chains at the active site are modified by covalent linkage to the cysteine and histidine side chains, respectively.15a-d This covalent linkage, in conjunction with coordination to the metal ion (Cu(II)), may modulate the energetics of tyrosine radical formation during the catalytic cycle.15a-d
  • An inactive form (X) of MnSOD has been observed in the second half of the catalytic cycle, as depicted in Scheme 8.147 During our density functional theory (DFT) geometry optimizations on the larger Mn3+(H2O)Superoxide dismutase (SOD) active site clusters,[42] we found that one of the protons of the water ligand, which originally H-bonded to the atom Oδ1 of the Asp ligand, gradually moved closer to Oδ1 and transferred to Oδ1
  • We have currently examined a model[234] containing the core structural features proposed by Burdi et al.230e consisting of a μ-oxo bridge, a terminal protonated oxygen ligand bound to the iron nearest Tyr[122], and a mono-oxygen bridge from Glu[238] in the core structure of X
  • The ability of charged Mg2+ to acidify H2O to form OH- proves critical for both proton transfers, where only the second occurs to the leaving group
Methods
  • Application of the variational principle yields a set of mean field one-electron equations giving one-electron energies and orbitals as well as the corresponding self-consistent-field (SCF) potential(s).
  • These SCF potentials are orbital dependent for hybrid potentials, while for “pure” DFT-GGA methods, all one-electron orbitals with the same spin share the same SCF potential.
  • For a discussion of both the fundamental and the practical aspects of using DFT methods, the authors refer to a very extensive literature.[19,26]
Results
  • Because mitochondria use over 90% of the cell’s oxygen, the mitochondrial electron transport chain produces a large quantity of oxygen radicals, and MnSOD is a primary biological defense against radical damage.[139,142,143].
Conclusion
  • Summary and Outlook

    In this work, the authors have provided a guided tour of high level quantum chemical studies of reaction mechanisms, and an assessment of related problems of intermediates and transition states for a wide variety of metalloenzymes.

    Some valuable parallels can be drawn between the mechanisms of protein tyrosine phosphatases (PTPases) and ribozyme chemistry.
  • In the Mg2+ aquo-catalyzed hammerhead ribozyme phosphate hydrolysis reaction, there is an associative transition state to a pentacoordinate (PO5) intermediate, with an early proton transfer, the first of two proton transfers overall.
  • These mechanisms look quite different, and yet there are some common themes.
  • The ability of charged Mg2+ to acidify H2O to form OH- proves critical for both proton transfers, where only the second occurs to the leaving group
Tables
  • Table1: Computational and Experimental Results of the Intramolecular [2+3] Cycloaddition of Scheme 7
  • Table2: Rate Constants for Catalysis by MnSOD from
  • Table3: Averaged Bond Distances (Å) of the FeMocoX (X ) C4-, N3-, O2-) Coresa bond
  • Table4: Calculated Redox Potentials (V) for Redox Transition (Oxidized FeMoco + e- f Resting FeMoco)
  • Table5: Gas-Phase and Protein Interaction Energies of the FeMoco Oxidation States oxidation states
  • Table6: Experimental and Calculated 57Fe Isomer Shifts (mm s-1) for the FeMoco Cluster oxidation state total chargea range
  • Table7: Calculated Net Spin Density for the Central Anion of FeMoco
Download tables as Excel
Funding
  • We thank the NIH for financial support (grants GM43278 and GM39914, and for earlier support GM50154)
  • F.H. thanks the Wenner-Gren Foundations for financial support
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