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Volumn 25, Issue 8, 2009, Pages 996-1003

Predicting helix-helix interactions from residue contacts in membrane proteins

Author keywords

[No Author keywords available]

Indexed keywords

MEMBRANE PROTEIN;

EID: 64549119506     PISSN: 13674803     EISSN: 14602059     Source Type: Journal    
DOI: 10.1093/bioinformatics/btp114     Document Type: Article
Times cited : (53)

References (46)
  • 1
    • 0030801002 scopus 로고    scopus 로고
    • Gapped BLAST and PSI-BLAST: A new generation of protein database search programs
    • Altschul,S.F. et al. (1997) Gapped BLAST and PSI-BLAST: A new generation of protein database search programs. Nucleic Acids Res. 25, 3389-3402.
    • (1997) Nucleic Acids Res , vol.25 , pp. 3389-3402
    • Altschul, S.F.1
  • 2
    • 0033954256 scopus 로고    scopus 로고
    • The protein data bank
    • Berman,H.M. et al. (2000) The protein data bank. Nucleic Acids Res., 28, 235-242.
    • (2000) Nucleic Acids Res , vol.28 , pp. 235-242
    • Berman, H.M.1
  • 3
    • 44449083478 scopus 로고    scopus 로고
    • Prediction of membrane-protein topology from first principles
    • Bernsel,A. et al. (2008) Prediction of membrane-protein topology from first principles. Proc. Natl Acad. Sci. USA, 105, 7177-7181.
    • (2008) Proc. Natl Acad. Sci. USA , vol.105 , pp. 7177-7181
    • Bernsel, A.1
  • 4
    • 4444382786 scopus 로고    scopus 로고
    • A knowledge-based scale for the analysis and prediction of buried and exposed faces of transmembrane domain proteins
    • Beuming,T. and Weinstein,H. (2004) A knowledge-based scale for the analysis and prediction of buried and exposed faces of transmembrane domain proteins. Bioinformatics, 20, 1822-1835.
    • (2004) Bioinformatics , vol.20 , pp. 1822-1835
    • Beuming, T.1    Weinstein, H.2
  • 5
    • 0002632234 scopus 로고
    • An introduction to empirical bayes data analysis
    • Casella,G. (1985)An introduction to empirical bayes data analysis. Am. Stat., 39, 83-87.
    • (1985) Am. Stat , vol.39 , pp. 83-87
    • Casella, G.1
  • 6
    • 0348129526 scopus 로고    scopus 로고
    • The ASTRAL Compendium in 2004
    • Chandonia,J.M. et al. (2004) The ASTRAL Compendium in 2004. Nucleic Acids Res., 32, D189-D192.
    • (2004) Nucleic Acids Res , vol.32
    • Chandonia, J.M.1
  • 8
    • 0019872825 scopus 로고
    • Helix to helix packing in proteins
    • Chothia,C. et al. (1981) Helix to helix packing in proteins. J. Mol. Biol., 145, 215-250.
    • (1981) J. Mol. Biol , vol.145 , pp. 215-250
    • Chothia, C.1
  • 9
    • 0037379072 scopus 로고    scopus 로고
    • How do helix-helix interactions help determine the folds of membrane proteins? Perspectives from the study of homo-oligomeric helical bundles
    • DeGrado,W.F. et al. (2003) How do helix-helix interactions help determine the folds of membrane proteins? Perspectives from the study of homo-oligomeric helical bundles. Protein Sci., 12, 647-665.
    • (2003) Protein Sci , vol.12 , pp. 647-665
    • DeGrado, W.F.1
  • 10
    • 3543089710 scopus 로고    scopus 로고
    • A perturbation-based method for calculating explicit likelihood of evolutionary co-variance in multiple sequence alignments
    • Dekker,J.P. et al. (2004) A perturbation-based method for calculating explicit likelihood of evolutionary co-variance in multiple sequence alignments. Bioinformatics, 20, 1565-1572.
    • (2004) Bioinformatics , vol.20 , pp. 1565-1572
    • Dekker, J.P.1
  • 11
    • 0036226583 scopus 로고    scopus 로고
    • Comparison of helix interactions in membrane and soluble alpha-bundle proteins
    • Eilers,M. et al. (2002) Comparison of helix interactions in membrane and soluble alpha-bundle proteins. Biophys. J., 82, 2720-2736.
    • (2002) Biophys. J , vol.82 , pp. 2720-2736
    • Eilers, M.1
  • 12
    • 0029619259 scopus 로고
    • Knowledge-based protein secondary structure assignment
    • Frishman,D. and Argos,P. (1995) Knowledge-based protein secondary structure assignment. Proteins, 23, 566-579.
    • (1995) Proteins , vol.23 , pp. 566-579
    • Frishman, D.1    Argos, P.2
  • 13
    • 36949003878 scopus 로고    scopus 로고
    • Co-evolving residues in membrane proteins
    • Fuchs,A. et al. (2007) Co-evolving residues in membrane proteins. Bioinformatics, 23, 3312-3319.
    • (2007) Bioinformatics , vol.23 , pp. 3312-3319
    • Fuchs, A.1
  • 14
    • 30344453347 scopus 로고    scopus 로고
    • CASP6 assessment of contact prediction
    • Grana, et al. (2005) CASP6 assessment of contact prediction. Proteins, 61, 214-224.
    • (2005) Proteins , vol.61 , pp. 214-224
    • Grana1
  • 15
    • 10044249042 scopus 로고    scopus 로고
    • Helical packing patterns in membrane and soluble proteins
    • Gimpelev,M. et al. (2004) Helical packing patterns in membrane and soluble proteins. Biophys. J., 87, 4075-4086.
    • (2004) Biophys. J , vol.87 , pp. 4075-4086
    • Gimpelev, M.1
  • 16
    • 0033585083 scopus 로고    scopus 로고
    • The cytochrome c oxidase from Paracoccus denitrificans does not change the metal center ligation upon reduction
    • Harrenga,A. and Michel,H. (1999) The cytochrome c oxidase from Paracoccus denitrificans does not change the metal center ligation upon reduction. J. Biol. Chem., 274, 33296-33299.
    • (1999) J. Biol. Chem , vol.274 , pp. 33296-33299
    • Harrenga, A.1    Michel, H.2
  • 17
    • 36749082814 scopus 로고    scopus 로고
    • Assessment of intramolecular contact predictions for CASP7
    • Izarzugaza,J.M. et al. (2007) Assessment of intramolecular contact predictions for CASP7. Proteins, 69 (Suppl 8), 152-158.
    • (2007) Proteins , vol.69 , Issue.SUPPL. 8 , pp. 152-158
    • Izarzugaza, J.M.1
  • 18
    • 34047151404 scopus 로고    scopus 로고
    • Improving the accuracy of transmembrane protein topology prediction using evolutionary information
    • Jones,D.T. (2007) Improving the accuracy of transmembrane protein topology prediction using evolutionary information. Bioinformatics 23, 538-544.
    • (2007) Bioinformatics , vol.23 , pp. 538-544
    • Jones, D.T.1
  • 19
    • 0036721218 scopus 로고    scopus 로고
    • Mapping pathways of allosteric communication in GroEL by analysis of correlated mutations
    • Kass,I. and Horovitz,A. (2002) Mapping pathways of allosteric communication in GroEL by analysis of correlated mutations. Proteins 48, 611-617.
    • (2002) Proteins , vol.48 , pp. 611-617
    • Kass, I.1    Horovitz, A.2
  • 20
    • 0032080907 scopus 로고    scopus 로고
    • Interaction of transmembrane helices by a knobs-into-holes packing characteristic of soluble coiled coils
    • Langosch,D. and Heringa,J. (1998) Interaction of transmembrane helices by a knobs-into-holes packing characteristic of soluble coiled coils. Proteins, 31, 150-159.
    • (1998) Proteins , vol.31 , pp. 150-159
    • Langosch, D.1    Heringa, J.2
  • 21
    • 0032125607 scopus 로고    scopus 로고
    • A set of van der Waals and coulombic radii of protein atoms for molecular and solvent-accessible surface calculation, packing evaluation, and docking
    • Li,A.J. and Nussinov,R. (1998) A set of van der Waals and coulombic radii of protein atoms for molecular and solvent-accessible surface calculation, packing evaluation, and docking. Proteins, 32, 111-127.
    • (1998) Proteins , vol.32 , pp. 111-127
    • Li, A.J.1    Nussinov, R.2
  • 22
    • 33745634395 scopus 로고    scopus 로고
    • Cd-hit: A fast program for clustering and comparing large sets of protein or nucleotide sequences
    • Li,W. and Godzick,A. (2006) Cd-hit: A fast program for clustering and comparing large sets of protein or nucleotide sequences. Bioinformatics, 22, 1658-1659.
    • (2006) Bioinformatics , vol.22 , pp. 1658-1659
    • Li, W.1    Godzick, A.2
  • 23
    • 4143110064 scopus 로고    scopus 로고
    • Application of sparse NMR restraints to large-scale protein structure prediction
    • Li,W. et al. (2004) Application of sparse NMR restraints to large-scale protein structure prediction. Biophys. J., 87, 1241-1248.
    • (2004) Biophys. J , vol.87 , pp. 1241-1248
    • Li, W.1
  • 24
    • 39749179168 scopus 로고    scopus 로고
    • Enhanced membrane protein topology prediction using a hierarchical classification method and a new scoring function
    • Lo,A. et al. (2008) Enhanced membrane protein topology prediction using a hierarchical classification method and a new scoring function. J. Proteome Res., 7, 487-496.
    • (2008) J. Proteome Res , vol.7 , pp. 487-496
    • Lo, A.1
  • 25
    • 33644747742 scopus 로고    scopus 로고
    • Smoothing: Local regression techniques
    • Gentle,J, eds, Springer-Verlag, Heidelberg, pp
    • Loader,C. (2004) Smoothing: Local regression techniques. In Gentle,J. (eds) Handbook of Computational Statistics. Springer-Verlag, Heidelberg, pp. 540-560.
    • (2004) Handbook of Computational Statistics , pp. 540-560
    • Loader, C.1
  • 26
    • 0016772212 scopus 로고
    • Comparison of the predicted and observed secondary structure of T4 phage lysozyme
    • Matthews,B.W. (1975) Comparison of the predicted and observed secondary structure of T4 phage lysozyme. Biochim. Biophys. Acta., 405 442-451.
    • (1975) Biochim. Biophys. Acta , vol.405 , pp. 442-451
    • Matthews, B.W.1
  • 27
    • 64549140969 scopus 로고    scopus 로고
    • Exact inference in categorical data
    • Mehta,C.R. and Patel,N.R. (1997) Exact inference in categorical data. Biometrics, 53, 112-117.
    • (1997) Biometrics , vol.53 , pp. 112-117
    • Mehta, C.R.1    Patel, N.R.2
  • 28
    • 47049101751 scopus 로고    scopus 로고
    • Using inferred residue contacts to distinguish between correct and incorrect protein models
    • Miller,C.S. and Eisenberg,D. (2008) Using inferred residue contacts to distinguish between correct and incorrect protein models. Bioinformatics, 24, 1575-1582.
    • (2008) Bioinformatics , vol.24 , pp. 1575-1582
    • Miller, C.S.1    Eisenberg, D.2
  • 29
    • 0004255908 scopus 로고    scopus 로고
    • WCB-McGraw-Hill, Boston, MA, pp
    • Mitchell,T.M. (1997) Machine Learning. WCB-McGraw-Hill, Boston, MA, pp. 96-97
    • (1997) Machine Learning , pp. 96-97
    • Mitchell, T.M.1
  • 30
    • 0030627941 scopus 로고    scopus 로고
    • Improving contact predictions by the combination of correlated mutations and other sources of sequence information
    • Olmea,O. and Valencia,A. (1997) Improving contact predictions by the combination of correlated mutations and other sources of sequence information. Fold Des., 2, S25-S32.
    • (1997) Fold Des , vol.2
    • Olmea, O.1    Valencia, A.2
  • 31
    • 0032613288 scopus 로고    scopus 로고
    • Ab initio folding of proteins using restraints derived from evolutionary information
    • Ortiz,A.R. et al. (1999) Ab initio folding of proteins using restraints derived from evolutionary information. Proteins (Suppl 3), 177-185.
    • (1999) Proteins , Issue.SUPPL. 3 , pp. 177-185
    • Ortiz, A.R.1
  • 32
    • 46449120907 scopus 로고    scopus 로고
    • Predicting protein folding rates from geometric contact and amino acid sequence
    • Ouyang,Z. and Liang,J. (2008) Predicting protein folding rates from geometric contact and amino acid sequence. Protein Sci., 17, 1256-1263.
    • (2008) Protein Sci , vol.17 , pp. 1256-1263
    • Ouyang, Z.1    Liang, J.2
  • 33
    • 34948861813 scopus 로고    scopus 로고
    • Prediction of the burial status of transmembrane residues of helical membrane proteins
    • Park,Y. et al. (2007) Prediction of the burial status of transmembrane residues of helical membrane proteins. BMC Bioinformatics, 8, 302.
    • (2007) BMC Bioinformatics , vol.8 , pp. 302
    • Park, Y.1
  • 34
    • 0033790343 scopus 로고    scopus 로고
    • Helical membrane protein folding, stability, and evolution
    • Popot,J.L. and Engelman,D.M. (2000) Helical membrane protein folding, stability, and evolution. Annu. Rev. Biochem., 69, 881-922.
    • (2000) Annu. Rev. Biochem , vol.69 , pp. 881-922
    • Popot, J.L.1    Engelman, D.M.2
  • 35
    • 21444454088 scopus 로고    scopus 로고
    • PROFcon: Novel prediction of long-range contacts
    • Punta,M. and Rost,B. (2005) PROFcon: Novel prediction of long-range contacts. Bioinformatics, 21, 2960-2968.
    • (2005) Bioinformatics , vol.21 , pp. 2960-2968
    • Punta, M.1    Rost, B.2
  • 36
    • 0034711953 scopus 로고    scopus 로고
    • The GxxxG motif: A framework for transmembrane helix-helix association
    • Russ,W.P. and Engelman,D.M. (2000) The GxxxG motif: A framework for transmembrane helix-helix association. J. Mol. Biol., 296, 911-919.
    • (2000) J. Mol. Biol , vol.296 , pp. 911-919
    • Russ, W.P.1    Engelman, D.M.2
  • 37
    • 34547131849 scopus 로고    scopus 로고
    • Specificity in transmembrane helix-helix interactions mediated by aromatic residues
    • Sal-Man,N. et al. (2007) Specificity in transmembrane helix-helix interactions mediated by aromatic residues. J. Biol. Chem., 282 19753-19761.
    • (2007) J. Biol. Chem , vol.282 , pp. 19753-19761
    • Sal-Man, N.1
  • 38
    • 0036700020 scopus 로고    scopus 로고
    • Quantifying the accessible surface area of protein residues in their local environment
    • Samanta,U. et al. (2002) Quantifying the accessible surface area of protein residues in their local environment. Protein Eng., 15, 659-667.
    • (2002) Protein Eng , vol.15 , pp. 659-667
    • Samanta, U.1
  • 39
    • 34548750953 scopus 로고    scopus 로고
    • Natively unstructured regions in proteins identified from contact predictions
    • Schlessinger,A. et al. (2007) Natively unstructured regions in proteins identified from contact predictions. Bioinformatics, 23, 2376-2384.
    • (2007) Bioinformatics , vol.23 , pp. 2376-2384
    • Schlessinger, A.1
  • 40
    • 36749031067 scopus 로고    scopus 로고
    • Contact prediction using mutual information and neural nets
    • Shackelford,G. and Karplus,K. (2007) Contact prediction using mutual information and neural nets. Proteins, 69 (Suppl 8), 159-164.
    • (2007) Proteins , vol.69 , Issue.SUPPL. 8 , pp. 159-164
    • Shackelford, G.1    Karplus, K.2
  • 41
    • 13444280419 scopus 로고    scopus 로고
    • PDB_TM: Selection and membrane localization of transmembrane proteins in the protein data bank
    • Tusnady,G.E. et al. (2005) PDB_TM: Selection and membrane localization of transmembrane proteins in the protein data bank. Nucleic Acids Res., 33, D275-D278.
    • (2005) Nucleic Acids Res , vol.33
    • Tusnady, G.E.1
  • 42
    • 38549172064 scopus 로고    scopus 로고
    • TOPDB: Topology data bank of transmembrane proteins
    • Tusnady,G.E. et al. (2008) TOPDB: Topology data bank of transmembrane proteins. Nucleic Acids Res., 36, D234-D239.
    • (2008) Nucleic Acids Res , vol.36
    • Tusnady, G.E.1
  • 43
    • 33748791763 scopus 로고    scopus 로고
    • Helix-packing motifs in membrane proteins
    • Walters,R.F. and DeGrado,W.F. (2006) Helix-packing motifs in membrane proteins. Proc. Natl Acad. Sci. USA, 103, 13658-13663.
    • (2006) Proc. Natl Acad. Sci. USA , vol.103 , pp. 13658-13663
    • Walters, R.F.1    DeGrado, W.F.2
  • 44
    • 34147130190 scopus 로고    scopus 로고
    • Computational design of peptides that target transmembrane helices
    • Yin,H. et al. (2007) Computational design of peptides that target transmembrane helices. Science, 315, 1817-1822.
    • (2007) Science , vol.315 , pp. 1817-1822
    • Yin, H.1
  • 45
    • 33646596891 scopus 로고    scopus 로고
    • Predicting the solvent accessibility of transmembrane residues from protein sequence
    • Yuan,Z. et al. (2006) Predicting the solvent accessibility of transmembrane residues from protein sequence. J. Proteome Res., 5, 1063-1070.
    • (2006) J. Proteome Res , vol.5 , pp. 1063-1070
    • Yuan, Z.1
  • 46
    • 0035956884 scopus 로고    scopus 로고
    • Polar residues drive association of polyleucine transmembrane helices
    • Zhou,F.X. et al. (2001) Polar residues drive association of polyleucine transmembrane helices. Proc. Natl Acad. Sci. USA, 98, 2250-2255.
    • (2001) Proc. Natl Acad. Sci. USA , vol.98 , pp. 2250-2255
    • Zhou, F.X.1


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.