Harish B, Swapna GV, Kornhaber GJ, Montelione GT, Carey J. Multiple helical
conformations of the helix-turn-helix region revealed by NOE-restrained MD
simulations of tryptophan aporepressor, TrpR. Proteins. 2017 Apr;85(4):731-740.
doi: 10.1002/prot.25252. Epub 2017 Feb 22. PubMed PMID: 28120439.

Sprenger J, Carey J, Svensson B, Wengel V, Persson L. Binding and inhibition of spermidine synthase from Plasmodium falciparum: Implications for in vitro inhbitor testing. PLoS One. 2016 Sep 23; 11(9):e163442. doi: 10.1371/journal.pone.0163442.

Csefalvay E, Lapkouski M, Guzanova A, Csefalvay L, Baikova T, Shevelev I, Bialevich V, Shamayeva K, Janscak P, Kuta Smatanova I, Panjikar S, Carey J, Weiserova M, Ettrich R. Functional coupling of duplex translocation to DNA cleavage in a type I restriction enzyme. PLoS One. 2015 Jun 3;10(6):e0128700. doi: 10.1371/journal.pone.0128700.

Sprenger J, Svensson B, Hålander J, Carey J, Persson L, Al-Karadaghi S. Three-dimensional structures of Plasmodium falciparum spermidine synthese with bound inhibitors suggest new strategies for drug design. Acta Cryst. D. 2015 Mar; 71(Pt3):484-493. doi:10.1107/S1399004714027011.

Řeha D, Harish B, Sinha D, Kukacka Z, McSally J, Ettrichova O, Novak P, Carey  J, Ettrich R. Molecular dynamics comparison of E. coli WrbA apoprotein and holoprotein. J Mol Model. 2014 Sep;20(9):2400. doi: 10.1007/s00894-014-2400-8.

Sinha D, Shamayeva K, Ramasubramani V, Řeha D, Bialevich V, Khabiri M, Guzanová A, Milbar N, Weiserová M, Csefalvay E, Carey J, Ettrich R. Interdomain communication in the endonuclease/motor subunit of type I restriction-modification enzyme EcoR124I. J Mol Model. 2014 Jul;20(7):2334. doi:  10.1007/s00894-014-2334-1.

Pandey SK, Řeha D, Zayats V, Melichercik M, Carey J, Ettrich R. Binding-competent states for L-arginine in E. coli arginine repressor apoprotein. J Mol Model. 2014 Jul;20(7):2330. doi: 10.1007/s00894-014-2330-5.

Kishko I, Carey J, Reha D, Brynda J, Winkler R, Harish B, Guerra R, Ettrichova O, Kukacka Z, Sheryemyetyeva O, Novak P, Kuty M, Kuta Smatanova I, Ettrich R, Lapkouski M. 1.2 Å resolution crystal structure of Escherichia coli WrbA holoprotein. Acta Crystallogr D Biol Crystallogr. 2013 Sep;69(Pt 9):1748-57. doi: 10.1107/S0907444913017162. Epub 2013 Aug 15. PubMed PMID: 23999298.

Slavov N, Carey J, Snogerup Linse S (2013) “Calmodulin transduces Ca2+ oscillations into differential regulation of its target proteins.” ACS Chemical Neuroscience Apr 17;4(4):601-12. doi: 10.1021/cn300218d. Epub 2013 Feb 5. PubMed PMID: 23384199; PubMed Central PMCID: PMC3629746.

Kopecky V Jr, Kohoutova J, Lapkouski M, Hofbauerova K, Sovova Z, Ettrichova O, González-Pérez S, Dulebo A, Kaftan D, Smatanova IK, Revuelta JL, Arellano JB, Carey J, Ettrich R. “Raman spectroscopy adds complementary detail to the high-resolution x-ray crystal structure of photosynthetic PsbP from Spinacia oleracea.” PLoS One. 2012;7(10):e46694. doi: 10.1371/journal.pone.0046694. Epub 2012 Oct 5. PubMed PMID: 23071614; PubMed Central PMCID: PMC3465285.

Kishko I, Harish B, Zayats V, Tenner B, Beri D, Gustavsson T, Ettrich R, Carey J (2012) “Biphasic kinetic behavior of E. coli WrbA, an FMN-dependent NAD(P)H:quinone oxidoreductase.” PLoS One 7(8):e43902. doi: 10.1371/journal.pone.0043902. Epub 2012 Aug 29. PubMed PMID: 22952804; PubMed Central PMCID: PMC3430622.

Carey J, Benoff B, Harish B, Yuan L, Lawson CL. Environment-dependent long-range structural distortion in a temperature-sensitive point mutant. Protein
Sci. 2012 Jan;21(1):63-74. doi: 10.1002/pro.759. Epub 2011 Dec 8. PubMed PMID: 22057811; PubMed Central PMCID: PMC3323781.

Carey J, Benoff B, Harish B, Yuan L, Lawson CL (2012) “Environment-dependent long-range structural distortion in a temperature-sensitive point mutant.” Protein Sci. 21, 63-74.

Strawn R, Melichercik M, Green M, Stockner T, Carey J*, Ettrich R (2010) “Concerted allosteric mechanism of hexameric E. coli arginine repressor exploits competition between L-arginine ligands and resident arginine residues.” (2010) PLoS Comput. Biol. 6 (6): e1000801. *corresponding author

Strawn R, Stockner, T., Melichercik, M., Jin, L., Xue, W.-F., Carey J*, Ettrich R (2010) “Synergy of molecular dynamics and isothermal titration calorimetry in studies of allostery.” Methods in Enzymology, 492, 151-188. *corresponding author

Wolfová J, Smatanová IK, Brynda J, Mesters JR, Lapkouski M, Kuty M, Natalello A, Chatterjee N, Chern S-Y, Ebbel E, Ricci A, Grandori R, Ettrich R, Carey J. (2009) “Structural organization of WrbA in apo- and holo-protein crystals,” Bioch. Biophys. Acta, 1794, 1288-1298. cover story

Xue W-F, Szczepankiewicz O, Thulin E, Linse S, Carey J. (2009) “Role of protein surface charge in monellin sweetness.” Bioch. Biophys. Acta 1794, 410-420.

Lapkouski M, Panjikar S, Janscak P, Smatanová IK, Carey J*, Ettrich R, Csefalvay E. (2009) “Structure of the motor subunit of type I restriction-modification complex EcoR124I.” Nature Structural and Molecular Biology 16, 94-95. *corresponding author

Carey J*, Brynda J, Wolfová J, Grandori R, Gustavsson T, Ettrich R, Smatanová IK. (2007) “WrbA bridges bacterial flavodoxins and eukaryotic NAD(P)H:quinone oxidoreductases,” Protein Science 16, 2301-2305. *corresponding author; cover story

Carey J, Lindman S, Bauer M, Linse S. (2007) “Protein fragment reconstitution and three-dimensional domain swapping, ” Protein Science 16, 2317-2333. cover story

Wolfová J, Mesters JR, Brynda J, Grandori R, Natalello A, Carey J, Smatanová IK. (2007) “Crystallization and preliminary diffraction analysis of E. coli WrbA in complex with its cofactor flavin mononucleotide,” Acta Cryst.F63, 571-575.

Brauner A, Carey J, Henriksson M. Sunnerhagen M, Ehrenborg E. (2007) “Open-ended assignments and student responsibility,” Biochemistry and Molecular Biology Education, 35, 187-192.

Natalello A, Doglia SM, Carey J, Grandori R. (2007) “Role of FMN in Thermostability and oligomerization of E. coli stress-defense protein WrbA,” Biochemistry 46, 543-553.

Ji H, Shen L, Carey J, Grandori R, Zhang H. (2006) “Weaker binding of FMN by WrbA than by flavodoxin: a molecular modeling study,” J. Molec. Struct. Theo. Chem., 764, 155-160.

Nöll G, Kozma E, Grandori R, Carey J, Schödl T, Hauska G, Daub J. (2006) “Spectroelectrochemical investigation of a flavoprotein with a flavin-modified gold electrode,” Langmuir 22, 2378-2383.

Wolfova J, Grandori R, Kozma E, Chatterjee N, Carey J, Smatanova I. (2005) “Crystallization of the flavoprotein WrbA optimized using additives and gels,” J. Cryst. Growth 284, 502-505.

Samalikova M, Carey J, Grandori R. (2005) “Assembly of the hexameric Escherichia coli arginine repressor investigated by nano-ESI-TOF mass spectrometry,” Rapid Comm. Mass Spec. 19, 2549-2552.

Patel, K.A., Bartoli, K., Ngatchou, A.N., Wocj, G., Carey, J., & Tanaka, J.C. (2005) “Impaired function and trafficking of cyclic nucleotide-gated channel mutants from human cone CNGA3 causing achromatopsia 2,” Invest. Ophthamol. Visual Sci. 46, 2282-2290.

Jin, L., Xue, W.-F., Fukayama, J.W., Yetter, J., Pickering, M., & Carey, J. (2005) “Asymmetric allosteric activation of the symmetric ArgR hexamer,” J. Mol. Biol. 346, 43-56.

Xue, W.-F., Carey, J., & Linse, S. (2004) “Multi-method global analysis of thermodynamics and kinetics in reconstitution of monellin,” Proteins: Structure, Function, and Bioinformatics, 57, 586-595.

Pursglove SE, Fladvad M, Bellanda M, Moshref A, Henriksson M, Carey J, Sunnerhagen M. (2004 ) “Biophysical properties of regions flanking the bHLH-Zip motif in the p22 Max protein,” Biochem Biophys Res Commun.323,750-9.

Lawson, C.L., Benhoff, B., Berger, T., Berman, H.M., & Carey, J. (2004) “E. coli trp repressor forms a domain-swapped array in aqueous alcohol,” Structure 12, 1098-1107.

Szwajkajzer, D. & Carey, J. (2003) “RaPID plots: Affinity and mechanism at a glance,” Biacore J. 3 (1), 19.

McWhirter, A. & Carey, J. (2003) “T-cell receptor recognition of peptide antigen/MHC complexes,” Biacore J. 3(1), 18.

Tyler, R., Pelczer, I., Carey, J., & Copie, V. (2002) “Three-dimensional solution NMR structure of apo-L75F-TrpR, a temperature-sensitive mutant of the tryptophan repressor protein,” Biochemistry 41, 11954-11962.

Szwajkajzer, D., Dai, L., Fukayama, J.W., Abramczyk, B., Fairman, R., & Carey, J. (2001) “Quantitative Analysis of DNA Binding by E. coli Arginine Repressor,” J. Mol. Biol. 312, 949-962.

Scott, S.-P., Weber, I.T., Harrison, R.W., Carey, J., & Tanaka, J.C. (2001) “A Functioning Chimera of the Cyclic Nucleotide-binding Domain from the Bovine Retinal Rod Ion Channel and the DNA-binding Domain from Catabolite Gene-Activating Protein,” Biochemistry 40, 7464-7473.

Carey, J. (2000) “A Systematic, General Proteolytic Method for Defining Structural and Functional Domains of Proteins,” Meths. Enzymol., 328, 499-514.

Carey, J. (2000) “Globularity and Protein Function,” J. Biomol. Str. Dyn. 11, 87-88.

Kang, X., & Carey, J. (1999) “Role of Heme in Structural Organization of Cytochrome c Probed by Semisynthesis,” Biochemistry 38, 15944-15951.

Wallqvist, A., Lavoie, T.A., Chanatry, J.A., Covell, D.G., & Carey, J. (1999) “Cooperative Folding Units in E. coli Tryptophan Repressor,” Biophys. J. 77, 1619-1626.

Kang, X., & Carey, J. (1999) “Structural Organization in Peptide Fragments of Cytochrome c by Heme Binding,” J. Mol. Biol. 285, 463-468.

Jin, L., Fukayama, J.W., Pelczer, I., & Carey, J. (1999) “Long-range Effects on Dynamics in a Temperature-sensitive Mutant of trp Repressor,” J. Mol. Biol. 285, 361-378.

Winters, M.A., Frankel, D.Z., Debenedetti, P.G., Carey, J., Devaney, M., & Przybycien, T.M. (1999) “Protein Purification with Vapor-Phase Carbon Dioxide,” Biotech. Bioeng., 62, 247-258.

Sunnerhagen, M., Denisov, V.P., Venu, K., Carey, J., Halle, B., & Otting, G. (1998) “Water Molecules in DNA Recognition. I. Hydration Lifetimes of the trp Operator in Solution Measured by NMR Spectroscopy,” J. Mol. Biol.282, 847-858.

Grandori, R., Khalifah, P., Boice, J.A., Fairman, R., Giovanielli, K., & Carey, J. (1998) “Biochemical Characterization of WrbA, Founding Member of a New Family of Multimeric Flavodoxins,” J. Biol. Chem. 273, 20960-20966.

Szwajkajzer, D. & Carey, J. (1997) “Molecular and Biological Constraints on Ligand-binding Affinity and Specificity,” Biopolymers 44, 181-198.

Sunnerhagen, M.S., Nilges, M., Otting, G., & Carey, J., (1997) “Solution Structure of the DNAbinding Domain and Model for the Complex of Multifunctional, Hexameric Arginine Repressor with DNA,” Nature Structural Biology 4, 819-825.

Grandori, R., Struck, K., Giovanielli, K., & Carey, J. (1997) “A Three-Step Protocol for Construction of Chimeric Proteins,” Protein Engineering 10, 1099-1100.

Winters, M.A., Debenedetti, P.G., Carey, J., Sparks, H.G., Sane, S.U., & Przybycien, T.M. (1997) “Long-Term Storage of Supercritically-Processed Microparticulate Protein Powders,” Pharm. Res. 14, 1370-1378.

Yang, J., Gunasekera, A., Lavoie, T.A., Jin, L., Lewis, D.E.A., & Carey, J. (1996) “In vivo and in vitro Studies of TrpR-DNA Interactions,” J. Mol. Biol. 258, 37-52.

Grandori, R., Lavoie, T.A., Pflumm, M., Tian, G., Niersbach, H., Maas, W.K., Fairman, R., & Carey, J., (1995) “The DNA-Binding Domain of the Hexameric Arginine Repressor, ” J. Mol. Biol. 254, 150-162.

Yang, J., & Carey, J. (1995) “Footprint Phenotypes: Structural Models for DNA-Binding Proteins from Chemical Modification-Protection Analysis of DNA,” Meths. Enzymol. 259, 452-468.

Lavoie, T.A., & Carey, J. (1994) “Being Direct,” Nature Str. Biol. 1, 679.

Grandori, R., & Carey, J. (1994b) “Six New Candidate Members of the α/β Twisted Open- Sheet Family Detected by Sequence Similarity to Flavodoxins,” Prot. Sci. 3, 2185-2193.

Martin, K.S., Royer, C.A., Howard, K.P., Carey, J., Liu, Y.-C., Matthews, K.S., Heyduk, E., and Lee, J.C. (1994) “Salt, High pH, and Corepressor Destabilize Higher Order Oligomers of the trp Repressor Dimer,” Biophys. J. 66, 1167-1173.

Wu, L.C., Grandori, R., & Carey, J. (1994) “Autonomous Subdomains in Protein Folding,”Protein Science 3, 369-371.

Lavoie, T.A. & Carey, J. (1994) “Adaptability and Specificity in DNA Binding by trp Repressor,” Nucleic Acids & Molecular Biology 8, 184-196.

Grandori, R., & Carey, J. (1994a) “Two Highly Homologous Putative DNA-Binding Proteins in Yeast and E. coli,” Trends in Biochemical Sciences 19, 72.

Lawson, C.L., & Carey, J. (1993) “Tandem Binding in Crystals of a trp Repressor/Operator Half-site Complex,” Nature, 366, 178-182.

Wu, L.C., Laub, P., Elöve, G., Carey, J., & Roder, H. (1993) “A Noncovalent Peptide Complex as a Model for an Early Folding Intermediate of Cytochrome c,” Biochemistry 32, 10271-10276.

Carey, J., Combatti, N., Lewis, D.E.A., & Lawson, C.L. (1993) “Cocrystals of E. coli trp Repressor Bound to an Alternative Operator DNA Sequence,” J. Mol. Biol. 234, 496-498.

Lewis, D.E.A., & Carey, J. (1993) “Analysis of trp Repressor-DNA Interactions Using Gel Electrophoresis,” Electrophoresis 14, 713-719.

Jin, L., Yang, J., & Carey, J. (1993) “Thermodynamic Analysis of Ligand Binding to trp Repressor,” Biochemistry32 7302-7309.

Tian, G., Lim, D., Carey, J., & Maas, W. K. (1992) “Binding of the Arginine Repressor of E.coli K-12 to Its Operator.” J. Mol. Biol. 226, 387-397.

Tasayco, M.-L. & Carey, J. (1992) “Ordered Self-Assembly of Polypeptide Fragments to Form Nativelike Dimeric trp Repressor.” Science 255, 594-597.

Carey, J., Lewis, D.E.A., Lavoie, T. A., & Yang, J. (1991) “How Does trp Repressor Bind to Its Operator?” J. Biol. Chem. 266, 24509-24513.

Carey, J. (1991) “Gel Retardation” in Methods in Enzymology (R.T. Sauer, ed.) 208, 103-117.

Arrowsmith, C.H., Carey, J., Treat-Clemons, L., and Jardetzky, O. (1989) “NMR Assignments for the Amino-terminal Residues of trp Repressor and Their Role in DNA Binding.” Biochemistry 28, 3875.

Carey, J. (1989) “trp Repressor Arms Contribute Binding Energy without Occupying Unique Locations on DNA.” J. Biol. Chem. 264, 1941.

Carey, J. (1988) “Gel Retardation at Low pH Resolves trp Repressor-DNA Complexes for Quantitative Study.” Proc. Natl. Acad. Sci. 85, 975.

Klig, L.S., Carey, J., and Yanofsky, C. (1988) “trp Repressor Interactions with the trp EDCBA, aro H, and trp R Operators: Comparison of Repressor Binding in vitro and Repression in vivo.” J. Mol. Biol. 202, 969.

Landick, R., Carey, J., and Yanofsky, C. (1987) “Detection of Transcription Pausing in vivo in the trp Operon Leader Region.” Proc. Natl. Acad. Sci. 84, 1507.

Landick, R., Carey, J., and Yanofsky, C. (1985) “Translation Activates the Paused Transcription Complex and Restores Transcription of E. coli trp Leader Region.” Proc. Natl. Acad. Sci. 82, 4663.

Uhlenbeck, O.C., Carey, J., Romaniuk, P., Lowary, P.T., and Beckett, D. (1984) “Interaction of R17 Coat Protein with Its RNA Binding Site for Translational Repression.” J. Molec. Struct. Dyn. 1, 539.

Carey, J., Cameron, V., Krug, M., deHaseth, P.L., and Uhlenbeck, O.C. (1984) “Failure of Translational Repression in the Phage f2 op3 Mutant Is Not Due to an Altered Coat Protein-RNA Interaction.” J. Biol. Chem. 259, 20.

Bauer, C., Carey, J., Kasper, L., Lynn, S., Waechter, D., and Gardner, J. (1983) “Attenuation in Bacterial Operons” in Gene Function in Prokaryotes, Cold Spring Harbor Laboratory Press.

Carey, J., Lowary, P.T., and Uhlenbeck. O.C., (1983) “Interaction of R17 Coat Protein with Synthetic Variants of Its RNA Binding Site.” Biochemistry 22, 4723.

Carey, J., and Uhlenbeck, O.C., (1983) “Kinetic and Thermodynamic Characterization of the R17 Coat Protein-RNA Interaction.” Biochemistry 22, 2610.

Carey, J., Cameron, V., deHaseth, P.L., and Uhlenbeck, O.C. (1983) “Sequence-Specific Interaction of R17 Coat Protein with Its Ribonucleic Acid Binding Site.” Biochemistry 22, 2601.