Last Name

James L Cole PhD

InstitutionUniversity of Connecticut
DepartmentMolecular and Cell Biology
Biology / Physics Building, U-3125
91 North Eagleville Road
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    Publications listed below are automatically derived from MEDLINE/PubMed and other sources, which might result in incorrect or missing publications. Faculty can login to make corrections and additions.
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    1. Mayo CB, Wong CJ, Lopez PE, Lary JW, Cole JL. Activation of PKR by short stem-loop RNAs containing single-stranded arms. RNA. 2016 Jul; 22(7):1065-75. PMID: 27208315.
      View in: PubMed
    2. Husain B, Mayo C, Cole JL. Role of the Interdomain Linker in RNA-Activated Protein Kinase Activation. Biochemistry. 2016 Jan 19; 55(2):253-61. PMID: 26678943.
      View in: PubMed
    3. Husain B, Hesler S, Cole JL. Regulation of PKR by RNA: Formation of Active and Inactive Dimers. Biochemistry. 2015 Nov 10; 54(44):6663-72. PMID: 26488609; PMCID: PMC4641775 [Available on 11/10/16].
    4. De S, Bubnys A, Alonzo F, Hyun J, Lary JW, Cole JL, Torres VJ, Olson R. The Relationship between Glycan Binding and Direct Membrane Interactions in Vibrio cholerae Cytolysin, a Channel-forming Toxin. J Biol Chem. 2015 Nov 20; 290(47):28402-15. PMID: 26416894; PMCID: PMC4653697 [Available on 11/20/16].
    5. Launer-Felty K, Wong CJ, Cole JL. Structural analysis of adenovirus VAI RNA defines the mechanism of inhibition of PKR. Biophys J. 2015 Feb 3; 108(3):748-57. PMID: 25650941; PMCID: PMC4317563 [Available on 02/03/16].
    6. Cole JL. Preface. Methods Enzymol. 2015; 562:xix-xx. PMID: 26412666.
      View in: PubMed
    7. Kaus K, Lary JW, Cole JL, Olson R. Glycan specificity of the Vibrio vulnificus hemolysin lectin outlines evolutionary history of membrane targeting by a toxin family. J Mol Biol. 2014 Jul 29; 426(15):2800-12. PMID: 24862282; PMCID: PMC4102649.
    8. Wowor AJ, Yan Y, Auclair SM, Yu D, Zhang J, May ER, Gross ML, Kendall DA, Cole JL. Analysis of SecA dimerization in solution. Biochemistry. 2014 May 20; 53(19):3248-60. PMID: 24786965; PMCID: PMC4030788.
    9. Launer-Felty K, Cole JL. Domain interactions in adenovirus VAI RNA mediate high-affinity PKR binding. J Mol Biol. 2014 Mar 20; 426(6):1285-95. PMID: 24394721; PMCID: PMC3961479.
    10. Yu D, Wowor AJ, Cole JL, Kendall DA. Defining the Escherichia coli SecA dimer interface residues through in vivo site-specific photo-cross-linking. J Bacteriol. 2013 Jun; 195(12):2817-25. PMID: 23585536; PMCID: PMC3697251.
    11. Ehlinger A, Park S, Fahmy A, Lary JW, Cole JL, Finley D, Walters KJ. Conformational dynamics of the Rpt6 ATPase in proteasome assembly and Rpn14 binding. Structure. 2013 May 7; 21(5):753-65. PMID: 23562395; PMCID: PMC3670613.
    12. Winnen B, Anderson E, Cole JL, King GF, Rowland SL. Role of the PAS sensor domains in the Bacillus subtilis sporulation kinase KinA. J Bacteriol. 2013 May; 195(10):2349-58. PMID: 23504013; PMCID: PMC3650535.
    13. Lyons DF, Lary JW, Husain B, Correia JJ, Cole JL. Are fluorescence-detected sedimentation velocity data reliable? Anal Biochem. 2013 Jun 15; 437(2):133-7. PMID: 23499970; PMCID: PMC3640771.
    14. Wostenberg C, Lary JW, Sahu D, Acevedo R, Quarles KA, Cole JL, Showalter SA. The role of human Dicer-dsRBD in processing small regulatory RNAs. PLoS One. 2012; 7(12):e51829. PMID: 23272173; PMCID: PMC3521659.
    15. Husain B, Mukerji I, Cole JL. Analysis of high-affinity binding of protein kinase R to double-stranded RNA. Biochemistry. 2012 Nov 6; 51(44):8764-70. PMID: 23062027; PMCID: PMC3495235.
    16. Anderson E, Pierre-Louis WS, Wong CJ, Lary JW, Cole JL. Heparin activates PKR by inducing dimerization. J Mol Biol. 2011 Nov 11; 413(5):973-84. PMID: 21978664; PMCID: PMC3268052.
    17. Cole JL, Correia JJ, Stafford WF. The use of analytical sedimentation velocity to extract thermodynamic linkage. Biophys Chem. 2011 Nov; 159(1):120-8. PMID: 21703752; PMCID: PMC3166974.
    18. Bryk R, Wu K, Raimundo BC, Boardman PE, Chao P, Conn GL, Anderson E, Cole JL, Duffy NP, Nathan C, Griffin JH. Identification of new inhibitors of protein kinase R guided by statistical modeling. Bioorg Med Chem Lett. 2011 Jul 1; 21(13):4108-14. PMID: 21632247.
      View in: PubMed
    19. Wowor AJ, Yu D, Kendall DA, Cole JL. Energetics of SecA dimerization. J Mol Biol. 2011 Apr 22; 408(1):87-98. PMID: 21315086; PMCID: PMC3070768.
    20. Wong CJ, Launer-Felty K, Cole JL. Analysis of PKR-RNA interactions by sedimentation velocity. Methods Enzymol. 2011; 488:59-79. PMID: 21195224; PMCID: PMC3058617.
    21. Launer-Felty K, Wong CJ, Wahid AM, Conn GL, Cole JL. Magnesium-dependent interaction of PKR with adenovirus VAI. J Mol Biol. 2010 Oct 1; 402(4):638-44. PMID: 20713064; PMCID: PMC2980848.
    22. Cole JL. Analysis of PKR activation using analytical ultracentrifugation. Macromol Biosci. 2010 Jul 7; 10(7):703-13. PMID: 20533534; PMCID: PMC2926283.
    23. Anderson E, Quartararo C, Brown RS, Shi Y, Yao X, Cole JL. Analysis of monomeric and dimeric phosphorylated forms of protein kinase R. Biochemistry. 2010 Feb 16; 49(6):1217-25. PMID: 20088595; PMCID: PMC2819637.
    24. Zhang N, Wang Q, Ehlinger A, Randles L, Lary JW, Kang Y, Haririnia A, Storaska AJ, Cole JL, Fushman D, Walters KJ. Structure of the s5a:k48-linked diubiquitin complex and its interactions with rpn13. Mol Cell. 2009 Aug 14; 35(3):280-90. PMID: 19683493; PMCID: PMC2748877.
    25. Heinicke LA, Wong CJ, Lary J, Nallagatla SR, Diegelman-Parente A, Zheng X, Cole JL, Bevilacqua PC. RNA dimerization promotes PKR dimerization and activation. J Mol Biol. 2009 Jul 10; 390(2):319-38. PMID: 19445956; PMCID: PMC2763119.
    26. VanOudenhove J, Anderson E, Krueger S, Cole JL. Analysis of PKR structure by small-angle scattering. J Mol Biol. 2009 Apr 10; 387(4):910-20. PMID: 19232355; PMCID: PMC2663012.
    27. Lemaire PA, Anderson E, Lary J, Cole JL. Mechanism of PKR Activation by dsRNA. J Mol Biol. 2008 Aug 29; 381(2):351-60. PMID: 18599071; PMCID: PMC2570377.
    28. Anderson E, Cole JL. Domain stabilities in protein kinase R (PKR): evidence for weak interdomain interactions. Biochemistry. 2008 Apr 29; 47(17):4887-97. PMID: 18393532; PMCID: PMC2729556.
    29. Cole JL, Lary JW, P Moody T, Laue TM. Analytical ultracentrifugation: sedimentation velocity and sedimentation equilibrium. Methods Cell Biol. 2008; 84:143-79. PMID: 17964931; PMCID: PMC2711687.
    30. Robertson PD, Warren EM, Zhang H, Friedman DB, Lary JW, Cole JL, Tutter AV, Walter JC, Fanning E, Eichman BF. Domain architecture and biochemical characterization of vertebrate Mcm10. J Biol Chem. 2008 Feb 8; 283(6):3338-48. PMID: 18065420; PMCID: PMC2753450.
    31. Yan Q, Malashkevich VN, Fedorov A, Fedorov E, Cao E, Lary JW, Cole JL, Nathenson SG, Almo SC. Structure of CD84 provides insight into SLAM family function. Proc Natl Acad Sci U S A. 2007 Jun 19; 104(25):10583-8. PMID: 17563375; PMCID: PMC1965556.
    32. White SR, Evans KJ, Lary J, Cole JL, Lauring B. Recognition of C-terminal amino acids in tubulin by pore loops in Spastin is important for microtubule severing. J Cell Biol. 2007 Mar 26; 176(7):995-1005. PMID: 17389232; PMCID: PMC2064084.
    33. Kang Y, Chen X, Lary JW, Cole JL, Walters KJ. Defining how ubiquitin receptors hHR23a and S5a bind polyubiquitin. J Mol Biol. 2007 May 25; 369(1):168-76. PMID: 17408689; PMCID: PMC3864866.
    34. Cao E, Zang X, Ramagopal UA, Mukhopadhaya A, Fedorov A, Fedorov E, Zencheck WD, Lary JW, Cole JL, Deng H, Xiao H, Dilorenzo TP, Allison JP, Nathenson SG, Almo SC. T cell immunoglobulin mucin-3 crystal structure reveals a galectin-9-independent ligand-binding surface. Immunity. 2007 Mar; 26(3):311-21. PMID: 17363302.
      View in: PubMed
    35. Ucci JW, Kobayashi Y, Choi G, Alexandrescu AT, Cole JL. Mechanism of interaction of the double-stranded RNA (dsRNA) binding domain of protein kinase R with short dsRNA sequences. Biochemistry. 2007 Jan 9; 46(1):55-65. PMID: 17198375.
      View in: PubMed
    36. Cole JL. Activation of PKR: an open and shut case? Trends Biochem Sci. 2007 Feb; 32(2):57-62. PMID: 17196820; PMCID: PMC2703476.
    37. Cao E, Ramagopal UA, Fedorov A, Fedorov E, Yan Q, Lary JW, Cole JL, Nathenson SG, Almo SC. NTB-A receptor crystal structure: insights into homophilic interactions in the signaling lymphocytic activation molecule receptor family. Immunity. 2006 Oct; 25(4):559-70. PMID: 17045824.
      View in: PubMed
    38. Lemaire PA, Tessmer I, Craig R, Erie DA, Cole JL. Unactivated PKR exists in an open conformation capable of binding nucleotides. Biochemistry. 2006 Aug 1; 45(30):9074-84. PMID: 16866353; PMCID: PMC2913708.
    39. Lemaire PA, Lary J, Cole JL. Mechanism of PKR activation: dimerization and kinase activation in the absence of double-stranded RNA. J Mol Biol. 2005 Jan 7; 345(1):81-90. PMID: 15567412.
      View in: PubMed
    40. Snyder D, Lary J, Chen Y, Gollnick P, Cole JL. Interaction of the trp RNA-binding attenuation protein (TRAP) with anti-TRAP. J Mol Biol. 2004 May 7; 338(4):669-82. PMID: 15099736.
      View in: PubMed
    41. Ucci JW, Cole JL. Global analysis of non-specific protein-nucleic interactions by sedimentation equilibrium. Biophys Chem. 2004 Mar 1; 108(1-3):127-40. PMID: 15043926; PMCID: PMC2924682.
    42. Cole JL. Analysis of heterogeneous interactions. Methods Enzymol. 2004; 384:212-32. PMID: 15081689; PMCID: PMC2924680.
    43. Shaw-Reid CA, Munshi V, Graham P, Wolfe A, Witmer M, Danzeisen R, Olsen DB, Carroll SS, Embrey M, Wai JS, Miller MD, Cole JL, Hazuda DJ. Inhibition of HIV-1 ribonuclease H by a novel diketo acid, 4-[5-(benzoylamino)thien-2-yl]-2,4-dioxobutanoic acid. J Biol Chem. 2003 Jan 31; 278(5):2777-80. PMID: 12480948.
      View in: PubMed
    44. Rinaldi DA, Lormand NA, Brierre JE, Cole JL, Stagg MP, Fontenot MF, Buller EJ, Rainey JM. Phase I trial of gemcitabine, administered as a standard and constant dose-rate infusion, in combination with paclitaxel in patients with advanced solid tumors (LOA-2). Am J Clin Oncol. 2002 Oct; 25(5):523-7. PMID: 12393998.
      View in: PubMed
    45. Rinaldi DA, Lormand NA, Brierre JE, Cole JL, Barnes BC, Mills G, Yadlapati S, Felicia Fontenot M, Buller EJ, Rainey JM. A Phase II trial of topotecan and gemcitabine in patients with previously treated, advanced nonsmall cell lung carcinoma. Cancer. 2002 Sep 15; 95(6):1274-8. PMID: 12216095.
      View in: PubMed
    46. Wojtuszewski K, Hawkins ME, Cole JL, Mukerji I. HU binding to DNA: evidence for multiple complex formation and DNA bending. Biochemistry. 2001 Feb 27; 40(8):2588-98. PMID: 11327882.
      View in: PubMed
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