메뉴 건너뛰기




Volumn 13, Issue 11, 2004, Pages 2939-2948

Position dependence of the 13C chemical shifts of α-helical model peptides. Fingerprint of the 20 naturally occurring amino acids

Author keywords

helical peptides; 13C chemical shifts; Helix breaker; Locally dense basis approach

Indexed keywords

ALANINE; AMINO ACID; ASPARAGINE; ASPARTIC ACID; LEUCINE; PEPTIDE; SERINE; THREONINE; CARBON;

EID: 7244247466     PISSN: 09618368     EISSN: None     Source Type: Journal    
DOI: 10.1110/ps.04930804     Document Type: Article
Times cited : (2)

References (54)
  • 1
    • 0025082921 scopus 로고
    • Helix-coil stability constants for the naturally occurring amino acids in water. XXIII. Proline parameters from random poly(hydroxybutylglutamineco-L- proline)
    • Altmann, K.H., Wojcik, J., Vásquez, M., and Scheraga, H.A. 1990. Helix-coil stability constants for the naturally occurring amino acids in water. XXIII. Proline parameters from random poly(hydroxybutylglutamineco-L-proline). Biopolymers 30: 107-120.
    • (1990) Biopolymers , vol.30 , pp. 107-120
    • Altmann, K.H.1    Wojcik, J.2    Vásquez, M.3    Scheraga, H.A.4
  • 2
    • 0007865406 scopus 로고
    • Helix-coil stability constants for the naturally occurring amino acids in water. III. Glycine parameters from random poly(hydroxybutylglutamine-co- glycine)
    • Ananthanarayanan, V.S., Andreatta, R.H., Poland, D., and Scheraga, H.A. 1971. Helix-coil stability constants for the naturally occurring amino acids in water. III. Glycine parameters from random poly(hydroxybutylglutamine-co- glycine). Macromolecules 4: 417-424.
    • (1971) Macromolecules , vol.4 , pp. 417-424
    • Ananthanarayanan, V.S.1    Andreatta, R.H.2    Poland, D.3    Scheraga, H.A.4
  • 3
    • 0028173780 scopus 로고
    • Rules for α-helix termination by glycine
    • Aurora, R., Srinivasan, R., and Rose, G. 1994. Rules for α-helix termination by glycine. Science 264: 1126-1130.
    • (1994) Science , vol.264 , pp. 1126-1130
    • Aurora, R.1    Srinivasan, R.2    Rose, G.3
  • 4
    • 0024278714 scopus 로고
    • Helix geometry in proteins
    • Barlow, D.J. and Thornton, J.M. 1988. Helix geometry in proteins. J. Mol. Biol. 201: 601-619.
    • (1988) J. Mol. Biol. , vol.201 , pp. 601-619
    • Barlow, D.J.1    Thornton, J.M.2
  • 5
    • 0025752606 scopus 로고
    • Side chain-backbone hydrogen bonding contributes to helix stability in peptides derived from an α-helical region of carboxypeptidase A
    • Bruch, M.D., Dhingra, M.M., and Gierasch, L.M. 1991. Side chain-backbone hydrogen bonding contributes to helix stability in peptides derived from an α-helical region of carboxypeptidase A. Proteins 10: 130-139.
    • (1991) Proteins , vol.10 , pp. 130-139
    • Bruch, M.D.1    Dhingra, M.M.2    Gierasch, L.M.3
  • 6
    • 0027367977 scopus 로고
    • Helix capping propensities in peptides parallel those in proteins
    • Chakrabartty, A., Doig, A.J., and Baldwin, R.L. 1993. Helix capping propensities in peptides parallel those in proteins. Proc. Natl. Acad. Sci. 90: 11332-11336.
    • (1993) Proc. Natl. Acad. Sci. , vol.90 , pp. 11332-11336
    • Chakrabartty, A.1    Doig, A.J.2    Baldwin, R.L.3
  • 7
    • 41349117339 scopus 로고    scopus 로고
    • Classification of amino acids based on statistical results of known structures and cooperativity of protein folding
    • Chen, H., Zhou, X., and Ou-Yang, Z.-C. 2003. Classification of amino acids based on statistical results of known structures and cooperativity of protein folding. Phys. Rev. E 65: 061907.
    • (2003) Phys. Rev. E , vol.65 , pp. 061907
    • Chen, H.1    Zhou, X.2    Ou-Yang, Z.-C.3
  • 8
    • 84988097454 scopus 로고
    • Locally dense basis-sets for chemical-shift calculations
    • Chesnut, D.B. and Moore, K.D. 1989. Locally dense basis-sets for chemical-shift calculations. J. Comp. Chem. 10: 648-659.
    • (1989) J. Comp. Chem. , vol.10 , pp. 648-659
    • Chesnut, D.B.1    Moore, K.D.2
  • 9
    • 0015967881 scopus 로고
    • Conformational parameters for amino-acids in helical, β-sheet, and random coil regions calculated from proteins
    • Chou, P.Y. and Fasman, G.D. 1974. Conformational parameters for amino-acids in helical, β-sheet, and random coil regions calculated from proteins. Biochemistry 13: 211-222.
    • (1974) Biochemistry , vol.13 , pp. 211-222
    • Chou, P.Y.1    Fasman, G.D.2
  • 10
    • 0029020484 scopus 로고
    • N- and C-capping preferences for all 20 amino acids in α-helical peptides
    • Doig, A.J. and Baldwin, R.L. 1995. N- and C-capping preferences for all 20 amino acids in α-helical peptides. Protein Sci. 4: 1325-1336.
    • (1995) Protein Sci. , vol.4 , pp. 1325-1336
    • Doig, A.J.1    Baldwin, R.L.2
  • 14
  • 15
    • 0014543022 scopus 로고
    • The influence of short-range interactions on protein conformation. III. Dipeptide distributions in proteins of known sequence and structure
    • Kotelchuck, D., Dygert, M., and Scheraga, H.A. 1969. The influence of short-range interactions on protein conformation. III. Dipeptide distributions in proteins of known sequence and structure. Proc. Natl. Acad. Sci. 63: 615-622.
    • (1969) Proc. Natl. Acad. Sci. , vol.63 , pp. 615-622
    • Kotelchuck, D.1    Dygert, M.2    Scheraga, H.A.3
  • 16
    • 70350674995 scopus 로고
    • On the shortest spanning sub tree of a graph and the traveling salesman problem
    • Kruskal Jr., J.B. 1956. On the shortest spanning sub tree of a graph and the traveling salesman problem. Proc. Am. Math. Soc. 7: 48-50.
    • (1956) Proc. Am. Math. Soc. , vol.7 , pp. 48-50
    • Kruskal Jr., J.B.1
  • 17
    • 0029202363 scopus 로고
    • The impact of direct refinement against C-13(α) and C-13(β) chemical-shifts on protein-structure determination by NMR
    • Kuszewski, J., Qin, J.A., Gronenborn, A.M., and Clore, G.M. 1995. The impact of direct refinement against C-13(α) and C-13(β) chemical-shifts on protein-structure determination by NMR. J. Magn. Reson. Ser. B 106: 92-96.
    • (1995) J. Magn. Reson. Ser. B , vol.106 , pp. 92-96
    • Kuszewski, J.1    Qin, J.A.2    Gronenborn, A.M.3    Clore, G.M.4
  • 18
    • 0028887772 scopus 로고
    • A basis size dependence study of Carbon-13 nuclear magnetic resonance spectroscopic shielding in Alanyl and Valyl fragments: Toward protein shielding hypersurfaces
    • Laws, D.D., Le, H., de Dios, A.C., Havlin, R.H., and Oldfield, E. 1995. A basis size dependence study of Carbon-13 nuclear magnetic resonance spectroscopic shielding in Alanyl and Valyl fragments: Toward protein shielding hypersurfaces. J. Am. Chem. Soc. 117: 9542-9546.
    • (1995) J. Am. Chem. Soc. , vol.117 , pp. 9542-9546
    • Laws, D.D.1    Le, H.2    De Dios, A.C.3    Havlin, R.H.4    Oldfield, E.5
  • 19
    • 0000982573 scopus 로고
    • Helix formation in apocytochrome b5: The role of a neutral histidine at the N-cap position
    • Lecomte, J.T.J. and Moore, C.D. 1991. Helix formation in apocytochrome b5: The role of a neutral histidine at the N-cap position. J. Am Chem. Soc. 113: 9663-9665.
    • (1991) J. Am Chem. Soc. , vol.113 , pp. 9663-9665
    • Lecomte, J.T.J.1    Moore, C.D.2
  • 20
    • 0014764945 scopus 로고
    • Helix probability profiles of denaturated proteins and their correlation with native structures
    • Lewis, P.N., Gō, N., Gō, M., Kotelchuck, D., and Scheraga, H.A. 1970. Helix probability profiles of denaturated proteins and their correlation with native structures. Proc. Natl. Acad. Sci. 65: 810-815.
    • (1970) Proc. Natl. Acad. Sci. , vol.65 , pp. 810-815
    • Lewis, P.N.1    Go, N.2    Go, M.3    Kotelchuck, D.4    Scheraga, H.A.5
  • 21
    • 84987317310 scopus 로고
    • Energy parameters in polypeptides. VI. Conformational energy analysis of the N-acetyl N′-methyl amides of the twenty naturally occurring amino acids
    • Lewis, P.N., Momany, F.A., and Scheraga, H.A. 1973. Energy parameters in polypeptides. VI. Conformational energy analysis of the N-acetyl N′-methyl amides of the twenty naturally occurring amino acids. Israel J. Chem. 11: 121-152.
    • (1973) Israel J. Chem. , vol.11 , pp. 121-152
    • Lewis, P.N.1    Momany, F.A.2    Scheraga, H.A.3
  • 22
    • 85023294180 scopus 로고
    • Position-dependent stabilizing effects in α-helices-N-terminal capping in synthetic model peptides
    • Lyu, P.C., Zhou H.X., Jelveh, N., Wemmer, D.E., and Kallenbach, N.R. 1992. Position-dependent stabilizing effects in α-helices-N-terminal capping in synthetic model peptides. J. Am. Chem. Soc. 114: 6560-6562.
    • (1992) J. Am. Chem. Soc. , vol.114 , pp. 6560-6562
    • Lyu, P.C.1    Zhou, H.X.2    Jelveh, N.3    Wemmer, D.E.4    Kallenbach, N.R.5
  • 23
    • 0025890946 scopus 로고
    • Influence of proline residues on protein conformation
    • MacArthur, M.W. and Thornton, J.M. 1991. Influence of proline residues on protein conformation. J. Mol. Biol. 213: 397-412.
    • (1991) J. Mol. Biol. , vol.213 , pp. 397-412
    • MacArthur, M.W.1    Thornton, J.M.2
  • 24
    • 5944250450 scopus 로고
    • Energy parameters in polypeptides. VII. Geometric parameters, partial atomic charges, nonbonded interactions, hydrogen bond interactions, and intrinsic torsional potentials for the naturally occurring amino acids
    • Momany, F.A., McGuire, R.F., Burgess, A.W., and Scheraga, H.A. 1975. Energy parameters in polypeptides. VII. Geometric parameters, partial atomic charges, nonbonded interactions, hydrogen bond interactions, and intrinsic torsional potentials for the naturally occurring amino acids. J. Phys. Chem. 79: 2361-2381.
    • (1975) J. Phys. Chem. , vol.79 , pp. 2361-2381
    • Momany, F.A.1    McGuire, R.F.2    Burgess, A.W.3    Scheraga, H.A.4
  • 25
    • 0035830438 scopus 로고    scopus 로고
    • Distributions of intramolecular distances in the reduced and denatured states of bovine pancreatic ribonuclease A. Folding initiation structures in the C-terminal portions of the reduced protein
    • Navon, A., Ittah, V., Landsman, P., Scheraga, H.A., and Haas, E. 2001. Distributions of intramolecular distances in the reduced and denatured states of bovine pancreatic ribonuclease A. Folding initiation structures in the C-terminal portions of the reduced protein. Biochemistry 40: 105-118.
    • (2001) Biochemistry , vol.40 , pp. 105-118
    • Navon, A.1    Ittah, V.2    Landsman, P.3    Scheraga, H.A.4    Haas, E.5
  • 27
    • 33845550595 scopus 로고
    • Energy parameters in polypeptides. 9. Updating of geometrical parameters, nonbonded interactions, and hydrogen bond interactions for the naturally occurring amino acids
    • Némethy, G., Pottle, M.S., and Scheraga, H.A. 1983. Energy parameters in polypeptides. 9. Updating of geometrical parameters, nonbonded interactions, and hydrogen bond interactions for the naturally occurring amino acids. J. Phys. Chem. 87: 1883-1887.
    • (1983) J. Phys. Chem. , vol.87 , pp. 1883-1887
    • Némethy, G.1    Pottle, M.S.2    Scheraga, H.A.3
  • 28
    • 0001731773 scopus 로고
    • Energy parameters in polypeptides. 10. Improved geometrical parameters and nonbonded interactions for use in the ECEPP/3 algorithm, with application to proline-containing peptides
    • Némethy, G., Gibson, K.D., Palmer, K.A., Yoon, C.N., Paterlini, G., Zagari, A., Rumsey, S., and Scheraga, H.A. 1992. Energy parameters in polypeptides. 10. Improved geometrical parameters and nonbonded interactions for use in the ECEPP/3 algorithm, with application to proline-containing peptides. J. Phys. Chem. 96: 6472-6484.
    • (1992) J. Phys. Chem. , vol.96 , pp. 6472-6484
    • Némethy, G.1    Gibson, K.D.2    Palmer, K.A.3    Yoon, C.N.4    Paterlini, G.5    Zagari, A.6    Rumsey, S.7    Scheraga, H.A.8
  • 29
    • 0024273441 scopus 로고
    • Enhanced protein thermo-stability from designed mutations that interact with α-helix dipoles
    • Nicholson, H., Becktel, W.J., and Matthews, B.W. 1988. Enhanced protein thermo-stability from designed mutations that interact with α-helix dipoles. Nature 336: 651-656.
    • (1988) Nature , vol.336 , pp. 651-656
    • Nicholson, H.1    Becktel, W.J.2    Matthews, B.W.3
  • 30
    • 0036025444 scopus 로고    scopus 로고
    • Chemical shifts in amino acids, peptides, and proteins: From quantum chemistry to drug design
    • Oldfield, E. 2002. Chemical shifts in amino acids, peptides, and proteins: From quantum chemistry to drug design. Annu. Rev. Phys. Chem. 53: 349-378.
    • (2002) Annu. Rev. Phys. Chem. , vol.53 , pp. 349-378
    • Oldfield, E.1
  • 33
    • 0024290488 scopus 로고
    • Helix signal in proteins
    • Presta, L.G. and Rose, G.D. 1988. Helix signal in proteins. Science 240: 1632-1641.
    • (1988) Science , vol.240 , pp. 1632-1641
    • Presta, L.G.1    Rose, G.D.2
  • 35
    • 0024290472 scopus 로고
    • Amino acid preferences for specific locations at the ends of α-helices
    • Richardson, J.S. and Richardson, D.C. 1988. Amino acid preferences for specific locations at the ends of α-helices. Science 240: 1648-1652.
    • (1988) Science , vol.240 , pp. 1648-1652
    • Richardson, J.S.1    Richardson, D.C.2
  • 36
    • 0024066560 scopus 로고
    • On the multiple-minima problem in the conformational analysis of polypeptides. II. An electrostatically driven Monte Carlo method-tests on poly(L-alanine)
    • Ripoll, D.R. and Scheraga, H.A. 1988. On the multiple-minima problem in the conformational analysis of polypeptides. II. An electrostatically driven Monte Carlo method-tests on poly(L-alanine). Biopolymers 27: 1283-1303.
    • (1988) Biopolymers , vol.27 , pp. 1283-1303
    • Ripoll, D.R.1    Scheraga, H.A.2
  • 37
    • 0001428018 scopus 로고
    • L conformation at the ends of helices
    • ed. R. Jaenicke, Elsevier/North-Holland, New York
    • L conformation at the ends of helices. In Protein folding (ed. R. Jaenicke), p. 53. Elsevier/North-Holland, New York.
    • (1980) Protein Folding , pp. 53
    • Schellman, C.1
  • 38
    • 84924719416 scopus 로고
    • On the dominance of short-range interactions in polypeptides and proteins
    • Scheraga, H.A. 1973. On the dominance of short-range interactions in polypeptides and proteins. Pure Appl. Chem. 36: 1-8.
    • (1973) Pure Appl. Chem. , vol.36 , pp. 1-8
    • Scheraga, H.A.1
  • 39
    • 0024972479 scopus 로고
    • Capping and α-helix stability
    • Serrano, L. and Fersht, A.R. 1989. Capping and α-helix stability. Nature 342: 296-299.
    • (1989) Nature , vol.342 , pp. 296-299
    • Serrano, L.1    Fersht, A.R.2
  • 40
    • 0026709329 scopus 로고
    • α-Helix stability in proteins. I. Empirical correlations concerning substitution of side-chains at the N- and C-caps and replacement of alanine by glycine or serine at solvent-exposed surfaces
    • Serrrano, L., Sancho, J., Hirshberg, M., and Fersht, A.R. 1992. α-Helix stability in proteins. I. Empirical correlations concerning substitution of side-chains at the N- and C-caps and replacement of alanine by glycine or serine at solvent-exposed surfaces. J. Mol. Biol. 227: 544-559.
    • (1992) J. Mol. Biol. , vol.227 , pp. 544-559
    • Serrrano, L.1    Sancho, J.2    Hirshberg, M.3    Fersht, A.R.4
  • 41
    • 27244454740 scopus 로고
    • Intermolecular potentials from crystal data. 6. Determination of empirical potentials for O-H⋯O = C hydrogen bonds from packing configurations
    • Sippl, M.J., Némethy, G., and Scheraga, H.A. 1984. Intermolecular potentials from crystal data. 6. Determination of empirical potentials for O-H⋯O = C hydrogen bonds from packing configurations. J. Phys. Chem. 88: 6231-6233.
    • (1984) J. Phys. Chem. , vol.88 , pp. 6231-6233
    • Sippl, M.J.1    Némethy, G.2    Scheraga, H.A.3
  • 42
    • 0347610773 scopus 로고
    • 13C nuclear magnetic resonance chemical shifts
    • 13C nuclear magnetic resonance chemical shifts. J. Am. Chem. Soc. 113: 5490-5492.
    • (1991) J. Am. Chem. Soc. , vol.113 , pp. 5490-5492
    • Spera, S.1    Bax, A.2
  • 43
    • 0036874286 scopus 로고    scopus 로고
    • Unblocked statistical-coil tetrapeptides in aqueous solution: A theoretical study
    • Vila, J.A., Ripoll, D.R., Baldoni, H.A., and Scheraga, H.A. 2002. Unblocked statistical-coil tetrapeptides in aqueous solution: A theoretical study. J. Biomol. NMR 24: 245-262.
    • (2002) J. Biomol. NMR , vol.24 , pp. 245-262
    • Vila, J.A.1    Ripoll, D.R.2    Baldoni, H.A.3    Scheraga, H.A.4
  • 44
    • 0038324565 scopus 로고    scopus 로고
    • Unblocked statistical-coil tetrapeptides in aqueous solution: Quantum-chemical computation of the Carbon-13 NMR chemical shifts
    • Vila, J.A., Baldoni, H.A., Ripoll, D.R., and Scheraga, H.A. 2003. Unblocked statistical-coil tetrapeptides in aqueous solution: Quantum-chemical computation of the Carbon-13 NMR chemical shifts. J. Biomol. NMR 26: 113-130.
    • (2003) J. Biomol. NMR , vol.26 , pp. 113-130
    • Vila, J.A.1    Baldoni, H.A.2    Ripoll, D.R.3    Scheraga, H.A.4
  • 45
    • 4444273246 scopus 로고    scopus 로고
    • 13C chemical shifts for an alanine-rich peptide
    • 13C chemical shifts for an alanine-rich peptide. Proteins Struct. Funct. Bioinf. 57: 87-98.
    • (2004) Proteins Struct. Funct. Bioinf. , vol.57 , pp. 87-98
  • 46
    • 0036129107 scopus 로고    scopus 로고
    • Probability-based protein secondary structure identification using combined NMR chemical-shift data
    • Wang, Y. and Jardetzky, O. 2002. Probability-based protein secondary structure identification using combined NMR chemical-shift data. Protein Sci. 11: 852-861.
    • (2002) Protein Sci. , vol.11 , pp. 852-861
    • Wang, Y.1    Jardetzky, O.2
  • 47
    • 0034923356 scopus 로고    scopus 로고
    • Use of chemical shifts in macromolecular structure determination
    • Wishart, D. and Case, D.A. 2001. Use of chemical shifts in macromolecular structure determination. Methods Enzymol. 338: 3-34.
    • (2001) Methods Enzymol. , vol.338 , pp. 3-34
    • Wishart, D.1    Case, D.A.2
  • 48
    • 0029181728 scopus 로고
    • H-1, C-I3 and N-15 random coil NMR chemical-shifts of the common amino-acids. 1. Investigations of nearest-neighbor effects
    • Wishart, D.S., Bigam, C.G., Holm, A., Hodges, R.S., and Sykes, B. 1995. H-1, C-I3 and N-15 random coil NMR chemical-shifts of the common amino-acids. 1. Investigations of nearest-neighbor effects. J. Biomol. NMR 5: 67-81.
    • (1995) J. Biomol. NMR , vol.5 , pp. 67-81
    • Wishart, D.S.1    Bigam, C.G.2    Holm, A.3    Hodges, R.S.4    Sykes, B.5
  • 49
    • 0025113815 scopus 로고
    • Helix-coil stability constants for the naturally occurring amino acids in water. XXIV. Half-cystine parameters from random Poly(hydroxybutylglutamine-co- S-methylthio-L-cysteine)
    • Wojcik, J., Altmann, K.H., and Scheraga, H.A. 1990. Helix-coil stability constants for the naturally occurring amino acids in water. XXIV. Half-cystine parameters from random Poly(hydroxybutylglutamine-co-S-methylthio-L-cysteine). Biopolymers 30: 121-134.
    • (1990) Biopolymers , vol.30 , pp. 121-134
    • Wojcik, J.1    Altmann, K.H.2    Scheraga, H.A.3
  • 50
    • 0035544152 scopus 로고    scopus 로고
    • 13C′ chemical shifts in proteins using a density functional database
    • 13C′ chemical shifts in proteins using a density functional database. J. Biomol. NMR 21: 321-333.
    • (2001) J. Biomol. NMR , vol.21 , pp. 321-333
    • Xu, X.-P.1    Case, D.A.2
  • 51
    • 0037114648 scopus 로고    scopus 로고
    • 13C′ chemical shifts in peptides using density functional theory
    • 13C′ chemical shifts in peptides using density functional theory. Biopolymers 65: 408-423.
    • (2002) Biopolymers , vol.65 , pp. 408-423
  • 52
    • 0027980822 scopus 로고
    • Contribution to global protein stabilization of the N-capping box in human growth hormone
    • Zhukovsky, E.A., Mulkerrin, M.G., and Presta, L.G. 1994. Contribution to global protein stabilization of the N-capping box in human growth hormone. Biochemistry 33: 9856-9864.
    • (1994) Biochemistry , vol.33 , pp. 9856-9864
    • Zhukovsky, E.A.1    Mulkerrin, M.G.2    Presta, L.G.3
  • 53
    • 0000668407 scopus 로고
    • Theory of the phase transition between helix and random coil in polypeptide chains
    • Zimm, B.H. and Bragg, J.K. 1959. Theory of the phase transition between helix and random coil in polypeptide chains. J. Chem. Phys. 31: 526-535.
    • (1959) J. Chem. Phys. , vol.31 , pp. 526-535
    • Zimm, B.H.1    Bragg, J.K.2
  • 54
    • 0017435119 scopus 로고
    • Conformational analysis of the 20 naturally occurring amino acid residues using ECEPP
    • Zimmerman, S.S., Pottle, M.S., Némethy, G., and Scheraga, H.A. 1977. Conformational analysis of the 20 naturally occurring amino acid residues using ECEPP. Macromolecules 10: 1-9.
    • (1977) Macromolecules , vol.10 , pp. 1-9
    • Zimmerman, S.S.1    Pottle, M.S.2    Némethy, G.3    Scheraga, H.A.4


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.