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Volumn 1753, Issue 1, 2005, Pages 121-130

Fibril modelling by sequence and structure conservation analysis combined with protein docking techniques: β2-microglobulin amyloidosis

Author keywords

2 microglobulin; Fibril modelling; Protein

Indexed keywords

BETA 2 MICROGLOBULIN; MONOMER;

EID: 27744531820     PISSN: 15709639     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.bbapap.2005.07.012     Document Type: Conference Paper
Times cited : (6)

References (55)
  • 2
    • 0035955555 scopus 로고    scopus 로고
    • β-2 microglobulin and its deaminated variant, N17D form amyloid fibrils with a range of morphologies in vitro
    • N.M. Kad, N.H. Thomson, D.P. Smith, D.A. Smith, and S.E. Radford β-2 microglobulin and its deaminated variant, N17D form amyloid fibrils with a range of morphologies in vitro J. Mol. Biol. 313 2001 559 571
    • (2001) J. Mol. Biol. , vol.313 , pp. 559-571
    • Kad, N.M.1    Thomson, N.H.2    Smith, D.P.3    Smith, D.A.4    Radford, S.E.5
  • 5
    • 0035293977 scopus 로고    scopus 로고
    • Dynamic of β2-microglobulin fibril formation and reabsorption: The role of proteolysis
    • V. Bellotti, M. Gallieni, S. Giorgetti, and D. Brancaccio Dynamic of β2-microglobulin fibril formation and reabsorption: the role of proteolysis Semin. Dial. 14 2001 117 122
    • (2001) Semin. Dial. , vol.14 , pp. 117-122
    • Bellotti, V.1    Gallieni, M.2    Giorgetti, S.3    Brancaccio, D.4
  • 7
    • 0035367287 scopus 로고    scopus 로고
    • Kidney dialysis-associated amyloidosis: A molecular role for copper in fiber formation
    • C.J. Morgan, M. Gelfand, C. Atreya, and A.D. Miranker Kidney dialysis-associated amyloidosis: a molecular role for copper in fiber formation J. Mol. Biol. 309 2001 339 345
    • (2001) J. Mol. Biol. , vol.309 , pp. 339-345
    • Morgan, C.J.1    Gelfand, M.2    Atreya, C.3    Miranker, A.D.4
  • 8
    • 0346103697 scopus 로고    scopus 로고
    • Glycosaminoglycans enhance the trifluoroethanol-induced extension of beta 2-microglobulin-related amyloid fibrils at a neutral pH
    • S. Yamamoto, I. Yamaguchi, K. Hasegawa, S. Tsutsumi, Y. Goto, F. Gejyo, and H. Naiki Glycosaminoglycans enhance the trifluoroethanol-induced extension of beta 2-microglobulin-related amyloid fibrils at a neutral pH J. Am. Soc. Nephrol. 15 2004 126 133
    • (2004) J. Am. Soc. Nephrol. , vol.15 , pp. 126-133
    • Yamamoto, S.1    Yamaguchi, I.2    Hasegawa, K.3    Tsutsumi, S.4    Goto, Y.5    Gejyo, F.6    Naiki, H.7
  • 9
    • 2942748436 scopus 로고    scopus 로고
    • Oligomeric assembly of native-like precursors precedes amyloid formation by beta-2 microglobulin
    • C.M. Eakin, F.J. Attenello, C.J. Morgan, and A.D. Miranker Oligomeric assembly of native-like precursors precedes amyloid formation by beta-2 microglobulin Biochemistry 43 2004 7808 7815
    • (2004) Biochemistry , vol.43 , pp. 7808-7815
    • Eakin, C.M.1    Attenello, F.J.2    Morgan, C.J.3    Miranker, A.D.4
  • 12
    • 0038351889 scopus 로고    scopus 로고
    • Role of the N and C-terminal strands of beta 2-microglobulin in amyloid formation at neutral pH
    • S. Jones, D.P. Smith, and S.E. Radford Role of the N and C-terminal strands of beta 2-microglobulin in amyloid formation at neutral pH J. Mol. Biol. 330 2003 935 941
    • (2003) J. Mol. Biol. , vol.330 , pp. 935-941
    • Jones, S.1    Smith, D.P.2    Radford, S.E.3
  • 16
    • 0034660206 scopus 로고    scopus 로고
    • The structure and stability of an HLA-A*0201/octameric tax peptide complex with an empty conserved peptide-N-terminal binding site.
    • A.R. Khan, B.M. Baker, P. Ghosh, W.E. Biddison, and D.C. Wiley The structure and stability of an HLA-A*0201/octameric tax peptide complex with an empty conserved peptide-N-terminal binding site. J. Immunol. 164 2000 6398 6405
    • (2000) J. Immunol. , vol.164 , pp. 6398-6405
    • Khan, A.R.1    Baker, B.M.2    Ghosh, P.3    Biddison, W.E.4    Wiley, D.C.5
  • 18
    • 0036172742 scopus 로고    scopus 로고
    • The intrachain disulfide bond of beta(2)-microglobulin is not essential for the immunoglobulin fold at neutral pH, but is essential for amyloid fibril formation at acidic pH
    • Y. Ohhashi, Y. Hagihara, G. Kozhukh, M. Hoshino, K. Hasegawa, I. Yamaguchi, H. Naiki, and Y. Goto The intrachain disulfide bond of beta(2)-microglobulin is not essential for the immunoglobulin fold at neutral pH, but is essential for amyloid fibril formation at acidic pH J. Biochem. 131 2002 45 52
    • (2002) J. Biochem. , vol.131 , pp. 45-52
    • Ohhashi, Y.1    Hagihara, Y.2    Kozhukh, G.3    Hoshino, M.4    Hasegawa, K.5    Yamaguchi, I.6    Naiki, H.7    Goto, Y.8
  • 19
    • 0037077209 scopus 로고    scopus 로고
    • Conformation of beta 2-microglobulin amyloid fibrils analyzed by reduction of the disulfide bond
    • D.P. Hong, M. Gozu, K. Hasegawa, H. Naiki, and Y. Goto Conformation of beta 2-microglobulin amyloid fibrils analyzed by reduction of the disulfide bond J. Biol. Chem. 277 2002 21554 21560
    • (2002) J. Biol. Chem. , vol.277 , pp. 21554-21560
    • Hong, D.P.1    Gozu, M.2    Hasegawa, K.3    Naiki, H.4    Goto, Y.5
  • 21
    • 0035037143 scopus 로고    scopus 로고
    • A proposed structural model for amyloid fibril elongation: Domain swapping forms an interdigitating β-structure polymer
    • N. Sinha, C.J. Tsai, and R. Nussinov A proposed structural model for amyloid fibril elongation: domain swapping forms an interdigitating β-structure polymer Protein Eng. 14 2001 93 103
    • (2001) Protein Eng. , vol.14 , pp. 93-103
    • Sinha, N.1    Tsai, C.J.2    Nussinov, R.3
  • 22
    • 0037155826 scopus 로고    scopus 로고
    • A designed system for assessing how sequence affects alpha to beta conformational transitions in proteins
    • B. Ciani, E.G. Hutchinson, R.B. Sessions, and D.N. Woolfson A designed system for assessing how sequence affects alpha to beta conformational transitions in proteins J. Biol. Chem. 277 2002 10150 10155
    • (2002) J. Biol. Chem. , vol.277 , pp. 10150-10155
    • Ciani, B.1    Hutchinson, E.G.2    Sessions, R.B.3    Woolfson, D.N.4
  • 23
    • 0036108484 scopus 로고    scopus 로고
    • 3D domain swapping: As domains continue to swap
    • Y. Liu, and D. Eisenberg 3D domain swapping: as domains continue to swap Protein Sci. 11 2002 1285 1299
    • (2002) Protein Sci. , vol.11 , pp. 1285-1299
    • Liu, Y.1    Eisenberg, D.2
  • 24
    • 0344407050 scopus 로고    scopus 로고
    • Conservation and amyloid formation: A study of the gelsolin-like family
    • H. Benyamini, K. Gunasekaran, H. Wolfson, and R. Nussinov Conservation and amyloid formation: a study of the gelsolin-like family Proteins 51 2003 266 282
    • (2003) Proteins , vol.51 , pp. 266-282
    • Benyamini, H.1    Gunasekaran, K.2    Wolfson, H.3    Nussinov, R.4
  • 25
    • 0028961335 scopus 로고
    • SCOP: A structural classification of proteins database for the investigation of sequences and structures
    • A.G. Murzin, S.E. Brenner, T. Hubbard, and C. Chothia SCOP: a structural classification of proteins database for the investigation of sequences and structures J. Mol. Biol. 247 1995 536 540
    • (1995) J. Mol. Biol. , vol.247 , pp. 536-540
    • Murzin, A.G.1    Brenner, S.E.2    Hubbard, T.3    Chothia, C.4
  • 26
    • 2442456104 scopus 로고    scopus 로고
    • A method for simultaneous alignment of multiple protein structures
    • M. Shatsky, R. Nussinov, and H.J. Wolfson A method for simultaneous alignment of multiple protein structures Proteins 56 2004 143 156
    • (2004) Proteins , vol.56 , pp. 143-156
    • Shatsky, M.1    Nussinov, R.2    Wolfson, H.J.3
  • 28
    • 0027968068 scopus 로고
    • Improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice
    • J.D. Thompson, D.G. Higgins, T.J. Gibson, and W. Clustal Improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice Nucleic Acids Res. 11 1994 4673 4680
    • (1994) Nucleic Acids Res. , vol.11 , pp. 4673-4680
    • Thompson, J.D.1    Higgins, D.G.2    Gibson, T.J.3    Clustal, W.4
  • 29
    • 0345062357 scopus 로고    scopus 로고
    • Universally conserved positions in protein folds: Reading evolutionary signals about stability, folding kinetics and function
    • L.A. Mirny, and E.I. Shakhnovich Universally conserved positions in protein folds: reading evolutionary signals about stability, folding kinetics and function J. Mol. Biol. 291 1999 177 196
    • (1999) J. Mol. Biol. , vol.291 , pp. 177-196
    • Mirny, L.A.1    Shakhnovich, E.I.2
  • 30
    • 0036190448 scopus 로고    scopus 로고
    • Determining the roles of different chain fragments in recognition of immunoglobulin fold
    • B. Reva, A. Kister, S. Topiol, and I. Gelfand Determining the roles of different chain fragments in recognition of immunoglobulin fold Protein Eng. 15 2002 13 19
    • (2002) Protein Eng. , vol.15 , pp. 13-19
    • Reva, B.1    Kister, A.2    Topiol, S.3    Gelfand, I.4
  • 32
    • 0037192778 scopus 로고    scopus 로고
    • Cleaved β2-microglobulin partially attains a conformation that has amyloidogenic features
    • N.H. Heegard, P. Roepstorff, S.G. Melberg, and M.H. Nissen Cleaved β2-microglobulin partially attains a conformation that has amyloidogenic features J. Biol. Chem. 277 2002 11184 11189
    • (2002) J. Biol. Chem. , vol.277 , pp. 11184-11189
    • Heegard, N.H.1    Roepstorff, P.2    Melberg, S.G.3    Nissen, M.H.4
  • 33
    • 0036295080 scopus 로고    scopus 로고
    • Transthyretin fibrillogenesis entails the assembly of monomers: A molecular model for in vitro assembled transthyretin amyloid-like fibrils
    • I. Cardoso, C.S. Goldsbury, S.A. Muller, V. Olivieri, S. Wirtz, A.M. Damas, U. Aebi, and M.J. Saraiva Transthyretin fibrillogenesis entails the assembly of monomers: a molecular model for in vitro assembled transthyretin amyloid-like fibrils J. Mol. Biol. 317 2002 683 695
    • (2002) J. Mol. Biol. , vol.317 , pp. 683-695
    • Cardoso, I.1    Goldsbury, C.S.2    Muller, S.A.3    Olivieri, V.4    Wirtz, S.5    Damas, A.M.6    Aebi, U.7    Saraiva, M.J.8
  • 35
    • 8844247180 scopus 로고    scopus 로고
    • Mechanism of prion propagation: Amyloid growth occurs by monomer addition
    • S.R. Collins, A. Douglass, R.D. Vale, and J.S. Weissman Mechanism of prion propagation: amyloid growth occurs by monomer addition PLoS Biol. 2 2004 e321
    • (2004) PLoS Biol. , vol.2 , pp. 321
    • Collins, S.R.1    Douglass, A.2    Vale, R.D.3    Weissman, J.S.4
  • 36
    • 0347755444 scopus 로고    scopus 로고
    • Predicting molecular interactions in silico: Ii. Protein-protein and protein-drug docking
    • D. Schneidman-Duhovny, R. Nussinov, and H.J. Wolfson Predicting molecular interactions in silico: Ii. Protein-protein and protein-drug docking Curr. Med. Chem. 11 2004 91 107
    • (2004) Curr. Med. Chem. , vol.11 , pp. 91-107
    • Schneidman-Duhovny, D.1    Nussinov, R.2    Wolfson, H.J.3
  • 38
    • 18844453949 scopus 로고    scopus 로고
    • Prediction of multimolecular assemblies by multiple docking
    • Y. Inbar, H. Benyamini, R. Nussinov, and H.J. Wolfson Prediction of multimolecular assemblies by multiple docking J. Mol. Biol. 349 2005 435 447
    • (2005) J. Mol. Biol. , vol.349 , pp. 435-447
    • Inbar, Y.1    Benyamini, H.2    Nussinov, R.3    Wolfson, H.J.4
  • 40
    • 0028166881 scopus 로고
    • Shape complementarity at protein-protein interfaces
    • R. Norel, S.L. Lin, H.J. Wolfson, and R. Nussinov Shape complementarity at protein-protein interfaces Biopolymers 34 1994 933 940
    • (1994) Biopolymers , vol.34 , pp. 933-940
    • Norel, R.1    Lin, S.L.2    Wolfson, H.J.3    Nussinov, R.4
  • 41
    • 0029089732 scopus 로고
    • Molecular surface complementarity at protein-protein interfaces: The critical role played by surface normals at well placed, sparse points in docking
    • R. Norel, S.L. Lin, H.J. Wolfson, and R. Nussinov Molecular surface complementarity at protein-protein interfaces: the critical role played by surface normals at well placed, sparse points in docking J. Mol. Biol. 252 1995 263 273
    • (1995) J. Mol. Biol. , vol.252 , pp. 263-273
    • Norel, R.1    Lin, S.L.2    Wolfson, H.J.3    Nussinov, R.4
  • 42
    • 0000933440 scopus 로고    scopus 로고
    • Examination of shape complementarity in docking of unbound proteins
    • R. Norel, D. Petrey, H.J. Wolfson, and R. Nussinov Examination of shape complementarity in docking of unbound proteins Protein Sci. 35 1999 403 419
    • (1999) Protein Sci. , vol.35 , pp. 403-419
    • Norel, R.1    Petrey, D.2    Wolfson, H.J.3    Nussinov, R.4
  • 43
    • 0036606483 scopus 로고    scopus 로고
    • Principles of docking: An overview of search algorithms and a guide to scoring functions
    • I. Halperin, B. Ma, H. Wolfson, and R. Nussinov Principles of docking: an overview of search algorithms and a guide to scoring functions Proteins 47 2002 409 443
    • (2002) Proteins , vol.47 , pp. 409-443
    • Halperin, I.1    Ma, B.2    Wolfson, H.3    Nussinov, R.4
  • 44
    • 0037183496 scopus 로고    scopus 로고
    • Formation of a copper specific binding site in non-native states of β-2 microglobulin
    • C.M. Eakin, J.D. Knight, C.J. Morgan, M.A. Gelfand, and A.D. Miranker Formation of a copper specific binding site in non-native states of β-2 microglobulin Biochemistry 41 2002 10646 10656
    • (2002) Biochemistry , vol.41 , pp. 10646-10656
    • Eakin, C.M.1    Knight, J.D.2    Morgan, C.J.3    Gelfand, M.A.4    Miranker, A.D.5
  • 45
    • 0042847751 scopus 로고    scopus 로고
    • Cryo-electron microscopy structure of an SH3 amyloid fibril and model of the molecular packing.
    • J.L. Jimenez, J.I. Guijaro, E. Orlova, J. Zurdo, C.M. Dobson, M. Sunde, and H.R. Saibil Cryo-electron microscopy structure of an SH3 amyloid fibril and model of the molecular packing. EMBO J. 18 1999 815 821
    • (1999) EMBO J. , vol.18 , pp. 815-821
    • Jimenez, J.L.1    Guijaro, J.I.2    Orlova, E.3    Zurdo, J.4    Dobson, C.M.5    Sunde, M.6    Saibil, H.R.7
  • 48
    • 0037059764 scopus 로고    scopus 로고
    • Investigation of a peptide responsible for amyloid fibril formation of beta 2-microglobulin by achromobacter protease i
    • G.V. Kozhukh, Y. Hagihara, T. Kawakami, K. Hasegawa, H. Naiki, and Y. Goto Investigation of a peptide responsible for amyloid fibril formation of beta 2-microglobulin by achromobacter protease i J. Biol. Chem. 277 2002 1310 1315
    • (2002) J. Biol. Chem. , vol.277 , pp. 1310-1315
    • Kozhukh, G.V.1    Hagihara, Y.2    Kawakami, T.3    Hasegawa, K.4    Naiki, H.5    Goto, Y.6
  • 49
    • 0037227173 scopus 로고    scopus 로고
    • Amyloid-forming peptides from β2-microglobulin-insights into the mechanism of fibril formation in vitro
    • S. Jones, J. Manning, N.M. Kad, and S.E. Radford Amyloid-forming peptides from β2-microglobulin-insights into the mechanism of fibril formation in vitro J. Mol. Biol. 325 2003 249 257
    • (2003) J. Mol. Biol. , vol.325 , pp. 249-257
    • Jones, S.1    Manning, J.2    Kad, N.M.3    Radford, S.E.4
  • 51
    • 0028043552 scopus 로고
    • Position-based sequence weights
    • S. Henikoff, and J.G. Henikoff Position-based sequence weights J. Mol. Biol. 243 1994 574 578
    • (1994) J. Mol. Biol. , vol.243 , pp. 574-578
    • Henikoff, S.1    Henikoff, J.G.2
  • 52
    • 0026342532 scopus 로고
    • Information-theoretical entropy as a measure of sequence variability
    • P.S. Shenkin, B. Erman, and L.D. Mastrandrea Information-theoretical entropy as a measure of sequence variability Proteins 11 1991 297 313
    • (1991) Proteins , vol.11 , pp. 297-313
    • Shenkin, P.S.1    Erman, B.2    Mastrandrea, L.D.3
  • 53
    • 0034486070 scopus 로고    scopus 로고
    • The identification of conserved interactions within the SH3 domain by alignment of sequences and structures
    • S.M. Larson, and A.R. Davidson The identification of conserved interactions within the SH3 domain by alignment of sequences and structures Protein Sci. 9 2000 2170 2180
    • (2000) Protein Sci. , vol.9 , pp. 2170-2180
    • Larson, S.M.1    Davidson, A.R.2
  • 54
    • 0015222647 scopus 로고
    • The interpretation of protein structures: Estimation of static accessibility
    • B. Lee, and F.M. Richards The interpretation of protein structures: estimation of static accessibility J. Mol. Biol. 55 1971 379 400
    • (1971) J. Mol. Biol. , vol.55 , pp. 379-400
    • Lee, B.1    Richards, F.M.2
  • 55
    • 0017187836 scopus 로고
    • The nature of the accessible and buried surface in proteins
    • C. Chothia The nature of the accessible and buried surface in proteins J. Mol. Biol. 105 1975 1 14
    • (1975) J. Mol. Biol. , vol.105 , pp. 1-14
    • Chothia, C.1


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