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Senear, Donald F.

TitleProfessor
InstitutionUniversity of California, Irvine
DepartmentMolecular Biology & Biochem
Address3230 McGaugh Hall
Zot 3900
CA 92697
Phone(949) 824-8014, 8013
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    COUPLING MECHANISMS--SITE-SPECIFIC PROTEIN-DNA ASSEMBLY
    NIH/NIGMS R29GM041465Dec 1, 1988 - Mar 31, 1995
    Role: Principal Investigator

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    Publications listed below are automatically derived from MEDLINE/PubMed and other sources, which might result in incorrect or missing publications. Researchers can login to make corrections and additions, or contact us for help.
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    1. Holt AK, Senear D. The cooperative binding energetics of CytR and cAMP receptor protein support a quantitative model of differential activation and repression of CytR-regulated class III Escherichia coli promoters. Biochemistry. 2013 Nov 19; 52(46):8209-18. PMID: 24138566.
      View in: PubMed
    2. Wallentine BD, Wang Y, Tretyachenko-Ladokhina V, Tan M, Senear D, Luecke H. Structures of oncogenic, suppressor and rescued p53 core-domain variants: mechanisms of mutant p53 rescue. Acta Crystallogr D Biol Crystallogr. 2013 Oct; 69(Pt 10):2146-56. PMID: 24100332; PMCID: PMC3792646.
    3. Moody CL, Tretyachenko-Ladokhina V, Laue TM, Senear D, Cocco MJ. Multiple conformations of the cytidine repressor DNA-binding domain coalesce to one upon recognition of a specific DNA surface. Biochemistry. 2011 Aug 09; 50(31):6622-32. PMID: 21688840.
      View in: PubMed
    4. Holt AK, Senear D. An unusual pattern of CytR and CRP binding energetics at Escherichia coli cddP suggests a unique blend of class I and class II mediated activation. Biochemistry. 2010 Jan 26; 49(3):432-42. PMID: 20000490.
      View in: PubMed
    5. Tan YH, Chen YM, Ye X, Lu Q, Tretyachenko-Ladokhina V, Yang W, Senear D, Luo R. Molecular mechanisms of functional rescue mediated by P53 tumor suppressor mutations. Biophys Chem. 2009 Nov; 145(1):37-44. PMID: 19748724; PMCID: PMC2794655.
    6. Senear D, Tretyachenko-Ladokhina V, Opel ML, Aeling KA, Hatfield GW, Franklin LM, Darlington RC, Alexander Ross JB. Pressure dissociation of integration host factor-DNA complexes reveals flexibility-dependent structural variation at the protein-DNA interface. Nucleic Acids Res. 2007; 35(6):1761-72. PMID: 17324943; PMCID: PMC1874591.
    7. Aeling KA, Steffen NR, Johnson M, Hatfield GW, Lathrop RH, Senear D. DNA deformation energy as an indirect recognition mechanism in protein-DNA interactions. IEEE/ACM Trans Comput Biol Bioinform. 2007 Jan-Mar; 4(1):117-25. PMID: 17277419.
      View in: PubMed
    8. Aeling KA, Opel ML, Steffen NR, Tretyachenko-Ladokhina V, Hatfield GW, Lathrop RH, Senear D. Indirect recognition in sequence-specific DNA binding by Escherichia coli integration host factor: the role of DNA deformation energy. J Biol Chem. 2006 Dec 22; 281(51):39236-48. PMID: 17035240.
      View in: PubMed
    9. Tretyachenko-Ladokhina V, Cocco MJ, Senear D. Flexibility and adaptability in binding of E. coli cytidine repressor to different operators suggests a role in differential gene regulation. J Mol Biol. 2006 Sep 15; 362(2):271-86. PMID: 16919681.
      View in: PubMed
    10. Chahla M, Wooll J, Laue TM, 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 Apr 08; 42(13):3812-25. PMID: 12667072.
      View in: PubMed
    11. Rusinova E, Tretyachenko-Ladokhina V, Vele OE, Senear D, Alexander Ross JB. Alexa and Oregon Green dyes as fluorescence anisotropy probes for measuring protein-protein and protein-nucleic acid interactions. Anal Biochem. 2002 Sep 01; 308(1):18-25. PMID: 12234459.
      View in: PubMed
    12. Tretyachenko-Ladokhina V, Ross JB, Senear D. Thermodynamics of E. coli cytidine repressor interactions with DNA: distinct modes of binding to different operators suggests a role in differential gene regulation. J Mol Biol. 2002 Feb 22; 316(3):531-46. PMID: 11866516.
      View in: PubMed
    13. Senear D, Mendelson RA, Stone DB, Luck LA, Rusinova E, Ross JB. Quantitative analysis of tryptophan analogue incorporation in recombinant proteins. Anal Biochem. 2002 Jan 01; 300(1):77-86. PMID: 11743694.
      View in: PubMed
    14. Gavigan SA, Nguyen T, Nguyen N, Senear D. Role of multiple CytR binding sites on cooperativity, competition, and induction at the Escherichia coli udp promoter. J Biol Chem. 1999 Jun 04; 274(23):16010-9. PMID: 10347150.
      View in: PubMed
    15. Senear D, Ross JB, Laue TM. Analysis of protein and DNA-mediated contributions to cooperative assembly of protein-DNA complexes. Methods. 1998 Sep; 16(1):3-20. PMID: 9774512.
      View in: PubMed
    16. Rhee KY, Senear D, Hatfield GW. Activation of gene expression by a ligand-induced conformational change of a protein-DNA complex. J Biol Chem. 1998 May 01; 273(18):11257-66. PMID: 9556617.
      View in: PubMed
    17. Senear D, Perini LT, Gavigan SA. Analysis of interactions between CytR and CRP at CytR-regulated promoters. Methods Enzymol. 1998; 295:403-24. PMID: 9750230.
      View in: PubMed
    18. Rusinova E, Ross JB, Laue TM, Sowers LC, Senear D. Linkage between operator binding and dimer to octamer self-assembly of bacteriophage lambda cI repressor. Biochemistry. 1997 Oct 21; 36(42):12994-3003. PMID: 9335560.
      View in: PubMed
    19. Barbier CS, Short SA, Senear D. Allosteric mechanism of induction of CytR-regulated gene expression. Cytr repressor-cytidine interaction. J Biol Chem. 1997 Jul 04; 272(27):16962-71. PMID: 9202008.
      View in: PubMed
    20. Huang YT, Rusinova E, Ross JB, Senear D. An aromatic stacking interaction between subunits helps mediate DNA sequence specificity: operator site discrimination by phage lambda cI repressor. J Mol Biol. 1997 Mar 28; 267(2):403-17. PMID: 9096234.
      View in: PubMed
    21. Perini LT, Doherty EA, Werner E, Senear D. Multiple specific CytR binding sites at the Escherichia coli deoP2 promoter mediate both cooperative and competitive interactions between CytR and cAMP receptor protein. J Biol Chem. 1996 Dec 27; 271(52):33242-55. PMID: 8969182.
      View in: PubMed
    22. Sato AK, Bitten ER, Senear D, Alexander Ross JB, Rousslang KW. Steady-state and time-resolved phosphorescence of wild-type and modified bacteriophage ?cI repressors. J Fluoresc. 1994 Jun; 4(2):195-201. PMID: 24233382.
      View in: PubMed
    23. Senear D, Dalma-Weiszhausz DD, Brenowitz M. Effects of anomalous migration and DNA to protein ratios on resolution of equilibrium constants from gel mobility-shift assays. Electrophoresis. 1993 Aug; 14(8):704-12. PMID: 8404813.
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    24. Senear D, Laue TM, Ross JB, Waxman E, Eaton S, Rusinova E. The primary self-assembly reaction of bacteriophage lambda cI repressor dimers is to octamer. Biochemistry. 1993 Jun 22; 32(24):6179-89. PMID: 8512927.
      View in: PubMed
    25. Laue TM, Senear D, Eaton S, Ross JB. 5-hydroxytryptophan as a new intrinsic probe for investigating protein-DNA interactions by analytical ultracentrifugation. Study of the effect of DNA on self-assembly of the bacteriophage lambda cI repressor. Biochemistry. 1993 Mar 16; 32(10):2469-72. PMID: 8448106.
      View in: PubMed
    26. Ross JB, Senear D, Waxman E, Kombo BB, Rusinova E, Huang YT, Laws WR, Hasselbacher CA. Spectral enhancement of proteins: biological incorporation and fluorescence characterization of 5-hydroxytryptophan in bacteriophage lambda cI repressor. Proc Natl Acad Sci U S A. 1992 Dec 15; 89(24):12023-7. PMID: 1465434; PMCID: PMC50690.
    27. Senear D, Brenowitz M. Determination of binding constants for cooperative site-specific protein-DNA interactions using the gel mobility-shift assay. J Biol Chem. 1991 Jul 25; 266(21):13661-71. PMID: 1856200.
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    28. Senear D, Batey R. Comparison of operator-specific and nonspecific DNA binding of the lambda cI repressor: [KCl] and pH effects. Biochemistry. 1991 Jul 09; 30(27):6677-88. PMID: 1829636.
      View in: PubMed
    29. Senear D, Ackers GK. Proton-linked contributions to site-specific interactions of lambda cI repressor and OR. Biochemistry. 1990 Jul 17; 29(28):6568-77. PMID: 2168735.
      View in: PubMed
    30. Brenowitz M, Senear D, Ackers GK. Flanking DNA-sequences contribute to the specific binding of cI-repressor and OR1. Nucleic Acids Res. 1989 May 25; 17(10):3747-55. PMID: 2525252; PMCID: PMC317855.
    31. Senear D, Brenowitz M, Shea MA, Ackers GK. Energetics of cooperative protein-DNA interactions: comparison between quantitative deoxyribonuclease footprint titration and filter binding. Biochemistry. 1986 Nov 18; 25(23):7344-54. PMID: 3026451.
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    32. Petra PH, Namkung PC, Senear D, McCrae DA, Rousslang KW, Teller DC, Ross JB. Molecular characterization of the sex steroid binding protein (SBP) of plasma. Re-examination of rabbit SBP and comparison with the human, macaque and baboon proteins. J Steroid Biochem. 1986 Aug; 25(2):191-200. PMID: 3747520.
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    33. Petra PH, Stanczyk FZ, Senear D, Namkung PC, Novy MJ, Ross JB, Turner E, Brown JA. Current status of the molecular structure and function of the plasma sex steroid-binding protein (SBP). J Steroid Biochem. 1983 Jul; 19(1B):699-706. PMID: 6684195.
      View in: PubMed
    34. Senear D, Teller DC. Thermodynamics of concanavalin A dimer-tetramer self-association: sedimentation equilibrium studies. Biochemistry. 1981 May 26; 20(11):3076-83. PMID: 7248268.
      View in: PubMed
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