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Selected Publications

Structure Function Group

  1. Xu Y, Moon AF, Xu S, Krahn JM, Liu J, Pederson LC. Structure Based Substrate Specificity Analysis of Heparan Sulfate 6-O-Sulfotransferases. ACS chemical biology 2017 12(1):73-82. [Abstract]
  2. Zheng X, Pedersen LC, Gabel SA, Mueller GA, DeRose EF, London RE. Unfolding the HIV-1 reverse transcriptase RNase H domain--how to lose a molecular tug-of-war. Nucleic acids research 2016 44(4):1776-1788. [Abstract]
  3. Moon AF, Krahn JM, Lu X, Cuneo MJ, Pedersen LC. Structural characterization of the virulence factor Sda1 nuclease from Streptococcus pyogenes. Nucleic acids research 2016 44(8):3946-3957. [Abstract]
  4. Mueller GA, Randall TA, Glesner J, Pedersen LC, Perera L, Edwards LL, Chapman MD, London RE, Pomes A. Serological, genomic and structural analyses of the major mite allergen Der p 23. Clinical and experimental allergy: journal of the British Society for Allergy and Clinical Immunology 2016 46(2):365-376. [Abstract]
  5. Pham P, Afif SA, Shimoda M, Maeda K, Sakaguchi N, Pedersen LC, Goodman MF. Structural analysis of the activation-induced deoxycytidine deaminase required in immunoglobulin diversification. DNA repair 2016 43():48-56. [Abstract]
  6. Pomes A, Chruszcz M, Gustchina A, Minor W, Mueller GA, Pedersen LC, Wlodawer A, Chapman MC. 100 Years later: Celebrating the contributions of x-ray crystallography to allergy and clinical immunology. Journal of Allergy and Clinical Immunology 2015 136(1):29-37. [Abstract]
  7. Moon AF, Gosavi RA, Kunkel TA, Pedersen LC, Bebenek K. Creative employment of template-dependent synthesis by Polymerase Mu. Proceedings of the National Academy of Sciences of the United States of America 112(33):E4530-E4536 (2015). [Abstract]
  8. Bebenek K, Pedersen LC, Kunkel TA. Structure-function studies of DNA polymerase λ. Biochemistry 53(17):2781-2792 (2014). [Abstract]
  9. Moon AF, Gaudu P, Pedersen LC. Structural characterization of the virulence factor nuclease A from Streptococcus agalactiae. Acta crystallographica. Section D, Biological crystallography 70(Pt 11):2937-2949 (2014). [Abstract]
  10. Liu C, Sheng J, Krahn JM, Perera L, Xu Y, Hsieh PH, Dou W, Liu J, Pedersen LC. Molecular mechanism of substrate specificity for heparan sulfate 2-O-sulfotransferase. The Journal of biological chemistry 289(19):13407-13418 (2014). [Abstract]
  11. Mutoh S, Sobhany M, Moore R, Perera L, Pedersen L, Sueyoshi T, Negishi M. Phenobarbital indirectly activates the constitutive active androstane receptor (CAR) by inhibition of epidermal growth factor receptor signaling. Science signaling 6(274):ra31- (2013). [Abstract]
  12. Moon AF, Xu Y, Woody SM, Krahn JM, Linhardt RJ, Liu, J. & PEDERSEN, L.C. (2012) Dissecting the substrate recognition of 3-O-sulfotransferase for the biosynthesis of anticoagulant heparin. Proc Natl Acad Sci U.S.A. 109:5265-70 (2012).
  13. Bebenek, K., PEDERSEN, L.C. & Kunkel, T.A. Replication infidelity via a mismatch with Watson-Crick geometry. Proc Natl Acad Sci U.S.A. 108:1862-7 (2011).
  14. Mueller, G.A., Gosavi, R.A., Pomés, A., Wünschmann, S., Moon, A.F., London, R.E. & PEDERSEN, L.C. Ara h 2: crystal structure and IgE binding distinguish two subpopulations of peanut allergic patients by epitope diversity. Allergy 66(7):878-885 (2011). [Abstract]
  15. Moon, A.F., Midon, M., Meiss, G., Pingoud, A., London, R.E. & PEDERSEN, L.C. Structural insights into catalytic and substrate binding mechanisms of the strategic EndA nuclease from Streptococcus pneumoniae. Nucleic Acids Research 39(7):2943-2953 (2011). [Abstract]
  16. Moon, A.F., Mueller, G.A., Zhong, X. & PEDERSEN, L.C. A synergistic approach to protein crystallization: combination of a fixed-arm carrier with surface entropy reduction. Protein Sci. 19:901-13 (2010). [Abstract]
  17. Arana, M.E., Holmes, S.F., Fortune, J.M., Moon, A.F., PEDERSEN, L.C. & Kunkel, T.A. Functional residues on the surface of the N-terminal domain of yeast Pms1. DNA Repair 9:448-57 (2010). [Abstract]
  18. Mueller, G.A., Edwards, L.L., Aloor, J.J., Fessler, M.B., Glesner, J., Pomes, A., Chapman, M.D., London, R.E. & PEDERSEN, L.C. The structure of the dust mite allergen Der p 7 reveals similarities to innate immune proteins. J. Allergy Clin Immunol. 125:909-17 (2010). [Abstract]
  19. Batra, V.K., Beard, W.A., Hou, E.W., PEDERSEN, L.C., Prasad, R. & Wilson, S.H. Mutagenic conformation of 8-oxo-7,8-dihydro-2'-dGTP in the confines of a DNA polymerase active site. Nat Struct Mol Biol. 17:889-890 (2010). [Abstract]
  20. Mueller, G.A., Gosavi, R.A., Krahn, J.M., Edwards, L.L., Cuneo, M.J., Glesner, J., Pomés, A., Chapman, M.D., London, R.E. &PEDERSEN, LC. The Der p 5 crystal structure provides insight into the Group 5 dust mite allergens. The Journal of biological chemistry, 285(33):25394-25401 (2010). [Abstract]
  21. Mueller, G.A., Edwards, L.L., Aloor, J.J., Fessler, M.B., Glesner, J., Pomes, A., Chapman, M.D., London, R.E. & PEDERSEN, L.C. The Structure of the House Dust Mite Allergen Der p 7 Reveals Similarities to the Innate Immune Protein Lipopolysaccharide Binding Protein. The Journal of allergy and clinical immunology. 125(4):909-917 (2010). [Abstract]
  22. Cisneros, G.A., Perera, L., Schaaper, R.M., PEDERSEN, L.C., London, R.E., Pedersen, L.G. & Darden, T.A. Reaction mechanism of the epsilon subunit of E. coli DNA polymerase III: insights into active site metal coordination and catalytically significant residues. J Am Chem Soc. 131:1550-6 (2009). [Abstract]
  23. Garcia-Diaz, M., Bebenek, K., Larrea, A.A., Havener, J.M., Perera, L., Krahn, J.M., PEDERSEN, L.C., Ramsden, D.A. & Kunkel, T.A. Template strand scrunching during DNA gap repair synthesis by human polymerase lambda. Nat. Struct Mol Biol. 16:967-72 (2009). [Abstract]
  24. Beard, W.A., Shock, D.D., Batra, V.K., PEDERSEN, L.C. & Wilson, S.H. DNA Polymerase Beta Substrate Specificity: Side chain modulation of the 'A-rule'. The Journal of biological chemistry, 284(46):31680-31689 (2009). [Abstract]
  25. Tone, Y., PEDERSEN, L.C., Yamamoto, T., Izumikawa, T., Kitagawa, H., Nishihara, J., Tamura, J., Negishi, M., &Sugahara K. 2-O-Phosphorylation of xylose and 6-O-sulfation of galactose in the protein linkage region of glycosaminoglycans influence the glucuronyltransferase-I activity involved in the linkage region synthesis. J Biol Chem, 283:16801-16807 (2008). [Abstract]
  26. Bethea, H.N., Xu, D., Liu, J., &PEDERSEN, L.C. Redirecting the substrate specificity of heparan sulfate 2-O-sulfotransferase by structurally guided mutagenesis. Proceedings of the National Academy of Sciences of the United States of America, 105(48):18724-18729 (2008). [Abstract]
  27. Ullah, H., Scappini, E.L., Moon, A.F., Williams, L.V., Armstrong, D.L., &PEDERSEN L.C. Structure of a signal transduction regulator, RACK1, from arabidopsis thaliana. Protein science : a publication of the Protein Society, 17(10):1771-1780 (2008). [Abstract]
  28. Lin, P., Batra, V.K., PEDERSEN, L.C., Beard, W.A., Wilson, S.H., &Pedersen, L.G. Incorrect nucleotide insertion at the active site of a G:A mismatch catalyzed by DNA polymerase beta. Proc Natl Acad Sci USA, 105:5670-5674 (2008). [Abstract]
  29. Batra, V.K., Beard, W.A., Shock, D.D., PEDERSEN, L.C., &Wilson, S.H. Structures of DNA polymerase beta with active site mismatches suggest a transient abasic site intermediate during misincorporation. Molecular cell 30(3):315-324 (2008). [Abstract]
  30. Xu, D., Moon, A.F., Song, D., PEDERSEN, L.C, &Liu, J. Engineering sulfotransferases to modify heparan sulfate. Nature chemical biology (2008) 4(3):200-202. [Abstract]
  31. Moon, A.F., Garcia-Diaz, M., Batra, V.K., Beard, W.A., Bebenek, K., Kunkel, T.A., Wilson, S.H., &PEDERSEN, L.C. The X family portrait: structural insights into biological functions of X family polymerases. DNA repair 6(12):1709-1725 (2007). [Abstract]
  32. Liu, J. & PEDERSEN, L.C. Anticoagulant heparan sulfate: structural specificity and biosynthesis. Appl Microbiol Biotechnol, 74:263-272 (2007). [Abstract]
  33. Xu, D., Song, D., PEDERSEN, L.C. & Liu, J. Mutational study of heparan sulfate 2-O-sulfotransferase and chondroitin sulfate 2-O-sulfotransferase. J Biol Chem, 282:8356-8367 (2007). [Abstract]
  34. Ghosh, M., Meiss, G., Pingoud, A., London, R.E. & PEDERSEN, L.C. The nuclease A-inhibitor complex is characterized by a novel metal ion bridge. J Biol Chem, 282:5682-5690 (2007). [Abstract]
  35. Sucato, C.A., Upton, T.G., Kashemirov, B.A., Batra, V.K., Martinek, V., Xiang, Y., Beard, W.A., PEDERSEN, L.C., Wilson, S.H., McKenna, C.E., Florian, J., Warshel, A. & Goodman, M.F. Modifying the beta,gamma Leaving-Group Bridging Oxygen Alters Nucleotide Incorporation Efficiency, Fidelity, and the Catalytic mechanism of DNA polymerase beta. Biochemistry, 42:461-471 (2007). [Abstract]
  36. Moon AF, Garcia-Diaz M, Bebenek K, Davis BJ, Zhong X, Ramsden DA, Kunkel TA, Pedersen LC. Structural insight into the substrate specificity of DNA polymerase mu. Nature structural & molecular biology, 14(7):45-53 (2007). [Abstract]
  37. Kirby, T.W., Harvey, S., DeRose, E.F., Chalov, S., Chikova, A., Perrino, F.W., Schaaper, R.M., London, R.E. & PEDERSEN, L.C. Structure of the Escherichia coli DNA Polymerase III epsilon-Hot proofreading complex. J Biol Chem, 281:38466:38471 (2006). [Abstract]
  38. Batra, V.K., Shock, D.D., Prasad, R., Beard, W.A., Hou, E.W., PEDERSEN, L.C., Sayer, J.M., Yagi, H., Kumar, S., Jerina, D.M. & Wilson, S.H. Structure of DNA polymerase beta with a benzo[c]phenanthrene diol epoxide-adducted template exhibits mutagenic features. Proc Natl Acad Sci USA, 103:17231-17236 (2006). [Abstract]
  39. Lin, P., PEDERSEN, L.C., Batra, V.K., Beard, W.A., Wilson, S.H. & Pedersen, L.G. Energy analysis of chemistry for correct insertion by DNA polymerase beta. Proc Natl Acad Sci USA, 103:13294-13299 (2006). [Abstract]
  40. Picher, A.J., Garcia-Diaz, M., Bebenek, K., PEDERSEN, L.C., Kunkel, T.A. & Blanco, L. Promiscuous mismatch extension by human DNA polymerase lambda. Nucleic Acids Research, 34:3259-3266 (2006). [Abstract]
  41. Batra, V.K., Beard, W.A., Shock, D.D., Krahn, J.M., PEDERSEN, L.C. & Wilson, S.H. Magnesium-induced assembly of a complete DNA polymerase catalytic complex. Structure, 14:757-766 (2006). [Abstract]
  42. Garcia-Diaz, M., Bebenek, K., Krahn, J.M., PEDERSEN, L.C. & Kunkel, T.A. Structural analysis of strand misalignment during DNA synthesis by a human DNA polymerase. Cell, 124:331-342 (2006). [Abstract]
  43. Chen, J., Avci, F.Y., Munoz, E.M., McDowell, L.M., Chen, M., PEDERSEN, L.C., Zhang, L., Linhardt, R.J. & Liu, J. Enzymatic redesigning of biologically active heparan sulfate. J Biol Chem, 280:42817-42825 (2005). [Abstract]
  44. Garcia-Diaz, M., Bebenek, K., Gao, G. PEDERSEN, L.C., London, R.E. & Kunkel, T.A. Structure-function studies of DNA polymerase lambda. DNA Repair, 4:1358-1367 (2005).  [Abstract]
  45. Prasad, Rajendra, Batra, V.K., Yang, X., Krahn, J.M., PEDERSEN, L.C., Beard, W.A. & Wilson, S.H. Structural insight into the DNA polymerase β deoxyribose phosphate lyase mechanism. DNA Repair, 4:1347-1357 (2005). [Abstract]
  46. Ghosh, M., Meiss, M., Pingoud, A., London, R.E. & PEDERSEN, L.C. Structural insight into the mechanism of Nuclease A, a ββα metal nuclease from Anabaena. J Biol Chem, 280:27990-7 (2005). [Abstract]
  47. Batra, V.K., Beard, W.A., Shock, D.D., PEDERSEN, L.C. & Wilson, S.H. Nucleotide-induced DNA polymerase active site motions accommodating a mutagenic DNA intermediate. Structure, 13:1225-1233 (2005). [Abstract]
  48. Garcia-Diaz, M., Bebenek, K., Krahn, J.M., Kunkel, T.A. & PEDERSEN, L.C. A closed conformation for the Pol lambda catalytic cycle. Nat Struct Mol Biol, 12:97-98 (2005). [Abstract]
  49. Ueda, A., Matsui, K., Yamamoto, Y. PEDERSEN, L.C., Sueyoshi, T. & Negishi, M. Thr 176 regulates the activity of the mouse nuclear receptor CAR and is conserved in the NR1I subfamily-members PXR and VDR. Biochem. J., 388:623-630 (2005). [Abstract]
  50. Moon, A.F., Edavettal, S.C., Krahn, J.M., Munoz, E.M., Negishi, M., Linhardt, R.J., Liu, J. & PEDERSEN, L.C. Structural analysis of the sulfotransferase (3-O-sulfotransferase isoform 3) involved in the biosynthesis of an entry receptor for herpes simplex virus 1. J Biol Chem, 279:45185-93 (2004). [Abstract]
  51. Edavettal, S.C., Lee, K.A., Negishi, M., Linhardt, R.J., Liu, J., PEDERSEN, L.C. Crystal structure and mutational analysis of heparan sulfate 3-O-sulfotransferase Isoform 1. J Biol Chem, 279:25789-97 (2004). [Abstract]
  52. Edavettal, S.C., Carrick, K., Shah, R.R., PEDERSEN, L.C., Tropsha, A., Pope, R.M. & Liu, J. A conformational change in heparan sulfate 3-O-sulfotransferase-1 is induced by binding to heparan sulfate. Biochemistry, 43:4680-8 (2004).  [Abstract]
  53. Garcia-Diaz, M., Bebenek, K., Krahn, J.M., Blanco, L., Kunkel, T.A. & PEDERSEN, L.C. A structural solution for the DNA polymerase lambda-dependent repair of DNA gaps with minimal homology. Mol Cell, 13:561-72 (2004). [Abstract]
  54. Inoue, K., Sobhany, M., Transue, T.R., Oguma, K., PEDERSEN, L.C. & Negishi, M. Structural analysis by X-ray crystallography and calorimetry of a haemagglutinin component (HA1) of the progenitor toxin from Clostridium botulinum. Microbiology, 149:3361-70 (2003). [Abstract]
  55. Lee, K.A., Fuda, H., Lee, Y.C., Negishi, M., Strott, C.A. & PEDERSEN, L.C. Crystal structure of human cholesterol sulfotransferase (SULT2B1b) in the presence of pregnenolone and PAP: rationale for specificity differences between prototypical SULT2A1 and the SULT2B1 isoforms. J Biol Chem, 278:44593-9 (2003). [Abstract]
  56. Shevtsov, S., Petrotchenko, E.V., PEDERSEN, L.C. & Negishi, M. Crystallographic analysis of a hydroxylated polychlorinated biphenyl (OH-PCB) bound to the catalytic estrogen binding site of human estrogen sulfotransferase. Environ Health Perspect, 111: 884-8 (2003). [Abstract]
  57. PEDERSEN, L.C., Dong, J., Taniguchi, F., Kitagawa, H., Krahn, J.M., Pedersen, L.G., Sugahara, K. & Negishi, M. Crystal structure of an alpha 1,4-N-acetylhexosaminyltransferase (EXTL2), a member of the exostosin gene family involved in heparan sulfate biosynthesis. J Biol Chem, 278:14420-8 (2003).  [Abstract]
  58. Mueller, S.O., Hall, J.M., Swope, D.L., PEDERSEN, L.C. & Korach, K.S. Molecular determinants of the stereoselectivity of agonist activity of estrogen receptors (ER) alpha and beta. J Biol Chem, 278:12255-62 (2003). [Abstract]
  59. Gorokhov, A., Negishi, M., Johnson, E.F., PEDERSEN, L.C., Perera, L., Darden, T.A. & Pedersen, L.G. Explicit water near the catalytic I helix Thr in the predicted solution structure of CYP2A4. Biophys J, 84:57-68 (2003). [Abstract]
  60. PEDERSEN, L.C., Petrotchenko, E., Shevtsov, S. & Negishi, M. Crystal structure of the human estrogen sulfotransferase-PAPS complex: evidence for catalytic role of Ser137 in the sulfuryl transfer reaction. J Biol Chem, 277:17928-32 (2002). [Abstract]
  61. PEDERSEN, L.C., Darden, T.A. & Negishi, M. Crystal structure of beta 1,3-glucuronyltransferase I in complex with active donor substrate UDP-GlcUA. J Biol Chem, 277:21869-73 (2002). [Abstract]