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Volumn 88, Issue 3, 2005, Pages 1970-1977

Molecular packing and packing defects in helical membrane proteins

Author keywords

[No Author keywords available]

Indexed keywords

AMINO ACID; CARRIER PROTEIN; GLOBULAR PROTEIN; MEMBRANE PROTEIN; ION CHANNEL; MULTIPROTEIN COMPLEX;

EID: 21244502261     PISSN: 00063495     EISSN: None     Source Type: Journal    
DOI: 10.1529/biophysj.104.049585     Document Type: Article
Times cited : (39)

References (35)
  • 1
    • 0031563818 scopus 로고    scopus 로고
    • Helix packing in membrane proteins
    • Bowie, J. U. 1997. Helix packing in membrane proteins. J. Mol. Biol. 272:780-789.
    • (1997) J. Mol. Biol. , vol.272 , pp. 780-789
    • Bowie, J.U.1
  • 2
    • 0016606973 scopus 로고
    • Structural invariants in protein folding
    • Chothia, C. 1975. Structural invariants in protein folding. Nature. 254: 304-308.
    • (1975) Nature , vol.254 , pp. 304-308
    • Chothia, C.1
  • 4
    • 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., H. Gratkowski, and J. D. Lear. 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    Gratkowski, H.2    Lear, J.D.3
  • 5
    • 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
  • 6
    • 0000929505 scopus 로고
    • The hydrophobic moment detects periodicity in protein hydrophobicity
    • Eisenberg, D., R. M. Weiss, and T. C. Terwilliger. 1984. The hydrophobic moment detects periodicity in protein hydrophobicity. Proc. Natl. Acad. Sci. USA. 81:140-144.
    • (1984) Proc. Natl. Acad. Sci. USA , vol.81 , pp. 140-144
    • Eisenberg, D.1    Weiss, R.M.2    Terwilliger, T.C.3
  • 7
    • 0036382758 scopus 로고    scopus 로고
    • A novel scoring function for predicting the conformations of tightly packed pairs of transmembrane α-helices
    • Fleishman, S. J., and N. Ben-Tal. 2002. A novel scoring function for predicting the 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
  • 8
    • 0034595515 scopus 로고    scopus 로고
    • Protein packing: Dependence on protein size, secondary structure and amino acid composition
    • Fleming, P. J., and F. M. Richards. 2000. Protein packing: dependence on protein size, secondary structure and amino acid composition. J. Mol. Biol. 299:487-498.
    • (2000) J. Mol. Biol. , vol.299 , pp. 487-498
    • Fleming, P.J.1    Richards, F.M.2
  • 9
    • 0034674164 scopus 로고    scopus 로고
    • Conservation of substructures in proteins: Interfaces of secondary structural elements in proteasomal subunits
    • Gille, C., A. Goede, R. Preissner, K. Rother, and C. Frömmel. 2000. Conservation of substructures in proteins: interfaces of secondary structural elements in proteasomal subunits. J. Mol. Biol. 299: 1147-1154.
    • (2000) J. Mol. Biol. , vol.299 , pp. 1147-1154
    • Gille, C.1    Goede, A.2    Preissner, R.3    Rother, K.4    Frömmel, C.5
  • 10
    • 0001136015 scopus 로고    scopus 로고
    • Voronoi cell: New method for allocation of space among atoms: Elimination of avoidable errors in calculation of atomic volume and density
    • Goede, A., R. Preissner, and C. Frömmel. 1997. Voronoi cell: new method for allocation of space among atoms: elimination of avoidable errors in calculation of atomic volume and density. J. Comput. Chem. 18: 1113-1123.
    • (1997) J. Comput. Chem. , vol.18 , pp. 1113-1123
    • Goede, A.1    Preissner, R.2    Frömmel, C.3
  • 11
    • 0442276416 scopus 로고    scopus 로고
    • Structural features of transmembrane helices
    • Hildebrand, P. W., R. Preissner, and C. Frömmel. 2004. Structural features of transmembrane helices. FEBS Lett. 559:145-151.
    • (2004) FEBS Lett. , vol.559 , pp. 145-151
    • Hildebrand, P.W.1    Preissner, R.2    Frömmel, C.3
  • 12
    • 0041489951 scopus 로고    scopus 로고
    • Structure and mechanism of the glycerol-3-phosphate transporter from Escherichia coli
    • Huang, Y., M. J. Lemieux, J. Song, M. Auer, and D. N. Wang. 2003. Structure and mechanism of the glycerol-3-phosphate transporter from Escherichia coli. Science. 301:616-620.
    • (2003) Science , vol.301 , pp. 616-620
    • Huang, Y.1    Lemieux, M.J.2    Song, J.3    Auer, M.4    Wang, D.N.5
  • 14
    • 0036787577 scopus 로고    scopus 로고
    • Uniformity, ideality, and hydrogen bonds in transmembrane α-helices
    • Kim, S., and T. A. Cross. 2002. Uniformity, ideality, and hydrogen bonds in transmembrane α-helices. Biophys. J. 83:2084-2095.
    • (2002) Biophys. J. , vol.83 , pp. 2084-2095
    • Kim, S.1    Cross, T.A.2
  • 15
    • 0030589519 scopus 로고    scopus 로고
    • Properties of the protein matrix revealed by the free energy of cavity formation
    • Kocher, J. P., M. Prevost, S. J. Wodak, and B. Lee. 1996. Properties of the protein matrix revealed by the free energy of cavity formation. Structure. 4:1517-1529.
    • (1996) Structure , vol.4 , pp. 1517-1529
    • Kocher, J.P.1    Prevost, M.2    Wodak, S.J.3    Lee, B.4
  • 16
    • 0032080907 scopus 로고    scopus 로고
    • Interaction of transmembrane helices by a knobs-into-holes packing characteristic of soluble coiled coils
    • Langosch, D., and J. Heringa. 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
  • 17
    • 0028235050 scopus 로고
    • Specificity and promiscuity in membrane helix interactions
    • Lemmon, M. A., and D. M. Engelman. 1994. Specificity and promiscuity in membrane helix interactions. FEBS Lett. 346:17-20.
    • (1994) FEBS Lett. , vol.346 , pp. 17-20
    • Lemmon, M.A.1    Engelman, D.M.2
  • 18
    • 1542268949 scopus 로고    scopus 로고
    • Helix packing moments reveal diversity and conservation in membrane protein structure
    • Liu, W., M. Eilers, A. B. Patel, and S. O. Smith. 2004. Helix packing moments reveal diversity and conservation in membrane protein structure. J. Mol. Biol. 337:713-729.
    • (2004) J. Mol. Biol. , vol.337 , pp. 713-729
    • Liu, W.1    Eilers, M.2    Patel, A.B.3    Smith, S.O.4
  • 19
    • 0041766317 scopus 로고    scopus 로고
    • Structural biology. Breaching the barrier
    • Locher, K. P., R. B. Bass, and D. C. Rees. 2003. Structural biology. Breaching the barrier. Science. 301:603-604.
    • (2003) Science , vol.301 , pp. 603-604
    • Locher, K.P.1    Bass, R.B.2    Rees, D.C.3
  • 20
    • 0032584233 scopus 로고    scopus 로고
    • Structure-based prediction of the stability of transmembrane helix-helix interactions: The sequence dependence of glycophorin a dimerization
    • MacKenzie, K. R., and D. M. Engelman. 1998. Structure-based prediction of the stability of transmembrane helix-helix interactions: the sequence dependence of glycophorin A dimerization. Proc. Natl. Acad. Sci. USA. 95:3583-3590.
    • (1998) Proc. Natl. Acad. Sci. USA , vol.95 , pp. 3583-3590
    • MacKenzie, K.R.1    Engelman, D.M.2
  • 21
    • 0036104783 scopus 로고    scopus 로고
    • Influence of the environment in the conformation of α-helices studied by protein database search and molecular dynamics simulations
    • Olivella, M., X. Deupi, C. Govaerts, and L. Pardo. 2002. Influence of the environment in the conformation of α-helices studied by protein database search and molecular dynamics simulations. Biophys. J. 52:3207-3213.
    • (2002) Biophys. J. , vol.52 , pp. 3207-3213
    • Olivella, M.1    Deupi, X.2    Govaerts, C.3    Pardo, L.4
  • 22
    • 0029411262 scopus 로고
    • Occluded molecular surface: Analysis of protein packing
    • Pattabiraman, N., K. B. Ward, and P. J. Fleming. 1995. Occluded molecular surface: analysis of protein packing. J. Mol. Recognit. 8:334-344.
    • (1995) J. Mol. Recognit. , vol.8 , pp. 334-344
    • Pattabiraman, N.1    Ward, K.B.2    Fleming, P.J.3
  • 23
    • 0037194760 scopus 로고    scopus 로고
    • Open channel structure of MscL and the gating mechanism of mechanosensitive channels
    • Perozo, E., D. M. Cortes, P. Sompornpisut, A. Kloda, and B. Martinac. 2002. Open channel structure of MscL and the gating mechanism of mechanosensitive channels. Nature. 418:942-948.
    • (2002) Nature , vol.418 , pp. 942-948
    • Perozo, E.1    Cortes, D.M.2    Sompornpisut, P.3    Kloda, A.4    Martinac, B.5
  • 24
    • 0033790343 scopus 로고    scopus 로고
    • Helical membrane protein folding, stability, and evolution
    • Popot, J. L., and D. M. Engelman. 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
  • 25
    • 0032736656 scopus 로고    scopus 로고
    • Spare parts for helix-helix interaction
    • Preissner, R., A. Goede, and C. Frommel. 1999. Spare parts for helix-helix interaction. Protein Eng. 12:825-832.
    • (1999) Protein Eng. , vol.12 , pp. 825-832
    • Preissner, R.1    Goede, A.2    Frommel, C.3
  • 26
    • 0032540856 scopus 로고    scopus 로고
    • Dictionary of interfaces in proteins (DIP). Data bank of complementary molecular surface patches
    • Preissner, R., A. Goede, and C. Frommel. 1998. Dictionary of interfaces in proteins (DIP). Data bank of complementary molecular surface patches. J. Mol. Biol. 280:535-550.
    • (1998) J. Mol. Biol. , vol.280 , pp. 535-550
    • Preissner, R.1    Goede, A.2    Frommel, C.3
  • 27
    • 0021755764 scopus 로고
    • Solvent accessible surface area and excluded volume in proteins. Analytical equations for overlapping spheres and implications for the hydrophobic effect
    • Richmond, T. J. 1984. Solvent accessible surface area and excluded volume in proteins. Analytical equations for overlapping spheres and implications for the hydrophobic effect. J. Mol. Biol. 178:63-89.
    • (1984) J. Mol. Biol. , vol.178 , pp. 63-89
    • Richmond, T.J.1
  • 28
    • 0242559057 scopus 로고    scopus 로고
    • Inhomogeneous molecular density: Reference packing densities and distribution of cavities within proteins
    • Rother, K., R. Preissner, A. Goede, and C. Frömmel. 2003. Inhomogeneous molecular density: reference packing densities and distribution of cavities within proteins. Bioinformatics. 19:2112-2121.
    • (2003) Bioinformatics , vol.19 , pp. 2112-2121
    • Rother, K.1    Preissner, R.2    Goede, A.3    Frömmel, C.4
  • 29
    • 0035979146 scopus 로고    scopus 로고
    • The Cα-H⋯O hydrogen bond: A determinant of stability and specificity in transmembrane helix interactions
    • Senes, A., I. Ubarretxena-Belandia, and D. M. Engelman. 2001. The Cα-H⋯O hydrogen bond: a determinant of stability and specificity in transmembrane helix interactions. Proc. Natl. Acad. Sci. USA. 98: 9056-9061.
    • (2001) Proc. Natl. Acad. Sci. USA , vol.98 , pp. 9056-9061
    • Senes, A.1    Ubarretxena-Belandia, I.2    Engelman, D.M.3
  • 30
    • 0027804108 scopus 로고
    • An effective solvation term based on atomic occupancies for use in protein simulations
    • Stouten, P. F. W., C. Frömmel, H. Nakamura, and C. Sander. 1993. An effective solvation term based on atomic occupancies for use in protein simulations. Mol. Simulat. 10:97-120.
    • (1993) Mol. Simulat. , vol.10 , pp. 97-120
    • Stouten, P.F.W.1    Frömmel, C.2    Nakamura, H.3    Sander, C.4
  • 31
    • 2542442467 scopus 로고    scopus 로고
    • Opening the gate in potassium channels
    • Swartz, K. J. 2004. Opening the gate in potassium channels. Nat. Struct. Mol. Biol. 11:499-501.
    • (2004) Nat. Struct. Mol. Biol. , vol.11 , pp. 499-501
    • Swartz, K.J.1
  • 32
    • 0033516705 scopus 로고    scopus 로고
    • The packing density in proteins: Standard radii and volumes
    • Tsai, J., R. Taylor, C. Chothia, and M. Gerstein. 1999. The packing density in proteins: standard radii and volumes. J. Mol. Biol. 290:253-266.
    • (1999) J. Mol. Biol. , vol.290 , pp. 253-266
    • Tsai, J.1    Taylor, R.2    Chothia, C.3    Gerstein, M.4
  • 33
    • 0032922193 scopus 로고    scopus 로고
    • SFCHECK: A unified set of procedures for evaluating the quality of macromolecular structure-factor data and their agreement with the atomic model
    • Vaguine, A. A., J. Richelle, and S. J. Wodak. 1999. SFCHECK: a unified set of procedures for evaluating the quality of macromolecular structure-factor data and their agreement with the atomic model. Acta Crystallogr. D Biol. Crystallogr. 55:191-205.
    • (1999) Acta Crystallogr. D Biol. Crystallogr. , vol.55 , pp. 191-205
    • Vaguine, A.A.1    Richelle, J.2    Wodak, S.J.3
  • 35
    • 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


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.