메뉴 건너뛰기




Volumn 5, Issue 12, 1996, Pages 2600-2616

Conformational analysis and clustering of short and medium size loops connecting regular secondary structures: A database for modeling and prediction

Author keywords

biological functions of; classes; conformation; loop analysis; protein secondary structure; structure modeling and prediction

Indexed keywords

PARVALBUMIN;

EID: 0030449155     PISSN: 09618368     EISSN: None     Source Type: Journal    
DOI: 10.1002/pro.5560051223     Document Type: Article
Times cited : (99)

References (61)
  • 3
    • 0024571640 scopus 로고
    • The helix-turn-helix DNA-binding motif
    • Brennan RG. Matthews BW. 1989. The helix-turn-helix DNA-binding motif. J Biol Chem 264:1903-1906.
    • (1989) J Biol Chem , vol.264 , pp. 1903-1906
    • Brennan, R.G.1    Matthews, B.W.2
  • 6
    • 0021422888 scopus 로고
    • Energetic approach to the packing of α-helices. 2. General treatment of nonequivalent and nonregular helices
    • Chou K-C, Nemethy G, Scherega HA. 1984. Energetic approach to the packing of α-helices. 2. General treatment of nonequivalent and nonregular helices. J Am Chem Soc 106:3161-3170.
    • (1984) J Am Chem Soc , vol.106 , pp. 3161-3170
    • Chou, K.-C.1    Nemethy, G.2    Scherega, H.A.3
  • 7
    • 0025767350 scopus 로고
    • β-Breakers: An aperiodic secondary structure
    • Colloc'h N, Cohen FE 1991. β-Breakers: An aperiodic secondary structure. J Mol Biol 221:603-613.
    • (1991) J Mol Biol , vol.221 , pp. 603-613
    • Colloc'h, N.1    Cohen, F.E.2
  • 9
    • 0342929492 scopus 로고
    • Structural and sequence patterns in the loops of βαβ units
    • Edwards M, Sternberg M, Thomton JM. 1987. Structural and sequence patterns in the loops of βαβ units. Protein Engng 1:173-181.
    • (1987) Protein Engng , vol.1 , pp. 173-181
    • Edwards, M.1    Sternberg, M.2    Thomton, J.M.3
  • 10
    • 0022565437 scopus 로고
    • Standard conformations of polypeptide chain in irregular regions of proteins
    • Efimov AV 1986. Standard conformations of polypeptide chain in irregular regions of proteins. Mol Biol (Moscow. USSR) 20:250-260.
    • (1986) Mol Biol (Moscow. USSR) , vol.20 , pp. 250-260
    • Efimov, A.V.1
  • 11
    • 0025974401 scopus 로고
    • Structure of α-α-hairpins with short connections
    • Efimov AV. 1991a. Structure of α-α-hairpins with short connections. Protein Engng 4:245-250.
    • (1991) Protein Engng , vol.4 , pp. 245-250
    • Efimov, A.V.1
  • 12
    • 0025803604 scopus 로고
    • Structure of coiled β-β-hairpins and β-β-comers
    • Efimov AV. 1991b. Structure of coiled β-β-hairpins and β-β-comers. FEBS Letters 284:288-292.
    • (1991) FEBS Letters , vol.284 , pp. 288-292
    • Efimov, A.V.1
  • 13
    • 4243527252 scopus 로고
    • Long and medium-sized irregular regions in proteins as combinations of small standard structures
    • Ramakrishnan C, Balaram P, eds., Bangalore: Indian Academy of Science
    • Efimov AV. 1991c. Long and medium-sized irregular regions in proteins as combinations of small standard structures. In: Ramakrishnan C, Balaram P, eds.), Molecular conformation and biological interactions. Bangalore: Indian Academy of Science. pp 19-29.
    • (1991) Molecular Conformation and Biological Interactions , pp. 19-29
    • Efimov, A.V.1
  • 14
    • 0027284308 scopus 로고
    • Patterns of loop regions in proteins
    • Efimov AV 1993a. Patterns of loop regions in proteins. Curr Opin Struc Biol 3:379-384.
    • (1993) Curr Opin Struc Biol , vol.3 , pp. 379-384
    • Efimov, A.V.1
  • 15
    • 0027428284 scopus 로고
    • Standard structures in proteins
    • Efimov AV. 1993b. Standard structures in proteins. Prog Biophys Mol Biol 60:201-239.
    • (1993) Prog Biophys Mol Biol , vol.60 , pp. 201-239
    • Efimov, A.V.1
  • 16
    • 79952608525 scopus 로고
    • Accurate bond and angle parameters for X-ray protein structure refinement
    • Engh RA, Huber R. 1991. Accurate bond and angle parameters for X-ray protein structure refinement. Acta Cryst A 47:392-400.
    • (1991) Acta Cryst A , vol.47 , pp. 392-400
    • Engh, R.A.1    Huber, R.2
  • 17
    • 0000461280 scopus 로고
    • Confidence limits on phylogenies: An approach using the bootstrap
    • Felsenstein J. 1985. Confidence limits on phylogenies: An approach using the bootstrap. Evolution 39:783-791.
    • (1985) Evolution , vol.39 , pp. 783-791
    • Felsenstein, J.1
  • 18
    • 0014211361 scopus 로고
    • Construction of phylogenetic trees
    • Fitch WM, Margoliash E. 1967. Construction of phylogenetic trees. Science 155:279-284.
    • (1967) Science , vol.155 , pp. 279-284
    • Fitch, W.M.1    Margoliash, E.2
  • 19
    • 0019028066 scopus 로고
    • Model for haptoglobin heavy chain based upon structural homology
    • Greer J. 1980. Model for haptoglobin heavy chain based upon structural homology. Proc Natl Acad Sci USA 77:3393-3397.
    • (1980) Proc Natl Acad Sci USA , vol.77 , pp. 3393-3397
    • Greer, J.1
  • 20
    • 0025287330 scopus 로고
    • Comparative modelling methods: Application 10 the family of the mammalian Ser proteinases
    • Greer J. 1990a. Comparative modelling methods: Application 10 the family of the mammalian Ser proteinases. Prot Struct Funct and Genes 7:317-334.
    • (1990) Prot Struct Funct and Genes , vol.7 , pp. 317-334
    • Greer, J.1
  • 21
    • 55549115744 scopus 로고
    • Comparative modelling of proteins in the design of novel renin inhibitors
    • Greer J 1990b. Comparative modelling of proteins in the design of novel renin inhibitors. Biophysical J 57:p.A.207
    • (1990) Biophysical J , vol.57
    • Greer, J.1
  • 22
    • 0025995844 scopus 로고
    • A structural taxonomy of DNA-binding domains
    • Harrison SC. 1991. A structural taxonomy of DNA-binding domains. Nature 353:715-719.
    • (1991) Nature , vol.353 , pp. 715-719
    • Harrison, S.C.1
  • 23
    • 0025310356 scopus 로고
    • DNA-recognition by proteins with the helix-turn-helix motif
    • Harrison SC, Aggarwal H. 1990. DNA-recognition by proteins with the helix-turn-helix motif. Ann Rev Biochem 59:933-969.
    • (1990) Ann Rev Biochem , vol.59 , pp. 933-969
    • Harrison, S.C.1    Aggarwal, H.2
  • 24
    • 0020997912 scopus 로고
    • Dictionary of protein secondary structure: Pattern recognition of hydrogen-bonded and geometrical features
    • Kabsch W, Sander C. 1983 Dictionary of protein secondary structure: Pattern recognition of hydrogen-bonded and geometrical features. Biopolymers 22:2577-2637.
    • (1983) Biopolymers , vol.22 , pp. 2577-2637
    • Kabsch, W.1    Sander, C.2
  • 25
    • 0002404088 scopus 로고
    • On the orthogonal transformation used for structural comparisons
    • Kearsley SK. 1989. On the orthogonal transformation used for structural comparisons. Acta Cryst A 45:208-210
    • (1989) Acta Cryst A , vol.45 , pp. 208-210
    • Kearsley, S.K.1
  • 26
    • 0026244229 scopus 로고
    • MOLSCRIPT: A program to produce both detailed and schematic plots of protein structures
    • Kraulis PJ. 1991. MOLSCRIPT: A program to produce both detailed and schematic plots of protein structures. J Applied Cryst 24:946-950.
    • (1991) J Applied Cryst , vol.24 , pp. 946-950
    • Kraulis, P.J.1
  • 27
    • 0018816959 scopus 로고
    • Structure and evolution of calcium-modulated proteins
    • Kretsinger RH. 1980. Structure and evolution of calcium-modulated proteins. CRC Crit Rev Biochem 8:119-174.
    • (1980) CRC Crit Rev Biochem , vol.8 , pp. 119-174
    • Kretsinger, R.H.1
  • 28
    • 0022981913 scopus 로고
    • Loops in globular proteins: A novel category of secondary structure
    • Leszczynski JF, Rose GD 1986. Loops in globular proteins: A novel category of secondary structure. Science 234.849-855.
    • (1986) Science , vol.234 , pp. 849-855
    • Leszczynski, J.F.1    Rose, G.D.2
  • 30
    • 0025690309 scopus 로고
    • Situations of γ-turns in proteins. Their relation to α-helices, β-sheets and ligand binding sites
    • Milner-White EJ. 1990. Situations of γ-turns in proteins. Their relation to α-helices, β-sheets and ligand binding sites J Mol Biol 216:385-397.
    • (1990) J Mol Biol , vol.216 , pp. 385-397
    • Milner-White, E.J.1
  • 31
    • 12644316877 scopus 로고
    • One type of γ-turn, rather than the other, gives rise to chain reversal in proteins
    • Milner-White EJ, Ross BM, Ismail R, Belhadj-Mastefa K, Poet R 1988. One type of γ-turn, rather than the other, gives rise to chain reversal in proteins. J Mol Biol 216:385-397.
    • (1988) J Mol Biol , vol.216 , pp. 385-397
    • Milner-White, E.J.1    Ross, B.M.2    Ismail, R.3    Belhadj-Mastefa, K.4    Poet, R.5
  • 33
    • 0029009067 scopus 로고
    • The hydrophobic-staple motif and a role for loop-residues in or-helix stability and protein folding
    • Muñoz V, Blanco FJ, Serrano L. 1995. The hydrophobic-staple motif and a role for loop-residues in or-helix stability and protein folding. Nature Struc Biol 2:380-385.
    • (1995) Nature Struc Biol , vol.2 , pp. 380-385
    • Muñoz, V.1    Blanco, F.J.2    Serrano, L.3
  • 34
    • 0027530219 scopus 로고
    • Termination of the right handed helices in proteins by residues in left handed helical conformations
    • Nagarajaram HA, Sowdhamini R, Ramakrishnan C, Balaram P. 1993. Termination of the right handed helices in proteins by residues in left handed helical conformations. FEBS Letters 321:79-83.
    • (1993) FEBS Letters , vol.321 , pp. 79-83
    • Nagarajaram, H.A.1    Sowdhamini, R.2    Ramakrishnan, C.3    Balaram, P.4
  • 36
    • 0025104478 scopus 로고
    • Tertiary structural constraints on protein evolutionary diversity: Templates, key residues and structure prediction
    • Overington J, Johnson MS, Sali A, Blundell TL. 1990a. Tertiary structural constraints on protein evolutionary diversity: Templates, key residues and structure prediction. Proc R Soc Lond B. 241:132-145.
    • (1990) Proc R Soc Lond B , vol.241 , pp. 132-145
    • Overington, J.1    Johnson, M.S.2    Sali, A.3    Blundell, T.L.4
  • 37
    • 3643138684 scopus 로고
    • Applications of environment specific amino acid substitution tables to identification of key residues in protein tertiary structure
    • Overington J, Johnson MS, Topham C, McLeod A, Sali A, Zhu Z-Y, Sibanda BL, Blundell TL. 1990b. Applications of environment specific amino acid substitution tables to identification of key residues in protein tertiary structure. Curr Sci 59:867-874.
    • (1990) Curr Sci , vol.59 , pp. 867-874
    • Overington, J.1    Johnson, M.S.2    Topham, C.3    McLeod, A.4    Sali, A.5    Zhu, Z.-Y.6    Sibanda, B.L.7    Blundell, T.L.8
  • 39
    • 0025612679 scopus 로고
    • A helix-turn-strand structural motif common in α-β proteins
    • Rice PA, Goldman A, Steitz TA. 1990. A helix-turn-strand structural motif common in α-β proteins. Proteins 8:334-340.
    • (1990) Proteins , vol.8 , pp. 334-340
    • Rice, P.A.1    Goldman, A.2    Steitz, T.A.3
  • 40
    • 0024290472 scopus 로고
    • Amino acid preferences for specific locations at the ends of α-helices
    • Richardson JS, Richardson DC. 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
  • 41
    • 0026530262 scopus 로고
    • Taxonomy and conformational analysis of loops in proteins
    • Ring CS, Kneller DG, Langridge R, Cohen FE. 1992. Taxonomy and conformational analysis of loops in proteins. J Mol Biol 224:685-699.
    • (1992) J Mol Biol , vol.224 , pp. 685-699
    • Ring, C.S.1    Kneller, D.G.2    Langridge, R.3    Cohen, F.E.4
  • 42
    • 0025326949 scopus 로고
    • Automatic definition of recurrent local structure motifs in proteins
    • Rooman MJ, Rodriguez J, Wodak SJ. 1990a. Automatic definition of recurrent local structure motifs in proteins. J Mol Biol 213:327-336.
    • (1990) J Mol Biol , vol.213 , pp. 327-336
    • Rooman, M.J.1    Rodriguez, J.2    Wodak, S.J.3
  • 43
    • 0025326950 scopus 로고
    • Relations between protein sequence and structure and their significance
    • Rooman MJ, Rodriguez J, Wodak SJ 1990b. Relations between protein sequence and structure and their significance. J Mol Biol 213:337-350.
    • (1990) J Mol Biol , vol.213 , pp. 337-350
    • Rooman, M.J.1    Rodriguez, J.2    Wodak, S.J.3
  • 45
    • 12644308819 scopus 로고    scopus 로고
    • Predicting the conformational class of short and medium size loops connecting regular secondary structures: Application to comparative modelling
    • In press
    • Rufino SD, Donate LE. Canard LHJ, Blundell TL. 1996. Predicting the conformational class of short and medium size loops connecting regular secondary structures: Application to comparative modelling. J Mol Biol. In press.
    • (1996) J Mol Biol
    • Rufino, S.D.1    Donate, L.E.2    Canard, L.H.J.3    Blundell, T.L.4
  • 46
    • 0025317502 scopus 로고
    • Definition of general topological equivalence in protein structures
    • Sali A, Blundell TL. 1990. Definition of general topological equivalence in protein structures. J Mol Biol 212.403-428.
    • (1990) J Mol Biol , vol.212 , pp. 403-428
    • Sali, A.1    Blundell, T.L.2
  • 47
    • 0024391832 scopus 로고
    • Conformation of β-hairpins in protein structures. A systematic classification with applications to modelling by homology, electron density fitting and protein engineering
    • Sibanda BL, Blundell TL, Thomton JM. 1989. Conformation of β-hairpins in protein structures. A systematic classification with applications to modelling by homology, electron density fitting and protein engineering. J Mol Biol 206:759-777.
    • (1989) J Mol Biol , vol.206 , pp. 759-777
    • Sibanda, B.L.1    Blundell, T.L.2    Thomton, J.M.3
  • 48
    • 0021844602 scopus 로고
    • β-Hairpin families in globular proteins
    • Sibanda BL, Thornton JM. 1985. β-Hairpin families in globular proteins. Nature 316:170-174.
    • (1985) Nature , vol.316 , pp. 170-174
    • Sibanda, B.L.1    Thornton, J.M.2
  • 49
    • 0028914725 scopus 로고
    • An automatic method involving cluster analysis of secondary structures for the identification of domains in proteins
    • Sowdharnini R, Blundell TL. 1995. An automatic method involving cluster analysis of secondary structures for the identification of domains in proteins. Protein Sci 4:506-520.
    • (1995) Protein Sci , vol.4 , pp. 506-520
    • Sowdharnini, R.1    Blundell, T.L.2
  • 51
    • 0345186059 scopus 로고
    • Analysis of short loops connecting secondary structural elements in proteins
    • Ramakrishnan C. Balaram P, eds., Bangalore: Indian Academy of Science
    • Srinivasan N, Sowdhamini R, Ramakrishnan C, Balaram P. 1991. Analysis of short loops connecting secondary structural elements in proteins. In: Ramakrishnan C. Balaram P, eds., Molecular conformation and biological interactions. Bangalore: Indian Academy of Science. pp. 59-73.
    • (1991) Molecular Conformation and Biological Interactions , pp. 59-73
    • Srinivasan, N.1    Sowdhamini, R.2    Ramakrishnan, C.3    Balaram, P.4
  • 52
    • 0025280401 scopus 로고
    • Structural studies of protein-nucleic acid interaction: The sources of sequence-specific binding
    • Steitz TA. 1990. Structural studies of protein-nucleic acid interaction: The sources of sequence-specific binding. Q Rev Biophys 23:205-280.
    • (1990) Q Rev Biophys , vol.23 , pp. 205-280
    • Steitz, T.A.1
  • 54
    • 0001433241 scopus 로고
    • Knowledge based modelling of homologous proteins, part I: Three-dimensional frameworks derived from the simultaneous superposition of multiple structures
    • Sutcliffe MJ, Haneef I, Carney D, Blundell TL 1987. Knowledge based modelling of homologous proteins, part I: Three-dimensional frameworks derived from the simultaneous superposition of multiple structures Protein Engng 1:377-384
    • (1987) Protein Engng , vol.1 , pp. 377-384
    • Sutcliffe, M.J.1    Haneef, I.2    Carney, D.3    Blundell, T.L.4
  • 55
    • 0028477609 scopus 로고
    • Loopy similarities
    • Swindells MB. 1994. Loopy similarities. Struc Biol 1:421-422.
    • (1994) Struc Biol , vol.1 , pp. 421-422
    • Swindells, M.B.1
  • 56
    • 0029147823 scopus 로고
    • Intrinsic φ,ψ propensities of amino acids, derived from the coil regions of known structures
    • Swindells MB, MacArthur MW, Thornton JM. 1995 Intrinsic φ,ψ propensities of amino acids, derived from the coil regions of known structures. Nature Struc Biol 2:596-603
    • (1995) Nature Struc Biol , vol.2 , pp. 596-603
    • Swindells, M.B.1    MacArthur, M.W.2    Thornton, J.M.3
  • 58
    • 0027439391 scopus 로고
    • Identification of key residues in structurally variable regions of proteins using conformationally-constrained environmental substitution tables: Applications to loop fragment ranking in modelling of protein structure
    • Topham CM, McLeod A, Eisenmenger F, Overington JP, Johnson MS, Blundell TL. 1993. Identification of key residues in structurally variable regions of proteins using conformationally-constrained environmental substitution tables: Applications to loop fragment ranking in modelling of protein structure. J Mol Biol 229:194-220.
    • (1993) J Mol Biol , vol.229 , pp. 194-220
    • Topham, C.M.1    McLeod, A.2    Eisenmenger, F.3    Overington, J.P.4    Johnson, M.S.5    Blundell, T.L.6
  • 59
    • 0024834425 scopus 로고
    • Structural determinant of the conformations of medium-sized loops in proteins
    • Tramontano A, Chothia C, Lesk AM 1989. Structural determinant of the conformations of medium-sized loops in proteins. Proteins 6:382-394.
    • (1989) Proteins , vol.6 , pp. 382-394
    • Tramontano, A.1    Chothia, C.2    Lesk, A.M.3
  • 60
    • 0029863769 scopus 로고    scopus 로고
    • Automatic classification and analysis of αα-turn motifs in proteins
    • Wintjens RT, Rooman MJ, Wodak SJ. 1996. Automatic classification and analysis of αα-turn motifs in proteins. J Mol Biol 255:235-253.
    • (1996) J Mol Biol , vol.255 , pp. 235-253
    • Wintjens, R.T.1    Rooman, M.J.2    Wodak, S.J.3
  • 61
    • 0027227316 scopus 로고
    • Repeat of a helix-turn-helix module in DNA-binding proteins
    • Yura K, Tomoda S, Go M. 1993. Repeat of a helix-turn-helix module in DNA-binding proteins. Protein Engng 6:621-628.
    • (1993) Protein Engng , vol.6 , pp. 621-628
    • Yura, K.1    Tomoda, S.2    Go, M.3


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.