Protein folding and protein evolution: common folding nucleus in different subfamilies of c-type cytochromes?

Abkevich, 1994, Specific nucleus as the transition state for protein folding, Biochemistry, 33, 10026, 10.1021/bi00199a029 Bashford, 1987, Determinants of a protein fold. Unique features of the globin amino acid sequences, J. Mol. Biol., 196, 199, 10.1016/0022-2836(87)90521-3 Benning, 1991, Molecular structure of cytochrome c2 isolated from Rhodobacter capsulatus determined at 2.5 angstroms resolution, J. Mol. Biol., 220, 673, 10.1016/0022-2836(91)90109-J Benning, 1994, X-ray structure of the cytochrome c2 isolated from Paracoccus denitrificans refined to 1.7 angstroms resolution, Arch. Biochem. Biophys., 310, 460, 10.1006/abbi.1994.1193 Bhatia, 1981 Bushnell, 1990, High-resolution three-dimensional structure of horse heart cytochtome c, J. Mol. Biol., 214, 585, 10.1016/0022-2836(90)90200-6 Carter, 1985, Crystal structure of Azotobacter cytochrome c5 at 2 Å resolution, J. Mol. Biol., 184, 279, 10.1016/0022-2836(85)90380-8 Chothia, 1986, The relation between the divergence of sequence and structure in proteins, EMBO J., 5, 823, 10.1002/j.1460-2075.1986.tb04288.x Coló, 1996, Side chain packing of the N and C-terminal helices plays a critical role in the kinetics of cytochrome c folding, Biochemistry, 35, 5538, 10.1021/bi960052u Coló, 1997, Identification of the predominant non-native histidine ligand in unfolded cytochrome c, Biochemistry, 36, 12535, 10.1021/bi971697c Creighton, 1993, 244 Daggett, 1996, Structure of the transition state for folding of a protein derived from experiment and simulation, J. Mol. Biol., 257, 430, 10.1006/jmbi.1996.0173 Dickerson, 1972, The structure and history of an ancient protein, Sci. Am., 226, 58, 10.1038/scientificamerican0472-58 Dickerson, 1976, The cytochrome c fold and the evolution of bacterial energy metabolism, J. Mol. Biol., 100, 479, 10.1016/S0022-2836(76)80041-1 Dolgikh, 1981, α-Lactalbumin, FEBS Letters, 136, 311, 10.1016/0014-5793(81)80642-4 Elö, 1992, Early steps in cytochrome c folding probed by time-resolved circular-dichroism and fluorescence spectroscopy, Biochemistry, 31, 6876, 10.1021/bi00145a003 Elö, 1994, Kinetic mechanism of cytochrome c folding, Biochemistry, 33, 6925, 10.1021/bi00188a023 Fersht, 1997, Nucleation mechanism of protein folding, Curr. Opin. Struct. Biol., 7, 3, 10.1016/S0959-440X(97)80002-4 Itzhaki, 1995, The structure of the transition state for folding of chymotrypsin inhibitor 2 analyzed by protein engineering methods, J. Mol. Biol., 254, 260, 10.1006/jmbi.1995.0616 Jackson, 1991, Folding of chymotrypsin inhibitor 2. 1. Evidence for a two-state transition, Biochemistry, 30, 10428, 10.1021/bi00107a010 Jackson, 1993, Structure of the hydrophobic core in the transition state for folding of chymotrypsin inhibitor 2, Biochemistry, 32, 11270, 10.1021/bi00093a002 Jeng, 1990, Structural description of acid-denatured cytochrome c by hydrogen exchange and 2D NMR, Biochemistry, 29, 10433, 10.1021/bi00498a001 Kabsch, 1983, Dictionary of protein secondary structure pattern recognition of hydrogen-bonds and geometrical features, Biopolymers, 22, 2537, 10.1002/bip.360221211 Lo, 1995, Structural studies of the roles of residues 82 and 85 at the interactive face of cytochrome c, Biochemistry, 34, 163, 10.1021/bi00001a020 Louie, 1990, High-resolution refinement of yeast iso-1-∗cytochrome c and comparisons with other eukaryotic cytochromes c, J. Mol. Biol., 214, 527, 10.1016/0022-2836(90)90197-T Marmorino, 1995, A native tertiary interaction stabilize the A state of cytochrome c, Biochemistry, 34, 3140, 10.1021/bi00010a002 Mathews, 1985, The structure, function and evolution of cytochromes, Prog. Biophys. Mol. Biol., 45, 1, 10.1016/0079-6107(85)90004-5 Matsuura, 1982, Structure of cytochrome c551 from P. Aeruginosa refined at 1.6 angstroms resolution and comparison of the two redox forms, J. Mol. Biol., 156, 389, 10.1016/0022-2836(82)90335-7 Matthews, 1993, Pathways of protein folding, Annu. Rev. Biochem., 62, 653, 10.1146/annurev.bi.62.070193.003253 Meyer, 1996, Evolution and classification of c-type cytochromes, 33 Murphy, 1992, Structure determination and analysis of yeast iso-2-cytochrome c and a composite mutant protein, J. Mol. Biol., 227, 160, 10.1016/0022-2836(92)90689-H Ochi, 1983, Structure of rice ferricytochrome c at 2.0 angstroms resolution, J. Mol. Biol., 166, 407, 10.1016/S0022-2836(83)80092-8 Otzen, 1994, Structure of the transition state for the folding-unfolding of the barley chymotrypsin inhibitor 2 and its implications for mechanism of protein folding, Proc. Natl Acad. Sci. USA, 91, 10422, 10.1073/pnas.91.22.10422 Perutz, 1996, Bedeutung der Wasserstoffbrucken fur die Physiologie, Naturwissenschaft Rundschau, 49, 215 Perutz, 1965, Structure and function of haemoglobin. II. Some relations between polypeptide chain configuration and amino acid sequence, J. Mol. Biol., 13, 669, 10.1016/S0022-2836(65)80134-6 Perutz, 1986, J. Am. Chem. Soc., 108, 1064, 10.1021/ja00265a036 Ptitsyn, 1972, Thermodinamic parameters of helix-coil transitions in polypeptide chains, Pure Appl. Chem., 31, 227, 10.1351/pac197231010227 Ptitsyn, 1973, Sequental mechanism of protein folding, Dokl. Akad. Nauk SSSR, 210, 1213 Ptitsyn, 1995, Molten globule and protein folding, Advan. Protein Chem., 47, 83, 10.1016/S0065-3233(08)60546-X Ptitsyn, 1996, How molten is the molten globule?, Nature Struct. Biol., 3, 488, 10.1038/nsb0696-488 Ptitsyn, 1980, Similarities of protein topologies, Quart. Rev. Biophys., 13, 339, 10.1017/S0033583500001724 Ptitsyn, 1980, Self-organization of proteins and the problem of their three-dimensional structure prediction, 101 Ptitsyn, 1990, Evidence for a molten globule state as a general intermediate in protein folding, FEBS Letters, 262, 20, 10.1016/0014-5793(90)80143-7 Roder, 1997, Kinetic role of early intermediates in protein folding, Curr. Opin. Struct. Biol., 7, 15, 10.1016/S0959-440X(97)80004-8 Roder, 1994, Early stages of protein folding, 26 Roder, 1988, Structural characterization of folding intermediates in cytochrome c by H-exchange labelling and proton NMR, Nature, 335, 700, 10.1038/335700a0 Sander, 1991, Database of homology-derived protein structure, Proteins: Struct. Funct. Genet., 9, 56, 10.1002/prot.340090107 Shakhnovich, 1997, Theoretical studies of protein-folding thermodynamics and kinetics, Curr. Opin. Struct. Biol., 7, 29, 10.1016/S0959-440X(97)80005-X Shakhnovich, 1993, Engineering of stable and fast-folding sequences of model proteins, Proc. Natl Acad. Sci. USA, 90, 7195, 10.1073/pnas.90.15.7195 Shakhnovich, 1993, A new approach to the design of stable proteins, Protein Eng., 6, 793, 10.1093/protein/6.8.793 Shakhnovich, 1996, Conserved residues and the mechanism of protein folding, Nature, 379, 96, 10.1038/379096a0 Sosnick, 1994, The barriers in protein folding, Nature Struct. Biol., 1, 149, 10.1038/nsb0394-149 Takano, 1984, Refinement of myoglobin and cytochrome c, 262 Tanaka, 1975, The crystal structure of bonito (katsuo) ferrocytochrome c at 2.3 angstroms resolution. II. Structure and function, J. Biochem. (Tokyo), 77, 147 Tsong, 1972, A sequential model of nucleation-dependent protein folding, J. Mol. Biol., 63, 457, 10.1016/0022-2836(72)90440-8 Uversky, 1994, “Partly folded” state, a new equilibrium state of protein molecules, Biochemistry, 3, 2782, 10.1021/bi00176a006 Uversky, 1996, Further evidence on the equilibrium “pre-molten globule” state, J Mol. Biol., 255, 215, 10.1006/jmbi.1996.0018 Wallqvist, 1997, Identification of cooperative folding units in a set of native proteins, Protein Sci., 6, 1627, 10.1002/pro.5560060804 Wu, 1993, A noncovalent peptide complex as a model for an early folding intermediate of cytochrome c, Biochemistry, 32, 10271, 10.1021/bi00089a050