메뉴 건너뛰기




Volumn 57, Issue 3, 2010, Pages 1238-1244

An evolutionary conserved motif is responsible for Immunoglobulin heavy chain packing in the B cell membrane

Author keywords

Immunoglobulin evolution; Immunoglobulin heavy chain; Immunoglobulin isotypes; Molecular dynamics; POPC lipid bilayer; Purifying selection; Transmembrane helix

Indexed keywords

IMMUNOGLOBULIN HEAVY CHAIN;

EID: 78649661317     PISSN: 10557903     EISSN: 10959513     Source Type: Journal    
DOI: 10.1016/j.ympev.2010.09.022     Document Type: Article
Times cited : (9)

References (47)
  • 1
    • 33847155026 scopus 로고    scopus 로고
    • Algorithms for incorporating prior topological information in HMMs: application to transmembrane proteins
    • Bagos P.G., Liakopoulos T.D., Hamodrakas S.J. Algorithms for incorporating prior topological information in HMMs: application to transmembrane proteins. BMC Bioinf. 2006, 7:189.
    • (2006) BMC Bioinf. , vol.7 , pp. 189
    • Bagos, P.G.1    Liakopoulos, T.D.2    Hamodrakas, S.J.3
  • 3
    • 35548988341 scopus 로고    scopus 로고
    • Common themes in the assembly and architecture of activating immune receptors
    • Call M.E., Wucherpfennig K.W. Common themes in the assembly and architecture of activating immune receptors. Nature 2007, 7:841-850.
    • (2007) Nature , vol.7 , pp. 841-850
    • Call, M.E.1    Wucherpfennig, K.W.2
  • 5
    • 0028103275 scopus 로고
    • The CCP4 suite: programs for protein crystallography
    • Collaborative Computational Project Number 4
    • The CCP4 suite: programs for protein crystallography. Acta Crystallogr. Sect. D 1994, 50:760-763. Collaborative Computational Project Number 4.
    • (1994) Acta Crystallogr. Sect. D , vol.50 , pp. 760-763
  • 7
    • 33845316118 scopus 로고    scopus 로고
    • Transmembrane helix-helix interactions: comparative simulations of the glycophorin a dimer
    • Cuthbertson J.M., Bond P.J., Sansom M.S. Transmembrane helix-helix interactions: comparative simulations of the glycophorin a dimer. Biochemistry 2006, 45:14298-14310.
    • (2006) Biochemistry , vol.45 , pp. 14298-14310
    • Cuthbertson, J.M.1    Bond, P.J.2    Sansom, M.S.3
  • 8
    • 33846823909 scopus 로고
    • Particle mesh Ewald: An N_log(N) method for Ewald sums in large systems
    • Darden T., York D., Pedersen L. Particle mesh Ewald: An N_log(N) method for Ewald sums in large systems. J. Chem. Phys. 1993, 98:10089-10092.
    • (1993) J. Chem. Phys. , vol.98 , pp. 10089-10092
    • Darden, T.1    York, D.2    Pedersen, L.3
  • 9
    • 0036301006 scopus 로고    scopus 로고
    • Motifs of serine and threonine can drive association of transmembrane helices
    • Dawson J.P., Weinger J.S., Engelman D.M. Motifs of serine and threonine can drive association of transmembrane helices. J. Mol. Biol. 2002, 316:799-805.
    • (2002) J. Mol. Biol. , vol.316 , pp. 799-805
    • Dawson, J.P.1    Weinger, J.S.2    Engelman, D.M.3
  • 12
    • 0036135139 scopus 로고    scopus 로고
    • A possible role for pi-stacking in the self-assembly of amyloid fibrils
    • Gazit E. A possible role for pi-stacking in the self-assembly of amyloid fibrils. FASEB J. 2002, 16:77-83.
    • (2002) FASEB J. , vol.16 , pp. 77-83
    • Gazit, E.1
  • 13
    • 0035969998 scopus 로고    scopus 로고
    • Polar side chains drive the association of model transmembrane peptides
    • Gratkowski H., Lear J.D., DeGrado W.F. Polar side chains drive the association of model transmembrane peptides. Proc. Natl Acad. Sci. USA 2001, 98:880-885.
    • (2001) Proc. Natl Acad. Sci. USA , vol.98 , pp. 880-885
    • Gratkowski, H.1    Lear, J.D.2    DeGrado, W.F.3
  • 14
    • 0242578620 scopus 로고    scopus 로고
    • A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood
    • Guindon S., Gascuel O.A. A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood. Syst. Biol. 2003, 52:696-704.
    • (2003) Syst. Biol. , vol.52 , pp. 696-704
    • Guindon, S.1    Gascuel, O.A.2
  • 15
    • 68149170743 scopus 로고    scopus 로고
    • Structural determinants of transmembrane helical proteins
    • Harrington S.E., Ben-Tal N. Structural determinants of transmembrane helical proteins. Structure 2009, 17:1092-1103.
    • (2009) Structure , vol.17 , pp. 1092-1103
    • Harrington, S.E.1    Ben-Tal, N.2
  • 16
    • 20444499328 scopus 로고    scopus 로고
    • Insights into the recognition and association of transmembrane alpha-helices. The free energy of alpha-helix dimerization in glycophorin A
    • Henin J., Pohorille A., Chipot C. Insights into the recognition and association of transmembrane alpha-helices. The free energy of alpha-helix dimerization in glycophorin A. J. Am. Chem. Soc. 2005, 127:8478-8484.
    • (2005) J. Am. Chem. Soc. , vol.127 , pp. 8478-8484
    • Henin, J.1    Pohorille, A.2    Chipot, C.3
  • 18
    • 0000207681 scopus 로고
    • TMbase-A database of membrane spanning proteins segments
    • Hofmann K., Stoffel W. TMbase-A database of membrane spanning proteins segments. Biol. Chem. Hoppe-Seyler 1993, 374:166.
    • (1993) Biol. Chem. Hoppe-Seyler , vol.374 , pp. 166
    • Hofmann, K.1    Stoffel, W.2
  • 19
    • 1942473116 scopus 로고    scopus 로고
    • Shorter side chains optimize helix-helix packing
    • Jiang S., Vakser I.A. Shorter side chains optimize helix-helix packing. Protein Sci. 2004, 13:1426-1429.
    • (2004) Protein Sci. , vol.13 , pp. 1426-1429
    • Jiang, S.1    Vakser, I.A.2
  • 20
    • 0020997912 scopus 로고
    • Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical features
    • Kabsch W., Sander C. Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical features. Biopolymers 1983, 22:2577-2637.
    • (1983) Biopolymers , vol.22 , pp. 2577-2637
    • Kabsch, W.1    Sander, C.2
  • 21
    • 0037076540 scopus 로고    scopus 로고
    • GXXXG and AXXXA: common alphahelical interaction motifs in proteins, particularly in extremophiles
    • Kleiger G., Grothe R., Mallick P., Eisenberg D. GXXXG and AXXXA: common alphahelical interaction motifs in proteins, particularly in extremophiles. Biochemistry 2002, 41:5990-5997.
    • (2002) Biochemistry , vol.41 , pp. 5990-5997
    • Kleiger, G.1    Grothe, R.2    Mallick, P.3    Eisenberg, D.4
  • 22
    • 17744396121 scopus 로고    scopus 로고
    • Not so different after all: a comparison of methods for detecting amino acid sites under selection
    • Kosakovsky Pond S.L., Frost S.D. Not so different after all: a comparison of methods for detecting amino acid sites under selection. Mol. Biol. Evol. 2005, 22:1208-1222.
    • (2005) Mol. Biol. Evol. , vol.22 , pp. 1208-1222
    • Kosakovsky Pond, S.L.1    Frost, S.D.2
  • 24
    • 0000243829 scopus 로고
    • PROCHECK: a program to check the stereochemical quality of protein structures
    • Laskowski R.A., MacArthur M.W., Moss M.D., Thornton J.M. PROCHECK: a program to check the stereochemical quality of protein structures. J. Appl. Cryst. 1993, 26:283-291.
    • (1993) J. Appl. Cryst. , vol.26 , pp. 283-291
    • Laskowski, R.A.1    MacArthur, M.W.2    Moss, M.D.3    Thornton, J.M.4
  • 25
    • 0027772959 scopus 로고
    • Shape complementarity at protein/protein interfaces
    • Lawrence M.C., Colman P.M. Shape complementarity at protein/protein interfaces. J. Mol. Biol. 1993, 234:946-950.
    • (1993) J. Mol. Biol. , vol.234 , pp. 946-950
    • Lawrence, M.C.1    Colman, P.M.2
  • 26
    • 45849154166 scopus 로고    scopus 로고
    • An improved general amino acid replacement matrix
    • Le S.Q., Gascuel O. An improved general amino acid replacement matrix. Mol. Biol. Evol. 2008, 25:1307-1320.
    • (2008) Mol. Biol. Evol. , vol.25 , pp. 1307-1320
    • Le, S.Q.1    Gascuel, O.2
  • 28
    • 0030932407 scopus 로고    scopus 로고
    • A transmembrane helix dimer: structure and implications
    • MacKenzie K.R., Prestegard J.H., Engelman D.M. A transmembrane helix dimer: structure and implications. Science 1997, 276:131-133.
    • (1997) Science , vol.276 , pp. 131-133
    • MacKenzie, K.R.1    Prestegard, J.H.2    Engelman, D.M.3
  • 29
    • 0032546782 scopus 로고    scopus 로고
    • Pi-Stacking interactions. Alive and well in proteins
    • McGaughey G.B., Gagné M., Rappé A.K. Pi-Stacking interactions. Alive and well in proteins. J. Biol. Chem. 1998, 273:15458-15463.
    • (1998) J. Biol. Chem. , vol.273 , pp. 15458-15463
    • McGaughey, G.B.1    Gagné, M.2    Rappé, A.K.3
  • 30
    • 24044506284 scopus 로고    scopus 로고
    • The importance of dynamic effects on the enzyme activity: X-ray structure and molecular dynamics of onconase
    • Merlino A., Mazzarella L., Di Fiore A., Carannante A., Notomista E., Di Donato A., Sica F. The importance of dynamic effects on the enzyme activity: X-ray structure and molecular dynamics of onconase. J. Biol. Chem. 2005, 280:17953-17960.
    • (2005) J. Biol. Chem. , vol.280 , pp. 17953-17960
    • Merlino, A.1    Mazzarella, L.2    Di Fiore, A.3    Carannante, A.4    Notomista, E.5    Di Donato, A.6    Sica, F.7
  • 31
    • 33646794342 scopus 로고    scopus 로고
    • Polyglutamine repeats and beta-helix structure: molecular dynamics study
    • Merlino A., Esposito L., Vitagliano L. Polyglutamine repeats and beta-helix structure: molecular dynamics study. Proteins 2006, 63:918-927.
    • (2006) Proteins , vol.63 , pp. 918-927
    • Merlino, A.1    Esposito, L.2    Vitagliano, L.3
  • 33
    • 33644844890 scopus 로고    scopus 로고
    • Energetics of the native and non-native states of the glycophorin transmembrane helix dimer
    • Mottamal M., Zhang J., Lazaridis T. Energetics of the native and non-native states of the glycophorin transmembrane helix dimer. Proteins 2006, 62:996-1009.
    • (2006) Proteins , vol.62 , pp. 996-1009
    • Mottamal, M.1    Zhang, J.2    Lazaridis, T.3
  • 34
    • 0343081370 scopus 로고    scopus 로고
    • X-Ray diffraction analysis of three-dimensional crystals of bovine rhodopsin obtained from mixed micelles
    • Okada T., Le Trong I., Fox B.A., Behnke C.A., Stenkamp R.E., Palczewski K. X-Ray diffraction analysis of three-dimensional crystals of bovine rhodopsin obtained from mixed micelles. J. Struct. Biol. 2000, 130:73-80.
    • (2000) J. Struct. Biol. , vol.130 , pp. 73-80
    • Okada, T.1    Le Trong, I.2    Fox, B.A.3    Behnke, C.A.4    Stenkamp, R.E.5    Palczewski, K.6
  • 37
    • 66149134063 scopus 로고    scopus 로고
    • Studying membrane proteins through the eyes of the genetic code revealed a strong uracil bias in their coding mRNAs
    • Prilusky J., Eitan B. Studying membrane proteins through the eyes of the genetic code revealed a strong uracil bias in their coding mRNAs. Proc. Natl Acad. Sci. USA 2009, 106:6662-6666.
    • (2009) Proc. Natl Acad. Sci. USA , vol.106 , pp. 6662-6666
    • Prilusky, J.1    Eitan, B.2
  • 38
    • 3142702159 scopus 로고    scopus 로고
    • Unprecedented multiplicity of Ig transmembrane and secretory mRNA forms in the cartilaginous fish
    • Rumfelt L.L., Diaz M., Lohr R.L., Mochon E., Flajnik M.F. Unprecedented multiplicity of Ig transmembrane and secretory mRNA forms in the cartilaginous fish. J. Immunol. 2004, 173:1129-1139.
    • (2004) J. Immunol. , vol.173 , pp. 1129-1139
    • Rumfelt, L.L.1    Diaz, M.2    Lohr, R.L.3    Mochon, E.4    Flajnik, M.F.5
  • 39
    • 5144227144 scopus 로고    scopus 로고
    • Motifs of two small residues can assist but are not sufficient to mediate transmembrane helix interactions
    • Schneider D., Engelman D.M. Motifs of two small residues can assist but are not sufficient to mediate transmembrane helix interactions. J. Mol. Biol. 2004, 343:799-804.
    • (2004) J. Mol. Biol. , vol.343 , pp. 799-804
    • Schneider, D.1    Engelman, D.M.2
  • 40
    • 0025008168 scopus 로고
    • Sequence logos: a new way to display consensus sequences
    • Schneider T.D., Stephens R.M. Sequence logos: a new way to display consensus sequences. Nucleic Acids Res. 1990, 18:6097-6100.
    • (1990) Nucleic Acids Res. , vol.18 , pp. 6097-6100
    • Schneider, T.D.1    Stephens, R.M.2
  • 41
    • 0034711958 scopus 로고    scopus 로고
    • Statistical analysis of amino acid patterns in transmembrane helices: the GxxxG motif occurs frequently and in association with beta-branched residues at neighboring positions
    • Senes A., Gerstein M., Engelman D.M. Statistical analysis of amino acid patterns in transmembrane helices: the GxxxG motif occurs frequently and in association with beta-branched residues at neighboring positions. J. Mol. Biol. 2000, 296:921-936.
    • (2000) J. Mol. Biol. , vol.296 , pp. 921-936
    • Senes, A.1    Gerstein, M.2    Engelman, D.M.3
  • 43
    • 0031574072 scopus 로고    scopus 로고
    • The CLUSTAL_X windows interface. Flexible strategies for multiple sequence alignment aided by quality analysis tools
    • Thompson J.D., Gibson T.J., Plewniak F., Jeanmougin F., Higgins D.G. The CLUSTAL_X windows interface. Flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res. 1997, 25:4876-4882.
    • (1997) Nucleic Acids Res. , vol.25 , pp. 4876-4882
    • Thompson, J.D.1    Gibson, T.J.2    Plewniak, F.3    Jeanmougin, F.4    Higgins, D.G.5
  • 45
    • 34548757937 scopus 로고    scopus 로고
    • Specificity of helix packing in transmembrane dimer of the cell death factor BNIP3: a molecular modeling study
    • Vereshaga Y.A., Volynsky P.E., Pustovalova J.E., Nolde D.E., Arseniev A.S., Efremov R.G. Specificity of helix packing in transmembrane dimer of the cell death factor BNIP3: a molecular modeling study. Proteins 2007, 69:309-325.
    • (2007) Proteins , vol.69 , pp. 309-325
    • Vereshaga, Y.A.1    Volynsky, P.E.2    Pustovalova, J.E.3    Nolde, D.E.4    Arseniev, A.S.5    Efremov, R.G.6
  • 46
    • 33748791763 scopus 로고    scopus 로고
    • Helix-packing motifs in membrane proteins
    • Walters R.F., DeGrado W.F. Helix-packing motifs in membrane proteins. Proc. Natl Acad. Sci. USA 2006, 103:13658-13663.
    • (2006) Proc. Natl Acad. Sci. USA , vol.103 , pp. 13658-13663
    • Walters, R.F.1    DeGrado, W.F.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.