메뉴 건너뛰기




Volumn 23, Issue 3, 2015, Pages 584-597

Nothing to Sneeze At: A Dynamic and Integrative Computational Model of an Influenza A Virion

Author keywords

[No Author keywords available]

Indexed keywords

FORSSMAN ANTIGEN; IMMUNOGLOBULIN G; VIRUS SPIKE PROTEIN; LIPID; PROTEIN BINDING; VIRUS RECEPTOR;

EID: 84923884183     PISSN: 09692126     EISSN: 18784186     Source Type: Journal    
DOI: 10.1016/j.str.2014.12.019     Document Type: Article
Times cited : (89)

References (67)
  • 1
    • 77957083058 scopus 로고
    • Lateral diffusion in membranes
    • R. Lipowsky, E. Sackmann, Handbook of Biological Physics North-Holland
    • P.F.F. Almeida, and W.L.C. Vaz Lateral diffusion in membranes R. Lipowsky, E. Sackmann, Structure and Dynamics of Membranes: From Cells to Vesicles Handbook of Biological Physics Vol. 1 1995 North-Holland 305 357
    • (1995) Structure and Dynamics of Membranes: From Cells to Vesicles , vol.1 , pp. 305-357
    • Almeida, P.F.F.1    Vaz, W.L.C.2
  • 2
    • 64749105956 scopus 로고    scopus 로고
    • Hybrid coarse-graining approach for lipid bilayers at large length and time scales
    • G.S. Ayton, and G.A. Voth Hybrid coarse-graining approach for lipid bilayers at large length and time scales J. Phys. Chem. B 113 2009 4413 4424
    • (2009) J. Phys. Chem. B , vol.113 , pp. 4413-4424
    • Ayton, G.S.1    Voth, G.A.2
  • 3
    • 64749106745 scopus 로고    scopus 로고
    • Systematic multiscale simulation of membranes protein systems
    • G.S. Ayton, and G.A. Voth Systematic multiscale simulation of membranes protein systems Curr. Opin. Struct. Biol. 19 2009 138 144
    • (2009) Curr. Opin. Struct. Biol. , vol.19 , pp. 138-144
    • Ayton, G.S.1    Voth, G.A.2
  • 4
    • 78349258978 scopus 로고    scopus 로고
    • Multiscale computer simulation of the immature HIV-1 virion
    • G.S. Ayton, and G.A. Voth Multiscale computer simulation of the immature HIV-1 virion Biophys. J. 99 2010 2757 2765
    • (2010) Biophys. J. , vol.99 , pp. 2757-2765
    • Ayton, G.S.1    Voth, G.A.2
  • 5
    • 27744475701 scopus 로고    scopus 로고
    • Anomalous diffusion of proteins due to molecular crowding
    • D.S. Banks, and C. Fradin Anomalous diffusion of proteins due to molecular crowding Biophys. J. 89 2005 2960 2971
    • (2005) Biophys. J. , vol.89 , pp. 2960-2971
    • Banks, D.S.1    Fradin, C.2
  • 9
    • 0027397591 scopus 로고
    • Biologic importance of neuraminidase stalk length in influenza A virus
    • M.R. Castrucci, and Y. Kawaoka Biologic importance of neuraminidase stalk length in influenza A virus J. Virol. 67 1993 759 764
    • (1993) J. Virol. , vol.67 , pp. 759-764
    • Castrucci, M.R.1    Kawaoka, Y.2
  • 11
    • 42949117368 scopus 로고    scopus 로고
    • Protein area occupancy at the center of the red blood cell membrane
    • A.D. Dupuy, and D.M. Engelman Protein area occupancy at the center of the red blood cell membrane Proc. Natl. Acad. Sci. USA 105 2008 2848 2852
    • (2008) Proc. Natl. Acad. Sci. USA , vol.105 , pp. 2848-2852
    • Dupuy, A.D.1    Engelman, D.M.2
  • 12
    • 84905484603 scopus 로고    scopus 로고
    • Lipidwrapper: An algorithm for generating large-scale membrane models of arbitrary geometry
    • J.D. Durrant, and R.E. Amaro Lipidwrapper: an algorithm for generating large-scale membrane models of arbitrary geometry PLoS Comp. Biol. 10 2014 e1003720
    • (2014) PLoS Comp. Biol. , vol.10 , pp. e1003720
    • Durrant, J.D.1    Amaro, R.E.2
  • 13
    • 0029946890 scopus 로고    scopus 로고
    • Constrained diffusion or immobile fraction on cell surfaces: A new interpretation
    • T.J. Feder, I. BrustMascher, J.P. Slattery, B. Baird, and W.W. Webb Constrained diffusion or immobile fraction on cell surfaces: A new interpretation Biophys. J. 70 1996 2767 2773
    • (1996) Biophys. J. , vol.70 , pp. 2767-2773
    • Feder, T.J.1    Brustmascher, I.2    Slattery, J.P.3    Baird, B.4    Webb, W.W.5
  • 14
    • 84877324091 scopus 로고    scopus 로고
    • At low pH, influenza virus matrix protein m1 undergoes a conformational change prior to dissociating from the membrane
    • J. Fontana, and A.C. Steven At low pH, influenza virus matrix protein m1 undergoes a conformational change prior to dissociating from the membrane J. Virol. 87 2013 5621 5628
    • (2013) J. Virol. , vol.87 , pp. 5621-5628
    • Fontana, J.1    Steven, A.C.2
  • 15
  • 16
    • 77956556232 scopus 로고    scopus 로고
    • Influenza hemagglutinin and neuraminidase membrane glycoproteins
    • S.J. Gamblin, and J.J. Skehel Influenza hemagglutinin and neuraminidase membrane glycoproteins J. Biol. Chem. 285 2010 28403 28409
    • (2010) J. Biol. Chem. , vol.285 , pp. 28403-28409
    • Gamblin, S.J.1    Skehel, J.J.2
  • 19
    • 84888634825 scopus 로고    scopus 로고
    • Transferable mixing of atomistic and coarse-grained water models
    • H.C. Gonzalez, L. Darre, and S. Pantano Transferable mixing of atomistic and coarse-grained water models J. Phys. Chem. B 117 2013 14438 14448
    • (2013) J. Phys. Chem. B , vol.117 , pp. 14438-14448
    • Gonzalez, H.C.1    Darre, L.2    Pantano, S.3
  • 20
    • 84876890599 scopus 로고    scopus 로고
    • Reduced lateral mobility of lipids and proteins in crowded membranes
    • J.E. Goose, and M.S.P. Sansom Reduced lateral mobility of lipids and proteins in crowded membranes PLoS Comp. Biol. 9 2013 e1003033
    • (2013) PLoS Comp. Biol. , vol.9 , pp. e1003033
    • Goose, J.E.1    Sansom, M.S.P.2
  • 21
    • 84885185774 scopus 로고    scopus 로고
    • Structural and energetic analysis of drug inhibition of the influenza A M2 proton channel
    • R.-X. Gu, L.A. Liu, and D.-Q. Wei Structural and energetic analysis of drug inhibition of the influenza A M2 proton channel Trends Pharmacol. Sci. 34 2013 571 580
    • (2013) Trends Pharmacol. Sci. , vol.34 , pp. 571-580
    • Gu, R.-X.1    Liu, L.A.2    Wei, D.-Q.3
  • 22
    • 0038240827 scopus 로고    scopus 로고
    • X-ray structure of the hemagglutinin of a potential H3 avian progenitor of the 1968 Hong Kong pandemic influenza virus
    • Y. Ha, D.J. Stevens, J.J. Skehel, and D.C. Wiley X-ray structure of the hemagglutinin of a potential H3 avian progenitor of the 1968 Hong Kong pandemic influenza virus Virology 309 2003 209 218
    • (2003) Virology , vol.309 , pp. 209-218
    • Ha, Y.1    Stevens, D.J.2    Skehel, J.J.3    Wiley, D.C.4
  • 24
    • 46249092554 scopus 로고    scopus 로고
    • GROMACS 4: Algorithms for highly efficient, load-balanced, and scalable molecular simulation
    • B. Hess, C. Kutzner, D. van der Spoel, and E. Lindahl GROMACS 4: algorithms for highly efficient, load-balanced, and scalable molecular simulation J. Chem. Theor. Comp. 4 2008 435 447
    • (2008) J. Chem. Theor. Comp. , vol.4 , pp. 435-447
    • Hess, B.1    Kutzner, C.2    Van Der Spoel, D.3    Lindahl, E.4
  • 28
    • 0019511629 scopus 로고
    • Anti-Forssman antibody in human-sera - Properties and decreased level in cancer patients
    • S. Kijimoto-Ochiai, W. Takahashi, and A. Makita Anti-Forssman antibody in human-sera - properties and decreased level in cancer patients Jpn. J. Exp. Med. 51 1981 149 155
    • (1981) Jpn. J. Exp. Med. , vol.51 , pp. 149-155
    • Kijimoto-Ochiai, S.1    Takahashi, W.2    Makita, A.3
  • 30
    • 80055020948 scopus 로고    scopus 로고
    • Consistent picture of lateral subdiffusion in lipid bilayers: Molecular dynamics simulation and exact results
    • G.R. Kneller, K. Baczynski, and M. Pasenkiewicz-Gierula Consistent picture of lateral subdiffusion in lipid bilayers: molecular dynamics simulation and exact results J. Chem. Phys. 135 2011 3651800
    • (2011) J. Chem. Phys. , vol.135 , pp. 3651800
    • Kneller, G.R.1    Baczynski, K.2    Pasenkiewicz-Gierula, M.3
  • 31
    • 84908326414 scopus 로고    scopus 로고
    • Lipid clustering correlates with membrane curvature as revealed by molecular simulations of complex lipid bilayers
    • H. Koldsø, D. Shorthouse, J. Hélie, and M.S.P. Sansom Lipid clustering correlates with membrane curvature as revealed by molecular simulations of complex lipid bilayers PLoS Comp. Biol. 10 2014 e1003911
    • (2014) PLoS Comp. Biol. , vol.10 , pp. e1003911
    • Koldsø, H.1    Shorthouse, D.2    Hélie, J.3    Sansom, M.S.P.4
  • 32
    • 84863645688 scopus 로고    scopus 로고
    • Virus capsid dissolution studied by microsecond molecular dynamics simulations
    • D.S.D. Larsson, L. Liljas, and D. van der Spoel Virus capsid dissolution studied by microsecond molecular dynamics simulations PLoS Comp. Biol. 8 2012 e1002502
    • (2012) PLoS Comp. Biol. , vol.8 , pp. e1002502
    • Larsson, D.S.D.1    Liljas, L.2    Van Der Spoel, D.3
  • 35
    • 0345098288 scopus 로고    scopus 로고
    • Molecular dynamics simulation of the formation, structure, and dynamics of small phospholipid vesicles
    • S.J. Marrink, and A.E. Mark Molecular dynamics simulation of the formation, structure, and dynamics of small phospholipid vesicles J. Am. Chem. Soc. 125 2003 15233 15242
    • (2003) J. Am. Chem. Soc. , vol.125 , pp. 15233-15242
    • Marrink, S.J.1    Mark, A.E.2
  • 36
    • 84882398607 scopus 로고    scopus 로고
    • Perspective on the Martini model
    • S.J. Marrink, and D.P. Tieleman Perspective on the Martini model Chem. Soc. Rev. 42 2013 6801 6822
    • (2013) Chem. Soc. Rev. , vol.42 , pp. 6801-6822
    • Marrink, S.J.1    Tieleman, D.P.2
  • 42
    • 84876934637 scopus 로고    scopus 로고
    • Formation of raft-like assemblies within clusters of influenza hemagglutinin observed by MD simulations
    • D.L. Parton, A. Tek, M. Baaden, and M.S.P. Sansom Formation of raft-like assemblies within clusters of influenza hemagglutinin observed by MD simulations PLoS Comp. Biol. 9 2013 e1003034
    • (2013) PLoS Comp. Biol. , vol.9 , pp. e1003034
    • Parton, D.L.1    Tek, A.2    Baaden, M.3    Sansom, M.S.P.4
  • 43
    • 40949088194 scopus 로고    scopus 로고
    • Progressive ordering with decreasing temperature of the phospholipids of influenza virus
    • I.V. Polozov, L. Bezrukov, K. Gawrisch, and J. Zimmerberg Progressive ordering with decreasing temperature of the phospholipids of influenza virus Nat. Chem. Biol. 4 2008 248 255
    • (2008) Nat. Chem. Biol. , vol.4 , pp. 248-255
    • Polozov, I.V.1    Bezrukov, L.2    Gawrisch, K.3    Zimmerberg, J.4
  • 46
    • 0024466223 scopus 로고
    • Hemagglutinins from 2 influenza-virus variants bind to sialic-acid derivatives with millimolar dissociation-constants - A 500-MHz proton nuclear magnetic-resonance study
    • N.K. Sauter, M.D. Bednarski, B.A. Wurzburg, J.E. Hanson, G.M. Whitesides, J.J. Skehel, and D.C. Wiley Hemagglutinins from 2 influenza-virus variants bind to sialic-acid derivatives with millimolar dissociation-constants - a 500-MHz proton nuclear magnetic-resonance study Biochemistry 28 1989 8388 8396
    • (1989) Biochemistry , vol.28 , pp. 8388-8396
    • Sauter, N.K.1    Bednarski, M.D.2    Wurzburg, B.A.3    Hanson, J.E.4    Whitesides, G.M.5    Skehel, J.J.6    Wiley, D.C.7
  • 47
    • 79955682195 scopus 로고    scopus 로고
    • Anomalous diffusion of oligomerized transmembrane proteins
    • U. Schmidt, and M. Weiss Anomalous diffusion of oligomerized transmembrane proteins J. Chem. Phys. 134 2011 165101
    • (2011) J. Chem. Phys. , vol.134 , pp. 165101
    • Schmidt, U.1    Weiss, M.2
  • 48
    • 26944491901 scopus 로고    scopus 로고
    • Influenza virus assembly and budding at the viral budozone
    • P. Roy, Advances in Virus Research Academic Press
    • A.P. Schmitt, and R.A. Lamb Influenza virus assembly and budding at the viral budozone P. Roy, Virus Structure and Assembly Advances in Virus Research Vol. 64 2005 Academic Press 383 416
    • (2005) Virus Structure and Assembly , vol.64 , pp. 383-416
    • Schmitt, A.P.1    Lamb, R.A.2
  • 49
    • 38749106195 scopus 로고    scopus 로고
    • Structure and mechanism of the M2 proton channel of influenza A virus
    • J.R. Schnell, and J.J. Chou Structure and mechanism of the M2 proton channel of influenza A virus Nature 451 2008 591 595
    • (2008) Nature , vol.451 , pp. 591-595
    • Schnell, J.R.1    Chou, J.J.2
  • 51
    • 0345599000 scopus 로고    scopus 로고
    • Differently anchored influenza hemagglutinin mutants display distinct interaction dynamics with mutual rafts
    • D.E. Shvartsman, M. Kotler, R.D. Tall, M.G. Roth, and Y.I. Henis Differently anchored influenza hemagglutinin mutants display distinct interaction dynamics with mutual rafts J. Cell Biol. 163 2003 879 888
    • (2003) J. Cell Biol. , vol.163 , pp. 879-888
    • Shvartsman, D.E.1    Kotler, M.2    Tall, R.D.3    Roth, M.G.4    Henis, Y.I.5
  • 53
    • 62849091082 scopus 로고    scopus 로고
    • Structures common to different glycans
    • A. Varki, R.D. Cummings, J.D. Esko, H.H. Freeze, P. Stanley, C.R. Bertozzi, G.W. Hart, M.E. Etzler, Cold Spring Harbor Laboratory Press
    • P. Stanley, and R.D. Cummings Structures common to different glycans A. Varki, R.D. Cummings, J.D. Esko, H.H. Freeze, P. Stanley, C.R. Bertozzi, G.W. Hart, M.E. Etzler, Essentials of Glycobiology 2009 Cold Spring Harbor Laboratory Press
    • (2009) Essentials of Glycobiology
    • Stanley, P.1    Cummings, R.D.2
  • 54
    • 80855156716 scopus 로고    scopus 로고
    • Molecular simulation approaches to membrane proteins
    • P.J. Stansfeld, and M.S.P. Sansom Molecular simulation approaches to membrane proteins Structure 19 2011 1562 1572
    • (2011) Structure , vol.19 , pp. 1562-1572
    • Stansfeld, P.J.1    Sansom, M.S.P.2
  • 55
    • 0036007087 scopus 로고    scopus 로고
    • Influenza A virus M-2 ion channel activity is essential for efficient replication in tissue culture
    • M. Takeda, A. Pekosz, K. Shuck, L.H. Pinto, and R.A. Lamb Influenza A virus M-2 ion channel activity is essential for efficient replication in tissue culture J. Virol. 76 2002 1391 1399
    • (2002) J. Virol. , vol.76 , pp. 1391-1399
    • Takeda, M.1    Pekosz, A.2    Shuck, K.3    Pinto, L.H.4    Lamb, R.A.5
  • 56
    • 0025895628 scopus 로고
    • 3-Dimensional structure of the neuraminidase of influenza virus-A/Tokyo/3/67 at 2.2 Å resolution
    • J.N. Varghese, and P.M. Colman 3-Dimensional structure of the neuraminidase of influenza virus-A/Tokyo/3/67 at 2.2 Å resolution J. Mol. Biol. 221 1991 473 486
    • (1991) J. Mol. Biol. , vol.221 , pp. 473-486
    • Varghese, J.N.1    Colman, P.M.2
  • 57
    • 84855969095 scopus 로고    scopus 로고
    • Association of influenza virus proteins with membrane rafts
    • M. Veit, and B. Thaa Association of influenza virus proteins with membrane rafts Adv. Virol. 2011 2011 370606
    • (2011) Adv. Virol. , vol.2011 , pp. 370606
    • Veit, M.1    Thaa, B.2
  • 58
    • 0000931789 scopus 로고
    • Volume, shape, and roundness of quartz particles
    • H. Wadell Volume, shape, and roundness of quartz particles J. Geol. 43 1935 250 280
    • (1935) J. Geol. , vol.43 , pp. 250-280
    • Wadell, H.1
  • 60
    • 84870299253 scopus 로고    scopus 로고
    • Distribution of surface glycoproteins on influenza A virus determined by electron cryotomography
    • S. Wasilewski, L.J. Calder, T. Grant, and P.B. Rosenthal Distribution of surface glycoproteins on influenza A virus determined by electron cryotomography Vaccine 30 2012 7368 7373
    • (2012) Vaccine , vol.30 , pp. 7368-7373
    • Wasilewski, S.1    Calder, L.J.2    Grant, T.3    Rosenthal, P.B.4
  • 61
    • 84875777145 scopus 로고    scopus 로고
    • Mixing MARTINI: Electrostatic coupling in hybrid atomistic-coarse-grained biomolecular simulations
    • T.A. Wassenaar, H.I. Ingolfsson, M. Priess, S.J. Marrink, and L.V. Schafer Mixing MARTINI: electrostatic coupling in hybrid atomistic-coarse-grained biomolecular simulations J. Phys. Chem. B 117 2013 3516 3530
    • (2013) J. Phys. Chem. B , vol.117 , pp. 3516-3530
    • Wassenaar, T.A.1    Ingolfsson, H.I.2    Priess, M.3    Marrink, S.J.4    Schafer, L.V.5
  • 63
    • 84871766072 scopus 로고    scopus 로고
    • Molecular genetic basis of the human Forssman glycolipid antigen negativity
    • M. Yamamoto, E. Cid, and F. Yamamoto Molecular genetic basis of the human Forssman glycolipid antigen negativity Sci. Rep. 2 2012 975
    • (2012) Sci. Rep. , vol.2 , pp. 975
    • Yamamoto, M.1    Cid, E.2    Yamamoto, F.3
  • 65
    • 84876033771 scopus 로고    scopus 로고
    • Structure and assembly of the influenza A virus ribonucleoprotein complex
    • W. Zheng, and Y.J. Tao Structure and assembly of the influenza A virus ribonucleoprotein complex FEBS Lett. 587 2013 1206 1214
    • (2013) FEBS Lett. , vol.587 , pp. 1206-1214
    • Zheng, W.1    Tao, Y.J.2
  • 66
    • 62649155309 scopus 로고    scopus 로고
    • Mechanical properties of the icosahedral shell of Southern Bean Mosaic Virus: A molecular dynamics study
    • M. Zink, and H. Grubmüller Mechanical properties of the icosahedral shell of Southern Bean Mosaic Virus: a molecular dynamics study Biophys. J. 96 2009 1350 1363
    • (2009) Biophys. J. , vol.96 , pp. 1350-1363
    • Zink, M.1    Grubmüller, H.2
  • 67
    • 77249145890 scopus 로고    scopus 로고
    • Primary changes of the mechanical properties of Southern Bean Mosaic Virus upon calcium removal
    • M. Zink, and H. Grubmüller Primary changes of the mechanical properties of Southern Bean Mosaic Virus upon calcium removal Biophys. J. 98 2010 687 695
    • (2010) Biophys. J. , vol.98 , pp. 687-695
    • Zink, M.1    Grubmüller, H.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.