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Volumn 95, Issue 11, 2008, Pages 5281-5295

α-helical topology prediction and generation of distance restraints in membrane proteins

Author keywords

[No Author keywords available]

Indexed keywords

MEMBRANE PROTEIN;

EID: 58149356273     PISSN: 00063495     EISSN: 15420086     Source Type: Journal    
DOI: 10.1529/biophysj.108.132241     Document Type: Article
Times cited : (13)

References (49)
  • 2
    • 0035109170 scopus 로고    scopus 로고
    • MPTopo: A database of membrane protein topology
    • Jayasinghe, S., K. Hristova, and S. H. White. 2000. MPTopo: a database of membrane protein topology. Protein Sci. 10:455-458.
    • (2000) Protein Sci , vol.10 , pp. 455-458
    • Jayasinghe, S.1    Hristova, K.2    White, S.H.3
  • 3
    • 61349097346 scopus 로고    scopus 로고
    • Predicting transmembrane protein topology with a hidden Markov model: Applications to complete genomes
    • Krogh, A., B. Larsson, G. von Heijne, and E. L. L. Sonnhammer. 2001. Predicting transmembrane protein topology with a hidden Markov model: applications to complete genomes. J. Mol. Biol. 157:105-132.
    • (2001) J. Mol. Biol , vol.157 , pp. 105-132
    • Krogh, A.1    Larsson, B.2    von Heijne, G.3    Sonnhammer, E.L.L.4
  • 4
    • 0031954925 scopus 로고    scopus 로고
    • Genome-wide analysis of integral membrane proteins from eubacterial, archaean, and eukaryotic organisms
    • Wallin, E., and G. von Heijne. 1998. Genome-wide analysis of integral membrane proteins from eubacterial, archaean, and eukaryotic organisms. Protein Sci. 7:1029-1038.
    • (1998) Protein Sci , vol.7 , pp. 1029-1038
    • Wallin, E.1    von Heijne, G.2
  • 6
    • 0028211273 scopus 로고
    • A model recognition approach to the prediction of all-helical membrane protein structure and topology
    • Jones, D. T., W. R. Taylor, and J. M. Thornton. 1994. A model recognition approach to the prediction of all-helical membrane protein structure and topology. Biochemistry. 33:3038-3049.
    • (1994) Biochemistry , vol.33 , pp. 3038-3049
    • Jones, D.T.1    Taylor, W.R.2    Thornton, J.M.3
  • 7
    • 0034899781 scopus 로고    scopus 로고
    • Evaluation of methods for the prediction of membrane spanning regions
    • Möller, S., M. D. R. Croning, and R. Apweiler. 2001. Evaluation of methods for the prediction of membrane spanning regions. Bioinformation. 17:646-653.
    • (2001) Bioinformation , vol.17 , pp. 646-653
    • Möller, S.1    Croning, M.D.R.2    Apweiler, R.3
  • 8
    • 0036132818 scopus 로고    scopus 로고
    • Transmembrane topology prediction methods: A reassessment and improvement by a consensus method using a dataset of experimentally characterized transmembrane topologies
    • Ikeda, M., M. Arai, D. M. Lao, and T. Shimizu. 2002. Transmembrane topology prediction methods: a reassessment and improvement by a consensus method using a dataset of experimentally characterized transmembrane topologies. In Silico Biol. 2:19-33.
    • (2002) In Silico Biol , vol.2 , pp. 19-33
    • Ikeda, M.1    Arai, M.2    Lao, D.M.3    Shimizu, T.4
  • 9
    • 3042579686 scopus 로고    scopus 로고
    • Best α-helical transmembrane protein topology predictions are achieved using hidden Markov models and evolutionary information
    • Viklund, H., and A. Elofsson. 2004. Best α-helical transmembrane protein topology predictions are achieved using hidden Markov models and evolutionary information. Protein Sci. 13:1908-1917.
    • (2004) Protein Sci , vol.13 , pp. 1908-1917
    • Viklund, H.1    Elofsson, A.2
  • 10
    • 9544252210 scopus 로고    scopus 로고
    • A hidden Markov model with molecular mechanics energy-scoring function for transmembrane helix prediction
    • Zheng, W. J., V. Z. Spassov, L. Yan, P. K. Flook, and S. Szalma. 2004. A hidden Markov model with molecular mechanics energy-scoring function for transmembrane helix prediction. Comput. Biol. Chem. 28:265-274.
    • (2004) Comput. Biol. Chem , vol.28 , pp. 265-274
    • Zheng, W.J.1    Spassov, V.Z.2    Yan, L.3    Flook, P.K.4    Szalma, S.5
  • 11
    • 1842789432 scopus 로고    scopus 로고
    • SVMtm: Support vector machines to predict transmembrane segments
    • Yuan, Z., J. S. Mattick, and R. D. Teasdale. 2004. SVMtm: support vector machines to predict transmembrane segments. J. Comput. Chem. 25:632-636.
    • (2004) J. Comput. Chem , vol.25 , pp. 632-636
    • Yuan, Z.1    Mattick, J.S.2    Teasdale, R.D.3
  • 12
    • 0842308529 scopus 로고    scopus 로고
    • ConPred-elite: A highly reliable approach to transmembrane topology prediction
    • Xia, J.-X., M. Ikeda, and T. Shimizu. 2004. ConPred-elite: a highly reliable approach to transmembrane topology prediction. Comput. Biol. Chem. 28:51-60.
    • (2004) Comput. Biol. Chem , vol.28 , pp. 51-60
    • Xia, J.-X.1    Ikeda, M.2    Shimizu, T.3
  • 13
    • 0032406838 scopus 로고    scopus 로고
    • Statistical analysis of predicted transmembrane α-helices
    • Arkin, I. T., and A. T. Brunger. 1998. Statistical analysis of predicted transmembrane α-helices. Biochim. Biophys. Acta. 1429:113-128.
    • (1998) Biochim. Biophys. Acta , vol.1429 , pp. 113-128
    • Arkin, I.T.1    Brunger, A.T.2
  • 15
    • 0036226583 scopus 로고    scopus 로고
    • Comparison of helix interactions in membrane and soluble α-bundle proteins
    • Eilers, M., A. B. Patel, W. Liu, and S. O. Smith. 2002. Comparison of helix interactions in membrane and soluble α-bundle proteins. Biophys. J. 82:2720-2736.
    • (2002) Biophys. J , vol.82 , pp. 2720-2736
    • Eilers, M.1    Patel, A.B.2    Liu, W.3    Smith, S.O.4
  • 16
    • 0035943429 scopus 로고    scopus 로고
    • Helix-helix packing and interfacial pairwise interactions of residues in membrane proteins
    • Adamian, L., and J. Liang. 2001. Helix-helix packing and interfacial pairwise interactions of residues in membrane proteins. J. Mol. Biol. 311:891-907.
    • (2001) J. Mol. Biol , vol.311 , pp. 891-907
    • Adamian, L.1    Liang, J.2
  • 17
    • 0031563818 scopus 로고    scopus 로고
    • Helix packing in membrane proteins
    • Bowie, J. 1997. Helix packing in membrane proteins. J. Mol. Biol. 272:780-789.
    • (1997) J. Mol. Biol , vol.272 , pp. 780-789
    • Bowie, J.1
  • 18
    • 0037436390 scopus 로고    scopus 로고
    • Higher-order interhelical spatial interactions in membrane proteins
    • Adamian, L., R. Jackups, Jr., T. A. Binkowski, and J. Liang. 2003. Higher-order interhelical spatial interactions in membrane proteins. J. Mol. Biol. 327:251-272.
    • (2003) J. Mol. Biol , vol.327 , pp. 251-272
    • Adamian, L.1    Jackups Jr., R.2    Binkowski, T.A.3    Liang, J.4
  • 19
    • 10044249042 scopus 로고    scopus 로고
    • Helical packing patterns in membrane and soluble proteins
    • Gimpelev, M., L. R. Forrest, D. Murray, and B. Honig. 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    Forrest, L.R.2    Murray, D.3    Honig, B.4
  • 20
    • 38549107644 scopus 로고    scopus 로고
    • Predicting transmembrane helix pair configurations with knowledge-based distance-dependent pair potentials
    • Wendel, C., and H. Gohlke. 2008. Predicting transmembrane helix pair configurations with knowledge-based distance-dependent pair potentials. Prot. Struct. Funct. Bioinf. 70:984-999.
    • (2008) Prot. Struct. Funct. Bioinf , vol.70 , pp. 984-999
    • Wendel, C.1    Gohlke, H.2
  • 21
    • 17744373462 scopus 로고    scopus 로고
    • Modeling and predicting all-a transmembrane proteins including helix-helix pairing
    • Waldispül, J., and J.-M. Steyaert. 2005. Modeling and predicting all-a transmembrane proteins including helix-helix pairing. Theor. Comput. Sci. 335:67-92.
    • (2005) Theor. Comput. Sci , vol.335 , pp. 67-92
    • Waldispül, J.1    Steyaert, J.-M.2
  • 22
    • 0042844582 scopus 로고    scopus 로고
    • Exploring the conformational space of membrane protein folds matching distance constraints
    • Faulon, J.-L., K. Sale, and M. Young. 2003. Exploring the conformational space of membrane protein folds matching distance constraints. Protein Sci. 12:1750-1761.
    • (2003) Protein Sci , vol.12 , pp. 1750-1761
    • Faulon, J.-L.1    Sale, K.2    Young, M.3
  • 23
    • 4644322798 scopus 로고    scopus 로고
    • Optimal bundling of transmembrane helices using sparse distance constraints
    • Sale, K., J.-L. Faulon, G. A. Gray, J. S. Schoeniger, and M. Young. 2004. Optimal bundling of transmembrane helices using sparse distance constraints. Protein Sci. 13:2613-2627.
    • (2004) Protein Sci , vol.13 , pp. 2613-2627
    • Sale, K.1    Faulon, J.-L.2    Gray, G.A.3    Schoeniger, J.S.4    Young, M.5
  • 24
    • 0037339560 scopus 로고    scopus 로고
    • Computer simulations of membrane protein folding: Structure and dynamics
    • Chen, C.-M., and C.-C. Chen. 2003. Computer simulations of membrane protein folding: structure and dynamics. Biophys. J. 84:1902-1908.
    • (2003) Biophys. J , vol.84 , pp. 1902-1908
    • Chen, C.-M.1    Chen, C.-C.2
  • 25
    • 0025249842 scopus 로고
    • Membrane protein folding and oligomerization-the two-stage model
    • Popot, J.-L., and D. M. Engelman. 1990. Membrane protein folding and oligomerization-the two-stage model. Biochemistry. 29:4031-4037.
    • (1990) Biochemistry , vol.29 , pp. 4031-4037
    • Popot, J.-L.1    Engelman, D.M.2
  • 26
    • 0032987478 scopus 로고    scopus 로고
    • Membrane protein folding and stability: Physical principles
    • White, S. H., and W. C. Wimley. 1999. Membrane protein folding and stability: physical principles. Annu. Rev. Biophys. Biomol. Struct. 28:319-365.
    • (1999) Annu. Rev. Biophys. Biomol. Struct , vol.28 , pp. 319-365
    • White, S.H.1    Wimley, W.C.2
  • 28
    • 0038458865 scopus 로고    scopus 로고
    • Modeling the 3D structure of GPCRs: Advances and application to drug discovery
    • Becker, O. M., S. Shacham, Y. Marantz, and S. Noiman. 2003. Modeling the 3D structure of GPCRs: advances and application to drug discovery. Curr. Opin. Drug Discov. Devel. 6:353-361.
    • (2003) Curr. Opin. Drug Discov. Devel , vol.6 , pp. 353-361
    • Becker, O.M.1    Shacham, S.2    Marantz, Y.3    Noiman, S.4
  • 30
    • 0038730774 scopus 로고    scopus 로고
    • A simple method for modeling transmembrane helix oligomers
    • Kim, S., A. K. Chamberlain, and J. U. Bowie. 2003. A simple method for modeling transmembrane helix oligomers. J. Mol. Biol. 329:831-840.
    • (2003) J. Mol. Biol , vol.329 , pp. 831-840
    • Kim, S.1    Chamberlain, A.K.2    Bowie, J.U.3
  • 31
    • 0036382758 scopus 로고    scopus 로고
    • Conformations of tightly packed pairs of transmembrane α-helices
    • Fleishman, S. J., and N. Ben-Tal. 2002. Conformations of tightly packed pairs of transmembrane α-helices. J. Mol. Biol. 321:363-378.
    • (2002) J. Mol. Biol , vol.321 , pp. 363-378
    • Fleishman, S.J.1    Ben-Tal, N.2
  • 32
    • 33645793799 scopus 로고    scopus 로고
    • Structure modeling of all identified G protein-coupled receptors in the human genome
    • Zhang, Y., M. E. Devries, and J. Skolnick. 2006. Structure modeling of all identified G protein-coupled receptors in the human genome. PLoS Comput. Biol. 2:e13.
    • (2006) PLoS Comput. Biol , vol.2
    • Zhang, Y.1    Devries, M.E.2    Skolnick, J.3
  • 33
    • 0043180474 scopus 로고    scopus 로고
    • PISCES: A protein sequence culling server
    • Wang, G., and R. L. Dunbrack. 2003. PISCES: a protein sequence culling server. Bioinformation. 19:1589-1591.
    • (2003) Bioinformation , vol.19 , pp. 1589-1591
    • Wang, G.1    Dunbrack, R.L.2
  • 34
    • 0033983453 scopus 로고    scopus 로고
    • Asparagine mediate self-association of a model transmembrane helix
    • Choma, C., H. Gratkowski, J. D. Lear, and W. F. DeGrado. 2000. Asparagine mediate self-association of a model transmembrane helix. Nat. Struct. Biol. 7:161-166.
    • (2000) Nat. Struct. Biol , vol.7 , pp. 161-166
    • Choma, C.1    Gratkowski, H.2    Lear, J.D.3    DeGrado, W.F.4
  • 35
    • 0007949690 scopus 로고    scopus 로고
    • Interhelical hydrogen bonding drives strong interactions in membrane proteins
    • Zhou, F. X., M. J. Cocco, W. P. Russ, A. T. Brunger, and D. M. Engelman. 2000. Interhelical hydrogen bonding drives strong interactions in membrane proteins. Nat. Struct. Biol. 7:154-160.
    • (2000) Nat. Struct. Biol , vol.7 , pp. 154-160
    • Zhou, F.X.1    Cocco, M.J.2    Russ, W.P.3    Brunger, A.T.4    Engelman, D.M.5
  • 36
    • 0025906146 scopus 로고
    • Contribution to the thermodynamics of protein folding from the reduction in water-accessible nonpolar surface area
    • Livingstone, J. R., R. S. Spolar, and M. T. Record, Jr. 1991. Contribution to the thermodynamics of protein folding from the reduction in water-accessible nonpolar surface area. Biochemistry. 30:4237-4244.
    • (1991) Biochemistry , vol.30 , pp. 4237-4244
    • Livingstone, J.R.1    Spolar, R.S.2    Record Jr., M.T.3
  • 37
    • 33751087497 scopus 로고    scopus 로고
    • A novel approach for α-helical topology prediction in globular proteins: Generation of interhelical restraints
    • McAllister, S. R., B. E. Mickus, J. L. Klepeis, and C. A. Floudas. 2006. A novel approach for α-helical topology prediction in globular proteins: generation of interhelical restraints. Prot. Struct. Funct. Bioinf. 65:930-952.
    • (2006) Prot. Struct. Funct. Bioinf , vol.65 , pp. 930-952
    • McAllister, S.R.1    Mickus, B.E.2    Klepeis, J.L.3    Floudas, C.A.4
  • 40
    • 85031354005 scopus 로고    scopus 로고
    • ILOG. 2003. CPLEX User's Manual 9.0. ILOG, Sunnyvale, CA and Genilly, France.
    • ILOG. 2003. CPLEX User's Manual 9.0. ILOG, Sunnyvale, CA and Genilly, France.
  • 41
    • 85031365522 scopus 로고    scopus 로고
    • Dash Optimization. 2003. Xpress-MP: Getting Started. Dash Optimization, Englewood Cliffs, NJ.
    • Dash Optimization. 2003. Xpress-MP: Getting Started. Dash Optimization, Englewood Cliffs, NJ.
  • 44
    • 4344581120 scopus 로고    scopus 로고
    • The retinal conformation and its environment in rhodopsin in light of a new 2.2 Å crystal structure
    • Okada, T., M. Sugihara, A.-N. Bondar, M. Elstner, P. Entel, and V. Buss. 2004. The retinal conformation and its environment in rhodopsin in light of a new 2.2 Å crystal structure. J. Mol. Biol. 342:571-583.
    • (2004) J. Mol. Biol , vol.342 , pp. 571-583
    • Okada, T.1    Sugihara, M.2    Bondar, A.-N.3    Elstner, M.4    Entel, P.5    Buss, V.6
  • 49
    • 85031354928 scopus 로고    scopus 로고
    • DeLano Scientific, Palo Alto, CA
    • DeLano, W. L. 2002. The PyMol Molecular Graphics System. DeLano Scientific, Palo Alto, CA. http://www.pymol.org.
    • (2002)
    • DeLano, W.L.1


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