메뉴 건너뛰기




Volumn 9, Issue 4, 2014, Pages

Intermolecular β-strand networks avoid hub residues and favor low interconnectedness: A potential protection mechanism against chain dissociation upon mutation

Author keywords

[No Author keywords available]

Indexed keywords

AMYLOID PRECURSOR PROTEIN; PROTEIN P53; AMINO ACID; AMYLOID; PROTEIN BINDING; TP53 PROTEIN, HUMAN;

EID: 84899633630     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0094745     Document Type: Article
Times cited : (8)

References (59)
  • 1
    • 52649130704 scopus 로고    scopus 로고
    • Protein-protein interaction and quaternary structure
    • Janin J, Bahadur RP, Chakrabarti P (2008) Protein-protein interaction and quaternary structure. Q Rev Biophys 41: 133-180.
    • (2008) Q Rev Biophys , vol.41 , pp. 133-180
    • Janin, J.1    Bahadur, R.P.2    Chakrabarti, P.3
  • 2
    • 65549157572 scopus 로고    scopus 로고
    • A survey of available tools and web servers for analysis of protein-protein interactions and interfaces
    • Tuncbag N, Kar G, Keskin O, Gursoy A, Nussinov R (2009) A survey of available tools and web servers for analysis of protein-protein interactions and interfaces. Briefings in Bioinformatics 10: 217.
    • (2009) Briefings in Bioinformatics , vol.10 , pp. 217
    • Tuncbag, N.1    Kar, G.2    Keskin, O.3    Gursoy, A.4    Nussinov, R.5
  • 3
    • 0036469060 scopus 로고    scopus 로고
    • Unraveling hot spots in binding interfaces: Progress and challenges
    • DeLano WL (2002) Unraveling hot spots in binding interfaces: progress and challenges. Current opinion in structural biology 12: 14-20.
    • (2002) Current Opinion in Structural Biology , vol.12 , pp. 14-20
    • Delano, W.L.1
  • 4
    • 79959593991 scopus 로고    scopus 로고
    • Characterization of proteinprotein interaction interfaces from a single species
    • Talavera D, Robertson DL, Lovell SC (2011) Characterization of proteinprotein interaction interfaces from a single species. PloS one 6: e21053.
    • (2011) PloS One , vol.6
    • Talavera, D.1    Robertson, D.L.2    Lovell, S.C.3
  • 5
    • 1042275583 scopus 로고    scopus 로고
    • A dissection of specific and non-specific protein-protein interfaces
    • DOI 10.1016/j.jmb.2003.12.073
    • Bahadur RP, Chakrabarti P, Rodier F, Janin J (2004) A dissection of specific and non-specific protein-protein interfaces. J Mol Biol 336: 943-955. (Pubitemid 38201541)
    • (2004) Journal of Molecular Biology , vol.336 , Issue.4 , pp. 943-955
    • Bahadur, R.P.1    Chakrabarti, P.2    Rodier, F.3    Janin, J.4
  • 6
    • 0028916599 scopus 로고
    • A hot spot of binding energy in a hormone-receptor interface
    • Clackson T, Wells JA (1995) A hot spot of binding energy in a hormone-receptor interface. Science 267: 383-386.
    • (1995) Science , vol.267 , pp. 383-386
    • Clackson, T.1    Wells, J.A.2
  • 7
    • 84858374665 scopus 로고    scopus 로고
    • The amyloid state of proteins in human diseases
    • Eisenberg D, Jucker M (2012) The Amyloid State of Proteins in Human Diseases. Cell 148: 1188-1203.
    • (2012) Cell , vol.148 , pp. 1188-1203
    • Eisenberg, D.1    Jucker, M.2
  • 8
    • 0036789017 scopus 로고    scopus 로고
    • Serpinopathies and the conformational dementias
    • Lomas DA, Carrell RW (2002) Serpinopathies and the conformational dementias. Nature Reviews Genetics 3: 759-768.
    • (2002) Nature Reviews Genetics , vol.3 , pp. 759-768
    • Lomas, D.A.1    Carrell, R.W.2
  • 10
    • 57049093241 scopus 로고    scopus 로고
    • Amyloidogenesis in its biological environment: Challenging a fundamental issue in protein misfolding diseases
    • Bellotti V, Chiti F (2008) Amyloidogenesis in its biological environment: challenging a fundamental issue in protein misfolding diseases. Current opinion in structural biology 18: 771-779.
    • (2008) Current Opinion in Structural Biology , vol.18 , pp. 771-779
    • Bellotti, V.1    Chiti, F.2
  • 14
    • 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
  • 15
    • 49249122738 scopus 로고    scopus 로고
    • The structural determinants that lead to the formation of particular oligomeric structures in the pancreatic-type ribonuclease family
    • Benito A, Laurents DV, Ribo M, Vilanova M (2008) The structural determinants that lead to the formation of particular oligomeric structures in the pancreatic-type ribonuclease family. Curr Protein Pept Sci 9: 370-393.
    • (2008) Curr Protein Pept Sci , vol.9 , pp. 370-393
    • Benito, A.1    Laurents, D.V.2    Ribo, M.3    Vilanova, M.4
  • 16
    • 0242668337 scopus 로고    scopus 로고
    • Common structure of soluble amyloid oligomers implies common mechanism of pathogenesis
    • DOI 10.1126/science.1079469
    • Kayed R, Head E, Thompson JL, McIntire TM, Milton SC, et al. (2003) Common structure of soluble amyloid oligomers implies common mechanism of pathogenesis. Science 300: 486-489. (Pubitemid 36444329)
    • (2003) Science , vol.300 , Issue.5618 , pp. 486-489
    • Kayed, R.1    Head, E.2    Thompson, J.L.3    McIntire, T.M.4    Milton, S.C.5    Cotman, C.W.6    Glabel, C.G.7
  • 18
    • 0033200063 scopus 로고    scopus 로고
    • Protein misfolding, evolution and disease
    • DOI 10.1016/S0968-0004(99)01445-0, PII S0968000499014450
    • Dobson CM (1999) Protein misfolding, evolution and disease. Trends Biochem Sci 24: 329-332. (Pubitemid 29421804)
    • (1999) Trends in Biochemical Sciences , vol.24 , Issue.9 , pp. 329-332
    • Dobson, C.M.1
  • 20
    • 0141733169 scopus 로고    scopus 로고
    • Structural organization of α-synuclein fibrils studied by site-directed spin labeling
    • DOI 10.1074/jbc.M305266200
    • Der-Sarkissian A, Jao CC, Chen J, Langen R (2003) Structural organization of alpha-synuclein fibrils studied by site-directed spin labeling. J Biol Chem 278: 37530-37535. (Pubitemid 37175274)
    • (2003) Journal of Biological Chemistry , vol.278 , Issue.39 , pp. 37530-37535
    • Der-Sarkissiant, A.1    Jao, C.C.2    Chen, J.3    Langen, R.4
  • 21
    • 16244376187 scopus 로고    scopus 로고
    • The parallel superpleated beta-structure as a model for amyloid fibrils of human amylin
    • DOI 10.1016/j.jmb.2005.02.029
    • Kajava AV, Aebi U, Steven AC (2005) The parallel superpleated beta-structure as a model for amyloid fibrils of human amylin. J Mol Biol 348: 247-252. (Pubitemid 40462093)
    • (2005) Journal of Molecular Biology , vol.348 , Issue.2 , pp. 247-252
    • Kajava, A.V.1    Aebi, U.2    Steven, A.C.3
  • 22
    • 20444474976 scopus 로고    scopus 로고
    • Structural insights into a yeast prion illuminate nucleation and strain diversity
    • DOI 10.1038/nature03679
    • Krishnan R, Lindquist SL (2005) Structural insights into a yeast prion illuminate nucleation and strain diversity. Nature 435: 765-772. (Pubitemid 40839721)
    • (2005) Nature , vol.435 , Issue.7043 , pp. 765-772
    • Krishnan, R.1    Lindquist, S.L.2
  • 24
    • 84861822461 scopus 로고    scopus 로고
    • Structural comparison of mouse and human alpha-synuclein amyloid fibrils by solid-state NMR
    • Lv G, Kumar A, Giller K, Orcellet ML, Riedel D, et al. (2012) Structural comparison of mouse and human alpha-synuclein amyloid fibrils by solid-state NMR. J Mol Biol 420: 99-111.
    • (2012) J Mol Biol , vol.420 , pp. 99-111
    • Lv, G.1    Kumar, A.2    Giller, K.3    Orcellet, M.L.4    Riedel, D.5
  • 25
    • 33845978790 scopus 로고    scopus 로고
    • Insight into the structure of amyloid fibrils from the analysis of globular proteins
    • Trovato A, Chiti F, Maritan A, Seno F (2006) Insight into the structure of amyloid fibrils from the analysis of globular proteins. PLoS computational biology 2: e170.
    • (2006) PLoS Computational Biology , vol.2
    • Trovato, A.1    Chiti, F.2    Maritan, A.3    Seno, F.4
  • 27
    • 5044235541 scopus 로고    scopus 로고
    • Prediction of sequence-dependent and mutational effects on the aggregation of peptides and proteins
    • DOI 10.1038/nbt1012
    • Fernandez-Escamilla A-M, Rousseau F, Schymkowitz J, Serrano L (2004) Prediction of sequence-dependent and mutational effects on the aggregation of peptides and proteins. Nature biotechnology 22: 1302-1306. (Pubitemid 39336784)
    • (2004) Nature Biotechnology , vol.22 , Issue.10 , pp. 1302-1306
    • Fernandez-Escamilla, A.-M.1    Rousseau, F.2    Schymkowitz, J.3    Serrano, L.4
  • 30
    • 79960005237 scopus 로고    scopus 로고
    • Prediction of amyloid aggregation in vivo
    • Belli M, Ramazzotti M, Chiti F (2011) Prediction of amyloid aggregation in vivo. EMBO Rep 12: 657-663.
    • (2011) EMBO Rep , vol.12 , pp. 657-663
    • Belli, M.1    Ramazzotti, M.2    Chiti, F.3
  • 31
    • 8844277625 scopus 로고    scopus 로고
    • ICBS: A database of interactions between protein chains mediated by β-sheet formation
    • DOI 10.1093/bioinformatics/bth326
    • Dou Y, Baisnée P-F, Pollastri G, Pécout Y, Nowick J, et al. (2004) ICBS: a database of interactions between protein chains mediated by b-sheet formation. Bioinformatics 20: 2767-2777. (Pubitemid 39530163)
    • (2004) Bioinformatics , vol.20 , Issue.16 , pp. 2767-2777
    • Dou, Y.1    Baisnee, P.-F.2    Pollastri, G.3    Pecout, Y.4    Nowick, J.5    Baldi, P.6
  • 32
    • 84859509789 scopus 로고    scopus 로고
    • Beta-strand interfaces of non-dimeric protein oligomers are characterized by scattered charged residue patterns
    • Feverati G, Achoch M, Zrimi J, Vuillon L, Lesieur C (2012) Beta-Strand Interfaces of Non-Dimeric Protein Oligomers Are Characterized by Scattered Charged Residue Patterns. PloS one 7: e32558.
    • (2012) PloS One , vol.7
    • Feverati, G.1    Achoch, M.2    Zrimi, J.3    Vuillon, L.4    Lesieur, C.5
  • 35
    • 79952115911 scopus 로고    scopus 로고
    • Oligomeric interfaces under the lens: Gemini
    • Feverati G, Lesieur C (2010) Oligomeric interfaces under the lens: gemini. PloS one 5: e9897.
    • (2010) PloS One , vol.5
    • Feverati, G.1    Lesieur, C.2
  • 37
    • 41149083129 scopus 로고    scopus 로고
    • Protein contacts, inter-residue interactions and side-chain modelling
    • Faure G, Bornot A, de Brevern AG (2008) Protein contacts, inter-residue interactions and side-chain modelling. Biochimie 90: 626-639.
    • (2008) Biochimie , vol.90 , pp. 626-639
    • Faure, G.1    Bornot, A.2    De Brevern, A.G.3
  • 38
    • 77958056909 scopus 로고    scopus 로고
    • Structural classification of proteins and structural genomics: New insights into protein folding and evolution
    • Andreeva A, Murzin AG (2011) Structural classification of proteins and structural genomics: new insights into protein folding and evolution. Acta Crystallogr Sect F Struct Biol Cryst Commun 66: 1190-1197.
    • (2011) Acta Crystallogr Sect F Struct Biol Cryst Commun , vol.66 , pp. 1190-1197
    • Andreeva, A.1    Murzin, A.G.2
  • 40
    • 0028961335 scopus 로고
    • SCOP: A structural classification of proteins database for the investigation of sequences and structures
    • Murzin AG, Brenner SE, Hubbard T, Chothia C (1995) SCOP: a structural classification of proteins database for the investigation of sequences and structures. J Mol Biol 247: 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
  • 41
    • 0034598946 scopus 로고    scopus 로고
    • Molecular dynamics simulations of a [beta]-hairpin fragment of protein G: Balance between side-chain and backbone forces1
    • Ma B, Nussinov R (2000) Molecular dynamics simulations of a [beta]-hairpin fragment of protein G: balance between side-chain and backbone forces1. Journal of molecular biology 296: 1091-1104.
    • (2000) Journal of Molecular Biology , vol.296 , pp. 1091-1104
    • Ma, B.1    Nussinov, R.2
  • 42
    • 0003187567 scopus 로고    scopus 로고
    • The atomic structure of protein-protein recognition sites
    • DOI 10.1006/jmbi.1998.2439
    • Lo Conte L, Chothia C, Janin J (1999) The atomic structure of protein-protein recognition sites. J Mol Biol 285: 2177-2198. (Pubitemid 29078179)
    • (1999) Journal of Molecular Biology , vol.285 , Issue.5 , pp. 2177-2198
    • Conte, L.L.1    Chothia, C.2    Janin, J.3
  • 43
    • 0028176595 scopus 로고
    • Measurement of the b-sheet-forming propensities of amino acids
    • Minor Jr. DL, Kim P (1994) Measurement of the b-sheet-forming propensities of amino acids. Nature 367: 660-663.
    • (1994) Nature , vol.367 , pp. 660-663
    • Minor Jr., D.L.1    Kim, P.2
  • 44
    • 0001117058 scopus 로고    scopus 로고
    • Construction and design of b-sheets
    • Smith CK, Regan L (1997) Construction and design of b-sheets. Acc Chem Res 30: 153-161.
    • (1997) Acc Chem Res , vol.30 , pp. 153-161
    • Smith, C.K.1    Regan, L.2
  • 46
    • 37349000392 scopus 로고    scopus 로고
    • β-Sheet capping: Signals that initiate and terminate β-sheet formation
    • DOI 10.1016/j.jsb.2007.09.024, PII S1047847707002389
    • FarzadFard F, Gharaei N, Pezeshk H, Marashi SA (2008) [beta]-Sheet capping: Signals that initiate and terminate [beta]-sheet formation. Journal of structural biology 161: 101-110. (Pubitemid 350298265)
    • (2008) Journal of Structural Biology , vol.161 , Issue.1 , pp. 101-110
    • FarzadFard, F.1    Gharaei, N.2    Pezeshk, H.3    Marashi, S.-A.4
  • 47
    • 0036597960 scopus 로고    scopus 로고
    • Beta-sheet breaker strategy for the treatment of Alzheimer's disease
    • DOI 10.1002/ddr.10074
    • Adessi C, Soto C (2002) Beta-sheet breaker strategy for the treatment of Alzheimer's disease. Drug development research 56: 184-193. (Pubitemid 35014941)
    • (2002) Drug Development Research , vol.56 , Issue.2 , pp. 184-193
    • Adessi, C.1    Soto, C.2
  • 50
    • 70349832423 scopus 로고    scopus 로고
    • Following evolutionary paths to protein-protein interactions with high affinity and selectivity
    • Levin KB, Dym O, Albeck S, Magdassi S, Keeble AH, et al. (2009) Following evolutionary paths to protein-protein interactions with high affinity and selectivity. Nature structural & molecular biology 16: 1049-1055.
    • (2009) Nature Structural & Molecular Biology , vol.16 , pp. 1049-1055
    • Levin, K.B.1    Dym, O.2    Albeck, S.3    Magdassi, S.4    Keeble, A.H.5
  • 51
    • 0242720597 scopus 로고    scopus 로고
    • Uncovering network systems within protein structures
    • DOI 10.1016/j.jmb.2003.08.061
    • Greene LH, Higman VA (2003) Uncovering network systems within protein structures. J Mol Biol 334: 781-791. (Pubitemid 37433891)
    • (2003) Journal of Molecular Biology , vol.334 , Issue.4 , pp. 781-791
    • Greene, L.H.1    Higman, V.A.2
  • 52
    • 0034721164 scopus 로고    scopus 로고
    • Error and attack tolerance of complex networks
    • DOI 10.1038/35019019
    • Albert R, Jeong H, Barabasi AL (2000) Error and attack tolerance of complex networks. Nature 406: 378-382. (Pubitemid 30625551)
    • (2000) Nature , vol.406 , Issue.6794 , pp. 378-382
    • Albert, R.1    Jeong, H.2    Barabasi, A.-L.3
  • 53
    • 0142077573 scopus 로고    scopus 로고
    • Topology of evolving networks: Local events and universality
    • DOI 10.1103/PhysRevLett.85.5234
    • Albert R, Barabasi AL (2000) Topology of evolving networks: local events and universality. Phys Rev Lett 85: 5234-5237. (Pubitemid 32871817)
    • (2000) Physical Review Letters , vol.85 , Issue.24 , pp. 5234-5237
    • Albert, R.1    Barabasi, A.-L.2
  • 55
    • 0742305866 scopus 로고    scopus 로고
    • Network biology: Understanding the cell's functional organization
    • DOI 10.1038/nrg1272
    • Barabasi AL, Oltvai ZN (2004) Network biology: understanding the cell's functional organization. Nat Rev Genet 5: 101-113. (Pubitemid 38160277)
    • (2004) Nature Reviews Genetics , vol.5 , Issue.2 , pp. 101-113
    • Barabasi, A.-L.1    Oltvai, Z.N.2
  • 57
    • 0030602896 scopus 로고    scopus 로고
    • A dataset of protein-protein interfaces generated with a sequence-order-independent comparison technique
    • DOI 10.1006/jmbi.1996.0424
    • Tsai CJ, Lin SL, Wolfson HJ, Nussinov R (1996) A dataset of protein-protein interfaces generated with a sequence-order-independent comparison technique. J Mol Biol 260: 604-620. (Pubitemid 26254246)
    • (1996) Journal of Molecular Biology , vol.260 , Issue.4 , pp. 604-620
    • Tsai, C.-J.1    Lin, S.L.2    Wolfson, H.J.3    Nussinov, R.4
  • 58
    • 0036291145 scopus 로고    scopus 로고
    • Predicting changes in the stability of proteins and protein complexes: A study of more than 1000 mutations
    • DOI 10.1016/S0022-2836(02)00442-4
    • Guerois R, Nielsen JE, Serrano L (2002) Predicting changes in the stability of proteins and protein complexes: a study of more than 1000 mutations. Journal of molecular biology 320: 369-387. (Pubitemid 34722226)
    • (2002) Journal of Molecular Biology , vol.320 , Issue.2 , pp. 369-387
    • Guerois, R.1    Nielsen, J.E.2    Serrano, L.3


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.