메뉴 건너뛰기




Volumn 8, Issue 3, 1999, Pages 573-586

Analysis of interactive packing of secondary structural elements in α/β units in proteins

Author keywords

Comparative modeling; Packing geometry; Protein structure prediction; helix; packing; strand

Indexed keywords

ALPHA CHAIN; ALPHA HELIX; ARTICLE; BETA CHAIN; HYDROGEN BOND; NONHUMAN; PREDICTION; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEIN FAMILY; PROTEIN PROTEIN INTERACTION; PROTEIN SECONDARY STRUCTURE; SEQUENCE ANALYSIS; STRUCTURE ANALYSIS; TARGET CELL;

EID: 0033016710     PISSN: 09618368     EISSN: None     Source Type: Journal    
DOI: 10.1110/ps.8.3.573     Document Type: Article
Times cited : (18)

References (56)
  • 1
    • 0021118489 scopus 로고
    • Evolution and the tertiary structure of globular proteins
    • Bajaj M, Blundell TL. 1984. Evolution and the tertiary structure of globular proteins. Ann Rev Biochem 13:453-491.
    • (1984) Ann Rev Biochem , vol.13 , pp. 453-491
    • Bajaj, M.1    Blundell, T.L.2
  • 2
    • 0027373337 scopus 로고
    • Knowledge-based model-building of proteins - Concepts and examples
    • Bajorath J, Stenkamp R, Arufto A. 1993. Knowledge-based model-building of proteins - Concepts and examples. Protein Sci 2:1798-1810.
    • (1993) Protein Sci , vol.2 , pp. 1798-1810
    • Bajorath, J.1    Stenkamp, R.2    Arufto, A.3
  • 4
    • 0024278714 scopus 로고
    • Helix geometry in proteins
    • Barlow DJ, Thornton JM. 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
  • 8
  • 9
    • 0031991297 scopus 로고    scopus 로고
    • Structural classification of αββ and ββα supersecondary structure units in proteins
    • Boutonnet NS, Kajava AV, Rooman MJ. 1998. Structural classification of αββ and ββα supersecondary structure units in proteins. Proteins 30:193-212.
    • (1998) Proteins , vol.30 , pp. 193-212
    • Boutonnet, N.S.1    Kajava, A.V.2    Rooman, M.J.3
  • 10
    • 0014693695 scopus 로고
    • A possible three-dimensional structure of bovine β-lactalbumin based on that of hen's egg white lysozyme
    • Browne WJ, North ACT, Philips DC, Brew K, Vanaman TC, Hill RL. 1969. A possible three-dimensional structure of bovine β-lactalbumin based on that of hen's egg white lysozyme. J Mol Biol 42:65-86.
    • (1969) J Mol Biol , vol.42 , pp. 65-86
    • Browne, W.J.1    North, A.C.T.2    Philips, D.C.3    Brew, K.4    Vanaman, T.C.5    Hill, R.L.6
  • 11
    • 0016352763 scopus 로고
    • Hydrophobic bonding and accessible surface area in proteins
    • Chothia C. 1974. Hydrophobic bonding and accessible surface area in proteins. Nature 248:338-339.
    • (1974) Nature , vol.248 , pp. 338-339
    • Chothia, C.1
  • 12
    • 0006980341 scopus 로고
    • Structural invarients in protein folding
    • Chothia C. 1975. Structural invarients in protein folding. Nature 254:705-708.
    • (1975) Nature , vol.254 , pp. 705-708
    • Chothia, C.1
  • 13
    • 0021118508 scopus 로고
    • Principles that determine the structure of proteins
    • Chothia C. 1984. Principles that determine the structure of proteins. Ann Rev Biochem 53:537-512.
    • (1984) Ann Rev Biochem , vol.53 , pp. 537-1512
    • Chothia, C.1
  • 14
    • 0020429363 scopus 로고
    • Evolution of proteins formed by β-sheets: 1. Plastocyanin and azurin
    • Chothia C, Lesk AM. 1982. Evolution of proteins formed by β-sheets: 1. Plastocyanin and azurin. J Mol Biol 160:325-342.
    • (1982) J Mol Biol , vol.160 , pp. 325-342
    • Chothia, C.1    Lesk, A.M.2
  • 15
    • 0022706389 scopus 로고
    • The relation between the divergence of sequence and structure in proteins
    • Chothia C, Lesk AM. 1986. The relation between the divergence of sequence and structure in proteins. EMBO J 5:823-826.
    • (1986) EMBO J , vol.5 , pp. 823-826
    • Chothia, C.1    Lesk, A.M.2
  • 18
    • 0343063933 scopus 로고
    • Structure of proteins: Packing of α-helices and pleated sheets
    • Chothia C, Levin M, Richardson D. 1977. Structure of proteins: Packing of α-helices and pleated sheets. Proc Natl Acad Sci USA 74:4130-4134.
    • (1977) Proc Natl Acad Sci USA , vol.74 , pp. 4130-4134
    • Chothia, C.1    Levin, M.2    Richardson, D.3
  • 19
    • 0022368919 scopus 로고
    • Interactions between an alpha-helix and a beta-sheet. Energetics of alpha/beta packing in proteins
    • Chou KC, Nemethy G, Rumsey S, Tuttle RW, Scheraga HA. 1985. Interactions between an alpha-helix and a beta-sheet. Energetics of alpha/beta packing in proteins. J Mol Biol 186:591-609.
    • (1985) J Mol Biol , vol.186 , pp. 591-609
    • Chou, K.C.1    Nemethy, G.2    Rumsey, S.3    Tuttle, R.W.4    Scheraga, H.A.5
  • 20
    • 0019997016 scopus 로고
    • Analysis and prediction of the packing of α-helices against a β-sheet in the tertiary structure of globular proteins
    • Cohen FE, Sternberg MJE, Taylor WR. 1982. Analysis and prediction of the packing of α-helices against a β-sheet in the tertiary structure of globular proteins. J Mol Biol 156:821-862.
    • (1982) J Mol Biol , vol.156 , pp. 821-862
    • Cohen, F.E.1    Sternberg, M.J.E.2    Taylor, W.R.3
  • 21
    • 0028953472 scopus 로고
    • Structural similarity between 2-layer alpha/beta-proteins and beta-proteins
    • Efimov AV. 1995. Structural similarity between 2-layer alpha/beta-proteins and beta-proteins. J Mol Biol 245:402-415.
    • (1995) J Mol Biol , vol.245 , pp. 402-415
    • Efimov, A.V.1
  • 22
    • 0025284257 scopus 로고
    • The evolution of alpha-beta-barrel enzymes
    • Farber GK, Petsko GA. 1990. The evolution of alpha-beta-barrel enzymes. TIBS 15:228-228.
    • (1990) TIBS , vol.15 , pp. 228-228
    • Farber, G.K.1    Petsko, G.A.2
  • 23
    • 0019888748 scopus 로고
    • Comparative model-building of the mammalian serine proteinases
    • Greer J. 1981. Comparative model-building of the mammalian serine proteinases. J Mol Biol 153:1027-1042.
    • (1981) J Mol Biol , vol.153 , pp. 1027-1042
    • Greer, J.1
  • 24
    • 0025364112 scopus 로고
    • De novo design of an alpha-beta-barrel protein
    • Handel T. 1990. De novo design of an alpha-beta-barrel protein. Protein Eng 3:233-234.
    • (1990) Protein Eng , vol.3 , pp. 233-234
    • Handel, T.1
  • 25
    • 0026018780 scopus 로고
    • A new method for building protein conformations from sequence alignments with homologues of known structure
    • Havel TF, Snow ME. 1991. A new method for building protein conformations from sequence alignments with homologues of known structure. J Mol Biol 217:1-7.
    • (1991) J Mol Biol , vol.217 , pp. 1-7
    • Havel, T.F.1    Snow, M.E.2
  • 26
    • 0027363912 scopus 로고
    • Structural relationships of homologous proteins as a fundamental principle in homology modeling
    • Hilbert M, Bohm G, Jaenicke R. 1993. Structural relationships of homologous proteins as a fundamental principle in homology modeling. Proteins 17:138-151.
    • (1993) Proteins , vol.17 , pp. 138-151
    • Hilbert, M.1    Bohm, G.2    Jaenicke, R.3
  • 27
    • 0019326109 scopus 로고
    • Packing of α-helices onto β-pleated sheet and the anatomy of αβ-proteins
    • Janin J, Chothia C. 1980. Packing of α-helices onto β-pleated sheet and the anatomy of αβ-proteins. J Mol Biol 143:95-128.
    • (1980) J Mol Biol , vol.143 , pp. 95-128
    • Janin, J.1    Chothia, C.2
  • 29
    • 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
  • 30
    • 0025372503 scopus 로고
    • The design of idealized α/β-barrels - Analysis of beta-sheet closure requirements
    • Lasters I, Wodak SJ, Pio F. 1990. The design of idealized α/β-barrels - Analysis of beta-sheet closure requirements. Proteins 7:249-256.
    • (1990) Proteins , vol.7 , pp. 249-256
    • Lasters, I.1    Wodak, S.J.2    Pio, F.3
  • 31
    • 0024529940 scopus 로고
    • Structural principles of alpha-beta-barrel proteins - The packing of the interior of the sheet
    • Lesk AM, Branden CI, Chothia C. 1989. Structural principles of alpha-beta-barrel proteins - The packing of the interior of the sheet. Proteins 5:139-148.
    • (1989) Proteins , vol.5 , pp. 139-148
    • Lesk, A.M.1    Branden, C.I.2    Chothia, C.3
  • 32
    • 0019332167 scopus 로고
    • How different amino acid sequences determine similar protein structures: The structure and evolutionary dynamics of the globins
    • Lesk AM, Chothia C. 1980. How different amino acid sequences determine similar protein structures: The structure and evolutionary dynamics of the globins. J Mol Biol 136:225-270.
    • (1980) J Mol Biol , vol.136 , pp. 225-270
    • Lesk, A.M.1    Chothia, C.2
  • 33
    • 0020429363 scopus 로고
    • Evolution of proteins formed by β-sheets: II. The core of immunoglobulin domains
    • Lesk AM, Chothia C. 1982. Evolution of proteins formed by β-sheets: II. The core of immunoglobulin domains. J Mol Biol 160:325-342
    • (1982) J Mol Biol , vol.160 , pp. 325-342
    • Lesk, A.M.1    Chothia, C.2
  • 34
    • 0000187138 scopus 로고
    • The response of protein structures to amino acid sequence changes
    • Lesk AM, Chothia C. 1986. The response of protein structures to amino acid sequence changes. Phil Trans Roy Soc Lond 317:345-356.
    • (1986) Phil Trans Roy Soc Lond , vol.317 , pp. 345-356
    • Lesk, A.M.1    Chothia, C.2
  • 35
    • 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
  • 37
    • 0028864205 scopus 로고
    • A critical-assessment of comparative molecular modeling of tertiary structures of proteins
    • Mosimann S, Meleshko R, James MNG. 1995. A critical-assessment of comparative molecular modeling of tertiary structures of proteins. Proteins Struct Funct Genet 23:301-317.
    • (1995) Proteins Struct Funct Genet , vol.23 , pp. 301-317
    • Mosimann, S.1    Meleshko, R.2    James, M.N.G.3
  • 38
    • 0028955505 scopus 로고
    • Predicting the helix packing of globular-proteins by self-correcting distance geometry
    • Mumenthaler C, Braun W. 1995. Predicting the helix packing of globular-proteins by self-correcting distance geometry. Protein Sci 4:863-871.
    • (1995) Protein Sci , vol.4 , pp. 863-871
    • Mumenthaler, C.1    Braun, W.2
  • 39
    • 0027999471 scopus 로고
    • The evolution of alternate core packing in eight fold alpha/beta-barrels
    • Raine ARC, Scrutton NS, Mathews FS. 1994. The evolution of alternate core packing in eight fold alpha/beta-barrels. Protein Sci 3:1889-1892.
    • (1994) Protein Sci , vol.3 , pp. 1889-1892
    • Raine, A.R.C.1    Scrutton, N.S.2    Mathews, F.S.3
  • 40
    • 0027507711 scopus 로고
    • Packing of secondary structural elements in proteins: Analysis and prediction of inter-helix distances
    • Reddy BVB, Blundell TL. 1993. Packing of secondary structural elements in proteins: Analysis and prediction of inter-helix distances. J Mot Biol 233:464-479.
    • (1993) J Mot Biol , vol.233 , pp. 464-479
    • Reddy, B.V.B.1    Blundell, T.L.2
  • 41
    • 0019443447 scopus 로고
    • The anatomy and taxonomy of protein structure
    • Richardson JS. 1981. The anatomy and taxonomy of protein structure. Adv Prot Chem 34:167-339.
    • (1981) Adv Prot Chem , vol.34 , pp. 167-339
    • Richardson, J.S.1
  • 42
    • 0017876485 scopus 로고
    • Packing of α-helices: Geometrical constraints and contact areas
    • Richmond TJ, Richards FM. 1978. Packing of α-helices: Geometrical constraints and contact areas. J Mol Biol 119:537-555.
    • (1978) J Mol Biol , vol.119 , pp. 537-555
    • Richmond, T.J.1    Richards, F.M.2
  • 43
    • 0029902780 scopus 로고    scopus 로고
    • Bringing the protein sequence-structure gap by structure predictions
    • Rost B, Sander C. 1996. Bringing the protein sequence-structure gap by structure predictions. Ann Rev Bioph and Biomole Str 25:113-136.
    • (1996) Ann Rev Bioph and Biomole Str , vol.25 , pp. 113-136
    • Rost, B.1    Sander, C.2
  • 45
    • 0028991962 scopus 로고
    • Modelling mutations and homologous proteins
    • Sali A. 1995. Modelling mutations and homologous proteins. Curr Opin Biotech 6:437-451.
    • (1995) Curr Opin Biotech , vol.6 , pp. 437-451
    • Sali, A.1
  • 46
    • 0025317502 scopus 로고
    • The definition of topological equivalence in homologous and analogous structures: A procedure involving a comparison of local properties and relationships
    • Sali A, Blundell TL. 1990. The definition of topological equivalence in homologous and analogous structures: A procedure involving a comparison of local properties and relationships. J Mol Biol 212:403-428.
    • (1990) J Mol Biol , vol.212 , pp. 403-428
    • Sali, A.1    Blundell, T.L.2
  • 47
    • 0027136282 scopus 로고
    • Comparative protein modelling by satisfaction of spatial restraints
    • Sali A, Blundell TL. 1993. Comparative protein modelling by satisfaction of spatial restraints. J Mol Biol 234:779-815.
    • (1993) J Mol Biol , vol.234 , pp. 779-815
    • Sali, A.1    Blundell, T.L.2
  • 49
    • 0030908273 scopus 로고    scopus 로고
    • Advances in comparative protein-structure modelling
    • Sanchez R, Sali A. 1997. Advances in comparative protein-structure modelling. Curr Opin Struct Biol 7:206-214.
    • (1997) Curr Opin Struct Biol , vol.7 , pp. 206-214
    • Sanchez, R.1    Sali, A.2
  • 51
    • 0027220648 scopus 로고
    • An evaluation of the performance of an automated procedure for comparative modelling of protein tertiary structure
    • Srinivasan N, Blundell TL. 1993 An evaluation of the performance of an automated procedure for comparative modelling of protein tertiary structure. Protein Eng 6:501-512.
    • (1993) Protein Eng , vol.6 , pp. 501-512
    • Srinivasan, N.1    Blundell, T.L.2
  • 52
    • 0027510701 scopus 로고
    • An automated-method for modeling proteins on known templates using distance geometry
    • Srinivasan S, March CJ, Sudarshanam S. 1993. An automated-method for modeling proteins on known templates using distance geometry. Protein Sci 2:277-289.
    • (1993) Protein Sci , vol.2 , pp. 277-289
    • Srinivasan, S.1    March, C.J.2    Sudarshanam, S.3
  • 53
    • 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. 1987a. Knowledge-based modelling of homologous proteins. Part I: Three dimensional frameworks derived from the simultaneous superposition of multiple structures. Protein Eng 1:377-384.
    • (1987) Protein Eng , vol.1 , pp. 377-384
    • Sutcliffe, M.J.1    Haneef, I.2    Carney, D.3    Blundell, T.L.4
  • 54
    • 0000179199 scopus 로고
    • Knowledge-based modelling of homologous proteins. Part II: Rules for the conformations of substituted side-chains
    • Sutcliffe MJ, Hayes FRF, Blundell TL. 1987b. Knowledge-based modelling of homologous proteins. Part II: Rules for the conformations of substituted side-chains. Protein Eng 1:385-392.
    • (1987) Protein Eng , vol.1 , pp. 385-392
    • Sutcliffe, M.J.1    Hayes, F.R.F.2    Blundell, T.L.3
  • 55
    • 0029867179 scopus 로고    scopus 로고
    • Principles of helix-helix packing in proteins - The helical lattice superposition model
    • Walther D, Eisenhaber F, Argos P. 1996. Principles of helix-helix packing in proteins - The helical lattice superposition model. J Mol Biol 255:536-553.
    • (1996) J Mol Biol , vol.255 , pp. 536-553
    • Walther, D.1    Eisenhaber, F.2    Argos, P.3
  • 56
    • 0028954109 scopus 로고
    • Packing constraints of hydrophobic side-chains in alpha/beta (8) barrels
    • Vtyurin N, Panov V. 1995. Packing constraints of hydrophobic side-chains in alpha/beta (8) barrels. Proteins 21:256-260.
    • (1995) Proteins , vol.21 , pp. 256-260
    • Vtyurin, N.1    Panov, V.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.