Stanford Advisors

All Publications

  • Formylglycine-generating enzyme binds substrate directly at a mononuclear Cu(I) center to initiate O2 activation. Proceedings of the National Academy of Sciences of the United States of America Appel, M. J., Meier, K. K., Lafrance-Vanasse, J., Lim, H., Tsai, C., Hedman, B., Hodgson, K. O., Tainer, J. A., Solomon, E. I., Bertozzi, C. R. 2019


    The formylglycine-generating enzyme (FGE) is required for the posttranslational activation of type I sulfatases by oxidation of an active-site cysteine to Calpha-formylglycine. FGE has emerged as an enabling biotechnology tool due to the robust utility of the aldehyde product as a bioconjugation handle in recombinant proteins. Here, we show that Cu(I)-FGE is functional in O2 activation and reveal a high-resolution X-ray crystal structure of FGE in complex with its catalytic copper cofactor. We establish that the copper atom is coordinated by two active-site cysteine residues in a nearly linear geometry, supporting and extending prior biochemical and structural data. The active cuprous FGE complex was interrogated directly by X-ray absorption spectroscopy. These data unambiguously establish the configuration of the resting enzyme metal center and, importantly, reveal the formation of a three-coordinate tris(thiolate) trigonal planar complex upon substrate binding as furthermore supported by density functional theory (DFT) calculations. Critically, inner-sphere substrate coordination turns on O2 activation at the copper center. These collective results provide a detailed mechanistic framework for understanding why nature chose this structurally unique monocopper active site to catalyze oxidase chemistry for sulfatase activation.

    View details for PubMedID 30824597

  • A Six-Coordinate Peroxynitrite Low-Spin Iron(III) Porphyrinate Complex-The Product of the Reaction of Nitrogen Monoxide (center dot NO(g)) with a Ferric-Superoxide Species JOURNAL OF THE AMERICAN CHEMICAL SOCIETY Sharma, S. K., Schaefer, A. W., Lim, H., Matsumura, H., Moenne-Loccoz, P., Hedman, B., Hodgson, K. O., Solomon, E. I., Karlin, K. D. 2017; 139 (48): 17421–30


    Peroxynitrite (-OON═O, PN) is a reactive nitrogen species (RNS) which can effect deleterious nitrative or oxidative (bio)chemistry. It may derive from reaction of superoxide anion (O2•-) with nitric oxide (·NO) and has been suggested to form an as-yet unobserved bound heme-iron-PN intermediate in the catalytic cycle of nitric oxide dioxygenase (NOD) enzymes, which facilitate a ·NO homeostatic process, i.e., its oxidation to the nitrate anion. Here, a discrete six-coordinate low-spin porphyrinate-FeIII complex [(PIm)FeIII(-OON═O)] (3) (PIm; a porphyrin moiety with a covalently tethered imidazole axial "base" donor ligand) has been identified and characterized by various spectroscopies (UV-vis, NMR, EPR, XAS, resonance Raman) and DFT calculations, following its formation at -80 °C by addition of ·NO(g) to the heme-superoxo species, [(PIm)FeIII(O2•-)] (2). DFT calculations confirm that 3 is a six-coordinate low-spin species with the PN ligand coordinated to iron via its terminal peroxidic anionic O atom with the overall geometry being in a cis-configuration. Complex 3 thermally transforms to its isomeric low-spin nitrato form [(PIm)FeIII(NO3-)] (4a). While previous (bio)chemical studies show that phenolic substrates undergo nitration in the presence of PN or PN-metal complexes, in the present system, addition of 2,4-di-tert-butylphenol (2,4DTBP) to complex 3 does not lead to nitrated phenol; the nitrate complex 4a still forms. DFT calculations reveal that the phenolic H atom approaches the terminal PN O atom (farthest from the metal center and ring core), effecting O-O cleavage, giving nitrogen dioxide (·NO2) plus a ferryl compound [(PIm)FeIV═O] (7); this rebounds to give [(PIm)FeIII(NO3-)] (4a).The generation and characterization of the long sought after ferriheme peroxynitrite complex has been accomplished.

    View details for PubMedID 29091732

  • Metalloprotein entatic control of ligand-metal bonds quantified by ultrafast x-ray spectroscopy SCIENCE Mara, M. W., Hadt, R. G., Reinhard, M., Kroll, T., Lim, H., Hartsock, R. W., Alonso-Mori, R., Chollet, M., Glownia, J. M., Nelson, S., Sokaras, D., Kunnus, K., Hodgson, K. O., Hedman, B., Bergmann, U., Gaffney, K. J., Solomon, E. I. 2017; 356 (6344): 1276-+


    The multifunctional protein cytochrome c (cyt c) plays key roles in electron transport and apoptosis, switching function by modulating bonding between a heme iron and the sulfur in a methionine residue. This Fe-S(Met) bond is too weak to persist in the absence of protein constraints. We ruptured the bond in ferrous cyt c using an optical laser pulse and monitored the bond reformation within the protein active site using ultrafast x-ray pulses from an x-ray free-electron laser, determining that the Fe-S(Met) bond enthalpy is ~4 kcal/mol stronger than in the absence of protein constraints. The 4 kcal/mol is comparable with calculations of stabilization effects in other systems, demonstrating how biological systems use an entatic state for modest yet accessible energetics to modulate chemical function.

    View details for PubMedID 28642436

    View details for PubMedCentralID PMC5706643

  • Hydroxo-Bridged Dicopper(II,III) and -(III,III) Complexes: Models for Putative Intermediates in Oxidation Catalysis JOURNAL OF THE AMERICAN CHEMICAL SOCIETY Halvagar, M. R., Solntsev, P. V., Lim, H., Hedman, B., Hodgson, K. O., Solomon, E. I., Cramer, C. J., Tolman, W. B. 2014; 136 (20): 7269-7272


    A macrocyclic ligand (L(4-)) comprising two pyridine(dicarboxamide) donors was used to target reactive copper species relevant to proposed intermediates in catalytic hydrocarbon oxidations by particulate methane monooxygenase and heterogeneous zeolite systems. Treatment of LH4 with base and Cu(OAc)2·H2O yielded (Me4N)2[L2Cu4(μ4-O)] (1) or (Me4N)[LCu2(μ-OH)] (2), depending on conditions. Complex 2 was found to undergo two reversible 1-electron oxidations via cyclic voltammetry and low-temperature chemical reactions. On the basis of spectroscopy and theory, the oxidation products were identified as novel hydroxo-bridged mixed-valent Cu(II)Cu(III) and symmetric Cu(III)2 species, respectively, that provide the first precedence for such moieties as oxidation catalysis intermediates.

    View details for DOI 10.1021/ja503629r

    View details for Web of Science ID 000336416600021

    View details for PubMedID 24821432

    View details for PubMedCentralID PMC4046753

  • Excited-state proton-relay dynamics of 7-hydroxyquinoline controlled by solvent reorganization in room temperature ionic liquids PHYSICAL CHEMISTRY CHEMICAL PHYSICS Lim, H., Jeong, H., Park, S., Lee, J. Y., Jang, D. 2012; 14 (1): 218-224


    The excited-state triple proton relay of 7-hydroxyquinoline (7HQ) along a hydrogen-bonded methanol chain in room temperature ionic liquids (RTILs) has been investigated using picosecond time-resolved fluorescence spectroscopy. The rate constant of the proton relay in a methanol-added RTIL is found to be slower by an order of magnitude than that in bulk methanol and to have unity in its kinetic isotope effect. These suggest that the excited-state tautomerization dynamics of 7HQ in methanol-added RTILs is mainly controlled by the solvent reorganization dynamics to form a cyclically hydrogen-bonded complex of 7HQ·(CH(3)OH)(2) upon absorption of a photon due to high viscosity values of RTILs. Because the cyclic complex of 7HQ·(CH(3)OH)(2) at the ground state is unstable in RTILs, the collision-induced slow formation of the cyclic complex should take place upon excitation prior to undergoing subsequent intrinsic proton transfer rapidly.

    View details for DOI 10.1039/c1cp22329a

    View details for Web of Science ID 000297593800025

    View details for PubMedID 22073404

  • Excited-State Double Proton Transfer of 7-Azaindole Dimers in a Low-Temperature Organic Glass PHOTOCHEMISTRY AND PHOTOBIOLOGY Lim, H., Park, S., Jang, D. 2011; 87 (4): 766-771


    The excited-state double proton transfer of model DNA base pairs, 7-azaindole (7AI) dimers, is explored in a low-temperature organic glass of n-dodecane using picosecond time-resolved fluorescence spectroscopy. Reaction mechanisms are found to depend on the conformations of 7AI dimers at the moment of excitation; whereas planar conformers tautomerize rapidly (<10 ps), twisted conformers undergo double proton transfer to form tautomeric dimers on the time scale of 250 ps at 8 K. The proton transfer is found to consist of two orthogonal steps: precursor-configurational optimization and intrinsic proton transfer via tunneling. The rate is almost isotope independent at cryogenic temperatures because configurational optimization is the rate-determining step of the overall proton transfer. This optimization is assisted by lattice vibrations below 150 K or by librational motions above 150 K.

    View details for DOI 10.1111/j.1751-1097.2011.00923.x

    View details for Web of Science ID 000292864200004

    View details for PubMedID 21413991

  • Excited-State Double Proton Transfer Dynamics of Model DNA Base Pairs: 7-Hydroxyquinoline Dimers JOURNAL OF PHYSICAL CHEMISTRY A Lim, H., Park, S., Jang, D. 2010; 114 (43): 11432-11435


    The excited-state double proton transfer of model DNA base pairs, 7-hydroxyquinoline dimers, in benzene has been investigated using picosecond time-resolved fluorescence spectroscopy. Upon excitation, whereas singly hydrogen-bonded noncyclic dimers do not go through tautomerization within the relaxation time of 1400 ps, doubly hydrogen-bonded cyclic dimers undergo excited-state double proton transfer on the time scale of 25 ps to form tautomeric dimers, which subsequently undergo a conformational change in 180 ps to produce singly hydrogen-bonded tautomers. The rate constant of the double proton transfer reaction is temperature-independent, showing a large kinetic isotope effect of 5.2, suggesting that the rate is governed mostly by tunneling.

    View details for DOI 10.1021/jp106301q

    View details for Web of Science ID 000283471900009

    View details for PubMedID 20939620