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Volumn 264, Issue 5, 1996, Pages 1180-1195

Deviations from planarity of the peptide bond in peptides and proteins

Author keywords

Chirality; Distortion; Distribution; Peptide bond; angles

Indexed keywords

AMINO ACID; PEPTIDE; PROTEIN;

EID: 0030596007     PISSN: 00222836     EISSN: None     Source Type: Journal    
DOI: 10.1006/jmbi.1996.0705     Document Type: Article
Times cited : (166)

References (61)
  • 2
    • 11644328584 scopus 로고
    • Systematic analysis of structural data as a research technique in organic chemistry
    • Allen, F. H., Kennard, O. & Taylor, R. (1983). Systematic analysis of structural data as a research technique in organic chemistry. Acc. Chem. Res. 16, 146-153.
    • (1983) Acc. Chem. Res. , vol.16 , pp. 146-153
    • Allen, F.H.1    Kennard, O.2    Taylor, R.3
  • 5
    • 0023140814 scopus 로고
    • Crystallographic R-factor refinement by molecular dynamics
    • Brünger, A. T., Kuriyan, J. & Karplus, M. (1987). Crystallographic R-factor refinement by molecular dynamics. Science, 235, 458-460.
    • (1987) Science , vol.235 , pp. 458-460
    • Brünger, A.T.1    Kuriyan, J.2    Karplus, M.3
  • 6
    • 84961983610 scopus 로고
    • Rotation about the C-N bond in formamide: An ab initio molecular orbital study of structure and energetics in the gas phase and in solution
    • Burton, N. A., Chiu, S. S.-L., Davidson, M. M., Green, D. V. S., Hillier, I. H., McDouall, J. J. W. & Vincent, M. A. (1993). Rotation about the C-N bond in formamide: an ab initio molecular orbital study of structure and energetics in the gas phase and in solution. J. Chem. Soc. Faraday Trans. 89, 2631-2635.
    • (1993) J. Chem. Soc. Faraday Trans. , vol.89 , pp. 2631-2635
    • Burton, N.A.1    Chiu, S.S.-L.2    Davidson, M.M.3    Green, D.V.S.4    Hillier, I.H.5    McDouall, J.J.W.6    Vincent, M.A.7
  • 7
    • 0002543237 scopus 로고
    • Fundamental dimensions of polypeptide chains
    • Corey, R. B. & Pauling, L. (1953). Fundamental dimensions of polypeptide chains. Proc. Roy. Soc. ser. B, 141, 10-20.
    • (1953) Proc. Roy. Soc. Ser. B , vol.141 , pp. 10-20
    • Corey, R.B.1    Pauling, L.2
  • 8
    • 36849133192 scopus 로고
    • Microwave spectrum and molecular structure of formamide
    • Costain, C. C. & Dowling, J. M. (1960). Microwave spectrum and molecular structure of formamide. J. Chem. Phys. 32, 158-165.
    • (1960) J. Chem. Phys. , vol.32 , pp. 158-165
    • Costain, C.C.1    Dowling, J.M.2
  • 10
    • 0001612915 scopus 로고
    • Crystallographic refinement of the structure of bovine pancreatic trypsin inhibitor at 1.5 A resolution
    • Deisenhofer, J. & Steigemann, W. (1975). Crystallographic refinement of the structure of bovine pancreatic trypsin inhibitor at 1.5 A resolution. Acta Crystallog. sect. B, 31, 238-250.
    • (1975) Acta Crystallog. Sect. B , vol.31 , pp. 238-250
    • Deisenhofer, J.1    Steigemann, W.2
  • 11
    • 0021112292 scopus 로고
    • Structure of porcine pancreatic phospholipase A2 at 2.6 Å resolution and comparison with bovine phospholipase A2
    • Dijkstra, B. W., Renetseder, R., Kalk, K. H., Hol, W. G. J. & Drenth, J. (1983). Structure of porcine pancreatic phospholipase A2 at 2.6 Å resolution and comparison with bovine phospholipase A2. J. Mol. Biol. 168, 163-179.
    • (1983) J. Mol. Biol. , vol.168 , pp. 163-179
    • Dijkstra, B.W.1    Renetseder, R.2    Kalk, K.H.3    Hol, W.G.J.4    Drenth, J.5
  • 12
    • 4243946831 scopus 로고
    • The crystal structure of cysteinylglycine-sodium iodide
    • Dryer, H. B. (1951). The crystal structure of cysteinylglycine-sodium iodide. Acta Crystallog. 4, 42-50.
    • (1951) Acta Crystallog. , vol.4 , pp. 42-50
    • Dryer, H.B.1
  • 13
    • 0028469350 scopus 로고
    • Calculations of one-, two- and three-bond nuclear spin-spin couplings in a model peptide and correlations with experimental data
    • Edison, A. S., Markley, J. L. & Weinhold, F. (1994). Calculations of one-, two- and three-bond nuclear spin-spin couplings in a model peptide and correlations with experimental data. J. Biomol. NMR, 4, 519-542.
    • (1994) J. Biomol. NMR , vol.4 , pp. 519-542
    • Edison, A.S.1    Markley, J.L.2    Weinhold, F.3
  • 14
    • 85004809734 scopus 로고
    • Intramolecular water bridge and a distorted trans peptide bond in the crystal structure of alpha-L-glutamyl-L-aspartic acid hydrate
    • Eggleston, D. S. & Hodgson, D. J. (1985). Intramolecular water bridge and a distorted trans peptide bond in the crystal structure of alpha-L-glutamyl-L-aspartic acid hydrate. Int. J. Pept. Protein Res. 26, 509-517.
    • (1985) Int. J. Pept. Protein Res. , vol.26 , pp. 509-517
    • Eggleston, D.S.1    Hodgson, D.J.2
  • 15
    • 79952608525 scopus 로고
    • Accurate bond and angle parameters for X-ray protein structure refinement
    • Engh, R. & Huber, R. (1991). Accurate bond and angle parameters for X-ray protein structure refinement. Acta Crystallog. sect. A, 47, 392-400.
    • (1991) Acta Crystallog. Sect. A , vol.47 , pp. 392-400
    • Engh, R.1    Huber, R.2
  • 17
    • 0001129057 scopus 로고
    • An independent crystallographic refinement of porcine phospholipase A2 at 2.4 Å resolution
    • Finzel, B. C., Ohlendorf, D. H., Weber, P. C. & Salemme, F. R. (1991). An independent crystallographic refinement of porcine phospholipase A2 at 2.4 Å resolution. Acta Crystallog. sect. B, 47, 558-559.
    • (1991) Acta Crystallog. Sect. B , vol.47 , pp. 558-559
    • Finzel, B.C.1    Ohlendorf, D.H.2    Weber, P.C.3    Salemme, F.R.4
  • 18
    • 0017078891 scopus 로고
    • Conformation of the cyclic tetrapeptide dihydrochlamydocin. Aib-L-Phe-D-Pro-L-Xaa, and experimental values for 3 → 1 intramolecular hydrogen bonds by X-ray diffraction
    • Flippen, J. L. & Karle, I. L. (1976). Conformation of the cyclic tetrapeptide dihydrochlamydocin. Aib-L-Phe-D-Pro-L-Xaa, and experimental values for 3 → 1 intramolecular hydrogen bonds by X-ray diffraction. Biopolymers, 15, 1081-1092.
    • (1976) Biopolymers , vol.15 , pp. 1081-1092
    • Flippen, J.L.1    Karle, I.L.2
  • 21
    • 0022333121 scopus 로고
    • Stereochemically restrained refinement of macromolecular structures
    • Hendrickson, W. A. (1985). Stereochemically restrained refinement of macromolecular structures. Methods Enzymol. 115, 252-270.
    • (1985) Methods Enzymol. , vol.115 , pp. 252-270
    • Hendrickson, W.A.1
  • 22
    • 0002860357 scopus 로고
    • Incorporation of stereochemical information into crystallographic refinement
    • (Diamond, R., Ramaseshan, S. & Venkatesan, K., eds), Indian Institute of Science, Bangalore
    • Hendrickson, W. A. & Konnert, J. H. (1980). Incorporation of stereochemical information into crystallographic refinement. In Computing in Crystallography (Diamond, R., Ramaseshan, S. & Venkatesan, K., eds), pp. 13.01-13.23, Indian Institute of Science, Bangalore.
    • (1980) Computing in Crystallography , pp. 1301-1323
    • Hendrickson, W.A.1    Konnert, J.H.2
  • 23
    • 0014966180 scopus 로고
    • Abbreviations and symbols for the description of the conformation of polypeptide chains
    • IUPAC-IUB Commission on Biochemical Nomenclature. (1970). Abbreviations and symbols for the description of the conformation of polypeptide chains. J. Mol. Biol. 52, 1-17.
    • (1970) J. Mol. Biol. , vol.52 , pp. 1-17
  • 24
    • 0000057645 scopus 로고
    • Predictions of protein backbone structural parameters from first principles: Systematic comparisons of calculated N-C(α)-C' angles with high-resolution protein crystallographic results
    • Jiang, X., Cao, M., Teppen, B., Newton, S. Q. & Schäfer, L. (1995). Predictions of protein backbone structural parameters from first principles: systematic comparisons of calculated N-C(α)-C' angles with high-resolution protein crystallographic results. J. Phys. Chem. 99, 10521-10525.
    • (1995) J. Phys. Chem. , vol.99 , pp. 10521-10525
    • Jiang, X.1    Cao, M.2    Teppen, B.3    Newton, S.Q.4    Schäfer, L.5
  • 25
    • 0001308955 scopus 로고
    • Conformational dependence of atomic multipole moments
    • Koch, U., Popelier, P. L. A. & Stone, A. J. (1995). Conformational dependence of atomic multipole moments. Chem. Phys. Letters, 238, 253-260.
    • (1995) Chem. Phys. Letters , vol.238 , pp. 253-260
    • Koch, U.1    Popelier, P.L.A.2    Stone, A.J.3
  • 26
    • 0016681595 scopus 로고
    • The nonplanar peptide unit. III. Quantum chemical calculations for related compounds and experimental X-ray diffraction data
    • Kolaskar, A. S., Lakshminaranayan, A. V., Sarathy, K. P. & Sasisekharan, V. (1975). The nonplanar peptide unit. III. Quantum chemical calculations for related compounds and experimental X-ray diffraction data. Biopolymers, 14, 1081-1094.
    • (1975) Biopolymers , vol.14 , pp. 1081-1094
    • Kolaskar, A.S.1    Lakshminaranayan, A.V.2    Sarathy, K.P.3    Sasisekharan, V.4
  • 27
    • 0000117718 scopus 로고
    • Molecular structure of L-Leu-L-Tyr, Gly-D,L-Met.p-toluenesulfonate and L-His-L-Leu
    • Krause, J. A., Baures, P. W. & Eggleston, D. S. (1993). Molecular structure of L-Leu-L-Tyr, Gly-D,L-Met.p-toluenesulfonate and L-His-L-Leu. Acta Crystallog. sect. B, 49, 123-130.
    • (1993) Acta Crystallog. Sect. B , vol.49 , pp. 123-130
    • Krause, J.A.1    Baures, P.W.2    Eggleston, D.S.3
  • 29
    • 0027169515 scopus 로고
    • Main-chain bond lengths and bond angles in protein structures
    • Laskowski, R. A., Moss, D. S. & Thornton, J. M. (1993a). Main-chain bond lengths and bond angles in protein structures. J. Mol. Biol. 231, 1049-1067.
    • (1993) J. Mol. Biol. , vol.231 , pp. 1049-1067
    • Laskowski, R.A.1    Moss, D.S.2    Thornton, J.M.3
  • 30
    • 0000243829 scopus 로고
    • PROCHECK: A program to check the stereochemical quality of protein structures
    • Laskowski, R. A., MacArthur, M. W., Moss, D. S. & Thornton, J. M. (1993b). PROCHECK: a program to check the stereochemical quality of protein structures. J. Appl. Crystallog. 26, 283-291.
    • (1993) J. Appl. Crystallog. , vol.26 , pp. 283-291
    • Laskowski, R.A.1    MacArthur, M.W.2    Moss, D.S.3    Thornton, J.M.4
  • 31
    • 0017309766 scopus 로고
    • Structural patterns in globular proteins
    • Levitt, M. & Chothia, C. (1976). Structural patterns in globular proteins. Nature, 261, 552-558.
    • (1976) Nature , vol.261 , pp. 552-558
    • Levitt, M.1    Chothia, C.2
  • 32
    • 0025890946 scopus 로고
    • Influence of proline residues on protein conformation
    • MacArthur, M. W. & Thornton, J. M. (1989). Influence of proline residues on protein conformation. J. Mol. Biol. 218, 397-412.
    • (1989) J. Mol. Biol. , vol.218 , pp. 397-412
    • MacArthur, M.W.1    Thornton, J.M.2
  • 33
    • 84977303841 scopus 로고
    • The geometry of the reactive site and of the peptide groups in trypsin, trypsinogen and its complexes with inhibitors
    • Marquart, M., Walter, J., Deisenhofer, J., Bode, W. & Huber, R. (1983). The geometry of the reactive site and of the peptide groups in trypsin, trypsinogen and its complexes with inhibitors. Acta Crystallog. sect. B, 39, 480-490.
    • (1983) Acta Crystallog. Sect. B , vol.39 , pp. 480-490
    • Marquart, M.1    Walter, J.2    Deisenhofer, J.3    Bode, W.4    Huber, R.5
  • 34
    • 0014941385 scopus 로고
    • Energy parameters in polypeptides III. Semiempirical molecular orbital calculations for hydrogen-bonded model peptides
    • Momany, F. A., McGuire, R. F., Yan, J. F. & Scheraga, H. (1970). Energy parameters in polypeptides III. Semiempirical molecular orbital calculations for hydrogen-bonded model peptides. J. Phys. Chem. 74, 2424-2438.
    • (1970) J. Phys. Chem. , vol.74 , pp. 2424-2438
    • Momany, F.A.1    McGuire, R.F.2    Yan, J.F.3    Scheraga, H.4
  • 36
    • 0011359696 scopus 로고
    • Crystal and molecular structure of Glycyl-L-alanine hydrochloride
    • Naganathan, P. S. & Venkatesan, K. (1972). Crystal and molecular structure of Glycyl-L-alanine hydrochloride. Acta Crystallog. sect. B, 28, 552-556.
    • (1972) Acta Crystallog. Sect. B , vol.28 , pp. 552-556
    • Naganathan, P.S.1    Venkatesan, K.2
  • 37
    • 0025935211 scopus 로고
    • X-ray analyses of aspartic proteinases IV: Structure and refinement at 2.2 Å resolution of bovine chymosin
    • Newman, M., Safro, M., Frazao, C., Kahn, G., Zdanov, A., Tickle, I. J., Blundell, T. L. & Andreeva, N. (1991). X-ray analyses of aspartic proteinases IV: structure and refinement at 2.2 Å resolution of bovine chymosin. J. Mol. Biol. 221, 1295-1309.
    • (1991) J. Mol. Biol. , vol.221 , pp. 1295-1309
    • Newman, M.1    Safro, M.2    Frazao, C.3    Kahn, G.4    Zdanov, A.5    Tickle, I.J.6    Blundell, T.L.7    Andreeva, N.8
  • 39
    • 0027220647 scopus 로고
    • Identification and classification of protein fold families
    • Orengo, C. A., Flores, T. P., Taylor, W. R. & Thornton, J. M. (1993). Identification and classification of protein fold families. Protein Eng. 6, 485-500.
    • (1993) Protein Eng. , vol.6 , pp. 485-500
    • Orengo, C.A.1    Flores, T.P.2    Taylor, W.R.3    Thornton, J.M.4
  • 40
    • 0001025589 scopus 로고
    • Structure of L-phenylalanyl-L-proline monohydrate
    • Panneerselvan, K. & Chacko, K. K. (1989). Structure of L-phenylalanyl-L-proline monohydrate. Acta Crystallog. sect. C. 45, 106-109.
    • (1989) Acta Crystallog. Sect. C. , vol.45 , pp. 106-109
    • Panneerselvan, K.1    Chacko, K.K.2
  • 42
    • 0020480005 scopus 로고
    • Crystal structure and electron transfer properties of cytochrome-C3
    • Pierrot, M., Haser, R., Frey, M., Payan, F. & Astier, J. P. (1982). Crystal structure and electron transfer properties of cytochrome-C3. J. Biol. Chem. 257, 4341-4348.
    • (1982) J. Biol. Chem. , vol.257 , pp. 4341-4348
    • Pierrot, M.1    Haser, R.2    Frey, M.3    Payan, F.4    Astier, J.P.5
  • 43
    • 0001628150 scopus 로고
    • Electrostatic models for polypeptides: Can we assume transferability?
    • Price, S. L. & Stone, A. J. (1992). Electrostatic models for polypeptides: can we assume transferability? J. Chem. Soc. Faraday Trans. 88, 1755-1763.
    • (1992) J. Chem. Soc. Faraday Trans. , vol.88 , pp. 1755-1763
    • Price, S.L.1    Stone, A.J.2
  • 44
    • 0024804106 scopus 로고
    • Crystallographic refinement of interleukin-1β at 2.0 Å resolution
    • Priestle, J. P., Schaer, H.-P. & Gruetter, M. G. (1989). Crystallographic refinement of interleukin-1β at 2.0 Å resolution. Proc. Natl Acad. Sci. USA, 86, 9667-9671.
    • (1989) Proc. Natl Acad. Sci. USA , vol.86 , pp. 9667-9671
    • Priestle, J.P.1    Schaer, H.-P.2    Gruetter, M.G.3
  • 45
    • 0016022524 scopus 로고
    • Molecular orbital calculations on the conformation of amino acid residues of proteins
    • Pullman, B. & Pullman, A. (1974). Molecular orbital calculations on the conformation of amino acid residues of proteins. Advan. Protein Chem. 28, 347-526.
    • (1974) Advan. Protein Chem. , vol.28 , pp. 347-526
    • Pullman, B.1    Pullman, A.2
  • 46
    • 0014347743 scopus 로고
    • Need for non-planar peptide units in polypeptide chains
    • Ramachandran, G. N. (1968). Need for non-planar peptide units in polypeptide chains. Biopolymers, 6, 1494-1496.
    • (1968) Biopolymers , vol.6 , pp. 1494-1496
    • Ramachandran, G.N.1
  • 47
    • 0015930763 scopus 로고
    • The non-planar peptide unit II. Comparison of theory with crystal structure data
    • Ramachandran, G. N. & Kolaskar, A. S. (1973). The non-planar peptide unit II. Comparison of theory with crystal structure data. Biochim. Biophys. Acta, 303, 385-388.
    • (1973) Biochim. Biophys. Acta , vol.303 , pp. 385-388
    • Ramachandran, G.N.1    Kolaskar, A.S.2
  • 49
    • 0015268796 scopus 로고
    • Stereochemical criteria for polypeptide and protein chain conformations
    • Ramakrishnan, C. & Balasubranian, R. (1972). Stereochemical criteria for polypeptide and protein chain conformations. Int. J. Pept. Protein Res. 4, 79-99.
    • (1972) Int. J. Pept. Protein Res. , vol.4 , pp. 79-99
    • Ramakrishnan, C.1    Balasubranian, R.2
  • 50
    • 0016662479 scopus 로고
    • The covalent and three dimensional structure of concanavelin A. IV. Atomic coordinates, hydrogen bonding, and quaternary structure
    • Reeke, G. N., Jr, Decker, J. W. & Edelman, G. M. (1975). The covalent and three dimensional structure of concanavelin A. IV. Atomic coordinates, hydrogen bonding, and quaternary structure. J. Biol. Chem. 250, 1525-1547.
    • (1975) J. Biol. Chem. , vol.250 , pp. 1525-1547
    • Reeke G.N., Jr.1    Decker, J.W.2    Edelman, G.M.3
  • 51
    • 0017169407 scopus 로고
    • Energetics of the deformation of the peptide unit: Semi-empirical molecular orbital and ab initio study of N-methyl acetamide and N-acetyl-L-alanine N-methyl amide
    • Renugopalakrishnan, V. & Rein, R. (1976). Energetics of the deformation of the peptide unit: semi-empirical molecular orbital and ab initio study of N-methyl acetamide and N-acetyl-L-alanine N-methyl amide. Biochim. Biophys. Acta, 434, 164-168.
    • (1976) Biochim. Biophys. Acta , vol.434 , pp. 164-168
    • Renugopalakrishnan, V.1    Rein, R.2
  • 52
    • 0017773191 scopus 로고
    • Theoretical studies of environmental effects on protein conformation. 1. Flexibility of the peptide bond
    • Scheiner, S. & Kern, C. W. (1977). Theoretical studies of environmental effects on protein conformation. 1. Flexibility of the peptide bond. J. Am. Chem. Soc. 99, 7042-7050.
    • (1977) J. Am. Chem. Soc. , vol.99 , pp. 7042-7050
    • Scheiner, S.1    Kern, C.W.2
  • 53
    • 0030059610 scopus 로고    scopus 로고
    • Ribonuclease from Streptomyces aureofaciens at atomic ressolution
    • Sevcik, J., Dauter, Z., Lamzin, V. S. & Wilson, K. S. (1996). Ribonuclease from Streptomyces aureofaciens at atomic ressolution. Acta Crystallog. sect. D, 52, 327-344.
    • (1996) Acta Crystallog. Sect. D , vol.52 , pp. 327-344
    • Sevcik, J.1    Dauter, Z.2    Lamzin, V.S.3    Wilson, K.S.4
  • 54
    • 0025003236 scopus 로고
    • Crystal structure of ovalbumin as a model for the reactive centre of serpins
    • Stein, P. E., Leslie, A. G. W., Finch, J. T. & Turnell, W. G. (1990). Crystal structure of ovalbumin as a model for the reactive centre of serpins. Nature, 347, 99-102.
    • (1990) Nature , vol.347 , pp. 99-102
    • Stein, P.E.1    Leslie, A.G.W.2    Finch, J.T.3    Turnell, W.G.4
  • 55
    • 0029147823 scopus 로고
    • Intrinsic φ,ψ propensities of amino acids, derived from the coil regions of known structures
    • Swindells, M. B., MacArthur, M. W. & Thornton, J. M. (1995). Intrinsic φ,ψ propensities of amino acids, derived from the coil regions of known structures. Nature Struct. Biol. 2, 596-603.
    • (1995) Nature Struct. Biol. , vol.2 , pp. 596-603
    • Swindells, M.B.1    MacArthur, M.W.2    Thornton, J.M.3
  • 57
    • 0029879363 scopus 로고    scopus 로고
    • Determination of the backbone dihedral angles φ in human ubiquitin from reparametrized empirical Karplus equations
    • Wang, A. C. & Bax, A. (1996). Determination of the backbone dihedral angles φ in human ubiquitin from reparametrized empirical Karplus equations. J. Am. Chem. Soc. 118, 2483-2494.
    • (1996) J. Am. Chem. Soc. , vol.118 , pp. 2483-2494
    • Wang, A.C.1    Bax, A.2
  • 58
    • 0018373262 scopus 로고
    • Conformations of twisted parallel β-sheets and the origin of chirality in protein structures
    • Weatherford, D. W. & Salemme, F. R. (1979). Conformations of twisted parallel β-sheets and the origin of chirality in protein structures. Proc. Natl Acad. Sci. USA, 76, 19-23.
    • (1979) Proc. Natl Acad. Sci. USA , vol.76 , pp. 19-23
    • Weatherford, D.W.1    Salemme, F.R.2
  • 59
    • 0015223121 scopus 로고
    • The non-planar amide group
    • Winkler, F. K. & Dunitz, J. D. (1971). The non-planar amide group. J. Mol. Biol. 59, 169-182.
    • (1971) J. Mol. Biol. , vol.59 , pp. 169-182
    • Winkler, F.K.1    Dunitz, J.D.2
  • 60
    • 0016158501 scopus 로고
    • A novel approach for studies of the molecular conformation in flexible polypeptides
    • Wuthrich, K. & Grathwohl, C. (1974). A novel approach for studies of the molecular conformation in flexible polypeptides. FEBS Letters, 43, 337-340.
    • (1974) FEBS Letters , vol.43 , pp. 337-340
    • Wuthrich, K.1    Grathwohl, C.2
  • 61


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