C-capping and helix stability: the pro C-capping motif

Journal of Molecular Biology - Tập 274 - Trang 276-288 - 1997
Jesús Prieto1, Luis Serrano1
1EMBL, Meyehofstrasse 1 69117 Heidelberg, Germany

Tài liệu tham khảo

Armstrong, 1993, Charged histidine affects α-helix stability at all positions in the helix by interacting with the backbone charges, Proc. Natl Acad. Sci. USA, 90, 11337, 10.1073/pnas.90.23.11337 Aurora, 1995, Rules for α-helix termination by glycine, Science, 264, 1126, 10.1126/science.8178170 Blaber, 1993, Structural basis of amino acid α-helix propensity, Science, 260, 1637, 10.1126/science.8503008 Blanco, 1995, Folding of protein G B1 domain studied by the conformational characterization of fragments comprising its secondary structure elements, Eur. J. Biochem., 230, 634, 10.1111/j.1432-1033.1995.tb20605.x Bodner, 1980, NMR study of 1:1 complexes between divalent sulfur and aromatic compounds, Biochem. Biophys. Res. Commun., 94, 807, 10.1016/0006-291X(80)91306-6 Bothner-By, 1984, Structure determination of a tetrasacharide, J. Am. Chem. Soc., 106, 811, 10.1021/ja00315a069 Bruch, 1991, Side chain backbone hydrogen bonding contributes to helix stability in peptides derived from an α-helical region of carboxypeptidase A, Proteins: Struct. Funct. Genet., 10, 130, 10.1002/prot.340100206 Chakrabartty, 1993, Aromatic side-chain contribution of far-ultraviolet circular dichroism of helical peptides and its effect on measurement of helix propensities, Biochemistry, 32, 5560, 10.1021/bi00072a010 Chakrabartty, 1994, Helix propensities of the amino-acids measured in alanine-based peptides without helix-stabilizing side chain interactions, Protein Sci., 3, 843, 10.1002/pro.5560030514 Chen, 1974, Determination of the helix and β form of proteins in aqueous solution by Circular dichroism, Biochemistry, 13, 3350, 10.1021/bi00713a027 Dasgupta, 1993, Design of helix ends, Int. J. Pept. Res., 41, 499, 10.1111/j.1399-3011.1993.tb00470.x Doig, 1995, N- and C-capping preferences fro all 20 amino acids in α-helical peptides, Protein Sci., 4, 1325, 10.1002/pro.5560040708 Flory, 1988 Gill, 1989, Calculation of protein extinction coefficients from amino acid sequence data, Anal. Biochem., 182, 319, 10.1016/0003-2697(89)90602-7 Gong, 1995, Structural analysis of the N- and C-termini in a peptide with consensus sequence, Protein Sci., 4, 1446, 10.1002/pro.5560040802 Harper, 1993, Helix stop signals in proteins and peptides, Biochemistry, 32, 7605, 10.1021/bi00081a001 Hobohm, 1992, Selection of representative protein data sets, Protein Sci., 1, 409, 10.1002/pro.5560010313 Horovitz, 1992, α-helix stability in proteins. II. Factors that influence stability at an internal position, J. Mol. Biol., 227, 560, 10.1016/0022-2836(92)90907-2 Kabsch, 1983, Dictionary of protein secondary structure, Biopolymers, 22, 2577, 10.1002/bip.360221211 Kumar, 1980, A two-dimensional nuclear Overhauser enhancement (2D NOE) experiment for the elucidation of complete proton-proton cross relaxation networks in biological macromolecules, Biochem. Biophys. Res. Commun., 95, 1, 10.1016/0006-291X(80)90695-6 Lyu, 1990, Side chain contributions to the stability of alpha-helical structures in peptides, Science, 250, 669, 10.1126/science.2237416 Lyu, 1992, Position-dependent stabilizing effect in α-helices, J. Am. Chem. Soc., 114, 6560, 10.1021/ja00042a047 Lyu, 1993, Capping interactions in isolated α-helices, Biochemistry, 32, 421, 10.1021/bi00053a006 Merutka, 1995, ‘Random coil’ 1H chemical shifts obtained as a function of temperature and trifluoroethanol concentration for the peptide series GGXGG, J. Biomol. NMR, 5, 14, 10.1007/BF00227466 Muñoz, 1994, Elucidating the folding problem of helical peptides using empirical parameters, Nature: Struct. Biol., 1, 399, 10.1038/nsb0694-399 Muñoz, 1995, Analysis of i, i + 5 and i, i + 8 hydrophobic interactions in a helical model peptide bearing the hydrophobic staple motif, Biochemistry, 34, 15301, 10.1021/bi00046a039 Muñoz, 1995, Elucidating the folding problem of helical peptides using empirical parameters. II, J. Mol. Biol., 245, 275, 10.1006/jmbi.1994.0023 Muñoz, 1995, Elucidating the folding problem of helical peptides using empirical parameters. III, J. Mol. Biol., 245, 297, 10.1006/jmbi.1994.0024 Muñoz, 1995, Intrinsic secondary structure propensities of the amino acids, using statistical φ and ψ matrices, Proteins: Struct. Funct. Genet., 20, 301, 10.1002/prot.340200403 Muñoz, 1997, Development of the multiple sequence approximation within the AGADIR model of α-helix formation. Comparison with Zimm-Bragg and Lifson-Roig formalisms, Biopolymers, 41, 495, 10.1002/(SICI)1097-0282(19970415)41:5<495::AID-BIP2>3.0.CO;2-H Muñoz, 1995, The hydrophobic-staple motif and a role for loop-residues in α-helix stability and protein folding, Nature Struct. Biol., 2, 380, 10.1038/nsb0595-380 Nemethy, 1981, Strong interaction between disulfide derivatives and aromatic groups in peptides and proteins, Biochem. Biophys. Res. Commun., 94, 807 O’Neil, 1990, A thermodynamic scale for the helix-forming tendencies of the commonly occurring amino acids, Science, 250, 646, 10.1126/science.2237415 Piantini, 1982, Multiple quantum filters for elucidating NMR coupling networks, J. Am. Chem. Soc., 104, 6800, 10.1021/ja00388a062 Rance, 1987, Improved techniques for homonuclear rotating-frame and isotropic mixing experiments, J. Magn. Reson., 74, 557 Richardson, 1988, Amino acid preferences for specific locations at the ends of α-helices, Science, 240, 1648, 10.1126/science.3381086 Schellman, 1980, Protein Folding Seale, 1994, Sequence determinants of the capping-box, a stabilizing motif at the N-termini of α-helices, Protein Sci., 3, 1741, 10.1002/pro.5560031014 Shoemaker, 1990, Side-chain interactions in the C-peptide helix, Biopolymers, 29, 1, 10.1002/bip.360290104 Stapley, 1995, Addition of side chain interactions to modified Lifson-Roig theory application of energetics of phenylalanine-methionine interactions, Protein Sci., 4, 2383, 10.1002/pro.5560041117 Viguera, 1995, Experimental analysis of the Schellman motif, J. Mol. Biol., 251, 150, 10.1006/jmbi.1995.0422 Viguera, 1995, Side-chain interactions between sulphur containing amino acids and phenyalanine, in α-helices, Biochemistry, 34, 8771, 10.1021/bi00027a028 Vriend, 1990, WHATIF, Mol. Graph., 8, 52, 10.1016/0263-7855(90)80070-V Wishart, 1995, H, C and N random coil NMR chemical shifts of the common amino acids. I. Investigations of nearest neighbor effects, J. Biomol. NMR, 5, 67, 10.1007/BF00227471 Wüthrich, 1986 Zhou, 1994, Structure of a C-terminal α-helix Cap in a synthetic peptide, J. Am. Chem. Soc., 116, 1139, 10.1021/ja00082a049 Padmanaban, 1994, Helix-stabilizing interaction between Tyr and Leu of Val when the spacing is I,I + 4, J. Mol. Biol., 241, 706, 10.1006/jmbi.1994.1545