PUBLICATIONS

Articles

·         Watkins, D., Mohan, S.,  Koudelka, G.B., Williams, L.D., (2010) Sequence Recognition of DNA by Protein-Induced Conformational Transitions. J. Mol. Biol., 396, 1145-64.

·         Lainhart, W., Stolfa, G., Koudelka, G.B. (2009) Shiga Toxin as a Bacterial Defense against a Eukaryotic Predator, Tetrahymena thermophila, , J. Bacteriol., 191, 5116-5122.

·         Watkins, D., Hsiao, C., Woods, K.K., Koudelka, G.B., Williams, L.D., (2008) P22 c2 Repressor-Operator Complex: Mechanisms of Direct and Indirect Readout. Biochemistry 47, 2325-2338.

·         Shkilnyj, P. and Koudelka, G.B. (2007) Effect of Salt Shock on the Stability of λimm434 Lysogens, J. Bacteriol., 189:3115-3123.

·         McCabe, B.C., Pawlowski, D.R., Koudelka, G.B. (2005) The bacteriophage 434 repressor dimer preferentially undergoes autoproteolysis by intramolecular mechanism. J. Bacteriol., 187 5624-30

·         Koudelka, G.B., Hufnagel, LA, Koudelka, A.P. (2004) Isolation, Purification and Characterization of a Repressor from the Toxin-encoding Bacteriophage 933W J. Bacteriol., 186 7659-7669.

·         Mauro, S.A., Koudelka, G.B. (2004) Monovalent Cations Direct Sequence Recognition by 434 Repressor, J. Mol. Biol 340 445-457.

·         Pawlowski, D.R., Koudelka, G.B. (2004) The Preferred Substrate for RecA-Mediated Cleavage of Bacteriophage 434 Repressor is the DNA-Bound Dimer  J. Bacteriol., 185 1-6.

·         Ciubotaru, M., Koudelka, G.B. (2003) DNA Allosterically Modulates the Cooperative DNA Binding Interactions of 434 Bacteriophage Repressor. Biochemistry, 42,4253-4264.

·         Mauro, S.A., Pawlowski, Koudelka, G.B. (2003) The Role of the Minor Groove Substituents in Indirect Readout of DNA Sequence by 434 Repressor, J. Biol. Chem, 278, 12955-12960.

·         Xu, J., Koudelka, G.B. (2001) Repression of Transcription Initiation at 434 PR by 434 Repressor: Effects on Transition of a Closed to an Open Promoter Complex. J. Mol. Biol. 309, 573-587.

·         Xu, J., McCabe, B.C., Koudelka, G.B. (2001) Function-Based Selection and Characterization of Base pair Polymorphisms in a Promoter of E. coli RNA polymerase-s70, J. Bacteriol., 183, 2866-2873.

·         Xu, J. Koudelka, G.B. (2000) DNA Sequence Requirements for the Activation of 434 PRM Transcription by 434 Repressor. DNA and Cell Biol. 19, 621-630.

·         Xu, J., Koudelka, G.B. (2000) Mutually Exclusive Utilization of PR and PRM Promoters in Bacteriophage 434 OR, J. Bacteriol. 182, 3165-3174

·         Ciubotaru, M., Bright, F.V., Ingersoll, C.M., Koudelka, G.B. (1999) DNA-Induced Conformational Changes in Bacteriophage 434 Repressor, J. Mol. Biol.,294, 859-873.

·         Donner, A.L., Paa, K. & Koudelka, G.B. (1998) Carboxyl-Terminal Domain Dimer Interface Mutant 434 Repressors Have Altered Dimerization and DNA Binding Specificities. J. Mol. Biol., 283, 931-946.

·         Xu, J., Koudelka, G.B. (1998) DNA-based Positive Control Mutants in the Binding Site of 434 Repressor.  J. Biol. Chem. 273, 24165-24172.

·         Koudelka, G.B. (1998) Recognition of DNA Structure by 434 Repressor, Nucleic Acids Res. 26, 669-675.

·         Hilchey, S.P., Wu, L. & Koudelka, G.B. (1997) Recognition of Nonconserved Bases in the P22 Operator by P22 Repressor Requires Specific Interaction Between Repressor and Conserved Bases J. Biol. Chem. 272, 19898-19906.

·         Donner, A.L., Carlson, P.A. & Koudelka, G.B. (1997) Dimerization Specificity of P22 and 434 Repressors Is Determined by Multiple Polypeptide Segments. J. Bacteriol. 179, 1273-1271.

·         Hilchey, S.P., Koudelka, G.B. (1997) DNA-Based Loss of Specificity Mutations: Effects of DNA Sequence on the Contacted and Noncontacted Base Preferences of Bacteriophage P22 Repressor. J. Biol. Chem. 272, 1646-1653

·         Bell, A.C. & Koudelka, G.B., (1995) How 434 Repressor Discriminates Between OR1 and OR3: The Influence of Contacted and Noncontacted Base Pairs J. Biol. Chem. 270, 1205-1212.

·         Carlson, P.A. & Koudelka, G.B. (1994) Expression, Purification and Functional Characterization of the Carboxyl Terminal Domain Fragment of 434 Repressor.  J. Bacteriol. 176, 6907-6914

·         Koudelka, G.B. & Lam, C.-Y. (1993) Differential Recognition of OR1 and OR3 by Bacteriophage 434 Repressor and Cro. J. Biol. Chem. 268, 23812-23817.

·         Bell, A.C. & Koudelka, G.B. (1993) Operator Sequence Context Influences Amino Acid-Base Pair Interactions in 434 Repressor-Operator Complexes. J. Mol. Biol. 234, 542-553.

·         Wu, L. & Koudelka, G.B. (1993) Sequence Dependent Differences in DNA Structure Affect the Affinity of P22 Operators for P22 Repressor. J. Biol. Chem. 268, 18975-18981.

·         Wu, L., Vertino, A., & Koudelka, G.B. (1992) Non-Contacted Bases in the P22 Operator Affect its Affinity for P22 Repressor, J. Biol. Chem. 267, 9134-9139.

·         Koudelka, G.B., & Carlson, P.A. (1992) DNA Twisting and the Effects of Non-Contacted Bases on the Affinity of 434 Operator for 434 Repressor, Nature 355, 89-91.

·         Koudelka, G.B. (1991) Bending of Synthetic Bacteriophage 434 Operators by Bacteriophage 434 Proteins, Nucl. Acids Res. 19, 4115-4119.

·         Koudelka, G.B., Harbury, P.B., Harrison, S.C., & Ptashne, M. (1988) DNA Twisting and the Affinity of Bacteriophage 434 Operator for Bacteriophage 434 Repressor. Proc. natl. Acad. Sci., USA 85, 4633-4637.

·         Harrison,S.C., Anderson, J.E., Koudelka, G.B., Mondragon, A., Subbiah, S. Wharton, R.P., Wolberger, C., & Ptashne, M. (1988) Recognition of DNA Sequences by the Repressor of Bacteriophage 434.  Biophys. Chem. 29, 31-37.

·         Koudelka, G.B., & Ettinger, M.J. (1988) Fluoride Effects on the Activity of Rhus Laccase and the Catalytic Mechanism Under Steady‑state Conditions J. Biol. Chem. 263, 3698-3705.

·         Koudelka, G.B., Harrison, S.C., Ptashne, M. (1987) Non‑contacted Bases In the 434 Operator Affect Its Affinity for 434 Repressor and Cro. Nature 326, 886‑888.

·         Koudelka, G.B., Hansen, F.B., & Ettinger, M.J. (1985) Solvent Isotope Effects and the pH Dependence of Laccase Activity under Steady‑state Conditions. J. Biol. Chem. 260, 15561.

·         Hansen, F.B., Koudelka, G.B., Noble, R.W., & Ettinger, M.J. (1984) Effects of a Single Reduction‑Reoxidation Cycle on the Kinetics of Copper Reduction in Rhus Laccase.  Biochemistry 23, 2057‑2064.

Invited Reviews (peer reviewed)

·         Koudelka, G.B., Mauro, S.A., Ciubotaru M. (2006) Indirect Readout of DNA Sequence by Proteins: The Roles of DNA Sequence-Dependent Intrinsic and Extrinsic Forces. Progress in Nucleic Acids Research, 81: 143-177.

·         Koudelka, G.B. (2000) Cooperativity: Action at a distance in a classic system. Current Biology 10:R704-R707.

·         Koudelka, G.B. (1998) Repressors in Encyclopedia of Molecular Biology (T. Creighton, ed.) Wiley, New York.

·         Koudelka G.B., Xu, J.& Hilchey, S.P. (1997) Effects of DNA Sequence Directed Structural Differences on Transcription in Prokaryotes. In Nucleic Acids and Molecular Biology, (D.M.J. Lilley, F. Eckstein, eds). Springer-Verlag, Berlin.

·         Koudelka, G.B. (1993) Indirects Effects of DNA Sequence on 434 Repressor-DNA Interactions. In Nucleic Acids and Molecular Biology, Volume 7, pp. 16-27 (D.M.J. Lilley, F. Eckstein, eds). Springer-Verlag, Berlin.

Book Chapters

·         Koudelka, G.B. Donner, A.L., Ciubotaru, M. (1999) Role of the N- and C- Terminal Dimer Interfaces of 434 Repressor in Recognizing Sequence-Dependent DNA Structure Biol. Struct and Dyn.

·         Koudelka, G.B., Bell, A.C., Hilchey, S.P. (1996) Indirect Effects of DNA Sequence on Protein-DNA Interactions Biol. Struct and Dyn.1, 135-153

·         Koudelka, G.B., Harrison, S.C., & Ptashne, M.P. (1987) DNA Structure Modulates the Affinity of 434 Operator for 434 Repressor and Cro. in "Protein Structure and Design", UCLA Symposia on Molecular and Cellular Biology, New Series, Volume 69, (Dale Oxender, ed.). Alan R. Liss, Inc. New York.