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Publications

  1. Mautner, H., Cole, J. and Belew, M. (1983) The labeling of an axonal membrane component with 4-(N-maleimido) benzyltrimethyl-ammonium, a reagent capable of affinity labeling the alpha-subunit of the nicotinic acetylcholine receptor. Biochem. Biophys. Res. Commun. 111, 61-66.
  2. Cole, J., Boska, M., Blough, N.V. and Sauer, K. (1986) Reversible and irreversible effects of alkaline pH on Photosystem II electron transfer reactions. Biochim. Biophys. Acta 848, 41-47.
  3. Yachandra, V.K., Guiles, R.D., McDermott, A., Britt, R.D., Cole, J., Dexheimer, S.L., Sauer, K. and Klein, M.P. (1986) The state of manganese in the photosynthetic apparatus determined by X-ray absorption spectroscopy. Journal de Physique 47-C8, 1121-1128.
  4. Cole, J., Yachandra, V.K., Guiles, R.D., McDermott, A.E., Britt, R.D., Dexheimer, S.L., Sauer, K. and Klein, M.P. (1987) Assignment of the g=4.1 EPR signal to manganese in the S2 state of the photosynthetic oxygen-evolving complex: An X-ray absorption spectroscopy study. Biochem. Biophys. Acta 890, 395-398.
  5. Cole, J. and Sauer, K. (1987) The flash number dependence of EPR Signal II as a probe for charge accumulation in Photosystem II.Biochem. Biophys. Acta 891, 40-48.
  6. Cole, J.L., Yachandra, V.K., McDermott, A.E., Guiles, R.D., Dexheimer, S.L., Britt, R.D., Sauer, K. and Klein, M.P. (1987) Structure of the manganese complex of Photosystem II upon removal of the 33 kilodalton extrinsic protein: An X-ray absorption spectroscopy study. Biochemistry 26, 5967-5973.
  7. Yachandra, V.K., Guiles, R.D., McDermott, A.E., Cole, J.L., Britt, R.D., Dexheimer, S.L., Sauer, K. and Klein, M.P. (1987) Comparison of the structure of the manganese complex in the S1 and S2 states of the photosynthetic oxygen-evolving complex: An X-ray absorption spectroscopy study. Biochemistry 26, 5974-5981.
  8. Yachandra, V.K., Guiles, R.D., McDermott, A. Cole, J., Britt, R.D., Dexheimer, S.L., Sauer, K. and Klein, M.P. (1987) The state of manganese in the photosynthetic apparatus: an X-ray absorption spectroscopy study. in Progress in Photosynthesis Research (Ed. Biggins, J.) Martinus Nijhoff, Dordrecht, The Netherlands, Vol. 1, pp. 557-560.
  9. McDermott, A.E., Yachandra, V.K., Guiles, R.D., Cole, J.L., Dexheimer, S.L., Britt, R.D., Sauer, K. and Klein, M.P. (1988) Characterization of the manganese oxygen-evolving complex and the iron-quinone acceptor complex of Photosystem II from a thermophilic cyanobacterium by electron paramagnetic resonance and X-ray absorption spectroscopy. Biochemistry 27, 4021-4031.
  10. Guiles, R.D., Zimmermann, J.-L., McDermott, A.E., Yachandra, V.K., Cole, J.L., Dexheimer, S.L., Britt, R.D., Wieghardt, K., Bossek, U., Sauer, K. and Klein, M.P. (1990) The S3 state of Photosystem II: Difference between the structure of the manganese complex in the S2 and S3 states determined by X-ray absorption spectroscopy. Biochemistry 29, 471-485
  11. Guiles, R.D., Yachandra, V.K., McDermott, A.E., Cole, J.L., Dexheimer, S.L., Britt, R.D., Sauer, K. and Klein, M.P. (1990) The S0 state of Photosystem II induced by hydroxylamine: Differences between the structure of the manganese complex in the S0 and S1 states determined by X-ray absorption spectroscopy. Biochemistry 29, 486-496.
  12. Cole, J.L., Tan, G.O., Yang, E.K., Hodgson, K.O. and Solomon, E.I. (1990) Reactivity of the laccase trinuclear copper active site with dioxygen: An X-ray absorption edge study. J. Am. Chem. Soc.112, 2243-2249.
  13. Cole, J.L., Clark, P.A. and Solomon, E.I. (1990) Spectroscopic and chemical studies of the laccase trinuclear copper active site: Geometric and electronic structure. J. Am. Chem. Soc. 112, 9534-9548.
  14. Cole, J.L., Avigliano, L., Morpurgo, L. and Solomon, E.I. (1991) Spectroscopic and chemical studies of the ascorbate oxidase trinuclear copper active site: Comparison to laccase. J. Am. Chem. Soc.113, 9080-9089.
  15. Cole, J.L., Ballou, D.P. and Solomon, E. I. (1991) Spectroscopic characterization of the peroxide intermediate in the reduction of dioxygen catalyzed by the multicopper oxidases. J. Am. Chem. Soc. 113, 8544-8546.
  16. Cole, J.L., Gehman, J.D., Shafer, J.A. and Kuo, L.C. (1993) Solution oligomerization of the rev protein of HIV-1: implications for function. Biochemistry 32, 11769-11775. [Abstract]
  17. Cole, J.L., Kuo, L.C and Olsen, D.B. (1995) Assay for influenza virus endonuclease using DNA polymerase extension of a specific cleavage product. Anal. Biochem. 231, 309-314. [Abstract]
  18. Cole, J.L., Carroll, S.S. and Kuo, L.C. (1996) Stoichiometry of 2,5-oligoadenylate-induced dimerization of ribonuclease L: A sedimentation equilibrium study. J. Biol. Chem. 271, 3979-3981. [Abstract] [Full Text]
  19. Olsen, D.B., Benseler, F., Cole, J.L., Stahlhut, M.W., Demski, R.E., Darke, P.L. and Kuo, L.C. (1996) Elucidation of the mechanistic and kinetic properties of influenza endonuclease using chemically synthesized RNAs. J. Biol. Chem. 271, 7435-7439. [Abstract] [Full Text]
  20. Darke, P.L., Cole, J.L., Waxman, L., Hall, D.H., Sardana, M.K. and Kuo, L.C. (1996) Active human cytomegalovirus protease is a dimer. J. Biol. Chem. 271, 7445-7449. [Abstract] [Full Text]
  21. Shin, W., Sundaram, U.M., Cole, J.L., Zhang, H.H., Hedman, B., Hodgson, K.O. and Solomon, E.I. (1996) Chemical and spectroscopic definition of the peroxide-level intermediate in the multicopper oxidases: relevance to the catalytic mechanism of dioxygen reduction to water. J. Am. Chem. Soc. 118, 3202-3215. [Full Text]
  22. Cole, J. L. (1996) Characterization of human cytomegalovirus protease dimerization by analytical sedimentation. Biochemistry 35, 15601-15610. [Abstract] [Full Text]
  23. Cole, J.L., Carroll, S.S., Blue, E.S., Viscount, T. and Kuo, L.C. (1997) Activation of RNase L: Biophysical characterization. J. Biol. Chem. 272, 19187-19192. [Abstract] [Full Text]
  24. Carroll, S.S., Cole, J.L., Viscount, T., Geib, J., Gehman, J. and Kuo, L.C. (1997) Activation of RNase L: Kinetic characterization. J. Biol. Chem. 272, 19193-19198. [Abstract] [Full Text]
  25. Yan, Y., Li, Y., Munshi, S., Sardana, V., Cole, J.L., Sardana, M., Steinkuehler, C., Tomei, L., De Francesco, R., Kuo, L.C. and Chen, Z. (1998) Complex of NS3 Protease and NS4A peptide of BK strain hepatitis C virus: a 2.2 Å resolution structure in a hexagonal crystal form. Protein Sci. 7, 837-847. [Abstract] [Full Text]
  26. Li Y., Yan Y., Zugay-Murphy J., Xu B., Cole J.L., Witmer M., Felock P., Wolfe A., Hazuda D., Sardana, M.K., Chen Z., Kuo L.C. and Sardana V.V. (1999) Purification, solution properties and crystallization of SIV integrase containing a continuous core and C-terminal domain. Acta Crystallogr. D Biol. Crystallogr. 55, 1906-1910. [Abstract] [Full Text]
  27. Espeseth, A.S., Felock, P., Wolfe, A., Witmer M., Grobler J., Anthony, N., Egbertson, M., Melamed, J.Y., Young S., Hamill, T., Cole, J.L. and Hazuda, D.J. (2000) HIV-1 integrase inhibitors which compete with the target DNA substrate define a unique strand transfer conformation for integrase. Proc. Natl. Acad. Sci. USA 97, 11244-11249. [Abstract] [Full Text]
  28. Wojtuszewski, K., Hawkins, M.E., Cole, J.L. and Mukerji, I.J. (2001) HU Binding to DNA: Evidence for multiple complex formation and DNA bending. Biochemistry 40, 2588-2598. [Abstract] [Full Text]
  29. Cole, J.L. and Garsky, V.M. (2001) Thermodynamics of peptide inhibitor binding to HIV-1 gp41. Biochemistry 40, 5633-5641. [Abstract] [Full text]
  30. Shaw-Reid, C.A., Munshi, V., Graham, P., Wolfe, A., Witmer, M., Danzeisen, R., Olsen, D.B., Carroll, S.S., Embrey, M., Wai, J.S., Miller, M.D., Cole, J.L. and Hazuda, D.J. (2002) Inhibition of HIV-1 Ribonuclease H by a Novel Diketo Acid: 4-[5-(Benzoylamino)thien-2-yl]-2,4-dioxobutanoic Acid. J. Biol. Chem. 278, 2777-2780. [Abstract] [Full Text]
  31. Ucci, J.W. and Cole, J.L. (2004) Global Analysis of Nonspecific Protein-Nucleic Interactions by Sedimentation Equilibrium. Biophys. Chem., 108, 127-140. [Abstract] [Full text]
  32. Snyder, S., Lary, J., Chen, Y., Gollnick, P. and Cole, J.L. (2004) Interaction of the Trp RNA-binding Attenuation Protein(TRAP) with Anti-TRAP. J. Mol. Biol. 338, 669-682. [Abstract] [Full text]
  33. Lemaire, P.A., Lary, J. and Cole, J.L. (2005) Mechanism of PKR activation: Dimerization and kinase activation in the absence of double-stranded RNA. J. Mol. Biol. 345, 81-90. [Abstract] [Full text]
  34. Liu, Y., Cheney, M.D., Gaudet, J.J., Chruszcz, M., Lukasik, S.M., Sugiyama, D., Lary, J., Cole, J.L., Dauter, Z., Minor, W., Speck, N.A. and Bushweller, J.H. (2006) The tetramer structure of the Nervy homology two domain (NHR2) is critical for AML1/ETO's activity. Cancer Cell 9, 249-260. [Abstract] [Full text]
  35. Lemaire, P.A., Tessmer, I., Craig, R., Erie , D.A. and Cole, J.L. (2006) Unactivated PKR exists in an open conformation capable of binding nucleotides. Biochemistry 45, 9074-9084. [Abstract] [Full text]
  36. Cao, E., Ramagopal, U., Fedorov, A., Fedorov, L.,Yan, Q., Lary, J.W., Cole, J.L., Nathenson, S.G. and Almo S.C. (2006) NTB-A crystal structure: implications for homophilic interactions and signaling within the SLAM family of receptors. Immunity 25, 559-570. [Abstract] [Full Text]
  37. Ucci, J. W., Kobayashi, Y., Choi, G., Alexandrescu, A. and Cole, J. L. (2007) The mechanism of interaction of the dsRNA binding domain of PKR with short dsRNA sequences. Biochemistry 46, 55-65. [Abstract] [Full Text]
  38. Cao, E., Zang, X., Ramagopal, U. A., Mukhopadhaya, A., Fedorov, A., Fedorov, E., Zencheck, W. D., Lary, J. W., Cole, J. L., Deng, H., Xiao, H., Dilorenzo, T. P., Allison, J. P., Nathenson, S. G. and Almo, S. C. (2007). T cell immunoglobulin mucin-3 crystal structure reveals a galectin-9-independent ligand-binding surface. Immunity 26, 311-321. [Abstract] [Full Text]
  39. White, S. R., Evans, K. J., Lary, J., Cole, J. L. and Lauring, B. (2007) Recognition of C-terminal amino acids in tubulin by pore loops in Spastin is important for microtubule severing. J. Cell Biol. 176, 995-1005. [Abstract] [Full Text]
  40. Kang, Y., Chen, X., Lary, J.W., Cole, J. L. and and Walters, K.J. (2007) Defining how ubiquitin receptors hHR23a and S5a bind polyubiquitin. J. Mol. Biol. 369, 168-176. [Abstract] [Full Text]
  41. Yan, Q., Malashkevich, V.N., Fedorov, A., Fedorov, E., Cao, E., Lary, J.W., Cole, J.L., Nathenson, S.G. and Almo S.C. (2007) Structure of CD84 provides insight into SLAM family function. Proc. Natl. Acad. Sci. USA 104, 10583-10588. [Abstract] [Full Text]
  42. Robertson, P.D., Warren, E.M., Zhang, H., Friedman, D.B., Lary, J.W., Cole, J.L., Tutter, A.V., Walter, J.C., Fanning, E., Eichman, B.F. (2008) Domain architecture and biochemical characterization of vertebrate MCM10. J. Biol. Chem. 83, 3338-3348. [Abstract] [Full Text]
  43. Tyukhtenko, S., Deshmukh, L., Kumar, V., Lary, J. Cole, J.L., Lemmon, V. and Vinogradova, O. (2008) Characterization of neuron specific L1-CAM cytoplasmic tail: naturally disordered in solution it exercises different binding modes for different adaptor proteins. Biochemistry 47, 4160-4168. [Abstract] [Full Text]
  44. Anderson, E. and Cole, J.L. (2008) Domain stabilities in PKR: Evidence for weak interdomain interactions. Biochemistry 47, 4887-4897. [Abstract] [Full Text]
  45. Lemaire, P.A., Anderson, E., Lary, J.W. and Cole, J.L. (2008) Mechanism of PKR activation by dsRNA. J. Mol. Biol. 381,351-360. [Abstract] [Full Text]
  46. VanOudenhove, J., Anderson, E., Kreuger, S. and Cole, J.L. (2009) Analysis of PKR structure by small angle scattering. J. Mol. Biol. 387, 910-920. [Abstract] [Full Text]
  47. Heinicke, L.A., Wong, C.J., Lary, J., Nallagatla, S.R., Deigelman-Parente, A., Zheng, X., Cole, J.L. and Bevilacqua, P.C. (2009) RNA Dimerization promotes PKR dimerization and activation. J. Mol. Biol. 390, 319-338. [Abstract] [Full Text]
  48. Zhang, N., Wang, Q. Ehlinger, A., Randles, L., Lary, J. W., Kang, Y., Haririnia, A., Storaska, A. J., Cole, J. L., Fushman, D. and Walters, K. J. (2009) Structure of the S5a:K48-Linked Diubiquitin Complex and Its Interactions with Rpn13. Mol. Cell 35, 280-290.[Abstract] [Full Text]
  49. Anderson E., Quartararo C., Brown R.S., Shi Y., Yao X. and Cole J.L. (2010) Analysis of Monomeric and Dimeric Phosphorylated Forms of Protein Kinase R. Biochemistry 49, 1217-1225. [Abstract] [Full Text]
  50. Launer-Felty, K., Wong, C.J., Wahid, A.M., Conn, G.L. and Cole, J.L. (2010) Magnesium-Dependent Interaction of PKR with adenovirus VAI RNA. J. Mol. Biol. 402, 638-644.[Abstract] [Full Text]
  51. Bryk, R., Wu, K., Raimundo, B.C., Boardman, P.E., Chao, P., Conn, G.L., Anderson, E., Cole, J.L., Duffy, N.P., Nathan, C. and Griffin, J.H. (2011) Identification of new inhibitors of protein kinase R guided by statistical modeling. Biorganic and Medicinal Chemistry Letters, 13, 4108-4114. [Abstract] [Full Text]
  52. Anderson, E., Pierre-Louis, W.S., Wong, C.J., Lary, J.W. and Cole, J.L. (2011) Heparin Activates PKR by Inducing Dimerization.J. Mol. Biol.413,973-984.[Abstract] [Full Text]

Reviews

  1. Sauer, K., Guiles, R.D., McDermott, A.E., Cole, J.L., Yachandra, V.K., Dexheimer, S.L., Britt, R.D., Zimmermann, J.-L. and Klein, M.P. (1988) Spectroscopic studies of manganese involvement in photosynthetic oxygen-evolution. Chimica Scripta 28A, 87-91.
  2. Solomon, E.I., Cole, J.L. and Baldwin, M.J. (1990) Structure function correlations in copper clusters in proteins. Pure Appl. Chem. 62, 1063-1066.
  3. Cole, J.L. (1996) Approaches to high-volume screening assays of viral polymerases and related proteins. Methods Enzymol. 275, 310-328. [Abstract] [Full Text]
  4. Cole, J.L. and Hansen, J.C. (1999) Analytical ultracentrifugation as a contemporary biomolecular research tool. J. Biomolecular Techniques 10, 163-174. [Full Text]
  5. Cole, J.L. (2000) Analytical Ultracentrifugation. in Encyclopedia of Separation Science, Academic Press, London., pp. 313-320.
  6. Cole, J.L. (2004) Analysis of heterogeneous interactions. Meth. Enzymol. 384, 212-232. [Abstract] [Full text]
  7. Cole, J.L. (2007) Activation of PKR: An open and shut case? Trends Biochem. Sci. 32, 57-62. [Abstract] [Full Text]
  8. Cole, J.L., Lary, J.W., Moody, T. and Laue, T.M. (2008) Analytical Ultracentrifugation: Sedimentation Velocity and Sedimentation Equilibrium. Methods Cell Biol. 84, 143-179.[Abstract]
  9. Cole, J.L. (2010) Analysis of PKR activation using analytical ultracentrifugation. Macromol. Biosci. 10, 703-710.[Abstract] [Full Text]
  10. Wong, C.J., Launer-Felty, K. and Cole, J.L. (2011) Analysis of PKR-RNA interactions by sedimentation velocity. Methods Enzymol. 488, 59-79.[Abstract] [Full Text]
  11. Cole, J.L, Correia, J.J. and Stafford, W.F. (2011) The use of analytical sedimentation velocity to extract thermodynamic linkage. Biophys. Chem. 159, 120-128. [Abstract] [Full Text]

Patents

  1. Cole, J.L., Olsen D.B. and Kuo, L.C. DNA Polymerase extension assay for influenza virus endonuclease. U.S. Patent #5,660,989 issued August 27, 1997.
  2. Benseler, F. Cole; J. L., Olsen; D. B. and Kuo, L.C. Capped synthetic RNA, analogs and aptamers. U.S. Patent #5,861,501 issued January 19, 1999.
  3. Cole, J.L., Olsen D.B. and Kuo, L.C. DNA Polymerase extension assay. U.S. Patent #6,100,028 issued August 8, 2000.
  4. Cole, J.L., Kuo, L.C., Olsen, D.B. and Benseler, F. Capped synthetic RNA, analogs and aptamers. U.S. Patent #6,369,208B1 issued April 9, 2002.

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