메뉴 건너뛰기




Volumn 256, Issue 4, 2009, Pages 607-624

Group theory of icosahedral virus capsid vibrations: A top-down approach

Author keywords

Biomolecular assembly; Normal modes of vibration; Viruses

Indexed keywords

THEORETICAL STUDY; TOP-DOWN APPROACH; VIBRATION; VIRUS;

EID: 58549110225     PISSN: 00225193     EISSN: 10958541     Source Type: Journal    
DOI: 10.1016/j.jtbi.2008.10.019     Document Type: Article
Times cited : (18)

References (53)
  • 1
    • 14144256567 scopus 로고    scopus 로고
    • Normal modes for predicting protein motions: a comprehensive database assessment and associated Web tool
    • Alexandrov V., Lehnert U., Echols N., Milburn D., Engelman D., and Gerstein M. Normal modes for predicting protein motions: a comprehensive database assessment and associated Web tool. Protein Sci. 14 (2005) 633
    • (2005) Protein Sci. , vol.14 , pp. 633
    • Alexandrov, V.1    Lehnert, U.2    Echols, N.3    Milburn, D.4    Engelman, D.5    Gerstein, M.6
  • 2
    • 0035132230 scopus 로고    scopus 로고
    • Anisotropy of fluctuation dynamics of proteins with an elastic network model
    • Atilgan A., Durell S., Jernigan R., Demirel M., Keskin O., and Bahar I. Anisotropy of fluctuation dynamics of proteins with an elastic network model. Biophys. J. 80 (2001) 505-515
    • (2001) Biophys. J. , vol.80 , pp. 505-515
    • Atilgan, A.1    Durell, S.2    Jernigan, R.3    Demirel, M.4    Keskin, O.5    Bahar, I.6
  • 3
    • 25844431698 scopus 로고    scopus 로고
    • Coarse-grained normal mode analysis in structural biology
    • Bahar I., and Rader A.J. Coarse-grained normal mode analysis in structural biology. Curr. Opin. Struct. Biol. 15 (2005) 586-592
    • (2005) Curr. Opin. Struct. Biol. , vol.15 , pp. 586-592
    • Bahar, I.1    Rader, A.J.2
  • 4
    • 58549093281 scopus 로고    scopus 로고
    • Baskerville, W.K., Vibrational spectrum of the B = 7 Skyrme soliton, hep-th/9906063.
    • Baskerville, W.K., Vibrational spectrum of the B = 7 Skyrme soliton, hep-th/9906063.
  • 6
    • 0000991642 scopus 로고
    • Harmonic dynamics of proteins: normal modes and fluctuations in bovine pancreatic trypsin inhibitor
    • Brooks B.R., and Karplus M. Harmonic dynamics of proteins: normal modes and fluctuations in bovine pancreatic trypsin inhibitor. Proc. Natl. Acad. Sci. 80 (1983) 6571
    • (1983) Proc. Natl. Acad. Sci. , vol.80 , pp. 6571
    • Brooks, B.R.1    Karplus, M.2
  • 7
    • 0022111715 scopus 로고
    • Normal modes for specific motions of macromolecules: application to the hinge-bending mode of lysozyme
    • Brooks B.R., and Karplus M. Normal modes for specific motions of macromolecules: application to the hinge-bending mode of lysozyme. Proc. Natl. Acad. Sci. 82 (1985) 4995
    • (1985) Proc. Natl. Acad. Sci. , vol.82 , pp. 4995
    • Brooks, B.R.1    Karplus, M.2
  • 8
    • 73649156890 scopus 로고
    • Physical principles in the construction of regular viruses
    • Caspar D., and Klug A. Physical principles in the construction of regular viruses. Cold Spring Harbor Symp. Quant. Biol. 27 (1962) 1-24
    • (1962) Cold Spring Harbor Symp. Quant. Biol. , vol.27 , pp. 1-24
    • Caspar, D.1    Klug, A.2
  • 10
    • 0028454915 scopus 로고
    • A new approach for determining low-frequency normal modes in macromolecules
    • Durand P., Trinquier G., and Sanejouand Y.-H. A new approach for determining low-frequency normal modes in macromolecules. Biophysics 34 (1994) 759-771
    • (1994) Biophysics , vol.34 , pp. 759-771
    • Durand, P.1    Trinquier, G.2    Sanejouand, Y.-H.3
  • 11
    • 40749090883 scopus 로고    scopus 로고
    • Low frequency mechanical modes of viral capsids: an atomistic approach
    • Dykeman E.C., and Sankey O.F. Low frequency mechanical modes of viral capsids: an atomistic approach. Phys. Rev. Lett. 100 (2008) 028101
    • (2008) Phys. Rev. Lett. , vol.100 , pp. 028101
    • Dykeman, E.C.1    Sankey, O.F.2
  • 12
    • 42749088837 scopus 로고    scopus 로고
    • Dynamical implications of viral tiling theory
    • arXiv:0711.0541 [q-bio.BM]
    • ElSawy K.M., Taormina A., Twarock R., and Vaughan L. Dynamical implications of viral tiling theory. J. Theor. Biol. 252 (2008) 357-369. http://xxx.lanl.gov/abs/0711.0541 arXiv:0711.0541 [q-bio.BM]
    • (2008) J. Theor. Biol. , vol.252 , pp. 357-369
    • ElSawy, K.M.1    Taormina, A.2    Twarock, R.3    Vaughan, L.4
  • 13
    • 51849114210 scopus 로고    scopus 로고
    • Englert, F., Peeters, K., Taormina, A., 2008. Twenty-four near-instabilities of Caspar-Klug viruses. Phys. Rev. E 78, 031908 arxiv:0804.4275.
    • Englert, F., Peeters, K., Taormina, A., 2008. Twenty-four near-instabilities of Caspar-Klug viruses. Phys. Rev. E 78, 031908 arxiv:0804.4275.
  • 14
    • 33644848399 scopus 로고    scopus 로고
    • Molecular dynamics simulations of the complete satellite tobacco mosaic virus
    • Freddolino P., Arkhipov A., Larson S., McPherson A., and Schulten K. Molecular dynamics simulations of the complete satellite tobacco mosaic virus. Structure 14 (2006) 437-449
    • (2006) Structure , vol.14 , pp. 437-449
    • Freddolino, P.1    Arkhipov, A.2    Larson, S.3    McPherson, A.4    Schulten, K.5
  • 15
    • 34548444203 scopus 로고    scopus 로고
    • Mechanical modeling of viral capsids
    • Gibbons M.M., and Klug W.S. Mechanical modeling of viral capsids. J. Material Sci. 42 (2007) 8995-9004
    • (2007) J. Material Sci. , vol.42 , pp. 8995-9004
    • Gibbons, M.M.1    Klug, W.S.2
  • 16
    • 0025066772 scopus 로고
    • Normal mode analysis of human lysozyme: study of the relative motion of the two domains and characterization of the harmonic motion
    • Gibrat J.F., and Go N. Normal mode analysis of human lysozyme: study of the relative motion of the two domains and characterization of the harmonic motion. Proteins 8 (1990) 258
    • (1990) Proteins , vol.8 , pp. 258
    • Gibrat, J.F.1    Go, N.2
  • 17
    • 0020771265 scopus 로고
    • Dynamics of a small globular protein in terms of low-frequency vibrational modes
    • Go N., Noguti T., and Nishikawa T. Dynamics of a small globular protein in terms of low-frequency vibrational modes. Proc. Natl. Acad. Sci. 80 (1983) 3696
    • (1983) Proc. Natl. Acad. Sci. , vol.80 , pp. 3696
    • Go, N.1    Noguti, T.2    Nishikawa, T.3
  • 18
    • 0021701376 scopus 로고
    • Variational calculation of the normal modes of a large macromolecule: methods and some initial results
    • Harrison R. Variational calculation of the normal modes of a large macromolecule: methods and some initial results. Biopolymers 23 (1984) 2943
    • (1984) Biopolymers , vol.23 , pp. 2943
    • Harrison, R.1
  • 19
    • 9144263145 scopus 로고    scopus 로고
    • Structural rigidity in the capsid assembly of cowpea chlorotic mottle virus
    • Hespenheide B., Jacobs D., and Thorpe M. Structural rigidity in the capsid assembly of cowpea chlorotic mottle virus. J. Phys. Condens. Matter 16 (2004) S5055-S5064
    • (2004) J. Phys. Condens. Matter , vol.16
    • Hespenheide, B.1    Jacobs, D.2    Thorpe, M.3
  • 20
    • 1842686516 scopus 로고    scopus 로고
    • Shapes and cycles arising at the steady bifurcation with icosahedral symmetry
    • Hoyle R.B. Shapes and cycles arising at the steady bifurcation with icosahedral symmetry. Physica D 191 (2004) 261-281
    • (2004) Physica D , vol.191 , pp. 261-281
    • Hoyle, R.B.1
  • 21
    • 58549106477 scopus 로고    scopus 로고
    • Humphreys, J.E., 1990. Reflection Groups and Coxeter Groups. Cambridge Studies in Advanced Mathematics, vol. 29. Cambridge University Press, Cambridge.
    • Humphreys, J.E., 1990. Reflection Groups and Coxeter Groups. Cambridge Studies in Advanced Mathematics, vol. 29. Cambridge University Press, Cambridge.
  • 22
    • 0000785338 scopus 로고
    • Generic rigidity percolation: the pebble game
    • Jacobs D.J., and Thorpe M.F. Generic rigidity percolation: the pebble game. Phys. Rev. Lett. 75 (1995) 4051-4054
    • (1995) Phys. Rev. Lett. , vol.75 , pp. 4051-4054
    • Jacobs, D.J.1    Thorpe, M.F.2
  • 23
    • 28944434207 scopus 로고    scopus 로고
    • A connection rule for α-carbon coarse-grained elastic network models using chemical bond information
    • Jeong J.I., Jang Y., and Kim M.K. A connection rule for α-carbon coarse-grained elastic network models using chemical bond information. J. Mol. Graphics Modelling 24 (2006) 296
    • (2006) J. Mol. Graphics Modelling , vol.24 , pp. 296
    • Jeong, J.I.1    Jang, Y.2    Kim, M.K.3
  • 24
    • 33745014804 scopus 로고    scopus 로고
    • Using harmonic analysis and optimization to study macromolecular dynamics
    • Jeong J.I., Jang Y., and Kim M.K. Using harmonic analysis and optimization to study macromolecular dynamics. Int. J. Control Autom. Syst. 4 (2006) 382
    • (2006) Int. J. Control Autom. Syst. , vol.4 , pp. 382
    • Jeong, J.I.1    Jang, Y.2    Kim, M.K.3
  • 25
    • 33747826334 scopus 로고    scopus 로고
    • UMMS: constrained harmonic and anharmonic analyses of macromolecules based on elastic network models
    • Jeong J.I., Jang Y., and Kim M.K. UMMS: constrained harmonic and anharmonic analyses of macromolecules based on elastic network models. Nucl. Acids Res. 34 (2006) W57
    • (2006) Nucl. Acids Res. , vol.34
    • Jeong, J.I.1    Jang, Y.2    Kim, M.K.3
  • 26
    • 21844471075 scopus 로고    scopus 로고
    • Assembly models of papovaviridae based on tiling theory
    • q-bio/0508031
    • Keef T., Taormina A., and Twarock R. Assembly models of papovaviridae based on tiling theory. Phys. Biol. 2 (2005) 175-188. http://xxx.lanl.gov/abs/q-bio/0508031 q-bio/0508031
    • (2005) Phys. Biol. , vol.2 , pp. 175-188
    • Keef, T.1    Taormina, A.2    Twarock, R.3
  • 27
    • 33645287743 scopus 로고    scopus 로고
    • Classification of capped tubular viral particles in the family of Papovaviridae
    • q-bio.BM/0510028
    • Keef T., Taormina A., and Twarock R. Classification of capped tubular viral particles in the family of Papovaviridae. J. Phys. Condens. Matter 18 (2006) S375-S387. http://xxx.lanl.gov/abs/q-bio.BM/0510028 q-bio.BM/0510028
    • (2006) J. Phys. Condens. Matter , vol.18
    • Keef, T.1    Taormina, A.2    Twarock, R.3
  • 28
    • 33645282189 scopus 로고    scopus 로고
    • Master equation approach to the assembly of viral capsids
    • q-bio.BM/0508030
    • Keef T., Micheletti C., and Twarock R. Master equation approach to the assembly of viral capsids. J. Theor. Biol. 242 (2006) 713-721. http://xxx.lanl.gov/abs/q-bio.BM/0508030 q-bio.BM/0508030
    • (2006) J. Theor. Biol. , vol.242 , pp. 713-721
    • Keef, T.1    Micheletti, C.2    Twarock, R.3
  • 29
    • 47849116168 scopus 로고    scopus 로고
    • Blueprints for viral capsids in the family of polyomaviridae
    • Keef T., Twarock R., and Elsawy K.M. Blueprints for viral capsids in the family of polyomaviridae. J. Theor. Biol. 253 (2008) 808-816
    • (2008) J. Theor. Biol. , vol.253 , pp. 808-816
    • Keef, T.1    Twarock, R.2    Elsawy, K.M.3
  • 30
    • 0041334008 scopus 로고    scopus 로고
    • An elastic network model of HK97 capsid maturation
    • Kim M., Jernigan R., and Chirikjian G. An elastic network model of HK97 capsid maturation. J. Struct. Biol. 143 (2003) 107-117
    • (2003) J. Struct. Biol. , vol.143 , pp. 107-117
    • Kim, M.1    Jernigan, R.2    Chirikjian, G.3
  • 31
    • 0014856102 scopus 로고    scopus 로고
    • Laman, G., 1970. On graphs and rigidity of plane skeletal structures, J. Eng. Math. 331-340.
    • Laman, G., 1970. On graphs and rigidity of plane skeletal structures, J. Eng. Math. 331-340.
  • 32
    • 84990678054 scopus 로고
    • Protein normal-mode dynamics: trypsin inhibitor, crambin, ribonuclease and lysozyme
    • Levitt M., Sander C., and Stern P. Protein normal-mode dynamics: trypsin inhibitor, crambin, ribonuclease and lysozyme. Int. J. Quantum Chem. 10 (1983) 181
    • (1983) Int. J. Quantum Chem. , vol.10 , pp. 181
    • Levitt, M.1    Sander, C.2    Stern, P.3
  • 33
    • 0029560322 scopus 로고
    • Hinge-bending motion in citrate synthase arising from normal mode calculations
    • Marques O., and Sanejouand Y.H. Hinge-bending motion in citrate synthase arising from normal mode calculations. Proteins 23 (1995) 557
    • (1995) Proteins , vol.23 , pp. 557
    • Marques, O.1    Sanejouand, Y.H.2
  • 35
    • 0029937635 scopus 로고    scopus 로고
    • Motions in hemoglobin studied by normal mode analysis and energy minimization: evidence for the existence of tertiary T-like, quaternary R-like intermediate structures
    • Mouawad L., and Perahia D. Motions in hemoglobin studied by normal mode analysis and energy minimization: evidence for the existence of tertiary T-like, quaternary R-like intermediate structures. J. Mol. Biol. 258 (1996) 393
    • (1996) J. Mol. Biol. , vol.258 , pp. 393
    • Mouawad, L.1    Perahia, D.2
  • 36
    • 0020488742 scopus 로고
    • Collective variable description of small-amplitude conformational fluctuations in a globular protein
    • Noguti T., and Go N. Collective variable description of small-amplitude conformational fluctuations in a globular protein. Nature 296 (1982) 776
    • (1982) Nature , vol.296 , pp. 776
    • Noguti, T.1    Go, N.2
  • 37
    • 0037155021 scopus 로고    scopus 로고
    • Affine extensions of noncrystallographic Coxeter groups and quasicrystals
    • Patera J., and Twarock R. Affine extensions of noncrystallographic Coxeter groups and quasicrystals. J. Phys. A 35 (2002) 1551-1574
    • (2002) J. Phys. A , vol.35 , pp. 1551-1574
    • Patera, J.1    Twarock, R.2
  • 38
    • 14844300852 scopus 로고    scopus 로고
    • Maturation dynamics of bacteriophage HK97
    • Rader A., Vlad D., and Bahar I. Maturation dynamics of bacteriophage HK97. Structure 13 (2005) 413-421
    • (2005) Structure , vol.13 , pp. 413-421
    • Rader, A.1    Vlad, D.2    Bahar, I.3
  • 39
    • 58549112290 scopus 로고    scopus 로고
    • Sanejouand, Y.-H., Les modes normaux de vibration de basse fréquence des protéines. Ph.D. Thesis, Ecole Normale Supérieure Lyon, 2007.
    • Sanejouand, Y.-H., Les modes normaux de vibration de basse fréquence des protéines. Ph.D. Thesis, Ecole Normale Supérieure Lyon, 2007.
  • 40
    • 24944492922 scopus 로고    scopus 로고
    • Efficient determination of low-frequency normal modes of large protein structures by cluster-NMA
    • Schuyler A.D., and Chirikjian G.S. Efficient determination of low-frequency normal modes of large protein structures by cluster-NMA. J. Mol. Graphics Modelling 24 (2005) 46-58
    • (2005) J. Mol. Graphics Modelling , vol.24 , pp. 46-58
    • Schuyler, A.D.1    Chirikjian, G.S.2
  • 42
    • 48549096060 scopus 로고
    • Normal modes of symmetric protein assemblies
    • Simonson T., and Perahia D. Normal modes of symmetric protein assemblies. Biophys. J. 61 (1992) 427
    • (1992) Biophys. J. , vol.61 , pp. 427
    • Simonson, T.1    Perahia, D.2
  • 43
    • 0036307741 scopus 로고    scopus 로고
    • The mechanism and pathway of pH induced swelling in cowpea chlorotic mottle virus
    • Tama F., and Brooks C.L. The mechanism and pathway of pH induced swelling in cowpea chlorotic mottle virus. J. Mol. Biol. 318 (2002) 733
    • (2002) J. Mol. Biol. , vol.318 , pp. 733
    • Tama, F.1    Brooks, C.L.2
  • 44
    • 9644266693 scopus 로고    scopus 로고
    • Diversity and identity of mechanical properties of icosahedral viral capsids studied with elastic network normal mode analysis
    • Tama F., and Brooks C.L. Diversity and identity of mechanical properties of icosahedral viral capsids studied with elastic network normal mode analysis. J. Mol. Biol. 345 (2005) 299
    • (2005) J. Mol. Biol. , vol.345 , pp. 299
    • Tama, F.1    Brooks, C.L.2
  • 45
    • 33745024278 scopus 로고    scopus 로고
    • Symmetry, form, and shape: guiding principles for robustness in macromolecular machines
    • Tama F., and Brooks C.L. Symmetry, form, and shape: guiding principles for robustness in macromolecular machines. Annu. Rev. Biophys. Biomol. Struct. 35 (2006) 115-133
    • (2006) Annu. Rev. Biophys. Biomol. Struct. , vol.35 , pp. 115-133
    • Tama, F.1    Brooks, C.L.2
  • 46
    • 0000197372 scopus 로고    scopus 로고
    • Large amplitude elastic motions in proteins from a single-parameter, atomic analysis
    • Tirion M.M. Large amplitude elastic motions in proteins from a single-parameter, atomic analysis. Phys. Rev. Lett. 77 (1996) 1905-1908
    • (1996) Phys. Rev. Lett. , vol.77 , pp. 1905-1908
    • Tirion, M.M.1
  • 47
    • 36048951075 scopus 로고    scopus 로고
    • Selective inactivation of micro-organisms with near-infrared femtosecond laser pulses
    • Tsen K.T., Tsen S.-W.D., Sankey O.F., and Kiang J.G. Selective inactivation of micro-organisms with near-infrared femtosecond laser pulses. J. Phys. Condens. Matter 19 (2007) 472201
    • (2007) J. Phys. Condens. Matter , vol.19 , pp. 472201
    • Tsen, K.T.1    Tsen, S.-W.D.2    Sankey, O.F.3    Kiang, J.G.4
  • 48
    • 0842283367 scopus 로고    scopus 로고
    • A tiling approach to virus capsid assembly explaining a structural puzzle in virology
    • Twarock R. A tiling approach to virus capsid assembly explaining a structural puzzle in virology. J. Theor. Biol. 226 (2004) 477
    • (2004) J. Theor. Biol. , vol.226 , pp. 477
    • Twarock, R.1
  • 49
    • 33845629453 scopus 로고    scopus 로고
    • Mathematical virology: a novel approach to the structure and assembly of viruses
    • Twarock R. Mathematical virology: a novel approach to the structure and assembly of viruses. Philos. Trans. R. Soc. 364 (2006) 3357-3373
    • (2006) Philos. Trans. R. Soc. , vol.364 , pp. 3357-3373
    • Twarock, R.1
  • 50
  • 51
    • 20444440419 scopus 로고    scopus 로고
    • Normal mode calculations of icosahedral viruses with full dihedral flexibility by use of molecular symmetry
    • Vlijmen H.W.T.v., and Karplus M. Normal mode calculations of icosahedral viruses with full dihedral flexibility by use of molecular symmetry. J. Mol. Biol. 350 (2005) 528-542
    • (2005) J. Mol. Biol. , vol.350 , pp. 528-542
    • Vlijmen, H.W.T.v.1    Karplus, M.2
  • 52
    • 58549112875 scopus 로고    scopus 로고
    • Wigner E., 1930. Göttinger Nachrichten, p. 133.
    • Wigner E., 1930. Göttinger Nachrichten, p. 133.
  • 53
    • 0042100474 scopus 로고
    • The normal modes and frequencies of vibration of the regular plane hexagon model of the benzene molecule
    • Wilson E. The normal modes and frequencies of vibration of the regular plane hexagon model of the benzene molecule. Phys. Rev. 45 (1934) 706-714
    • (1934) Phys. Rev. , vol.45 , pp. 706-714
    • Wilson, E.1


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.