Experts and Doctors on protein conformation in Irvine, California, United States


Locale: Irvine, California, United States
Topic: protein conformation

Top Publications

  1. Wang X, Chemmama I, Yu C, Huszagh A, Xu Y, Viner R, et al. The proteasome-interacting Ecm29 protein disassembles the 26S proteasome in response to oxidative stress. J Biol Chem. 2017;292:16310-16320 pubmed publisher
  2. 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
  3. Roskamp K, Montelongo D, Anorma C, Bandak D, Chua J, Malecha K, et al. Multiple Aggregation Pathways in Human ?S-Crystallin and Its Aggregation-Prone G18V Variant. Invest Ophthalmol Vis Sci. 2017;58:2397-2405 pubmed publisher
    ..The resulting aggregates differ in their ThT fluorescence and turbidity, suggesting that at least two different aggregation pathways are accessible to both proteins under the conditions tested. ..
  4. Hu Y, Fay A, Lee C, Yoshizawa J, Ribbe M. Assembly of nitrogenase MoFe protein. Biochemistry. 2008;47:3973-81 pubmed publisher
  5. Sevrioukova I, Poulos T. Pyridine-substituted desoxyritonavir is a more potent inhibitor of cytochrome P450 3A4 than ritonavir. J Med Chem. 2013;56:3733-41 pubmed publisher
    ..Additionally, Ser119 was identified as a key residue assisting binding of ritonavir-like inhibitors, which emphasizes the importance of polar interactions in the CYP3A4-ligand association. ..
  6. Hinde E, Cardarelli F, Digman M, Gratton E. Changes in chromatin compaction during the cell cycle revealed by micrometer-scale measurement of molecular flow in the nucleus. Biophys J. 2012;102:691-7 pubmed publisher
    ..For the first time, to our knowledge, we were able to probe chromatin compaction on the micrometer scale, where the regulation of molecular diffusion may become relevant for many cellular processes. ..
  7. Javidpour P, Das A, Khosla C, Tsai S. Structural and biochemical studies of the hedamycin type II polyketide ketoreductase (HedKR): molecular basis of stereo- and regiospecificities. Biochemistry. 2011;50:7426-39 pubmed publisher
    ..The molecular features of hedKR important for regio- and stereospecificities can potentially be applied to biosynthesize new polyketides via protein engineering that rationally controls polyketide ketoreduction. ..
  8. Hu Y, Ribbe M. Decoding the nitrogenase mechanism: the homologue approach. Acc Chem Res. 2010;43:475-84 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. 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. ..
  2. 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. ..
  3. 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. ..
  4. 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]. ..
  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. 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. ..
  7. Kaiser P, Wohlschlegel J. Identification of ubiquitination sites and determination of ubiquitin-chain architectures by mass spectrometry. Methods Enzymol. 2005;399:266-77 pubmed
    ..This chapter describes mass spectrometric approaches for identifying ubiquitin acceptor lysines on target proteins and analyzing the ubiquitin chain topology. ..
  8. 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. ..
  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. Salveson P, Spencer R, Nowick J. X-ray Crystallographic Structure of Oligomers Formed by a Toxic ?-Hairpin Derived from ?-Synuclein: Trimers and Higher-Order Oligomers. J Am Chem Soc. 2016;138:4458-67 pubmed publisher
    ..The oligomers formed by peptide 1a are fundamentally different than the proposed models of the fibrils formed by ?-synuclein and suggest that ?-Syn36-55, rather than the NAC, may nucleate oligomer formation. ..
  11. Jasion V, Poulos T. Leishmania major peroxidase is a cytochrome c peroxidase. Biochemistry. 2012;51:2453-60 pubmed publisher
    ..These results suggest that the biological function of LmP is to act as a cytochrome c peroxidase. ..
  12. Zhang S, Kozak J, Jiang W, Yeromin A, Chen J, Yu Y, et al. Store-dependent and -independent modes regulating Ca2+ release-activated Ca2+ channel activity of human Orai1 and Orai3. J Biol Chem. 2008;283:17662-71 pubmed publisher
    ..The Orai3 current induced by 2-APB may reflect a store-independent mode of CRAC channel activation that opens a relatively nonselective cation pore. ..
  13. 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...
  14. Silberg J, Tapley T, Hoff K, Vickery L. Regulation of the HscA ATPase reaction cycle by the co-chaperone HscB and the iron-sulfur cluster assembly protein IscU. J Biol Chem. 2004;279:53924-31 pubmed
    ..ATP T-state is regenerated. Because HscA nucleotide exchange is fast, the overall rate of the chaperone cycle in vivo will be determined by the availability of the IscU-HscB substrate-co-chaperone complex. ..
  15. 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...
  16. 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. ..
  17. Moody C, Tretyachenko Ladokhina V, Laue T, Senear D, Cocco M. Multiple conformations of the cytidine repressor DNA-binding domain coalesce to one upon recognition of a specific DNA surface. Biochemistry. 2011;50:6622-32 pubmed publisher
    ..Aspects of CytR activity are unique among repressors; we identify here structural properties that are also distinct and that might underlie the different functional properties. ..
  18. Balashov S, Imasheva E, Wang J, Lanyi J. Excitation energy-transfer and the relative orientation of retinal and carotenoid in xanthorhodopsin. Biophys J. 2008;95:2402-14 pubmed publisher
    ..The results establish xanthorhodopsin as the simplest biological excited-state donor-acceptor system for collecting light...
  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. 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
  21. Churbanova I, Poulos T, Sevrioukova I. Production and characterization of a functional putidaredoxin reductase-putidaredoxin covalent complex. Biochemistry. 2010;49:58-67 pubmed publisher
  22. 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. ..
  23. 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. ..
  24. Amaro R, Swift R, Votapka L, Li W, Walker R, Bush R. Mechanism of 150-cavity formation in influenza neuraminidase. Nat Commun. 2011;2:388 pubmed publisher
    ..This result provides an atomic-level structural understanding of the recent finding that antiviral compounds designed to take advantage of contacts in the 150-cavity can inactivate both 2009 H1N1 pandemic and avian H5N1 viruses. ..
  25. Lee M, Ames B, Tsai S. Insight into the molecular basis of aromatic polyketide cyclization: crystal structure and in vitro characterization of WhiE-ORFVI. Biochemistry. 2012;51:3079-91 pubmed publisher
    ..A unified ARO/CYC-mediated cyclization mechanism is proposed on the basis of these structural and functional results. ..
  26. 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. ..
  27. Ficici E, Jeong D, Andricioaei I. Electric-Field-Induced Protein Translocation via a Conformational Transition in SecDF: An MD Study. Biophys J. 2017;112:2520-2528 pubmed publisher
    ..Our results show that the interaction of the P1 domain dipole moment with the TM electrical field considerably lowers the free-energy barrier in the direction of F-form to I-form transition. ..
  28. Young A, Carter W, Doyle H, Mamula M, Aswad D. Structural integrity of histone H2B in vivo requires the activity of protein L-isoaspartate O-methyltransferase, a putative protein repair enzyme. J Biol Chem. 2001;276:37161-5 pubmed
    ..The propensity of H2B to generate isoAsp in vivo may help explain why this histone in particular is found as a major antigen in autoimmune diseases such as lupus erythematosus. ..
  29. 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...
  30. Subramanian V, Marchant J, Said H. Apical membrane targeting and trafficking of the human proton-coupled transporter in polarized epithelia. Am J Physiol Cell Physiol. 2008;294:C233-40 pubmed
    ..For the first time, our data present information regarding structure-function and membrane targeting of the hPCFT polypeptide, as well as the mechanisms that control its steady-state expression in polarized cells. ..
  31. Chen H, Luo R. Binding induced folding in p53-MDM2 complex. J Am Chem Soc. 2007;129:2930-7 pubmed
    ..Within the stable helices, helix II in bound MDM2 is more nativelike than that in apo-MDM2. However, helix I and IV in bound MDM2 are less nativelike than those in apo-MDM2. ..
  32. Subramanian V, Marchant J, Said H. Targeting and trafficking of the human thiamine transporter-2 in epithelial cells. J Biol Chem. 2006;281:5233-45 pubmed
    ..Finally, we compared the behavior of hTHTR2 with that of hTHTR1 and the human reduced folate carrier (SLC19A1) to underscore commonalities in the cell surface targeting mechanisms of the entire SLC19A gene family. ..
  33. Gao Sheridan H, Kemper M, Khayat R, Tilley G, Armstrong F, Sridhar V, et al. A T14C variant of Azotobacter vinelandii ferredoxin I undergoes facile [3Fe-4S]0 to [4Fe-4S]2+ conversion in vitro but not in vivo. J Biol Chem. 1998;273:33692-701 pubmed
    ..However, unlike native FdI which does not undergo facile cluster conversion, the 7Fe form T14C FdI quickly converts to the 8Fe form with a high efficiency under reducing conditions. ..
  34. 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. ..
  35. Manville R, Neverisky D, Abbott G. SMIT1 Modifies KCNQ Channel Function and Pharmacology by Physical Interaction with the Pore. Biophys J. 2017;113:613-626 pubmed publisher
  36. Li H, Raman C, Glaser C, Blasko E, Young T, Parkinson J, et al. Crystal structures of zinc-free and -bound heme domain of human inducible nitric-oxide synthase. Implications for dimer stability and comparison with endothelial nitric-oxide synthase. J Biol Chem. 1999;274:21276-84 pubmed
    ..The structural comparison also reveals that pterin binding does not preferentially stabilize the dimer interface of NOS-2 over NOS-3. ..
  37. 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
  38. Andersson M, Mattle D, Sitsel O, Klymchuk T, Nielsen A, Møller L, et al. Copper-transporting P-type ATPases use a unique ion-release pathway. Nat Struct Mol Biol. 2014;21:43-8 pubmed publisher
    ..The ion pathway explains why certain Menkes' and Wilson's disease mutations impair protein function and points to a site for inhibitors targeting pathogens. ..
  39. Chahla M, Wooll J, Laue T, Nguyen N, Senear D. Role of protein-protein bridging interactions on cooperative assembly of DNA-bound CRP-CytR-CRP complex and regulation of the Escherichia coli CytR regulon. Biochemistry. 2003;42:3812-25 pubmed
    ..Instead, cytidine binding must induce a CytR conformation that is more rigid or in some other way less tolerant of the variation in the geometric arrangement of operator sites between different promoters. ..
  40. 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
  41. 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. ..
  42. Li M, Bermak J, Wang Z, Zhou Q. Modulation of dopamine D(2) receptor signaling by actin-binding protein (ABP-280). Mol Pharmacol. 2000;57:446-52 pubmed
    ..Our results suggest a new molecular mechanism of modulating D(2) receptor signaling by cytoskeletal protein interaction. ..
  43. Srikrishnan S, Randall A, Baldi P, Da Silva N. Rationally selected single-site mutants of the Thermoascus aurantiacus endoglucanase increase hydrolytic activity on cellulosic substrates. Biotechnol Bioeng. 2012;109:1595-9 pubmed publisher
    ..This work further demonstrates that non-catalytic amino acid residues can be engineered to enhance catalytic efficiency in pretreatment enzymes of interest. ..
  44. 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...
  45. Shu Z, Vijayakumar S, Chen C, Chen P, Lee W. Purified human SUV3p exhibits multiple-substrate unwinding activity upon conformational change. Biochemistry. 2004;43:4781-90 pubmed
    ..0, adopts a conformation similar to that of SUV3-70, suggesting a conformational change in SUV3-83 is required for its helicase activity. The physiological relevance of the multiple-substrate helicase activity of human SUV3 is discussed. ..
  46. Patel D, Isas J, Ladokhin A, Jao C, Kim Y, Kirsch T, et al. The conserved core domains of annexins A1, A2, A5, and B12 can be divided into two groups with different Ca2+-dependent membrane-binding properties. Biochemistry. 2005;44:2833-44 pubmed
    ..The biological implications of this subdivision are discussed. ..
  47. Tapley T, Cupp Vickery J, Vickery L. Structural determinants of HscA peptide-binding specificity. Biochemistry. 2006;45:8058-66 pubmed
  48. Dalmau M, Lim S, Wang S. pH-triggered disassembly in a caged protein complex. Biomacromolecules. 2009;10:3199-206 pubmed publisher
    ..These results suggest that altering the degree of electrostatic repulsion at subunit interfaces could be a generally applicable strategy for designing pH-triggered assembly in protein macromolecular structures. ..
  49. 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. ..
  50. 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...
  51. 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. ..
  52. 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...