Secondary Structure Switching in Cro Protein Evolution

Abel, 1996, An alpha to beta conformational switch in EF-Tu, Structure, 4, 1153, 10.1016/S0969-2126(96)00123-2

Albright, 1998, Crystal structure of lambda-Cro bound to a consensus operator at 3.0 Å resolution, J. Mol. Biol., 280, 137, 10.1006/jmbi.1998.1848

Altschul, 1997, Gapped BLAST and PSI-BLAST, Nucleic Acids Res., 25, 3389, 10.1093/nar/25.17.3389

Arseniev, 1988, Three-dimensional structure of rabbit liver [Cd7]metallothionein-2a in aqueous solution determined by nuclear magnetic resonance, J. Mol. Biol., 201, 637, 10.1016/0022-2836(88)90644-4

Aurora, 1998, Helix capping, Protein Sci., 7, 21, 10.1002/pro.5560070103

Bax, 1994, Measurement of homo- and heteronuclear J couplings from quantitative J correlation, Methods Enzymol., 239, 79, 10.1016/S0076-6879(94)39004-5

Bolten, 2001, Clustering protein sequences—structure prediction by transitive homology, Bioinformatics, 17, 935, 10.1093/bioinformatics/17.10.935

Branden, 1991

Brunger, 1998, Crystallography & NMR system, Acta Crystallogr. D Biol. Crystallogr., 54, 905, 10.1107/S0907444998003254

Bystroff, 1998, Prediction of local structure in proteins using a library of sequence-structure motifs, J. Mol. Biol., 281, 565, 10.1006/jmbi.1998.1943

Casjens, 2003, Prophages and bacterial genomics, Mol. Microbiol., 49, 277, 10.1046/j.1365-2958.2003.03580.x

Cordes, 1999, Evolution of a protein fold in vitro, Science, 284, 325, 10.1126/science.284.5412.325

Cordes, 2000, An evolutionary bridge to a new protein fold, Nat. Struct. Biol., 7, 1129, 10.1038/81985

Darling, 2000, Coupled energetics of lambda cro repressor self-assembly and site- specific DNA operator binding I, Biochemistry, 39, 11500, 10.1021/bi000935s

Delaglio, 1995, NMRPipe, J. Biomol. NMR, 6, 277, 10.1007/BF00197809

Doolittle, 1981, Similar amino acid sequences, Science, 214, 149, 10.1126/science.7280687

Gansner, 2000, An open graph visualization system and its applications to software engineering, Software Pract. Exp., 30, 1203, 10.1002/1097-024X(200009)30:11<1203::AID-SPE338>3.0.CO;2-N

Grishin, 2001, Fold change in evolution of protein structures, J. Struct. Biol., 134, 167, 10.1006/jsbi.2001.4335

Huang, 1995, Structure and stability of monomeric lambda repressor, Biochemistry, 34, 3884, 10.1021/bi00012a003

Huang, 1991, A time-efficient, linear-space local similarity algorithm, Adv. Appl. Math., 12, 337, 10.1016/0196-8858(91)90017-D

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

Johnson, 1994, NMRView. A computer program for the visualization and analysis of NMR data, J. Biomol. NMR, 4, 603, 10.1007/BF00404272

Johnson, 1979, Interactions between DNA-bound repressors govern regulation by the lambda phage repressor, Proc. Natl. Acad. Sci. USA, 76, 5061, 10.1073/pnas.76.10.5061

Kinch, 2002, Evolution of protein structures and functions, Curr. Opin. Struct. Biol., 12, 400, 10.1016/S0959-440X(02)00338-X

Koradi, 1996, Molmol, J. Mol. Graph., 14, 51, 10.1016/0263-7855(96)00009-4

Kraulis, 1991, Molscript, J. Appl. Crystallogr., 24, 946, 10.1107/S0021889891004399

Laskowski, 1996, Aqua and procheck-nmr, J. Biomol. NMR, 8, 477, 10.1007/BF00228148

Lauber, 2003, Homologous proteins with different folds, J. Mol. Biol., 328, 205, 10.1016/S0022-2836(03)00245-6

LeFevre, 2003, Retroevolution of lambda Cro toward a stable monomer, Proc. Natl. Acad. Sci. USA, 100, 2345, 10.1073/pnas.0537925100

Matsuo, 1995, Three-dimensional dimer structure of the lambda-Cro repressor in solution as determined by heteronuclear multidimensional NMR, J. Mol. Biol., 254, 668, 10.1006/jmbi.1995.0646

Merritt, 1997, Raster3D, Methods Enzymol., 277, 505, 10.1016/S0076-6879(97)77028-9

Mondragon, 1989, Structure of the amino-terminal domain of phage 434 repressor at 2.0 Å resolution, J. Mol. Biol., 205, 189, 10.1016/0022-2836(89)90375-6

Mondragon, 1989, Structure of phage 434 Cro protein at 2.35 A resolution, J. Mol. Biol., 205, 179, 10.1016/0022-2836(89)90374-4

Mossing, 1990, Stable, monomeric variants of lambda Cro obtained by insertion of a designed beta-hairpin sequence, Science, 250, 1712, 10.1126/science.2148648

Mount, 2001

Murzin, 1998, How far divergent evolution goes in proteins, Curr. Opin. Struct. Biol., 8, 380, 10.1016/S0959-440X(98)80073-0

Murzin, 1995, Scop, J. Mol. Biol., 247, 536, 10.1016/S0022-2836(05)80134-2

Neri, 1992, Determination of the nuclear magnetic resonance solution structure of the DNA-binding domain (residues 1 to 69) of the 434 repressor and comparison with the X-ray crystal structure, J. Mol. Biol., 223, 743, 10.1016/0022-2836(92)90987-U

Neri, 1989, Stereospecific nuclear magnetic resonance assignments of the methyl groups of valine and leucine in the DNA-binding domain of the 434 repressor by biosynthetically directed fractional 13C labeling, Biochemistry, 28, 7510, 10.1021/bi00445a003

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

Orengo, 1997, Cath, Structure, 5, 1093, 10.1016/S0969-2126(97)00260-8

Pabo, 1982, The operator-binding domain of lambda repressor, Nature, 298, 443, 10.1038/298443a0

Padmanabhan, 1997, Three-dimensional solution structure and stability of phage 434 Cro protein, Biochemistry, 36, 6424, 10.1021/bi970085p

Pan, 1993, Conversion of alpha-helices into beta-sheets features in the formation of the scrapie prion proteins, Proc. Natl. Acad. Sci. USA, 90, 10962, 10.1073/pnas.90.23.10962

Pearson, 1996, Effective protein sequence comparison, Methods Enzymol., 266, 227, 10.1016/S0076-6879(96)66017-0

Poteete, 1986, Bacteriophage P22 Cro protein, Biochemistry, 25, 251, 10.1021/bi00349a035

Ptashne, 1986

Rice, 2000, Emboss, Trends Genet., 16, 276, 10.1016/S0168-9525(00)02024-2

Sauer, 1982, Homology among DNA-binding proteins suggests use of a conserved super-secondary structure, Nature, 298, 447, 10.1038/298447a0

Shepard, 1998, Identification of a membrane-spanning domain of the thiol-activated pore-forming toxin Clostridium perfringens perfringolysin O, Biochemistry, 37, 14563, 10.1021/bi981452f

Strzelecka, 1995, The solution structure of the Mu Ner protein reveals a helix-turn-helix DNA recognition motif, Structure, 3, 1087, 10.1016/S0969-2126(01)00244-1

Thompson, 1997, The CLUSTAL_X windows interface, Nucleic Acids Res., 25, 4876, 10.1093/nar/25.24.4876

Van Leerdam, 1982, Ner, a cro-like function of bacteriophage Mu, Virology, 123, 19, 10.1016/0042-6822(82)90291-4

Vuister, 1993, Quantitative J correlation, J. Am. Chem. Soc., 115, 7772, 10.1021/ja00070a024

Wishart, 1992, The chemical shift index, Biochemistry, 31, 1647, 10.1021/bi00121a010

Woody, 1978, Aromatic side-chain contributions to the far ultraviolet circular dichroism of peptides and proteins, Biopolymers, 17, 1451, 10.1002/bip.1978.360170606