메뉴 건너뛰기




Volumn 16, Issue 1, 2015, Pages

Capturing coevolutionary signals inrepeat proteins

Author keywords

Co evolution; Direct coupling analysis; Direct information; Repeat proteins

Indexed keywords

AMINO ACIDS; STATISTICAL MECHANICS;

EID: 84934269306     PISSN: None     EISSN: 14712105     Source Type: Journal    
DOI: 10.1186/s12859-015-0648-3     Document Type: Article
Times cited : (14)

References (43)
  • 1
    • 0015597839 scopus 로고
    • Nucleation, rapid folding, and globular intrachain regions in proteins
    • Wetlaufer DB. Nucleation, rapid folding, and globular intrachain regions in proteins. Proc Natl Acad Sci USA. 1973; 70(3):697-701.
    • (1973) Proc Natl Acad Sci USA , vol.70 , Issue.3 , pp. 697-701
    • Wetlaufer, D.B.1
  • 2
    • 36749020130 scopus 로고    scopus 로고
    • Protein engineers turned evolutionists
    • Peisajovich SG, Tawfik DS. Protein engineers turned evolutionists. Nat Methods. 2007; 4(12):991-4.
    • (2007) Nat Methods , vol.4 , Issue.12 , pp. 991-994
    • Peisajovich, S.G.1    Tawfik, D.S.2
  • 3
    • 0017771466 scopus 로고
    • Evolution and tinkering
    • Jacob F. Evolution and tinkering. Science. 1977; 196(4295):1161-6.
    • (1977) Science , vol.196 , Issue.4295 , pp. 1161-1166
    • Jacob, F.1
  • 6
    • 84886688567 scopus 로고    scopus 로고
    • Detecting repetitions and periodicities in proteins by tiling the structural space
    • Parra RG, Espada R, Sánchez IE, Sippl MJ, Ferreiro DU. Detecting repetitions and periodicities in proteins by tiling the structural space. J Phys Chem B. 2013; 117(42):12887-97.
    • (2013) J Phys Chem B , vol.117 , Issue.42 , pp. 12887-12897
    • Parra, R.G.1    Espada, R.2    Sánchez, I.E.3    Sippl, M.J.4    Ferreiro, D.U.5
  • 8
    • 84865174088 scopus 로고    scopus 로고
    • Tandem repeats in proteins: from sequence to structure
    • Kajava AV. Tandem repeats in proteins: from sequence to structure. J Struct Biol. 2012; 179(3):279-88.
    • (2012) J Struct Biol , vol.179 , Issue.3 , pp. 279-288
    • Kajava, A.V.1
  • 10
    • 0029952910 scopus 로고    scopus 로고
    • Symmetry and the energy landscapes of biomolecules
    • Wolynes PG. Symmetry and the energy landscapes of biomolecules. Proc Natl Acad Sci U S A. 1996; 93(25):14249.
    • (1996) Proc Natl Acad Sci U S A , vol.93 , Issue.25 , pp. 14249
    • Wolynes, P.G.1
  • 11
    • 44949165528 scopus 로고    scopus 로고
    • The energy landscapes of repeat-containing proteins: topology, cooperativity, and the folding funnels of one-dimensional architectures
    • Ferreiro DU, Walczak AM, Komives EA, Wolynes PG. The energy landscapes of repeat-containing proteins: topology, cooperativity, and the folding funnels of one-dimensional architectures. PLoS Comput Biol. 2008; 4(5):1000070.
    • (2008) PLoS Comput Biol , vol.4 , Issue.5 , pp. 1000070
    • Ferreiro, D.U.1    Walczak, A.M.2    Komives, E.A.3    Wolynes, P.G.4
  • 13
    • 0028125904 scopus 로고
    • How frequent are correlated changes in families of protein sequences?
    • Neher E. How frequent are correlated changes in families of protein sequences?. Proc Natl Acad Sci. 1994; 91(1):98-102.
    • (1994) Proc Natl Acad Sci , vol.91 , Issue.1 , pp. 98-102
    • Neher, E.1
  • 14
    • 58549114185 scopus 로고    scopus 로고
    • Identification of direct residue contacts in protein-protein interaction by message passing
    • Weigt M, White RA, Szurmant H, Hoch JA, Hwa T. Identification of direct residue contacts in protein-protein interaction by message passing. Proc Natl Acad Sci. 2009; 106(1):67-72.
    • (2009) Proc Natl Acad Sci , vol.106 , Issue.1 , pp. 67-72
    • Weigt, M.1    White, R.A.2    Szurmant, H.3    Hoch, J.A.4    Hwa, T.5
  • 16
    • 84862647180 scopus 로고    scopus 로고
    • Three-dimensional structures of membrane proteins from genomic sequencing
    • 10.1016/j.cell.2012.04.012
    • Hopf TA, Colwell LJ, Sheridan R, Rost B, Sander C, Marks DS. Three-dimensional structures of membrane proteins from genomic sequencing. Cell. 2012; 149(7):1607-21. doi: 10.1016/j.cell.2012.04.012 .
    • (2012) Cell , vol.149 , Issue.7 , pp. 1607-1621
    • Hopf, T.A.1    Colwell, L.J.2    Sheridan, R.3    Rost, B.4    Sander, C.5    Marks, D.S.6
  • 17
    • 79955774472 scopus 로고    scopus 로고
    • The mempack alpha-helical transmembrane protein structure prediction server
    • 10.1093/bioinformatics/btr096
    • Nugent T, Ward S, Jones DT. The mempack alpha-helical transmembrane protein structure prediction server. Bioinformatics. 2011; 27(10):1438-9. doi: 10.1093/bioinformatics/btr096 .
    • (2011) Bioinformatics , vol.27 , Issue.10 , pp. 1438-1439
    • Nugent, T.1    Ward, S.2    Jones, D.T.3
  • 18
    • 83755178457 scopus 로고    scopus 로고
    • Direct-coupling analysis of residue coevolution captures native contacts across many protein families
    • Morcos F, Pagnani A, Lunt B, Bertolino A, Marks DS, Sander C, et al. Direct-coupling analysis of residue coevolution captures native contacts across many protein families. Proc Natl Acad Sci. 2011; 108(49):1293-301.
    • (2011) Proc Natl Acad Sci , vol.108 , Issue.49 , pp. 1293-1301
    • Morcos, F.1    Pagnani, A.2    Lunt, B.3    Bertolino, A.4    Marks, D.S.5    Sander, C.6
  • 19
    • 84907863038 scopus 로고    scopus 로고
    • Direct coupling analysis for protein contact prediction
    • Morcos F, Hwa T, Onuchic JN, Weigt M. Direct coupling analysis for protein contact prediction. Methods Mol Biol. 2014; 1137:55-70.
    • (2014) Methods Mol Biol , vol.1137 , pp. 55-70
    • Morcos, F.1    Hwa, T.2    Onuchic, J.N.3    Weigt, M.4
  • 20
    • 0032567972 scopus 로고    scopus 로고
    • Net prophets
    • Brenner S. Net prophets. Curr Biol. 1998; 8(5):147.
    • (1998) Curr Biol , vol.8 , Issue.5 , pp. 147
    • Brenner, S.1
  • 22
    • 84862192588 scopus 로고    scopus 로고
    • Accurate de novo structure prediction of large transmembrane protein domains using fragment-assembly and correlated mutation analysis
    • Nugent T, Jones DT. Accurate de novo structure prediction of large transmembrane protein domains using fragment-assembly and correlated mutation analysis. Proc Natl Acad Sci. 2012; 109(24):1540-7.
    • (2012) Proc Natl Acad Sci , vol.109 , Issue.24 , pp. 1540-1547
    • Nugent, T.1    Jones, D.T.2
  • 23
    • 84890816704 scopus 로고    scopus 로고
    • Coevolutionary signals across protein lineages help capture multiple protein conformations
    • Morcos F, Jana B, Hwa T, Onuchic JN. Coevolutionary signals across protein lineages help capture multiple protein conformations. Proc Natl Acad Sci USA. 2013; 110(51):20533-0538.
    • (2013) Proc Natl Acad Sci USA , vol.110 , Issue.51 , pp. 20533-20538
    • Morcos, F.1    Jana, B.2    Hwa, T.3    Onuchic, J.N.4
  • 25
    • 84893476565 scopus 로고    scopus 로고
    • Toward rationally redesigning bacterial two-component signaling systems using coevolutionary information
    • Cheng RR, Morcos F, Levine H, Onuchic JN. Toward rationally redesigning bacterial two-component signaling systems using coevolutionary information. Proc Natl Acad Sci USA. 2014; 111(5):563-71.
    • (2014) Proc Natl Acad Sci USA , vol.111 , Issue.5 , pp. 563-571
    • Cheng, R.R.1    Morcos, F.2    Levine, H.3    Onuchic, J.N.4
  • 26
    • 84886578448 scopus 로고    scopus 로고
    • The network of stabilizing contacts in proteins studied by coevolutionary data
    • Lui S, Tiana G. The network of stabilizing contacts in proteins studied by coevolutionary data. J Chem Phys. 2013; 139(15):155103.
    • (2013) J Chem Phys , vol.139 , Issue.15 , pp. 155103
    • Lui, S.1    Tiana, G.2
  • 27
    • 84872521100 scopus 로고    scopus 로고
    • Improved contact prediction in proteins: using pseudolikelihoods to infer potts models
    • Ekeberg M, Lövkvist C, Lan Y, Weigt M, Aurell E. Improved contact prediction in proteins: using pseudolikelihoods to infer potts models. Phys Rev E. 2013; 87(1):012707.
    • (2013) Phys Rev E , vol.87 , Issue.1 , pp. 012707
    • Ekeberg, M.1    Lövkvist, C.2    Lan, Y.3    Weigt, M.4    Aurell, E.5
  • 29
    • 84912100015 scopus 로고    scopus 로고
    • Improved contact predictions using the recognition of protein like contact patterns
    • 10.1371/journal.pcbi.1003889
    • Skwark MJ, Raimondi D, Michel M, Elofsson A. Improved contact predictions using the recognition of protein like contact patterns. PLoS Comput Biol. 2014; 10(11):1003889. doi: 10.1371/journal.pcbi.1003889 .
    • (2014) PLoS Comput Biol , vol.10 , Issue.11 , pp. 1003889
    • Skwark, M.J.1    Raimondi, D.2    Michel, M.3    Elofsson, A.4
  • 30
    • 84856090271 scopus 로고    scopus 로고
    • Psicov: precise structural contact prediction using sparse inverse covariance estimation on large multiple sequence alignments
    • 10.1093/bioinformatics/btr638
    • Jones DT, Buchan DWA, Cozzetto D, Pontil M. Psicov: precise structural contact prediction using sparse inverse covariance estimation on large multiple sequence alignments. Bioinformatics. 2012; 28(2):184-90. doi: 10.1093/bioinformatics/btr638 .
    • (2012) Bioinformatics , vol.28 , Issue.2 , pp. 184-190
    • Jones, D.T.1    Buchan, D.W.A.2    Cozzetto, D.3    Pontil, M.4
  • 31
    • 84929144039 scopus 로고    scopus 로고
    • Metapsicov: Combining coevolution methods for accurate prediction of contacts and long range hydrogen bonding in proteins
    • Jones DT, Singh T, Kosciolek T, Tetchner S. Metapsicov: Combining coevolution methods for accurate prediction of contacts and long range hydrogen bonding in proteins. Bioinformatics. 2015; 31(7):999-1006.
    • (2015) Bioinformatics , vol.31 , Issue.7 , pp. 999-1006
    • Jones, D.T.1    Singh, T.2    Kosciolek, T.3    Tetchner, S.4
  • 33
    • 61849158225 scopus 로고    scopus 로고
    • Analysis of repeat protein folding using nearest-neighbor statistical mechanical models
    • Aksel T, Barrick D. Analysis of repeat protein folding using nearest-neighbor statistical mechanical models. Methods Enzymol. 2009; 455:95-125.
    • (2009) Methods Enzymol , vol.455 , pp. 95-125
    • Aksel, T.1    Barrick, D.2
  • 34
    • 48249126206 scopus 로고    scopus 로고
    • The capillarity picture and the kinetics of one-dimensional protein folding
    • Ferreiro DU, Wolynes PG. The capillarity picture and the kinetics of one-dimensional protein folding. Proc Natl Acad Sci. 2008; 105(29):9853-854.
    • (2008) Proc Natl Acad Sci , vol.105 , Issue.29 , pp. 9853-9854
    • Ferreiro, D.U.1    Wolynes, P.G.2
  • 35
    • 58149464544 scopus 로고    scopus 로고
    • Predicting repeat protein folding kinetics from an experimentally determined folding energy landscape
    • Street TO, Barrick D. Predicting repeat protein folding kinetics from an experimentally determined folding energy landscape. Protein Sci. 2009; 18(1):58-68.
    • (2009) Protein Sci , vol.18 , Issue.1 , pp. 58-68
    • Street, T.O.1    Barrick, D.2
  • 36
    • 38049063892 scopus 로고    scopus 로고
    • Folding and unfolding mechanism of highly stable full-consensus ankyrin repeat proteins
    • Wetzel SK, Settanni G, Kenig M, Binz HK, Plückthun A. Folding and unfolding mechanism of highly stable full-consensus ankyrin repeat proteins. J Mol Biol. 2008; 376(1):241-57.
    • (2008) J Mol Biol , vol.376 , Issue.1 , pp. 241-257
    • Wetzel, S.K.1    Settanni, G.2    Kenig, M.3    Binz, H.K.4    Plückthun, A.5
  • 37
    • 27744531924 scopus 로고    scopus 로고
    • The energy landscape of modular repeat proteins: topology determines folding mechanism in the ankyrin family
    • Ferreiro DU, Cho SS, Komives EA, Wolynes PG. The energy landscape of modular repeat proteins: topology determines folding mechanism in the ankyrin family. J Mol Biol. 2005; 354(3):679-92.
    • (2005) J Mol Biol , vol.354 , Issue.3 , pp. 679-692
    • Ferreiro, D.U.1    Cho, S.S.2    Komives, E.A.3    Wolynes, P.G.4
  • 39
    • 79959931985 scopus 로고    scopus 로고
    • Hmmer web server: interactive sequence similarity searching
    • Finn RD, Clements J, Eddy SR. Hmmer web server: interactive sequence similarity searching. Nucleic Acids Res. 2011; 39(Web Server issue):W29-W37.
    • (2011) Nucleic Acids Res , vol.39 , Issue.WEB SERVER ISSUE , pp. W29-W37
    • Finn, R.D.1    Clements, J.2    Eddy, S.R.3
  • 41
    • 0028043552 scopus 로고
    • Position-based sequence weights
    • Henikoff S, Henikoff JG. Position-based sequence weights. J Mol Biol. 1994; 243(4):574-8.
    • (1994) J Mol Biol , vol.243 , Issue.4 , pp. 574-578
    • Henikoff, S.1    Henikoff, J.G.2
  • 42
    • 40049099114 scopus 로고    scopus 로고
    • Defining clusters from a hierarchical cluster tree: the dynamic tree cut package for r
    • Langfelder P, Zhang B, Horvath S. Defining clusters from a hierarchical cluster tree: the dynamic tree cut package for r. Bioinformatics. 2008; 24(5):719-20.
    • (2008) Bioinformatics , vol.24 , Issue.5 , pp. 719-720
    • Langfelder, P.1    Zhang, B.2    Horvath, S.3


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.