메뉴 건너뛰기




Volumn 1, Issue 3-4, 2010, Pages 271-283

A fresh look at the Ramachandran plot and the occurrence of standard structures in proteins

Author keywords

linear groups; polypeptide conformation; Ramachandran plot, secondary structure; torsion angles

Indexed keywords


EID: 80053296212     PISSN: 18685021     EISSN: 1868503X     Source Type: Journal    
DOI: 10.1515/bmc.2010.022     Document Type: Review
Times cited : (272)

References (59)
  • 3
    • 0014347799 scopus 로고
    • Stereochemical criteria for polypeptides and proteins v Conformation of a system of three linked peptide units
    • Venkatachalam CM. Stereochemical criteria for polypeptides and proteins. V. Conformation of a system of three linked peptide units. Biopolymers 1968; 6: 1425-36
    • (1968) Biopolymers , Issue.6 , pp. 1425-1436
    • Venkatachalam, C.M.1
  • 7
    • 75549085702 scopus 로고    scopus 로고
    • Protein geometry database: A flexible engine to explore backbone conformations and their relationships to covalent geometry
    • Berkholz DS, Krenesky PB, Davidson JR, Karplus PA. Protein geometry database: a flexible engine to explore backbone conformations and their relationships to covalent geometry. Nucleic Acids Res 2010; 38: D320-5
    • (2010) Nucleic Acids Res , vol.38 , pp. D320-D325
    • Berkholz, D.S.1    Krenesky, P.B.2    Davidson, J.R.3    Karplus, P.A.4
  • 8
    • 0000243829 scopus 로고
    • PROCHECK - A program to check the stereochemical quality of protein structure
    • Laskowski RA, MacArthur MW, Moss DS, Thornton JM. PROCHECK - a program to check the stereochemical quality of protein structure. J Appl Cryst 1993; 26: 283-91
    • (1993) J Appl Cryst , vol.26 , pp. 283-291
    • Laskowski, R.A.1    MacArthur, M.W.2    Moss, D.S.3    Thornton, J.M.4
  • 9
    • 0030589514 scopus 로고    scopus 로고
    • Phi/psi-chology: Ramachandran revisited
    • Kleywegt GJ, Jones TA. Phi/psi-chology: Ramachandran revisited. Structure 1996; 4: 1395-400
    • (1996) Structure , vol.4 , pp. 1395-1400
    • Kleywegt, G.J.1    Jones, T.A.2
  • 10
    • 3242886389 scopus 로고    scopus 로고
    • MOLPROBITY: Structure validation and all-Atom contact analysis for nucleic acids and their complexes
    • Davis IW, Murray LW, Richardson JS, Richardson DC. MOLPROBITY: structure validation and all-Atom contact analysis for nucleic acids and their complexes. Nucleic Acids Res 2004; 32: W615-9
    • (2004) Nucleic Acids Res , vol.32 , pp. W615-W619
    • Davis, I.W.1    Murray, L.W.2    Richardson, J.S.3    Richardson, D.C.4
  • 11
    • 50449111518 scopus 로고    scopus 로고
    • The intrinsic conformational propensities of the 20 naturally occurring amino acids and reflection of these propensities in proteins
    • Beck DA, Alonso DO, Inoyama D, Daggett V. The intrinsic conformational propensities of the 20 naturally occurring amino acids and reflection of these propensities in proteins. Proc Natl Acad Sci USA 2008; 105: 12259-64
    • (2008) Proc Natl Acad Sci USA , vol.105 , pp. 12259-12264
    • Beck, D.A.1    Alonso, D.O.2    Inoyama, D.3    Daggett, V.4
  • 12
    • 0025113022 scopus 로고
    • Beta-turns and their distortions: A proposed new nomenclature
    • Wilmot CM, Thornton JM. Beta-turns and their distortions: a proposed new nomenclature. Protein Eng 1990; 3: 479-93
    • (1990) Protein Eng , vol.3 , pp. 479-493
    • Wilmot, C.M.1    Thornton, J.M.2
  • 13
    • 0027428284 scopus 로고
    • Standard structures in proteins
    • Efimov AV. Standard structures in proteins. Prog Biophys Mol Biol 1993; 60: 201-39
    • (1993) Prog Biophys Mol Biol , vol.60 , pp. 201-239
    • Efimov, A.V.1
  • 15
    • 0026009212 scopus 로고
    • Prediction of protein backbone conformation based on seven structure assignments. Influence of local interactions
    • Rooman MJ, Kocher JP, Wodak SJ. Prediction of protein backbone conformation based on seven structure assignments. Influence of local interactions. J Mol Biol 1991; 221: 961-79
    • (1991) J Mol Biol , vol.221 , pp. 961-979
    • Rooman, M.J.1    Kocher, J.P.2    Wodak, S.J.3
  • 16
    • 46449114017 scopus 로고    scopus 로고
    • Structures, basins, and energies: A deconstruction of the Protein Coil Library
    • Perskie LL, Street TO, Rose GD. Structures, basins, and energies: a deconstruction of the Protein Coil Library. Protein Sci 2008; 17: 1151-61
    • (2008) Protein Sci , vol.17 , pp. 1151-1161
    • Perskie, L.L.1    Street, T.O.2    Rose, G.D.3
  • 17
    • 67650526041 scopus 로고    scopus 로고
    • Circular dichroism spectrum of peptides in the poly(Pro)II conformation
    • Woody RW. Circular dichroism spectrum of peptides in the poly(Pro)II conformation. J Am Chem Soc 2009; 131: 8234-45
    • (2009) J Am Chem Soc , vol.131 , pp. 8234-8245
    • Woody, R.W.1
  • 19
    • 0027474991 scopus 로고
    • Left-handed polyproline II helices commonly occur in globular proteins
    • Adzhubei AA, Sternberg MJ. Left-handed polyproline II helices commonly occur in globular proteins. J Mol Biol 1993; 229: 472-93
    • (1993) J Mol Biol , vol.229 , pp. 472-493
    • Adzhubei, A.A.1    Sternberg, M.J.2
  • 20
    • 0001312299 scopus 로고
    • The gamma turn, a possible folded conformation of the peptide chain Comparison with the betaturn
    • Nëethy G, Printz MP. The gamma turn, a possible folded conformation of the peptide chain. Comparison with the betaturn. Macromolecules 1972; 5: 755-8
    • (1972) Macromolecules , vol.5 , pp. 755-758
    • Neethy, G.1    Printz, M.P.2
  • 22
    • 0030010605 scopus 로고    scopus 로고
    • Experimentally observed conformation-dependent geometry and hidden strain in proteins
    • Karplus PA. Experimentally observed conformation-dependent geometry and hidden strain in proteins. Protein Sci 1996; 5: 1406-20
    • (1996) Protein Sci , vol.5 , pp. 1406-1420
    • Karplus, P.A.1
  • 26
    • 22244450719 scopus 로고    scopus 로고
    • Protein families and their evolution - A structural perspective
    • Orengo CA, Thornton JM. Protein families and their evolution - a structural perspective. Annu Rev Biochem 2005; 74: 867-900
    • (2005) Annu Rev Biochem , vol.74 , pp. 867-900
    • Orengo, C.A.1    Thornton, J.M.2
  • 27
    • 0014842661 scopus 로고
    • IUPAC-iub commission on biochemical nomenclature abbreviations and symbols for the description of the conformation of polypeptide chains
    • International Union of Pure and Applied Chemistry (IUPAC)
    • International Union of Pure and Applied Chemistry (IUPAC). IUPAC-IUB Commission on biochemical nomenclature. Abbreviations and symbols for the description of the conformation of polypeptide chains. Biochemistry 1970; 9: 3471-9
    • (1970) Biochemistry , vol.9 , pp. 3471-3479
  • 30
    • 76549252207 scopus 로고
    • The structure of proteins; Two hydrogen-bonded helical configurations of the polypeptide chain
    • Pauling L, Corey RB, Branson HR. The structure of proteins; two hydrogen-bonded helical configurations of the polypeptide chain. Proc Natl Acad Sci USA 1951; 37: 205-11
    • (1951) Proc Natl Acad Sci USA , vol.37 , pp. 205-211
    • Pauling, L.1    Corey, R.B.2    Branson, H.R.3
  • 31
    • 0027616709 scopus 로고
    • How my interest in proteins developed
    • Pauling L. How my interest in proteins developed. Protein Sci 1993; 2: 1060-3
    • (1993) Protein Sci , vol.2 , pp. 1060-1063
    • Pauling, L.1
  • 32
    • 0000591348 scopus 로고
    • New X-ray evidence on the configuration of polypeptide chains
    • Perutz MF. New X-ray evidence on the configuration of polypeptide chains. Nature 1951; 167: 1053-4
    • (1951) Nature , vol.167 , pp. 1053-1054
    • Perutz, M.F.1
  • 33
    • 0013820507 scopus 로고
    • X-ray diffraction studies on polypeptide conformations
    • Davies DR. X-ray diffraction studies on polypeptide conformations. Prog Biophys Mol Biol 1965; 15: 189-222
    • (1965) Prog Biophys Mol Biol , vol.15 , pp. 189-222
    • Davies, D.R.1
  • 34
    • 0037103092 scopus 로고    scopus 로고
    • Variants of 310-helices in proteins
    • Pal L, Basu G, Chakrabarti P. Variants of 310-helices in proteins. Proteins 2002; 48: 571-9
    • (2002) Proteins , vol.48 , pp. 571-579
    • Pal, L.1    Basu, G.2    Chakrabarti, P.3
  • 36
    • 0032692474 scopus 로고    scopus 로고
    • Novel protein structural motifs containing twoturn and longer 310-helices
    • Pal L, Basu G. Novel protein structural motifs containing twoturn and longer 310-helices. Protein Eng 1999; 12: 811-4
    • (1999) Protein Eng , vol.12 , pp. 811-814
    • Pal, L.1    Basu, G.2
  • 37
    • 76549238253 scopus 로고
    • The pleated sheet, a new layer configuration of polypeptide chains
    • Pauling L, Corey RB. The pleated sheet, a new layer configuration of polypeptide chains. Proc Natl Acad Sci USA 1951; 37: 251-6
    • (1951) Proc Natl Acad Sci USA , vol.37 , pp. 251-256
    • Pauling, L.1    Corey, R.B.2
  • 38
    • 0019443447 scopus 로고
    • The anatomy and taxonomy of protein structure
    • Richardson JS. The anatomy and taxonomy of protein structure. Adv Protein Chem 1981; 34: 167-339
    • (1981) Adv Protein Chem , vol.34 , pp. 167-339
    • Richardson, J.S.1
  • 39
    • 0017615801 scopus 로고
    • Logical analysis of the mechanism of protein folding. IV. Super-secondary structures
    • Nagano K. Logical analysis of the mechanism of protein folding. IV. Super-secondary structures. J Mol Biol 1977; 109: 235-50
    • (1977) J Mol Biol , vol.109 , pp. 235-250
    • Nagano, K.1
  • 40
    • 0001567029 scopus 로고
    • Structure of poly-L-proline II.
    • Sasisekharan V. Structure of poly-L-proline II. Acta Crystallogr 1959; 12: 897-903
    • (1959) Acta Crystallogr , vol.12 , pp. 897-903
    • Sasisekharan, V.1
  • 41
    • 0014416148 scopus 로고
    • The structure of poly-L-proline II
    • Arnott S, Dover SD. The structure of poly-L-proline II. Acta Crystallogr B 1968; 24: 599-601
    • (1968) Acta Crystallogr B , vol.24 , pp. 599-601
    • Arnott, S.1    Dover, S.D.2
  • 42
    • 0141821477 scopus 로고
    • Conformational analysis of macromolecules. III. Helical structures of polyglycine and poly-Lalanine
    • Scott RA, Scheraga HA. Conformational analysis of macromolecules. III. Helical structures of polyglycine and poly-Lalanine. J Chem Phys 1966; 45: 2091-101
    • (1966) J Chem Phys , vol.45 , pp. 2091-2101
    • Scott, R.A.1    Scheraga, H.A.2
  • 43
    • 0036400325 scopus 로고    scopus 로고
    • Is polyproline II a major backbone conformation in unfolded proteinš
    • Shi Z, Woody RW, Kallenbach NR. Is polyproline II a major backbone conformation in unfolded proteinš. Adv Protein Chem 2002; 62: 163-240
    • (2002) Adv Protein Chem , vol.62 , pp. 163-240
    • Shi, Z.1    Woody, R.W.2    Kallenbach, N.R.3
  • 44
    • 0000556407 scopus 로고
    • Hydrogen bonded helical configurations of the polypeptide chain
    • Donohue J. Hydrogen bonded helical configurations of the polypeptide chain. Proc Natl Acad Sci USA 1953; 39: 470-8
    • (1953) Proc Natl Acad Sci USA , vol.39 , pp. 470-478
    • Donohue, J.1
  • 45
    • 0001142723 scopus 로고
    • The pi-helix - A hydrogen bonded configuration of the polypeptide chain
    • Low B, Baybutt R. The pi-helix - a hydrogen bonded configuration of the polypeptide chain. J Am Chem Soc 1952; 74: 5806-7
    • (1952) J Am Chem Soc , vol.74 , pp. 5806-5807
    • Low, B.1    Baybutt, R.2
  • 46
    • 0033978466 scopus 로고    scopus 로고
    • The pi-helix translates structure into function
    • Weaver TM. The pi-helix translates structure into function. Protein Sci 2000; 9: 201-6
    • (2000) Protein Sci , vol.9 , pp. 201-206
    • Weaver, T.M.1
  • 47
    • 53249105518 scopus 로고    scopus 로고
    • Pi-Turns: Types, systematics and the context of their occurrence in protein structures
    • Dasgupta B, Chakrabarti P. pi-Turns: types, systematics and the context of their occurrence in protein structures. BMC Struct Biol 2008; 8: 39
    • (2008) BMC Struct Biol , vol.8 , pp. 39
    • Dasgupta, B.1    Chakrabarti, P.2
  • 48
    • 0036276409 scopus 로고    scopus 로고
    • Occurrence, conformational features and amino acid propensities for the p-helix
    • Fodje MN, Al-Karadaghi S. Occurrence, conformational features and amino acid propensities for the p-helix. Protein Eng 2002; 15: 353-8
    • (2002) Protein Eng , vol.15 , pp. 353-358
    • Fodje, M.N.1    Al-Karadaghi, S.2
  • 49
    • 0035915130 scopus 로고    scopus 로고
    • Paulings left-handed a-helix
    • Dunitz J. Paulings left-handed a-helix. Angew Chem Int Ed 2001; 40: 4167-73
    • (2001) Angew Chem Int Ed , vol.40 , pp. 4167-4173
    • Dunitz, J.1
  • 50
    • 0028566270 scopus 로고
    • A revised set of potentials for b-turn formation in proteins
    • Hutchinson EG, Thornton JM. A revised set of potentials for b-turn formation in proteins. Protein Sci 1994; 3: 2207-16
    • (1994) Protein Sci , vol.3 , pp. 2207-2216
    • Hutchinson, E.G.1    Thornton, J.M.2
  • 52
    • 0025326949 scopus 로고
    • Automatic definition of recurrent local structure motifs in proteins
    • Rooman MJ, Rodriguez J, Wodak SJ. Automatic definition of recurrent local structure motifs in proteins. J Mol Biol 1990; 213: 327-36
    • (1990) J Mol Biol , vol.213 , pp. 327-336
    • Rooman, M.J.1    Rodriguez, J.2    Wodak, S.J.3
  • 53
  • 54
    • 0029860175 scopus 로고    scopus 로고
    • Local structural motifs of protein backbones are classified by self-organizing neural networks
    • Schuchhardt J, Schneider G, Reichelt J, Schomburg D, Wrede P. Local structural motifs of protein backbones are classified by self-organizing neural networks. Protein Eng 1996; 9: 833-42
    • (1996) Protein Eng , vol.9 , pp. 833-842
    • Schuchhardt, J.1    Schneider, G.2    Reichelt, J.3    Schomburg, D.4    Wrede, P.5
  • 55
    • 0029863769 scopus 로고    scopus 로고
    • Automatic classification and analysis of a a-turn motifs in proteins
    • Wintjens RT, Rooman MJ, Wodak SJ. Automatic classification and analysis of a a-turn motifs in proteins. J Mol Biol 1996; 255: 235-53
    • (1996) J Mol Biol , vol.255 , pp. 235-253
    • Wintjens, R.T.1    Rooman, M.J.2    Wodak, S.J.3
  • 56
    • 0031052447 scopus 로고    scopus 로고
    • Patterns, structures, and amino acid frequencies in structural building blocks, a protein secondary structure classification scheme
    • Fetrow JS, Palumbo MJ, Berg G. Patterns, structures, and amino acid frequencies in structural building blocks, a protein secondary structure classification scheme. Proteins 1997; 27: 249-71
    • (1997) Proteins , vol.27 , pp. 249-271
    • Fetrow, J.S.1    Palumbo, M.J.2    Berg, G.3
  • 57
    • 0031927279 scopus 로고    scopus 로고
    • Typical interaction patterns in ab and ba turn motifs
    • Wintjens R, Wodak SJ, Rooman M. Typical interaction patterns in ab and ba turn motifs. Protein Eng 1998; 11: 505-22
    • (1998) Protein Eng , vol.11 , pp. 505-522
    • Wintjens, R.1    Wodak, S.J.2    Rooman, M.3
  • 59
    • 17744361862 scopus 로고    scopus 로고
    • Visualization of conformational distribution of short to medium size segments in globular proteins and identification of local structural motifs
    • Ikeda K, Tomii K, Yokomizo T, Mitomo D, Maruyama K, Suzuki S, Higo J. Visualization of conformational distribution of short to medium size segments in globular proteins and identification of local structural motifs. Protein Sci 2005; 14: 1253-65
    • (2005) Protein Sci , vol.14 , pp. 1253-1265
    • Ikeda, K.1    Tomii, K.2    Yokomizo, T.3    Mitomo, D.4    Maruyama, K.5    Suzuki, S.6    Higo, J.7


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.