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Volumn 26, Issue 10, 2012, Pages 1171-1185

Statistical analyses and computational prediction of helical kinks in membrane proteins

Author keywords

Computational prediction; Helical kinks; Molecular dynamics simulations

Indexed keywords

CLUSTERING ALGORITHMS; COMPUTATIONAL CHEMISTRY; CRYSTAL STRUCTURE; FORECASTING; HYDROGEN BONDS; PROTEINS; STATISTICAL METHODS;

EID: 84869495285     PISSN: 0920654X     EISSN: 15734951     Source Type: Journal    
DOI: 10.1007/s10822-012-9607-5     Document Type: Article
Times cited : (12)

References (46)
  • 1
    • 0032987478 scopus 로고    scopus 로고
    • Membrane protein folding and stability: Physical principles
    • White SH, Wimley WC (1999) Membrane protein folding and stability: physical principles. Annu Rev Bioph Biomol Struct 28:319-365
    • (1999) Annu Rev Bioph Biomol Struct , vol.28 , pp. 319-365
    • White, S.H.1    Wimley, W.C.2
  • 2
    • 0034677966 scopus 로고    scopus 로고
    • Drug discovery: A historical perspective
    • Drews J (2000) Drug discovery: a historical perspective. Science 287(5460):1960-1964
    • (2000) Science , vol.287 , Issue.5460 , pp. 1960-1964
    • Drews, J.1
  • 3
    • 33845890639 scopus 로고    scopus 로고
    • It's a GPCR world
    • Filmore D (2004) It's a GPCR world. Mod Drug Discov 7:24-26
    • (2004) Mod Drug Discov , vol.7 , pp. 24-26
    • Filmore, D.1
  • 4
    • 28444488355 scopus 로고    scopus 로고
    • Solving the membrane protein folding problem
    • doi:10.1038/nature04395
    • Bowie JU (2005) Solving the membrane protein folding problem. Nature 438(7068):581-589. doi:10.1038/nature04395
    • (2005) Nature , vol.438 , Issue.7068 , pp. 581-589
    • Bowie, J.U.1
  • 5
    • 0026661869 scopus 로고
    • Spontaneous insertion of polypeptidechains into membranes - A Monte-Carlo model
    • Milik M, Skolnick J (1992) Spontaneous insertion of polypeptidechains into membranes - a Monte-Carlo model. Proc Natl Acad Sci USA 89(20):9391-9395
    • (1992) Proc Natl Acad Sci USA , vol.89 , Issue.20 , pp. 9391-9395
    • Milik, M.1    Skolnick, J.2
  • 6
    • 4243379922 scopus 로고    scopus 로고
    • Lattice model of transmembrane polypeptide folding
    • Chen CM (2001) Lattice model of transmembrane polypeptide folding. Phys Rev E 63(1):010901
    • (2001) Phys Rev e , vol.63 , Issue.1 , pp. 010901
    • Chen, C.M.1
  • 7
    • 0034718560 scopus 로고    scopus 로고
    • Molecular mechanisms underlying differential odor responses of a mouse olfactory receptor
    • Floriano WB, Vaidehi N, Goddard WA, Singer MS, Shepherd GM (2000) Molecular mechanisms underlying differential odor responses of a mouse olfactory receptor. Proc Natl Acad Sci USA 97(20):10712-10716
    • (2000) Proc Natl Acad Sci USA , vol.97 , Issue.20 , pp. 10712-10716
    • Floriano, W.B.1    Vaidehi, N.2    Goddard, W.A.3    Singer, M.S.4    Shepherd, G.M.5
  • 8
    • 0037110551 scopus 로고    scopus 로고
    • Optimal potentials for predicting inter-helical packing in transmembrane proteins
    • doi:10.1002/prot.10229
    • Dobbs H, Orlandini E, Bonaccini R, Seno F (2002) Optimal potentials for predicting inter-helical packing in transmembrane proteins. Proteins 49(3):342-349. doi:10.1002/prot.10229
    • (2002) Proteins , vol.49 , Issue.3 , pp. 342-349
    • Dobbs, H.1    Orlandini, E.2    Bonaccini, R.3    Seno, F.4
  • 9
    • 0037339560 scopus 로고    scopus 로고
    • Computer Simulations of membrane protein folding: Structure and dynamics
    • Chen CM, Chen CC (2003) Computer Simulations of membrane protein folding: structure and dynamics. Biophys J 84(3):1902- 1908
    • (2003) Biophys J , vol.84 , Issue.3 , pp. 1902-1908
    • Chen, C.M.1    Chen, C.C.2
  • 10
    • 2942639959 scopus 로고    scopus 로고
    • Self-assembly of transmembrane helices of bacteriorhodopsin by a replica-exchange Monte Carlo simulation
    • -):. doi:10.1016/j. cplett.2004.04.112
    • Kokubo H, Okamoto Y (2004) Self-assembly of transmembrane helices of bacteriorhodopsin by a replica-exchange Monte Carlo simulation. Chem Phys Lett 392(1-3):168-175. doi:10.1016/j. cplett.2004.04.112
    • (2004) Chem Phys Lett , vol.392 , Issue.1-3 , pp. 168-175
    • Kokubo, H.1    Okamoto, Y.2
  • 11
    • 57149146836 scopus 로고    scopus 로고
    • A dual-scale approach toward structure prediction of retinal proteins
    • doi:10.1016/j.jsb.2008.10.001
    • Chen CC, Chen CM (2009) A dual-scale approach toward structure prediction of retinal proteins. J Struct Biol 165(1): 37-46. doi:10.1016/j.jsb.2008.10.001
    • (2009) J Struct Biol , vol.165 , Issue.1 , pp. 37-46
    • Chen, C.C.1    Chen, C.M.2
  • 12
    • 42649115134 scopus 로고    scopus 로고
    • Packing of transmembrane helices in bacteriorhodopsin folding: Structure and thermodynamics
    • doi:10.1016/ j.jsb.2008.01.003
    • Chen CC, Wei CC, Sun YC, Chen CM (2008) Packing of transmembrane helices in bacteriorhodopsin folding: structure and thermodynamics. J Struct Biol 162(2):237-247. doi:10.1016/ j.jsb.2008.01.003
    • (2008) J Struct Biol , vol.162 , Issue.2 , pp. 237-247
    • Chen, C.C.1    Wei, C.C.2    Sun, Y.C.3    Chen, C.M.4
  • 13
    • 0024290472 scopus 로고
    • Amino acid preferences for specific locations at the ends of alpha helices
    • Richardson JS, Richardson DC (1988) Amino acid preferences for specific locations at the ends of alpha helices. Science 240(4859):1648-1652
    • (1988) Science , vol.240 , Issue.4859 , pp. 1648-1652
    • Richardson, J.S.1    Richardson, D.C.2
  • 15
    • 1842866228 scopus 로고    scopus 로고
    • Proline residues in transmembrane segment IV are critical for activity, expression and targeting of the Na+/H+ exchanger isoform 1
    • Pt ):. doi:10.1042/BJ20030884
    • Slepkov ER, Chow S, Lemieux MJ, Fliegel L (2004) Proline residues in transmembrane segment IV are critical for activity, expression and targeting of the Na+/H+ exchanger isoform 1. Biochem J 379(Pt 1):31-38. doi:10.1042/ BJ20030884
    • (2004) Biochem J , vol.379 , Issue.1 , pp. 31-38
    • Slepkov, E.R.1    Chow, S.2    Lemieux, M.J.3    Fliegel, L.4
  • 16
    • 0036343993 scopus 로고    scopus 로고
    • Conformational dynamics of helix S6 from Shaker potassium channel: Simulation studies
    • doi:10.1002/ bip.10197
    • Bright JN, Shrivastava IH, Cordes FS, Sansom MS (2002) Conformational dynamics of helix S6 from Shaker potassium channel: simulation studies. Biopolymers 64(6):303-313. doi:10.1002/ bip.10197
    • (2002) Biopolymers , vol.64 , Issue.6 , pp. 303-313
    • Bright, J.N.1    Shrivastava, I.H.2    Cordes, F.S.3    Sansom, M.S.4
  • 18
    • 33344465109 scopus 로고    scopus 로고
    • Amino acid propensities for secondary structures are influenced by the protein structural class
    • doi:10.1016/j.bbrc.2006.01.159
    • Costantini S, Colonna G, Facchiano AM (2006) Amino acid propensities for secondary structures are influenced by the protein structural class. Biochem Biophys Res Commun 342(2):441-451. doi:10.1016/j.bbrc.2006.01.159
    • (2006) Biochem Biophys Res Commun , vol.342 , Issue.2 , pp. 441-451
    • Costantini, S.1    Colonna, G.2    Facchiano, A.M.3
  • 19
    • 0035895421 scopus 로고    scopus 로고
    • Non-alphahelical elements modulate polytopic membrane protein architecture
    • doi:10.1006/jmbi.2000.4402
    • Riek RP, Rigoutsos I, Novotny J, Graham RM (2001) Non-alphahelical elements modulate polytopic membrane protein architecture. J Mol Biol 306(2):349-362. doi:10.1006/jmbi.2000.4402
    • (2001) J Mol Biol , vol.306 , Issue.2 , pp. 349-362
    • Riek, R.P.1    Rigoutsos, I.2    Novotny, J.3    Graham, R.M.4
  • 20
    • 67349266230 scopus 로고    scopus 로고
    • Position of helical kinks in membrane protein crystal structures and the accuracy of computational prediction
    • doi:10.1016/j.jmgm.2009.02.004
    • Hall SE, Roberts K, Vaidehi N (2009) Position of helical kinks in membrane protein crystal structures and the accuracy of computational prediction. J Mol Graph Model 27(8):944-950. doi:10.1016/j.jmgm.2009.02.004
    • (2009) J Mol Graph Model , vol.27 , Issue.8 , pp. 944-950
    • Hall, S.E.1    Roberts, K.2    Vaidehi, N.3
  • 21
    • 0742288411 scopus 로고    scopus 로고
    • The evolution of transmembrane helix kinks and the structural diversity of G protein-coupled receptors
    • doi:10.1073/pnas.0306077101
    • Yohannan S, Faham S, Yang D, Whitelegge JP, Bowie JU (2004) The evolution of transmembrane helix kinks and the structural diversity of G protein-coupled receptors. Proc Natl Acad Sci USA 101(4):959-963. doi:10.1073/pnas.0306077101
    • (2004) Proc Natl Acad Sci USA , vol.101 , Issue.4 , pp. 959-963
    • Yohannan, S.1    Faham, S.2    Yang, D.3    Whitelegge, J.P.4    Bowie, J.U.5
  • 22
    • 84861434240 scopus 로고    scopus 로고
    • Shifting hydrogen bonds may produce flexible transmembrane helices
    • doi:10.1073/pnas.1201298109
    • Cao Z, Bowie JU (2012) Shifting hydrogen bonds may produce flexible transmembrane helices. Proc Natl Acad Sci USA 109(21):8121-8126. doi:10.1073/pnas.1201298109
    • (2012) Proc Natl Acad Sci USA , vol.109 , Issue.21 , pp. 8121-8126
    • Cao, Z.1    Bowie, J.U.2
  • 23
    • 78650702465 scopus 로고    scopus 로고
    • Improved helix and kink characterization in membrane proteins allows evaluation of kink sequence predictors
    • doi:10.1021/ci100324n
    • Langelaan DN, Wieczorek M, Blouin C, Rainey JK (2010) Improved helix and kink characterization in membrane proteins allows evaluation of kink sequence predictors. J Chem Inf Model 50(12):2213-2220. doi:10.1021/ci100324n
    • (2010) J Chem Inf Model , vol.50 , Issue.12 , pp. 2213-2220
    • Langelaan, D.N.1    Wieczorek, M.2    Blouin, C.3    Rainey, J.K.4
  • 24
    • 79959336987 scopus 로고    scopus 로고
    • TMKink: A method to predict transmembrane helix kinks
    • doi:10.1002/pro.653
    • Meruelo AD, Samish I, Bowie JU (2011) TMKink: a method to predict transmembrane helix kinks. Protein Sci 20(7):1256-1264. doi:10.1002/pro.653
    • (2011) Protein Sci , vol.20 , Issue.7 , pp. 1256-1264
    • Meruelo, A.D.1    Samish, I.2    Bowie, J.U.3
  • 25
    • 82355168443 scopus 로고    scopus 로고
    • String kernels and high-quality data set for improved prediction of kinked helices in alpha-helical membrane proteins
    • doi:10.1021/ci200278w
    • Kneissl B, Mueller SC, Tautermann CS, Hildebrandt A (2011) String kernels and high-quality data set for improved prediction of kinked helices in alpha-helical membrane proteins. J Chem Inf Model 51(11):3017-3025. doi:10.1021/ci200278w
    • (2011) J Chem Inf Model , vol.51 , Issue.11 , pp. 3017-3025
    • Kneissl, B.1    Mueller, S.C.2    Tautermann, C.S.3    Hildebrandt, A.4
  • 26
    • 84863106674 scopus 로고    scopus 로고
    • Replica exchange Monte- Carlo simulations of helix bundle membrane proteins: Rotational parameters of helices
    • doi:10.1007/s10822-012-9562-1
    • Wu HH, Chen CC, Chen CM (2012) Replica exchange Monte- Carlo simulations of helix bundle membrane proteins: rotational parameters of helices. J Comput Aided Mol Des 26(3):363-374. doi:10.1007/s10822-012-9562-1
    • (2012) J Comput Aided Mol des , vol.26 , Issue.3 , pp. 363-374
    • Wu, H.H.1    Chen, C.C.2    Chen, C.M.3
  • 27
    • 0043180474 scopus 로고    scopus 로고
    • PISCES: A protein sequence culling server
    • Wang G, Dunbrack RL Jr (2003) PISCES: a protein sequence culling server. Bioinformatics 19(12):1589-1591
    • (2003) Bioinformatics , vol.19 , Issue.12 , pp. 1589-1591
    • Wang, G.1    Dunbrack Jr., R.L.2
  • 28
    • 10944245838 scopus 로고    scopus 로고
    • A method for structural analysis of alpha-helices of membrane proteins
    • -):. doi:10.1007/s00894-004-0212-y
    • Mohapatra PK, Khamari A, Raval MK (2004) A method for structural analysis of alpha-helices of membrane proteins. J Mol Model 10(5-6):393-398. doi:10.1007/s00894-004-0212-y
    • (2004) J Mol Model , vol.10 , Issue.5-6 , pp. 393-398
    • Mohapatra, P.K.1    Khamari, A.2    Raval, M.K.3
  • 30
    • 22544450619 scopus 로고
    • Molecular dynamics study of a membrane-water interface
    • Zhou F, Schulten K (1995) Molecular dynamics study of a membrane-water interface. J Phys Chem 99(7):2194-2207
    • (1995) J Phys Chem , vol.99 , Issue.7 , pp. 2194-2207
    • Zhou, F.1    Schulten, K.2
  • 31
    • 0025310046 scopus 로고
    • Electrical modulation of membrane proteins: Enforced conformational oscillations and biological energy and signal transductions
    • doi:10.1146/annurev.bb.19.060190.000503
    • Tsong TY (1990) Electrical modulation of membrane proteins: enforced conformational oscillations and biological energy and signal transductions. Annu Rev Biophys Biophys Chem 19:83-106. doi:10.1146/annurev.bb.19.060190.000503
    • (1990) Annu Rev Biophys Biophys Chem , vol.19 , pp. 83-106
    • Tsong, T.Y.1
  • 32
    • 17144410761 scopus 로고    scopus 로고
    • Thermostat algorithms for molecular dynamics simulations
    • doi: 10.1007/B99427
    • Hunenberger P (2005) Thermostat algorithms for molecular dynamics simulations. Adv Polym Sci 173:105-147. doi: 10.1007/B99427
    • (2005) Adv Polym Sci , vol.173 , pp. 105-147
    • Hunenberger, P.1
  • 33
    • 1942519275 scopus 로고    scopus 로고
    • SPICKER: A clustering approach to identify near-native protein folds
    • Zhang Y, Skolnick J (2004) SPICKER: a clustering approach to identify near-native protein folds. J Comput Chem 25(6):865-871
    • (2004) J Comput Chem , vol.25 , Issue.6 , pp. 865-871
    • Zhang, Y.1    Skolnick, J.2
  • 34
    • 0015859467 scopus 로고
    • Principles that govern the folding of protein chains
    • Anfinsen CB (1973) Principles that govern the folding of protein chains. Science 181(96):223-230
    • (1973) Science , vol.181 , Issue.96 , pp. 223-230
    • Anfinsen, C.B.1
  • 35
    • 0032530578 scopus 로고    scopus 로고
    • Clustering of low-energy conformations near the native structures of small proteins
    • Shortle D, Simons KT, Baker D (1998) Clustering of low-energy conformations near the native structures of small proteins. Proc Natl Acad Sci USA 95(19):11158-11162
    • (1998) Proc Natl Acad Sci USA , vol.95 , Issue.19 , pp. 11158-11162
    • Shortle, D.1    Simons, K.T.2    Baker, D.3
  • 36
    • 0032552880 scopus 로고    scopus 로고
    • The preference of tryptophan for membrane interfaces
    • doi:10.1021/bi980809c
    • Yau WM, Wimley WC, Gawrisch K, White SH (1998) The preference of tryptophan for membrane interfaces. Biochemistry 37(42):14713-14718. doi:10.1021/bi980809c
    • (1998) Biochemistry , vol.37 , Issue.42 , pp. 14713-14718
    • Yau, W.M.1    Wimley, W.C.2    Gawrisch, K.3    White, S.H.4
  • 37
    • 0032817780 scopus 로고    scopus 로고
    • Helix packing in polytopic membrane proteins: Role of glycine in transmembrane helix association
    • doi:10.1016/S0006-3495(99)77009-8
    • Javadpour MM, Eilers M, Groesbeek M, Smith SO (1999) Helix packing in polytopic membrane proteins: role of glycine in transmembrane helix association. Biophys J 77(3):1609-1618. doi:10.1016/S0006-3495(99)77009-8
    • (1999) Biophys J , vol.77 , Issue.3 , pp. 1609-1618
    • Javadpour, M.M.1    Eilers, M.2    Groesbeek, M.3    Smith, S.O.4
  • 38
    • 77955984919 scopus 로고    scopus 로고
    • Internally bridging water molecule in transmembrane alpha-helical kink
    • doi:10.1016/j.sbi.2010. 05.008
    • Miyano M, Ago H, Saino H, Hori T, Ida K (2010) Internally bridging water molecule in transmembrane alpha-helical kink. Curr Opin Struct Biol 20(4):456-463. doi:10.1016/j.sbi.2010. 05.008
    • (2010) Curr Opin Struct Biol , vol.20 , Issue.4 , pp. 456-463
    • Miyano, M.1    Ago, H.2    Saino, H.3    Hori, T.4    Ida, K.5
  • 39
    • 0030983047 scopus 로고    scopus 로고
    • Architecture of helix bundle membrane proteins: An analysis of cytochrome c oxidase from bovine mitochondria
    • doi:10.1002/pro.5560060407
    • Wallin E, Tsukihara T, Yoshikawa S, von Heijne G, Elofsson A (1997) Architecture of helix bundle membrane proteins: an analysis of cytochrome c oxidase from bovine mitochondria. Protein Sci 6(4):808-815. doi:10.1002/pro. 5560060407
    • (1997) Protein Sci , vol.6 , Issue.4 , pp. 808-815
    • Wallin, E.1    Tsukihara, T.2    Yoshikawa, S.3    Von Heijne, G.4    Elofsson, A.5
  • 40
    • 80755133615 scopus 로고    scopus 로고
    • Classification and visualization of the social science network by the minimum span clustering method
    • doi: 10.1002/Asi.21634
    • Chang YF, Chen CM (2011) Classification and visualization of the social science network by the minimum span clustering method. J Am Soc Inform Sci Technol 62(12):2404-2413. doi: 10.1002/Asi.21634
    • (2011) J Am Soc Inform Sci Technol , vol.62 , Issue.12 , pp. 2404-2413
    • Chang, Y.F.1    Chen, C.M.2
  • 41
    • 17644392830 scopus 로고    scopus 로고
    • TM-align: A protein structure alignment algorithm based on the TM-score
    • doi:10.1093/nar/gki524
    • Zhang Y, Skolnick J (2005) TM-align: a protein structure alignment algorithm based on the TM-score. Nucleic Acids Res 33(7):2302-2309. doi:10.1093/nar/gki524
    • (2005) Nucleic Acids Res , vol.33 , Issue.7 , pp. 2302-2309
    • Zhang, Y.1    Skolnick, J.2
  • 42
    • 0033670439 scopus 로고    scopus 로고
    • MaxSub: An automated measure for the assessment of protein structure prediction quality
    • Siew N, Elofsson A, Rychlewski L, Fischer D (2000) MaxSub: an automated measure for the assessment of protein structure prediction quality. Bioinformatics 16(9):776-785
    • (2000) Bioinformatics , vol.16 , Issue.9 , pp. 776-785
    • Siew, N.1    Elofsson, A.2    Rychlewski, L.3    Fischer, D.4
  • 43
    • 0042622381 scopus 로고    scopus 로고
    • LGA: A method for finding 3D similarities in protein structures
    • Zemla A (2003) LGA: a method for finding 3D similarities in protein structures. Nucleic Acids Res 31(13):3370-3374
    • (2003) Nucleic Acids Res , vol.31 , Issue.13 , pp. 3370-3374
    • Zemla, A.1
  • 44
    • 0025249842 scopus 로고
    • Membrane protein folding and oligomerization: The two-stage model
    • Popot JL, Engelman DM (1990) Membrane protein folding and oligomerization: the two-stage model. Biochemistry 29(17): 4031-4037
    • (1990) Biochemistry , vol.29 , Issue.17 , pp. 4031-4037
    • Popot, J.L.1    Engelman, D.M.2
  • 45
    • 0026642866 scopus 로고
    • Bacteriorhodopsin can be refolded from two independently stable transmembrane helices and the complementary five-helix fragment
    • Kahn TW, Engelman DM (1992) Bacteriorhodopsin can be refolded from two independently stable transmembrane helices and the complementary five-helix fragment. Biochemistry 31(26):6144-6151
    • (1992) Biochemistry , vol.31 , Issue.26 , pp. 6144-6151
    • Kahn, T.W.1    Engelman, D.M.2
  • 46
    • 0030003278 scopus 로고    scopus 로고
    • Co assembly of synthetic segments of shaker K+ channel within phospholipid membranes
    • doi: 10.1021/bi952988t
    • Peled-Zehavi H, Arkin IT, Engelman DM, Shai Y (1996) Co assembly of synthetic segments of shaker K+ channel within phospholipid membranes. Biochemistry 35(21):6828-6838. doi: 10.1021/bi952988t
    • (1996) Biochemistry , vol.35 , Issue.21 , pp. 6828-6838
    • Peled-Zehavi, H.1    Arkin, I.T.2    Engelman, D.M.3    Shai, Y.4


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