Slow Assembly and Disassembly of λ Cro Repressor Dimers

Davidson, 2002, A genomic regulatory network for development, Science, 295, 1669, 10.1126/science.1069883 Ronen, 2002, Assigning numbers to the arrows: parameterizing a gene regulation network by using accurate expression kinetics, Proc. Natl Acad. Sci. USA, 99, 10555, 10.1073/pnas.152046799 von Hippel, 1996, Specificity mechanisms in the control of transcription, Biophys. Chem., 59, 231, 10.1016/0301-4622(96)00006-3 Record, 1991, Analysis of equilibrium and kinetic measurements to determine thermodynamic origins of stability and specificity and mechanism of formation of site-specific complexes between proteins and helical DNA, Methods Enzymol., 208, 291, 10.1016/0076-6879(91)08018-D Ptashne, 2004 Takeda, 1977, Cro regulatory protein specified by bacteriophage lambda. Structure, DNA-binding, and repression of RNA synthesis, J. Biol. Chem., 252, 6177, 10.1016/S0021-9258(17)40047-0 Johnson, 1980, Bacteriophage lambda repressor and cro protein: interactions with operator DNA, Methods Enzymol., 65, 839, 10.1016/S0076-6879(80)65078-2 Smith, 1998, Cro, CAP and lambda repressor led the way, Nature Struct. Biol., 5, 29, 10.1038/nsb0198-29 Johnson, 1978, Mechanism of action of the cro protein of bacteriophage lambda, Proc. Natl Acad. Sci. USA, 75, 1783, 10.1073/pnas.75.4.1783 Boschelli, 1982, Lambda phage cro repressor. DNA sequence-dependent interactions seen by tyrosine fluorescence, J. Mol. Biol., 162, 251, 10.1016/0022-2836(82)90525-3 Hochschild, 1986, How lambda repressor and lambda Cro distinguish between OR1 and OR3, Cell, 47, 807, 10.1016/0092-8674(86)90523-4 Pakula, 1986, Bacteriophage lambda cro mutations: effects on activity and intracellular degradation, Proc. Natl Acad. Sci. USA, 83, 8829, 10.1073/pnas.83.23.8829 Mossing, 1990, Stable, monomeric variants of lambda Cro obtained by insertion of a designed beta-hairpin sequence, Science, 250, 1712, 10.1126/science.2148648 Pakula, 1989, Amino acid substitutions that increase the thermal stability of the lambda Cro protein, Proteins: Struct. Funct. Genet., 5, 202, 10.1002/prot.340050303 Griko, 1992, Domains in lambda Cro repressor. A calorimetric study, Biochemistry, 31, 12701, 10.1021/bi00165a022 Jana, 1997, A folded monomeric intermediate in the formation of lambda Cro dimer-DNA complexes, J. Mol. Biol., 273, 402, 10.1006/jmbi.1997.1256 Ohlendorf, 1982, The molecular basis of DNA-protein recognition inferred from the structure of cro repressor, Nature, 298, 718, 10.1038/298718a0 Albright, 1998, Crystal structure of lambda-Cro bound to a consensus operator at 3.0Å resolution, J. Mol. Biol., 280, 137, 10.1006/jmbi.1998.1848 Rupert, 2000, The structural basis for enhanced stability and reduced DNA binding seen in engineered second-generation Cro monomers and dimers, J. Mol. Biol., 296, 1079, 10.1006/jmbi.1999.3498 Darling, 2000, Coupled energetics of lambda cro repressor self-assembly and site-specific DNA operator binding I: analysis of cro dimerization from nanomolar to micromolar concentrations, Biochemistry, 39, 11500, 10.1021/bi000935s Jana, 1998, Single-chain lambda Cro repressors confirm high intrinsic dimer–DNA affinity, Biochemistry, 37, 6446, 10.1021/bi980152v Pakula, 1990, Reverse hydrophobic effects relieved by amino-acid substitutions at a protein surface, Nature, 344, 363, 10.1038/344363a0 Ohlendorf, 1998, Refined structure of Cro repressor protein from bacteriophage lambda suggests both flexibility and plasticity, J. Mol. Biol., 280, 129, 10.1006/jmbi.1998.1849 Albright, 1996, High-resolution structure of an engineered Cro monomer shows changes in conformation relative to the native dimer, Biochemistry, 35, 735, 10.1021/bi951958n Mollah, 1996, Core packing defects in an engineered Cro monomer corrected by combinatorial mutagenesis, Biochemistry, 35, 743, 10.1021/bi951959f Hubbard, 1990, Role of the Cro repressor carboxy-terminal domain and flexible dimer linkage in operator and nonspecific DNA binding, Biochemistry, 29, 9241, 10.1021/bi00491a019 Satumba, 2002, Folding and assembly of lambda Cro repressor dimers are kinetically limited by proline isomerization, Biochemistry, 41, 14216, 10.1021/bi026777h Wu, 1994, Resonance energy transfer: methods and applications, Anal. Biochem., 218, 1, 10.1006/abio.1994.1134 Jonsson, 1996, Nonlinear free energy relationships in Arc repressor unfolding imply the existence of unstable, native-like folding intermediates, Biochemistry, 35, 4795, 10.1021/bi953056s Wendt, 1995, Kinetics of folding of leucine zipper domains, Biochemistry, 34, 4097, 10.1021/bi00012a028 Liu, 2002, 3D domain swapping: as domains continue to swap, Protein Sci., 11, 1285, 10.1110/ps.0201402 Filimonov, 1996, Reversible association of the equilibrium unfolding intermediate of lambda Cro repressor, J. Mol. Biol., 255, 767, 10.1006/jmbi.1996.0062 Shea, 1985, The OR control system of bacteriophage lambda. A physical–chemical model for gene regulation, J. Mol. Biol., 181, 211, 10.1016/0022-2836(85)90086-5 Arkin, 1998, Stochastic kinetic analysis of developmental pathway bifurcation in phage lambda-infected Escherichia coli cells, Genetics, 149, 1633, 10.1093/genetics/149.4.1633 Aurell, 2002, Stability puzzles in phage lambda, Phys. Rev. E, 65, 051914, 10.1103/PhysRevE.65.051914 Santillan, 2004, Why the lysogenic state of phage lambda is so stable: a mathematical modeling approach, Biophys. J., 86, 75, 10.1016/S0006-3495(04)74085-0 Little, 1999, Robustness of a gene regulatory circuit, EMBO J., 18, 4299, 10.1093/emboj/18.15.4299 Rentzeperis, 1999, Acceleration of the refolding of Arc repressor by nucleic acids and other polyanions, Nature Struct. Biol., 6, 569, 10.1038/9353 Cranz, 2004, Monomeric and dimeric bZIP transcription factor GCN4 bind at the same rate to their target DNA site, Biochemistry, 43, 718, 10.1021/bi0355793 Kohler, 2001, Effects of nucleic acids and polyanions on dimer formation and DNA binding by bZIP and bHLHZip transcription factors, Bioorg. Med. Chem., 9, 2435, 10.1016/S0968-0896(01)00221-8 Bradford, 1976, A rapid and sensitive method for the quantitation of microgram quantities of protein utilizing the principle of protein–dye binding, Anal. Biochem., 72, 248, 10.1016/0003-2697(76)90527-3