Experts and Doctors on molecular models in Irvine, California, United States


Locale: Irvine, California, United States
Topic: molecular models

Top Publications

  1. Kuznetsov V, Poulos T, Sevrioukova I. Putidaredoxin-to-cytochrome P450cam electron transfer: differences between the two reductive steps required for catalysis. Biochemistry. 2006;45:11934-44 pubmed
  2. Cornell C, Perera R, Brunner J, Semler B. Strand-specific RNA synthesis determinants in the RNA-dependent RNA polymerase of poliovirus. J Virol. 2004;78:4397-407 pubmed
    ..In some constructs, the partial reestablishment of PV1 amino acid sequences in this region was capable of rescuing RNA replication in vitro and in cell culture. ..
  3. Sevrioukova I, Poulos T, Churbanova I. Crystal structure of the putidaredoxin reductase x putidaredoxin electron transfer complex. J Biol Chem. 2010;285:13616-20 pubmed publisher
  4. Barrows T, Bhaskar B, Poulos T. Electrostatic control of the tryptophan radical in cytochrome c peroxidase. Biochemistry. 2004;43:8826-34 pubmed
    ..When taken together, these results demonstrate a strong correlation between the experimentally determined stability of the Trp191 radical, the enzyme activity, and the calculated electrostatic stabilization of the Trp191 radical. ..
  5. Meharenna Y, Doukov T, Li H, Soltis S, Poulos T. Crystallographic and single-crystal spectral analysis of the peroxidase ferryl intermediate. Biochemistry. 2010;49:2984-6 pubmed publisher
    ..The low-dose structure correlates well with an Fe(IV) horizontal lineO bond, while we postulate that the high-dose structure is the cryo-trapped Fe(III)-OH species previously thought to be an Fe(IV)-OH species. ..
  6. Shimizu H, Schuller D, Lanzilotta W, Sundaramoorthy M, Arciero D, Hooper A, et al. Crystal structure of Nitrosomonas europaea cytochrome c peroxidase and the structural basis for ligand switching in bacterial di-heme peroxidases. Biochemistry. 2001;40:13483-90 pubmed
    ..Most importantly, a Glu residue situated near the peroxide binding site could possibly serve as an acid-base catalytic group required for cleavage of the peroxide O--O bond. ..
  7. Ma C, Tran J, Li C, Ganesan L, Wood D, Morrissette N. Secondary mutations correct fitness defects in Toxoplasma gondii with dinitroaniline resistance mutations. Genetics. 2008;180:845-56 pubmed publisher
    ..These lines have reduced dinitroaniline resistance but most perform better than parental lines in competition assays, indicating that there is a trade-off between resistance and replication fitness. ..
  8. Hu Y, Fay A, Lee C, Yoshizawa J, Ribbe M. Assembly of nitrogenase MoFe protein. Biochemistry. 2008;47:3973-81 pubmed publisher
  9. Yoshizawa J, Blank M, Fay A, Lee C, Wiig J, Hu Y, et al. Optimization of FeMoco maturation on NifEN. J Am Chem Soc. 2009;131:9321-5 pubmed publisher

More Information


  1. Ladokhin A, Isas J, Haigler H, White S. Determining the membrane topology of proteins: insertion pathway of a transmembrane helix of annexin 12. Biochemistry. 2002;41:13617-26 pubmed
    ..2001) J. Biol. Chem. 276, 32395-32398]. ..
  2. Khakshoor O, Demeler B, Nowick J. Macrocyclic beta-sheet peptides that mimic protein quaternary structure through intermolecular beta-sheet interactions. J Am Chem Soc. 2007;129:5558-69 pubmed
  3. Meharenna Y, Oertel P, Bhaskar B, Poulos T. Engineering ascorbate peroxidase activity into cytochrome c peroxidase. Biochemistry. 2008;47:10324-32 pubmed publisher
    ..While wild-type CCP shows no APX activity, CCP2APX catalyzes the peroxidation of ascorbate at a rate of approximately 12 min (-1), indicating that the engineered ascorbate-binding loop can bind ascorbate. ..
  4. Bonagura C, Bhaskar B, Shimizu H, Li H, Sundaramoorthy M, McRee D, et al. High-resolution crystal structures and spectroscopy of native and compound I cytochrome c peroxidase. Biochemistry. 2003;42:5600-8 pubmed
    ..87 A, suggesting a single Fe(IV)-O bond and not the generally accepted double bond. ..
  5. Larson S, Day J, Barba de la Rosa A, Keen N, McPherson A. First crystallographic structure of a xylanase from glycoside hydrolase family 5: implications for catalysis. Biochemistry. 2003;42:8411-22 pubmed
    ..The first 13 N-terminal residues form one beta-strand of this domain. Residues 44, 45, and 316-322 form the linkers between this domain and the catalytic domain. ..
  6. Freites J, Choi Y, Tobias D. Molecular dynamics simulations of a pulmonary surfactant protein B peptide in a lipid monolayer. Biophys J. 2003;84:2169-80 pubmed
  7. Hu Y, Fay A, Schmid B, Makar B, Ribbe M. Molecular insights into nitrogenase FeMoco insertion: TRP-444 of MoFe protein alpha-subunit locks FeMoco in its binding site. J Biol Chem. 2006;281:30534-41 pubmed
    ..Our results provide some of the initial molecular insights into the FeMoco insertion process and, moreover, have useful implications for the overall scheme of nitrogenase assembly. ..
  8. Korman T, Tan Y, Wong J, Luo R, Tsai S. Inhibition kinetics and emodin cocrystal structure of a type II polyketide ketoreductase. Biochemistry. 2008;47:1837-47 pubmed publisher
    ..The results lay the foundation for the design of novel aromatic polyketide natural products with different reduction patterns. ..
  9. Khakshoor O, Lin A, Korman T, Sawaya M, Tsai S, Eisenberg D, et al. X-ray crystallographic structure of an artificial beta-sheet dimer. J Am Chem Soc. 2010;132:11622-8 pubmed publisher
  10. Solorzano C, Antonietti F, Duranti A, Tontini A, Rivara S, Lodola A, et al. Synthesis and structure-activity relationships of N-(2-oxo-3-oxetanyl)amides as N-acylethanolamine-hydrolyzing acid amidase inhibitors. J Med Chem. 2010;53:5770-81 pubmed publisher
  11. Cartailler J, Luecke H. X-ray crystallographic analysis of lipid-protein interactions in the bacteriorhodopsin purple membrane. Annu Rev Biophys Biomol Struct. 2003;32:285-310 pubmed
    ..A brief discussion of the possibility that bacteriorhodopsin functions as a light-driven inward hydroxide pump rather than an outward proton pump is also presented...
  12. Kemper M, Stout C, Lloyd S, Prasad G, Fawcett S, Armstrong F, et al. Y13C Azotobacter vinelandii ferredoxin I. A designed [Fe-S] ligand motif contains a cysteine persulfide. J Biol Chem. 1997;272:15620-7 pubmed
    ..It is interesting to note that neither of the two free cysteines present in FdI was modified. Thus, if NifS is involved in modifying the introduced cysteine there must be specificity to the reaction. ..
  13. Smith D, Woerpel K. Electrostatic interactions in cations and their importance in biology and chemistry. Org Biomol Chem. 2006;4:1195-201 pubmed
    ..These conformational biases, along with stereoelectronic effects, can control the stereoselectivity of reactions involving carbocationic intermediates. ..
  14. Jung Y, Bonagura C, Tilley G, Gao Sheridan H, Armstrong F, Stout C, et al. Structure of C42D Azotobacter vinelandii FdI. A Cys-X-X-Asp-X-X-Cys motif ligates an air-stable [4Fe-4S]2+/+ cluster. J Biol Chem. 2000;275:36974-83 pubmed
    ..The cluster conversion was ultimately accomplished using a new electrochemical method. Hydrophobic and electrostatic interaction and the lack of Gly residues adjacent to the Asp ligand explain the remarkable stability of this cluster. ..
  15. Dounay A, Humphreys P, Overman L, Wrobleski A. Total synthesis of the strychnos alkaloid (+)-minfiensine: tandem enantioselective intramolecular Heck-iminium ion cyclization. J Am Chem Soc. 2008;130:5368-77 pubmed publisher
    ..A distinctive feature of this sequence is the use of palladium-catalyzed reactions to form all carbon-carbon bonds in the transformation of these simple precursors to (+)-minfiensine...
  16. Foehr E, Raffioni S, Murray Rust J, Bradshaw R. The role of tyrosine residues in fibroblast growth factor receptor 1 signaling in PC12 cells. Systematic site-directed mutagenesis in the endodomain. J Biol Chem. 2001;276:37529-36 pubmed
    ..However, it does require Tyr(677) and/or Tyr(701), which may function to stabilize the active conformation directly or indirectly. ..
  17. Chen K, Bonagura C, Tilley G, McEvoy J, Jung Y, Armstrong F, et al. Crystal structures of ferredoxin variants exhibiting large changes in [Fe-S] reduction potential. Nat Struct Biol. 2002;9:188-92 pubmed
    ..The smaller (50--100 mV) increases observed for the neutral form are proposed to occur by directing a Hdelta+--Ndelta- dipole toward the reduced form of the cluster. ..
  18. Evans W, Fang M, Zucchi G, Furche F, Ziller J, Hoekstra R, et al. Isolation of dysprosium and yttrium complexes of a three-electron reduction product in the activation of dinitrogen, the (N2)3- radical. J Am Chem Soc. 2009;131:11195-202 pubmed publisher
    ..The DFT studies suggest that the unpaired electron is localized primarily in a dinitrogen pi orbital isolated spatially, energetically, and by symmetry from the metal orbitals...
  19. Chen D, Lanyi J. Structural changes in the N and N' states of the bacteriorhodopsin photocycle. Biophys J. 2009;96:2779-88 pubmed publisher
    ..The structural changes reverse their directions and decay in the N' state. ..
  20. Schuller D, Zhu W, Stojiljkovic I, Wilks A, Poulos T. Crystal structure of heme oxygenase from the gram-negative pathogen Neisseria meningitidis and a comparison with mammalian heme oxygenase-1. Biochemistry. 2001;40:11552-8 pubmed
    ..Key glycine residues provide the flexibility for the helical kink, allow close contact of the helix backbone with the heme, and may interact directly with heme ligands...
  21. Zeng W, de Greef J, Chen Y, Chien R, Kong X, Gregson H, et al. Specific loss of histone H3 lysine 9 trimethylation and HP1gamma/cohesin binding at D4Z4 repeats is associated with facioscapulohumeral dystrophy (FSHD). PLoS Genet. 2009;5:e1000559 pubmed publisher
    ..Based on these results, we propose a new model in which the epigenetic change initiated at 4q D4Z4 spreads its effect to other genomic regions, which compromises muscle-specific gene regulation leading to FSHD pathogenesis. ..
  22. Voronine D, Abramavicius D, Mukamel S. Chirality-based signatures of local protein environments in two-dimensional optical spectroscopy of two species photosynthetic complexes of green sulfur bacteria: simulation study. Biophys J. 2008;95:4896-907 pubmed publisher
    ..Pulse polarization configurations are designed that can separate the coherent and incoherent exciton dynamics contributions to the two-dimensional spectra. ..
  23. Balashov S, Imasheva E, Choi A, Jung K, Liaaen Jensen S, Lanyi J. Reconstitution of gloeobacter rhodopsin with echinenone: role of the 4-keto group. Biochemistry. 2010;49:9792-9 pubmed publisher
    ..We suggest that the 4-keto group in salinixanthin and echinenone allows for the twisted conformation of the ring around the C6-C7 bond and probably is engaged in an interaction that locks the carotenoid in the binding site. ..
  24. Li H, Das A, Sibhatu H, Jamal J, Sligar S, Poulos T. Exploring the electron transfer properties of neuronal nitric-oxide synthase by reversal of the FMN redox potential. J Biol Chem. 2008;283:34762-72 pubmed publisher
  25. Schuller D, Wilks A, Ortiz de Montellano P, Poulos T. Crystal structure of human heme oxygenase-1. Nat Struct Biol. 1999;6:860-7 pubmed
    ..Regioselective oxygenation of the alpha-meso heme carbon is due primarily to steric influence of the distal helix. ..
  26. Yano J, Koo L, Schuller D, Li H, Ortiz de Montellano P, Poulos T. Crystal structure of a thermophilic cytochrome P450 from the archaeon Sulfolobus solfataricus. J Biol Chem. 2000;275:31086-92 pubmed publisher
    ..An additional feature of the 4-phenylimidazole-bound structure is a zinc ion tetrahedrally bound by symmetry-related His and Glu residues...
  27. Lanzilotta W, Schuller D, Thorsteinsson M, Kerby R, Roberts G, Poulos T. Structure of the CO sensing transcription activator CooA. Nat Struct Biol. 2000;7:876-80 pubmed publisher
  28. Hoff K, Cupp Vickery J, Vickery L. Contributions of the LPPVK motif of the iron-sulfur template protein IscU to interactions with the Hsc66-Hsc20 chaperone system. J Biol Chem. 2003;278:37582-9 pubmed publisher
    ..The results are discussed in the context of a structural model based on the crystallographic structure of the DnaK peptide-binding domain...
  29. Day J, Kuznetsov Y, Larson S, Greenwood A, McPherson A. Biophysical studies on the RNA cores of satellite tobacco mosaic virus. Biophys J. 2001;80:2364-71 pubmed
    ..The intimate association of amino acid residues 2 through 25 with RNA likely contributes to the stability of the condensed conformation of the nucleic acid cores...
  30. Prosise G, Wu J, Luecke H. Crystal structure of Tritrichomonas foetus inosine monophosphate dehydrogenase in complex with the inhibitor ribavirin monophosphate reveals a catalysis-dependent ion-binding site. J Biol Chem. 2002;277:50654-9 pubmed
    ..Exploitation of these differences may lead to novel inhibitors, which favor the microbial form of the enzyme...
  31. Chen K, Jung Y, Bonagura C, Tilley G, Prasad G, Sridhar V, et al. Azotobacter vinelandii ferredoxin I: a sequence and structure comparison approach to alteration of [4Fe-4S]2+/+ reduction potential. J Biol Chem. 2002;277:5603-10 pubmed
  32. Tapley T, Cupp Vickery J, Vickery L. Structural determinants of HscA peptide-binding specificity. Biochemistry. 2006;45:8058-66 pubmed
  33. Dioumaev A, Brown L, Needleman R, Lanyi J. Coupling of the reisomerization of the retinal, proton uptake, and reprotonation of Asp-96 in the N photointermediate of bacteriorhodopsin. Biochemistry. 2001;40:11308-17 pubmed
    ..The reisomerization of the retinal occurs only after recovery from a long-living protein conformation in which reprotonation of Asp-96 is either entirely blocked or blocked at low pH. ..
  34. Shakkottai V, Regaya I, Wulff H, Fajloun Z, Tomita H, Fathallah M, et al. Design and characterization of a highly selective peptide inhibitor of the small conductance calcium-activated K+ channel, SkCa2. J Biol Chem. 2001;276:43145-51 pubmed
    ..Lei-Dab(7) will be a useful tool to investigate the functional role of SKCa2 in mammalian tissues. ..
  35. Wulff H, Gutman G, Cahalan M, Chandy K. Delineation of the clotrimazole/TRAM-34 binding site on the intermediate conductance calcium-activated potassium channel, IKCa1. J Biol Chem. 2001;276:32040-5 pubmed
    ..The heterocyclic moiety may project into the selectivity filter and obstruct the ion-conducting pathway from the inside. ..
  36. Raman C, Li H, Martasek P, Southan G, Masters B, Poulos T. Crystal structure of nitric oxide synthase bound to nitro indazole reveals a novel inactivation mechanism. Biochemistry. 2001;40:13448-55 pubmed
    ..We also present three crystal structures that reveal how alterations at the substrate site facilitate 7-NIBr and structurally dissimilar ligands to occupy the cofactor site. ..
  37. Delker S, Ji H, Li H, Jamal J, Fang J, Xue F, et al. Unexpected binding modes of nitric oxide synthase inhibitors effective in the prevention of a cerebral palsy phenotype in an animal model. J Am Chem Soc. 2010;132:5437-42 pubmed publisher
    ..A new hot spot generated as a result of enzyme elasticity provides important information for the future fragment-based design of selective NOS inhibitors. ..
  38. Patel D, Jao C, Mailliard W, Isas J, Langen R, Haigler H. Calcium-dependent binding of annexin 12 to phospholipid bilayers: stoichiometry and implications. Biochemistry. 2001;40:7054-60 pubmed
    ..Overall, these studies suggest that ANX12 is well suited to being a Ca2+ sensor for rapid all-or-none intercellular membrane-related events. ..
  39. Smith P, Zhou B, Ho N, Yuan Y, Su L, Tsai S, et al. 2.6 A X-ray crystal structure of human p53R2, a p53-inducible ribonucleotide reductase . Biochemistry. 2009;48:11134-41 pubmed publisher
    ..Insight gained from this structural work will be used in the identification of biological function, regulation mechanism, and inhibitor selection in RNR small subunits. ..
  40. Walter B, Parsley T, Ehrenfeld E, Semler B. Distinct poly(rC) binding protein KH domain determinants for poliovirus translation initiation and viral RNA replication. J Virol. 2002;76:12008-22 pubmed
    ..Our data have implications for differential picornavirus template utilization during viral translation and RNA replication and suggest that specific PCBP2 domains may have distinct roles in these activities. ..
  41. Li H, Shimizu H, Flinspach M, Jamal J, Yang W, Xian M, et al. The novel binding mode of N-alkyl-N'-hydroxyguanidine to neuronal nitric oxide synthase provides mechanistic insights into NO biosynthesis. Biochemistry. 2002;41:13868-75 pubmed
  42. White S, von Heijne G. How translocons select transmembrane helices. Annu Rev Biophys. 2008;37:23-42 pubmed publisher
    ..We review this progress and consider the connection between the physical principles of membrane protein stability and translocon selection of transmembrane helices. ..
  43. Lad L, Friedman J, Li H, Bhaskar B, Ortiz de Montellano P, Poulos T. Crystal structure of human heme oxygenase-1 in a complex with biliverdin. Biochemistry. 2004;43:3793-801 pubmed
    ..Biliverdin adopts a more linear conformation and moves from the heme site to an internal cavity. These structural results provide insight into the rate-limiting step in HO-1 catalysis, which is product, biliverdin, release. ..
  44. Swartz L, Kuchinskas M, Li H, Poulos T, Lanzilotta W. Redox-dependent structural changes in the Azotobacter vinelandii bacterioferritin: new insights into the ferroxidase and iron transport mechanism. Biochemistry. 2006;45:4421-8 pubmed
    ..Taken together, these data allow a molecular movie of the ferroxidase gating mechanism to be developed and provide further insight into the iron uptake and/or release and mineralization mechanism of bacterioferritins in general...
  45. Ho W, Li H, Nishida C, de Montellano P, Poulos T. Crystal structure and properties of CYP231A2 from the thermoacidophilic archaeon Picrophilus torridus. Biochemistry. 2008;47:2071-9 pubmed publisher
    ..The increase in thermal stability instead is best correlated with the smaller size and shorter loops in CYP231A2 compared to other P450s...
  46. Vickery L, Cupp Vickery J. Molecular chaperones HscA/Ssq1 and HscB/Jac1 and their roles in iron-sulfur protein maturation. Crit Rev Biochem Mol Biol. 2007;42:95-111 pubmed
    ..Additional genetic and biochemical studies are needed to extend these findings to mtHsp70 activities in higher eukaryotes. ..