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Volumn 5, Issue 10, 2010, Pages

Detection and alignment of 3D domain swapping proteins using angle-distance image-based secondary structural matching techniques

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; CLASSIFICATION ALGORITHM; CONTROLLED STUDY; CORRELATION COEFFICIENT; FEASIBILITY STUDY; HINGE REGION; IMAGE ANALYSIS; PROTEIN DOMAIN; PROTEIN SECONDARY STRUCTURE; SENSITIVITY ANALYSIS; SENSITIVITY AND SPECIFICITY; SEQUENCE ANALYSIS; STRUCTURAL BIOINFORMATICS; STRUCTURAL HOMOLOGY; STRUCTURE ANALYSIS; THREE DIMENSIONAL IMAGING; AMINO ACID SEQUENCE; CHEMICAL STRUCTURE; CHEMISTRY; MOLECULAR EVOLUTION; MOLECULAR GENETICS; SEQUENCE HOMOLOGY;

EID: 78149443849     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0013361     Document Type: Article
Times cited : (11)

References (61)
  • 1
    • 0028865843 scopus 로고
    • 3D domain swapping: A mechanism for oligomer assembly
    • Bennett MJ, Schlunegger MP, Eisenberg D (1995) 3D domain swapping: a mechanism for oligomer assembly. Protein Sci 4: 2455-2468.
    • (1995) Protein Sci , vol.4 , pp. 2455-2468
    • Bennett, M.J.1    Schlunegger, M.P.2    Eisenberg, D.3
  • 2
    • 0036108484 scopus 로고    scopus 로고
    • 3D domain swapping: As domains continue to swap
    • Liu Y, Eisenberg D (2002) 3D domain swapping: as domains continue to swap. Protein Sci 11: 1285-1299.
    • (2002) Protein Sci , vol.11 , pp. 1285-1299
    • Liu, Y.1    Eisenberg, D.2
  • 3
    • 4143058003 scopus 로고    scopus 로고
    • The evolving role of 3D domain swapping in proteins
    • Bennett MJ, Eisenberg D (2004) The evolving role of 3D domain swapping in proteins. Structure 12: 1339-1341.
    • (2004) Structure , vol.12 , pp. 1339-1341
    • Bennett, M.J.1    Eisenberg, D.2
  • 4
  • 5
    • 0028077637 scopus 로고
    • Refined structure of dimeric diphtheria toxin at 2.0 A resolution
    • Bennett MJ, Choe S, Eisenberg D (1994) Refined structure of dimeric diphtheria toxin at 2.0 A resolution. Protein Sci 3: 1444-1463.
    • (1994) Protein Sci , vol.3 , pp. 1444-1463
    • Bennett, M.J.1    Choe, S.2    Eisenberg, D.3
  • 6
    • 0035127031 scopus 로고    scopus 로고
    • A domain-swapped RNase A dimer with implications for amyloid formation
    • Liu Y, Gotte G, Libonati M, Eisenberg D (2001) A domain-swapped RNase A dimer with implications for amyloid formation. Nat Struct Biol 8: 211-214.
    • (2001) Nat Struct Biol , vol.8 , pp. 211-214
    • Liu, Y.1    Gotte, G.2    Libonati, M.3    Eisenberg, D.4
  • 7
    • 0032584210 scopus 로고    scopus 로고
    • The crystal structure of a 3D domain-swapped dimer of RNase A at a 2.1-A resolution
    • Liu Y, Hart PJ, Schlunegger MP, Eisenberg D (1998) The crystal structure of a 3D domain-swapped dimer of RNase A at a 2.1-A resolution. Proc Natl Acad Sci U S A 95: 3437-3442.
    • (1998) Proc Natl Acad Sci U S A , vol.95 , pp. 3437-3442
    • Liu, Y.1    Hart, P.J.2    Schlunegger, M.P.3    Eisenberg, D.4
  • 9
    • 0035069135 scopus 로고    scopus 로고
    • Human cystatin C, an amyloidogenic protein, dimerizes through three-dimensional domain swapping
    • Janowski R, Kozak M, Jankowska E, Grzonka Z, Grubb A, et al. (2001) Human cystatin C, an amyloidogenic protein, dimerizes through three-dimensional domain swapping. Nat Struct Biol 8: 316-320.
    • (2001) Nat Struct Biol , vol.8 , pp. 316-320
    • Janowski, R.1    Kozak, M.2    Jankowska, E.3    Grzonka, Z.4    Grubb, A.5
  • 11
    • 0035801540 scopus 로고    scopus 로고
    • Three-dimensional domain swapping in the folded and molten-globule states of cystatins, an amyloid-forming structural superfamily
    • Staniforth RA, Giannini S, Higgins LD, Conroy MJ, Hounslow AM, et al. (2001) Three-dimensional domain swapping in the folded and molten-globule states of cystatins, an amyloid-forming structural superfamily. Embo J 20: 4774-4781.
    • (2001) Embo J , vol.20 , pp. 4774-4781
    • Staniforth, R.A.1    Giannini, S.2    Higgins, L.D.3    Conroy, M.J.4    Hounslow, A.M.5
  • 12
    • 0034619431 scopus 로고    scopus 로고
    • Dimer formation through domain swapping in the crystal structure of the Grb2-SH2- Ac-pYVNV complex
    • Schiering N, Casale E, Caccia P, Giordano P, Battistini C (2000) Dimer formation through domain swapping in the crystal structure of the Grb2-SH2- Ac-pYVNV complex. Biochemistry 39: 13376-13382.
    • (2000) Biochemistry , vol.39 , pp. 13376-13382
    • Schiering, N.1    Casale, E.2    Caccia, P.3    Giordano, P.4    Battistini, C.5
  • 13
    • 0035697173 scopus 로고    scopus 로고
    • Structure of the SH3-guanylate kinase module from PSD-95 suggests a mechanism for regulated assembly of MAGUK scaffolding proteins
    • McGee AW, Dakoji SR, Olsen O, Bredt DS, Lim WA, et al. (2001) Structure of the SH3-guanylate kinase module from PSD-95 suggests a mechanism for regulated assembly of MAGUK scaffolding proteins. Mol Cell 8: 1291-1301.
    • (2001) Mol Cell , vol.8 , pp. 1291-1301
    • McGee, A.W.1    Dakoji, S.R.2    Olsen, O.3    Bredt, D.S.4    Lim, W.A.5
  • 14
    • 0037133242 scopus 로고    scopus 로고
    • Mechanism of action and NAD+-binding mode revealed by the crystal structure of Lhistidinol dehydrogenase
    • Barbosa JA, Sivaraman J, Li Y, Larocque R, Matte A, et al. (2002) Mechanism of action and NAD+-binding mode revealed by the crystal structure of Lhistidinol dehydrogenase. Proc Natl Acad Sci U S A 99: 1859-1864.
    • (2002) Proc Natl Acad Sci U S A , vol.99 , pp. 1859-1864
    • Barbosa, J.A.1    Sivaraman, J.2    Li, Y.3    Larocque, R.4    Matte, A.5
  • 15
    • 0030927104 scopus 로고    scopus 로고
    • Crystal structure of human glyoxalase I-evidence for gene duplication and 3D domain swapping
    • Cameron AD, Olin B, Ridderstrom M, Mannervik B, Jones TA (1997) Crystal structure of human glyoxalase I-evidence for gene duplication and 3D domain swapping. Embo J 16: 3386-3395.
    • (1997) Embo J , vol.16 , pp. 3386-3395
    • Cameron, A.D.1    Olin, B.2    Ridderstrom, M.3    Mannervik, B.4    Jones, T.A.5
  • 16
    • 0033571222 scopus 로고    scopus 로고
    • Nterminal domain swapping and metal ion binding in nitric oxide synthase dimerization
    • Crane BR, Rosenfeld RJ, Arvai AS, Ghosh DK, Ghosh S, et al. (1999) Nterminal domain swapping and metal ion binding in nitric oxide synthase dimerization. Embo J 18: 6271-6281.
    • (1999) Embo J , vol.18 , pp. 6271-6281
    • Crane, B.R.1    Rosenfeld, R.J.2    Arvai, A.S.3    Ghosh, D.K.4    Ghosh, S.5
  • 18
    • 0035826713 scopus 로고    scopus 로고
    • Threedimensional domain swapping in p13suc1 occurs in the unfolded state and is controlled by conserved proline residues
    • Rousseau F, Schymkowitz JW, Wilkinson HR, Itzhaki LS (2001) Threedimensional domain swapping in p13suc1 occurs in the unfolded state and is controlled by conserved proline residues. Proc Natl Acad Sci U S A 98: 5596-5601.
    • (2001) Proc Natl Acad Sci U S A , vol.98 , pp. 5596-5601
    • Rousseau, F.1    Schymkowitz, J.W.2    Wilkinson, H.R.3    Itzhaki, L.S.4
  • 19
    • 0034869693 scopus 로고    scopus 로고
    • Crystal structure of the human prion protein reveals a mechanism for oligomerization
    • Knaus KJ, Morillas M, Swietnicki W, Malone M, Surewicz WK, et al. (2001) Crystal structure of the human prion protein reveals a mechanism for oligomerization. Nat Struct Biol 8: 770-774.
    • (2001) Nat Struct Biol , vol.8 , pp. 770-774
    • Knaus, K.J.1    Morillas, M.2    Swietnicki, W.3    Malone, M.4    Surewicz, W.K.5
  • 21
    • 0035757051 scopus 로고    scopus 로고
    • 3D domain swapping, protein oligomerization, and amyloid formation
    • Jaskolski M (2001) 3D domain swapping, protein oligomerization, and amyloid formation. Acta Biochim Pol 48: 807-827.
    • (2001) Acta Biochim Pol , vol.48 , pp. 807-827
    • Jaskolski, M.1
  • 25
    • 0028843420 scopus 로고
    • Single-chain Fvs
    • Raag R, Whitlow M (1995) Single-chain Fvs. FASEB J 9: 73-80.
    • (1995) FASEB J , vol.9 , pp. 73-80
    • Raag, R.1    Whitlow, M.2
  • 26
    • 0026354773 scopus 로고
    • High resolution structure of an oligomeric eye lens beta-crystallin. Loops, arches, linkers and interfaces in beta B2 dimer compared to a monomeric gammacrystallin
    • Lapatto R, Nalini V, Bax B, Driessen H, Lindley PF, et al. (1991) High resolution structure of an oligomeric eye lens beta-crystallin. Loops, arches, linkers and interfaces in beta B2 dimer compared to a monomeric gammacrystallin. J Mol Biol 222: 1067-1083.
    • (1991) J Mol Biol , vol.222 , pp. 1067-1083
    • Lapatto, R.1    Nalini, V.2    Bax, B.3    Driessen, H.4    Lindley, P.F.5
  • 27
    • 0028171466 scopus 로고
    • Dimerization of beta B2-crystallin: The role of the linker peptide and the N- and C-terminal extensions
    • Trinkl S, Glockshuber R, Jaenicke R (1994) Dimerization of beta B2-crystallin: the role of the linker peptide and the N- and C-terminal extensions. Protein Sci 3: 1392-1400.
    • (1994) Protein Sci , vol.3 , pp. 1392-1400
    • Trinkl, S.1    Glockshuber, R.2    Jaenicke, R.3
  • 28
  • 29
    • 3042581007 scopus 로고    scopus 로고
    • Flexible structure alignment by chaining aligned fragment pairs allowing twists
    • Ye Y, Godzik A (2003) Flexible structure alignment by chaining aligned fragment pairs allowing twists. Bioinformatics 19 Suppl 2: ii246-255.
    • (2003) Bioinformatics , vol.19 , Issue.SUPPL 2
    • Ye, Y.1    Godzik, A.2
  • 30
    • 12944271968 scopus 로고    scopus 로고
    • FAST: A novel protein structure alignment algorithm
    • Zhu J, Weng Z (2005) FAST: a novel protein structure alignment algorithm. Proteins 58: 618-627.
    • (2005) Proteins , vol.58 , pp. 618-627
    • Zhu, J.1    Weng, Z.2
  • 31
    • 17644392830 scopus 로고    scopus 로고
    • TM-align: A protein structure alignment algorithm based on the TM-score
    • Zhang Y, Skolnick J (2005) TM-align: a protein structure alignment algorithm based on the TM-score. Nucleic Acids Res 33: 2302-2309.
    • (2005) Nucleic Acids Res , vol.33 , pp. 2302-2309
    • Zhang, Y.1    Skolnick, J.2
  • 32
    • 0027440362 scopus 로고
    • Protein structure comparison by alignment of distance matrices
    • Holm L, Sander C (1993) Protein structure comparison by alignment of distance matrices. J Mol Biol 233: 123-138.
    • (1993) J Mol Biol , vol.233 , pp. 123-138
    • Holm, L.1    Sander, C.2
  • 33
    • 0031715982 scopus 로고    scopus 로고
    • Protein structure alignment by incremental combinatorial extension (CE) of the optimal path
    • Shindyalov IN, Bourne PE (1998) Protein structure alignment by incremental combinatorial extension (CE) of the optimal path. Protein Eng 11: 739-747.
    • (1998) Protein Eng , vol.11 , pp. 739-747
    • Shindyalov, I.N.1    Bourne, P.E.2
  • 34
  • 35
    • 0036888353 scopus 로고    scopus 로고
    • Improvements in the analysis of domain motions in proteins from conformational change: DynDom version 1.50
    • Hayward S, Lee RA (2002) Improvements in the analysis of domain motions in proteins from conformational change: DynDom version 1.50. J Mol Graph Model 21: 181-183.
    • (2002) J Mol Graph Model , vol.21 , pp. 181-183
    • Hayward, S.1    Lee, R.A.2
  • 38
    • 56749132934 scopus 로고    scopus 로고
    • Angle-distance image matching techniques for protein structure comparison
    • Chu CH, Tang CY, Tang CY, Pai TW (2008) Angle-distance image matching techniques for protein structure comparison. J Mol Recognit 21: 442-452.
    • (2008) J Mol Recognit , vol.21 , pp. 442-452
    • Chu, C.H.1    Tang, C.Y.2    Tang, C.Y.3    Pai, T.W.4
  • 40
    • 0032169688 scopus 로고    scopus 로고
    • PQS: A protein quaternary structure file server
    • Henrick K, Thornton JM (1998) PQS: a protein quaternary structure file server. Trends Biochem Sci 23: 358-361.
    • (1998) Trends Biochem Sci , vol.23 , pp. 358-361
    • Henrick, K.1    Thornton, J.M.2
  • 41
    • 0034479757 scopus 로고    scopus 로고
    • TOP: A new method for protein structure comparisons and similarity searches
    • Lu GG (2000) TOP: a new method for protein structure comparisons and similarity searches. Journal of Applied Crystallography 33: 176-183.
    • (2000) Journal of Applied Crystallography , vol.33 , pp. 176-183
    • Lu, G.G.1
  • 43
    • 13444307044 scopus 로고    scopus 로고
    • Secondary-structure matching (SSM), a new tool for fast protein structure alignment in three dimensions
    • Krissinel E, Henrick K (2004) Secondary-structure matching (SSM), a new tool for fast protein structure alignment in three dimensions. Acta Crystallogr D Biol Crystallogr 60: 2256-2268.
    • (2004) Acta Crystallogr D Biol Crystallogr , vol.60 , pp. 2256-2268
    • Krissinel, E.1    Henrick, K.2
  • 44
    • 0030017889 scopus 로고    scopus 로고
    • Analysis of topological and nontopological structural similarities in the PDB: New examples with old structures
    • Alexandrov NN, Fischer D (1996) Analysis of topological and nontopological structural similarities in the PDB: new examples with old structures. Proteins 25: 354-365.
    • (1996) Proteins , vol.25 , pp. 354-365
    • Alexandrov, N.N.1    Fischer, D.2
  • 45
    • 0034237578 scopus 로고    scopus 로고
    • Large-scale comparison of protein sequence alignment algorithms with structure alignments
    • Sauder JM, Arthur JW, Dunbrack RL, Jr. (2000) Large-scale comparison of protein sequence alignment algorithms with structure alignments. Proteins 40: 6-22.
    • (2000) Proteins , vol.40 , pp. 6-22
    • Sauder, J.M.1    Arthur, J.W.2    Dunbrack Jr., R.L.3
  • 49
    • 84858617091 scopus 로고    scopus 로고
    • Java OpenGL [http://jogamp.org/].
    • Java OpenGL
  • 50
    • 67849101183 scopus 로고    scopus 로고
    • iSARST: An integrated SARST web server for rapid protein structural similarity searches
    • Lo WC, Lee CY, Lee CC, Lyu PC (2009) iSARST: an integrated SARST web server for rapid protein structural similarity searches. Nucleic Acids Res 37: W545-551.
    • (2009) Nucleic Acids Res , vol.37
    • Lo, W.C.1    Lee, C.Y.2    Lee, C.C.3    Lyu, P.C.4
  • 51
    • 46249109058 scopus 로고    scopus 로고
    • CPSARST: An efficient circular permutation search tool applied to the detection of novel protein structural relationships
    • Lo WC, Lyu PC (2008) CPSARST: an efficient circular permutation search tool applied to the detection of novel protein structural relationships. Genome Biol 9: R11.
    • (2008) Genome Biol , vol.9
    • Lo, W.C.1    Lyu, P.C.2
  • 52
  • 53
    • 3142745171 scopus 로고    scopus 로고
    • Alternative alignments from comparison of protein structures
    • Shih ES, Hwang MJ (2004) Alternative alignments from comparison of protein structures. Proteins 56: 519-527.
    • (2004) Proteins , vol.56 , pp. 519-527
    • Shih, E.S.1    Hwang, M.J.2
  • 55
    • 84893482610 scopus 로고
    • A solution for the best rotation to relate two sets of vectors
    • Kabsch W (1976) A solution for the best rotation to relate two sets of vectors. Acta Crystallographica Section A 32: 922-923.
    • (1976) Acta Crystallographica Section A , vol.32 , pp. 922-923
    • Kabsch, W.1
  • 56
    • 66549119395 scopus 로고    scopus 로고
    • Advances and pitfalls of protein structural alignment
    • Hasegawa H, Holm L (2009) Advances and pitfalls of protein structural alignment. Curr Opin Struct Biol 19: 341-348.
    • (2009) Curr Opin Struct Biol , vol.19 , pp. 341-348
    • Hasegawa, H.1    Holm, L.2
  • 57
    • 0026458378 scopus 로고
    • Amino acid substitution matrices from protein blocks
    • Henikoff S, Henikoff JG (1992) Amino acid substitution matrices from protein blocks. Proc Natl Acad Sci U S A 89: 10915-10919.
    • (1992) Proc Natl Acad Sci U S A , vol.89 , pp. 10915-10919
    • Henikoff, S.1    Henikoff, J.G.2
  • 58
    • 33644869455 scopus 로고    scopus 로고
    • Flexible secondary structure based protein structure comparison applied to the detection of circular permutation
    • Vesterstrom J, Taylor WR (2006) Flexible secondary structure based protein structure comparison applied to the detection of circular permutation. J Comput Biol 13: 43-63.
    • (2006) J Comput Biol , vol.13 , pp. 43-63
    • Vesterstrom, J.1    Taylor, W.R.2
  • 59
    • 0033833116 scopus 로고    scopus 로고
    • Protein structure alignment using environmental profiles
    • Jung J, Lee B (2000) Protein structure alignment using environmental profiles. Protein Eng 13: 535-543.
    • (2000) Protein Eng , vol.13 , pp. 535-543
    • Jung, J.1    Lee, B.2
  • 60
    • 33847249065 scopus 로고    scopus 로고
    • QSCOP-SCOP quantified by structural relationships
    • Suhrer SJ, Wiederstein M, Sippl MJ (2007) QSCOP-SCOP quantified by structural relationships. Bioinformatics 23: 513-514.
    • (2007) Bioinformatics , vol.23 , pp. 513-514
    • Suhrer, S.J.1    Wiederstein, M.2    Sippl, M.J.3
  • 61
    • 13444279981 scopus 로고    scopus 로고
    • Comprehensive evaluation of protein structure alignment methods: Scoring by geometric measures
    • Kolodny R, Koehl P, Levitt M (2005) Comprehensive evaluation of protein structure alignment methods: scoring by geometric measures. J Mol Biol 346: 1173-1188.
    • (2005) J Mol Biol , vol.346 , pp. 1173-1188
    • Kolodny, R.1    Koehl, P.2    Levitt, M.3


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