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Volumn 5, Issue 6, 2010, Pages

Hydrophilicity matching - A potential prerequisite for the formation of protein-protein complexes in the cell

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; BINDING SITE; CELL TRANSPORT; CYTOPLASM; DEPENDENT VARIABLE; DOCKGROUND; ENERGY TRANSFER; HYDRATION; HYDROPHILICITY; INTRACELLULAR SPACE; PHYSICAL CHEMISTRY; PROTEIN DATABASE; PROTEIN LOCALIZATION; PROTEIN PROTEIN INTERACTION; PROTEIN STRUCTURE;

EID: 77955288869     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0011169     Document Type: Article
Times cited : (6)

References (34)
  • 3
    • 56349130674 scopus 로고    scopus 로고
    • Towards quantitative predictions in cell biology using chemical properties of proteins
    • Vendruscolo M, Tartaglia GG (2008) Towards quantitative predictions in cell biology using chemical properties of proteins. Mol Biosyst 4: 1170-1175.
    • (2008) Mol Biosyst , vol.4 , pp. 1170-1175
    • Vendruscolo, M.1    Tartaglia, G.G.2
  • 4
    • 63149130741 scopus 로고    scopus 로고
    • Bimodal protein solubility distribution revealed by an aggregation analysis of the entire ensemble of Escherichia coli proteins
    • Niwa T, Ying BW, Saito K, Jin W, Takada S, et al. (2009) Bimodal protein solubility distribution revealed by an aggregation analysis of the entire ensemble of Escherichia coli proteins. Proc Natl Acad Sci USA 106: 4201-4206.
    • (2009) Proc Natl Acad Sci USA , vol.106 , pp. 4201-4206
    • Niwa, T.1    Ying, B.W.2    Saito, K.3    Jin, W.4    Takada, S.5
  • 6
    • 43849103490 scopus 로고    scopus 로고
    • Coarse-grained molecular simulation of diffusion and reaction kinetics in a crowded virtual cytoplasm
    • Ridgway D, Broderick G, Lopez-Campistrous A, Ru'aini M, Winter P, et al. (2008) Coarse-grained molecular simulation of diffusion and reaction kinetics in a crowded virtual cytoplasm. Biophys J 94: 3748-3759.
    • (2008) Biophys J , vol.94 , pp. 3748-3759
    • Ridgway, D.1    Broderick, G.2    Lopez-Campistrous, A.3    Ru'aini, M.4    Winter, P.5
  • 7
    • 58149360317 scopus 로고    scopus 로고
    • Influence of macromolecular crowding on protein-protein association rates - a Brownian dynamics study
    • Wieczorek G, Zielenkiewicz P (2008) Influence of macromolecular crowding on protein-protein association rates - a Brownian dynamics study. Biophys J 95: 5030-5036.
    • (2008) Biophys J , vol.95 , pp. 5030-5036
    • Wieczorek, G.1    Zielenkiewicz, P.2
  • 8
    • 2342469914 scopus 로고    scopus 로고
    • Stochastic model of protein-protein interaction: Why signaling proteins need to be colocalized
    • Batada NN, Shepp LA, Siegmund DO (2004) Stochastic model of protein-protein interaction: Why signaling proteins need to be colocalized. Proc Natl Acad Sci U S A 101: 6445-6449.
    • (2004) Proc Natl Acad Sci U S A , vol.101 , pp. 6445-6449
    • Batada, N.N.1    Shepp, L.A.2    Siegmund, D.O.3
  • 10
  • 11
    • 0037086447 scopus 로고    scopus 로고
    • Addressing protein localization within the nucleus
    • Bickmore WA, Sutherland HGE (2002) Addressing protein localization within the nucleus. EMBO J 21: 1248-1254.
    • (2002) EMBO J , vol.21 , pp. 1248-1254
    • Bickmore, W.A.1    Sutherland, H.G.E.2
  • 12
    • 0035445626 scopus 로고    scopus 로고
    • Large-scale identification of mammalian proteins localized to nuclear sub-compartments
    • Sutherland HGE, Mumford GK, Newton K, Ford LV, Farrall R, et al. (2001) Large-scale identification of mammalian proteins localized to nuclear sub-compartments. Hum Mol Genet 10: 1995-2011.
    • (2001) Hum Mol Genet , vol.10 , pp. 1995-2011
    • Sutherland, H.G.E.1    Mumford, G.K.2    Newton, K.3    Ford, L.V.4    Farrall, R.5
  • 13
    • 33846010187 scopus 로고    scopus 로고
    • Prediction of protein submitochondria locations by hybridizing pseudo-amino acid composition with various physicochemical features of segmented sequence
    • doi:10.1186/1471-2105-7-518
    • Du PF, Li YD (2006) Prediction of protein submitochondria locations by hybridizing pseudo-amino acid composition with various physicochemical features of segmented sequence. BMC Bioinformatics 7: doi:10.1186/1471-2105-7-518.
    • (2006) BMC Bioinformatics , pp. 7
    • Du, P.F.1    Li, Y.D.2
  • 14
    • 33748476481 scopus 로고    scopus 로고
    • Electrostatic properties of protein-protein complexes
    • Kundrotas PJ, Alexov E (2006) Electrostatic properties of protein-protein complexes. Biophys J 91: 1724-1736.
    • (2006) Biophys J , vol.91 , pp. 1724-1736
    • Kundrotas, P.J.1    Alexov, E.2
  • 15
    • 36749060694 scopus 로고    scopus 로고
    • DOCKGROUND system of databases for protein recognition studies: Unbound structures for docking
    • Gao Y, Douguet D, Tovchigrechko A, Vakser IA (2007) DOCKGROUND system of databases for protein recognition studies: Unbound structures for docking. Proteins 69: 845-851.
    • (2007) Proteins , vol.69 , pp. 845-851
    • Gao, Y.1    Douguet, D.2    Tovchigrechko, A.3    Vakser, I.A.4
  • 16
    • 0003037157 scopus 로고
    • Intraclass correlation coefficient. Encyclopedia of statistical sciences
    • editors
    • Kotz S, Johnson NL, Read CB, editors. (1983) Intraclass correlation coefficient. Encyclopedia of statistical sciences. New York: Wiley. vol. 4. pp. 212-217.
    • (1983) New York: Wiley , vol.4 , pp. 212-217
    • Kotz, S.1    Johnson, N.L.2    Read, C.B.3
  • 17
    • 48249153186 scopus 로고
    • Intraclass correlations - uses in assessing rater reliability
    • Shrout PE, Fleiss JL (1979) Intraclass correlations - uses in assessing rater reliability. Psychol Bull 86: 420-428.
    • (1979) Psychol Bull , vol.86 , pp. 420-428
    • Shrout, P.E.1    Fleiss, J.L.2
  • 18
    • 4043171970 scopus 로고    scopus 로고
    • The GB/SA continuum model for solvation. A fast analytical method for the calculation of approximate Born radii
    • Qiu D, Shenkin PS, Hollinger FP, Still WC (1997) The GB/SA continuum model for solvation. A fast analytical method for the calculation of approximate Born radii. J Phys Chem A 101: 3005-3014.
    • (1997) J Phys Chem A , vol.101 , pp. 3005-3014
    • Qiu, D.1    Shenkin, P.S.2    Hollinger, F.P.3    Still, W.C.4
  • 19
    • 41949100049 scopus 로고    scopus 로고
    • Recent advances in implicit solvent-based methods for biomolecular simulations
    • Chen JH, Brooks CL, Khandogin J (2008) Recent advances in implicit solvent-based methods for biomolecular simulations. Curr Opin Struct Biol 18: 140-148.
    • (2008) Curr Opin Struct Biol , vol.18 , pp. 140-148
    • Chen, J.H.1    Brooks, C.L.2    Khandogin, J.3
  • 20
    • 0037195486 scopus 로고    scopus 로고
    • Mathematical correlations for predicting protein retention times in hydrophobic interaction chromatography
    • Lienqueo ME, Mahn A, Asenjo JA (2002) Mathematical correlations for predicting protein retention times in hydrophobic interaction chromatography. J Chromatogr A 978: 71-79.
    • (2002) J Chromatogr A , vol.978 , pp. 71-79
    • Lienqueo, M.E.1    Mahn, A.2    Asenjo, J.A.3
  • 21
    • 59849088376 scopus 로고    scopus 로고
    • Methods of calculating protein hydrophobicity and their application in developing correlations to predict hydrophobic interaction chromatography retention
    • Mahn A, Lienqueo ME, Salgado JC (2009) Methods of calculating protein hydrophobicity and their application in developing correlations to predict hydrophobic interaction chromatography retention. J Chromatogr A 1216: 1838-1844.
    • (2009) J Chromatogr A , vol.1216 , pp. 1838-1844
    • Mahn, A.1    Lienqueo, M.E.2    Salgado, J.C.3
  • 22
    • 13844255387 scopus 로고    scopus 로고
    • Natively unfolded proteins
    • Fink AL (2005) Natively unfolded proteins. Curr Opin Struct Biol 15: 35-41.
    • (2005) Curr Opin Struct Biol , vol.15 , pp. 35-41
    • Fink, A.L.1
  • 23
    • 62149141206 scopus 로고    scopus 로고
    • Geometric cue for protein localization in a bacterium
    • Ramamurthi KS, Lecuyer S, Stone HA, Losick R (2009) Geometric cue for protein localization in a bacterium. Science 323: 1354-1357.
    • (2009) Science , vol.323 , pp. 1354-1357
    • Ramamurthi, K.S.1    Lecuyer, S.2    Stone, H.A.3    Losick, R.4
  • 24
    • 69449106111 scopus 로고    scopus 로고
    • Negative membrane curvature as a cue for subcellular localization of a bacterial protein
    • Ramamurthi KS, Losick R (2009) Negative membrane curvature as a cue for subcellular localization of a bacterial protein. Proc Natl Acad Sci USA 106: 13541-13545.
    • (2009) Proc Natl Acad Sci USA , vol.106 , pp. 13541-13545
    • Ramamurthi, K.S.1    Losick, R.2
  • 25
    • 0033777047 scopus 로고    scopus 로고
    • Random walks and cell size
    • Agutter PS, Wheatley DN (2000) Random walks and cell size. Bioessays 22: 1018-1023.
    • (2000) Bioessays , vol.22 , pp. 1018-1023
    • Agutter, P.S.1    Wheatley, D.N.2
  • 27
    • 34547559704 scopus 로고    scopus 로고
    • PDB2PQR: Expanding and upgrading automated preparation of biomolecular structures for molecular simulations
    • Dolinsky TJ, Czodrowski P, Li H, Nielsen JE, Jensen JH, et al. (2007) PDB2PQR: expanding and upgrading automated preparation of biomolecular structures for molecular simulations. Nucleic Acids Res 35: W522-W525.
    • (2007) Nucleic Acids Res , vol.35
    • Dolinsky, T.J.1    Czodrowski, P.2    Li, H.3    Nielsen, J.E.4    Jensen, J.H.5
  • 28
    • 33745628037 scopus 로고    scopus 로고
    • The geometry of the ribosomal polypeptide exit tunnel
    • Voss NR, Gerstein M, Steitz TA, Moore PB (2006) The geometry of the ribosomal polypeptide exit tunnel. J Mol Biol 360: 893-906.
    • (2006) J Mol Biol , vol.360 , pp. 893-906
    • Voss, N.R.1    Gerstein, M.2    Steitz, T.A.3    Moore, P.B.4
  • 29
    • 0020997912 scopus 로고
    • Dictionary of protein secondary structure: Pattern recognition of hydrogen-bonded and geometrical features
    • Kabsch W, Sander C (1983) Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical features. Biopolymers 22: 2577-2637.
    • (1983) Biopolymers , vol.22 , pp. 2577-2637
    • Kabsch, W.1    Sander, C.2
  • 30
    • 0242443693 scopus 로고    scopus 로고
    • Force fields for protein simulations
    • Ponder JW, Case DA (2003) Force fields for protein simulations. Adv Protein Chem 66: 27-85.
    • (2003) Adv Protein Chem , vol.66 , pp. 27-85
    • Ponder, J.W.1    Case, D.A.2
  • 31
    • 0029912748 scopus 로고    scopus 로고
    • Development and testing of the OPLS all-atom force field on conformational energetics and properties of organic liquids
    • Jorgensen WL, Maxwell DS, TiradoRives J (1996) Development and testing of the OPLS all-atom force field on conformational energetics and properties of organic liquids. J Am Chem Soc 118: 11225-11236.
    • (1996) J Am Chem Soc , vol.118 , pp. 11225-11236
    • Jorgensen, W.L.1    Maxwell, D.S.2    Tiradorives, J.3
  • 32
    • 0029633168 scopus 로고
    • GROMACS - A message-passing parallel molecular dynamics implementation
    • Berendsen HJC, van der Spoel D, van Drunen R (1995) GROMACS - A message-passing parallel molecular dynamics implementation. Comp Phys Comm 91: 43-56.
    • (1995) Comp Phys Comm , vol.91 , pp. 43-56
    • Berendsen, H.J.C.1    van der Spoel, D.2    van Drunen, R.3
  • 33
    • 20544433165 scopus 로고
    • Van der Waals volumes+radii
    • Bondi A (1964) Van der Waals volumes+radii. J Phys Chem 68: 441-452.
    • (1964) J Phys Chem , vol.68 , pp. 441-452
    • Bondi, A.1
  • 34
    • 33748546968 scopus 로고    scopus 로고
    • Intermolecular nonbonded contact distances in organic crystal structures: Comparison with distances expected from van der Waals radii
    • Rowland RS, Taylor R (1996) Intermolecular nonbonded contact distances in organic crystal structures: Comparison with distances expected from van der Waals radii. J Phys Chem 100: 7384-7391
    • (1996) J Phys Chem , vol.100 , pp. 7384-7391
    • Rowland, R.S.1    Taylor, R.2


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