메뉴 건너뛰기




Volumn 9, Issue 3-4, 2008, Pages 245-256

Polyomaviridae assembly polymorphism from an energy landscape perspective

Author keywords

Assembly polymorphism; Energy landscape; SV40; Viral tiling theory

Indexed keywords

AGGREGATES; CALCIUM COMPOUNDS; COMPUTATION THEORY; CRYSTAL STRUCTURE; FREE ENERGY; IONS; POLYMORPHISM; PROTEINS; SULFUR COMPOUNDS; VIRUSES;

EID: 48549105510     PISSN: 1748670X     EISSN: 17486718     Source Type: Journal    
DOI: 10.1080/17486700802167983     Document Type: Conference Paper
Times cited : (3)

References (38)
  • 1
    • 0035964342 scopus 로고    scopus 로고
    • Electrostatics of nanosystems: Application to microtubules and the ribosome
    • Baker, N. A., Sept, D., Joseph, S., Holst, M. J. and McCammon, J. A. (2001) Electrostatics of nanosystems: Application to microtubules and the ribosome. 98, pp. 10037-10041.
    • (2001) , vol.98 , pp. 10037-10041
    • Baker, N.A.1    Sept, D.2    Joseph, S.3    Holst, M.J.4    McCammon, J.A.5
  • 2
    • 0036199391 scopus 로고    scopus 로고
    • Structural requirements for the assembly of Norwalk virus-like particles
    • Bertolotti-Ciarlet, A., White, L. J., Chen, R., Prasad, B. V. and Estes, M. K. (2002) Structural requirements for the assembly of Norwalk virus-like particles. 76, pp. 4044-4055.
    • (2002) , vol.76 , pp. 4044-4055
    • Bertolotti-Ciarlet, A.1    White, L.J.2    Chen, R.3    Prasad, B.V.4    Estes, M.K.5
  • 3
    • 84986512474 scopus 로고
    • CHARMM - A program for macromolecular energy, minimization, and dynamics calculations
    • Brooks, B. R., Bruccoleri, R. E., Olafson, B. D., States, D. J., Swaminathan, S. and Karplus, M. (1983) CHARMM-a program for macromolecular energy, minimization, and dynamics calculations. 4, pp. 187-217.
    • (1983) , vol.4 , pp. 187-217
    • Brooks, B.R.1    Bruccoleri, R.E.2    Olafson, B.D.3    States, D.J.4    Swaminathan, S.5    Karplus, M.6
  • 4
  • 5
    • 73649156890 scopus 로고
    • Physical principles in the construction of regular viruses
    • Caspar, D. L. and Klug, A. (1962) Physical principles in the construction of regular viruses. 27, pp. 1-24.
    • (1962) , vol.27 , pp. 1-24
    • Caspar, D.L.1    Klug, A.2
  • 6
    • 0017340452 scopus 로고
    • Characterization of components released by alkali disruption of simian virus 40
    • Christiansen, G., Landers, T., Griffith, J. and Berg, P. (1977) Characterization of components released by alkali disruption of simian virus 40. 21, pp. 1079-1084.
    • (1977) , vol.21 , pp. 1079-1084
    • Christiansen, G.1    Landers, T.2    Griffith, J.3    Berg, P.4
  • 7
    • 26944458918 scopus 로고    scopus 로고
    • The physical determinants of the DNA conformational landscape: An analysis of the potential energy surface of single-strand dinucleotides in the conformational space of duplex DNA
    • ElSawy, K. M., Hodgson, M. K. and Caves, L. S. D. (2005) The physical determinants of the DNA conformational landscape: An analysis of the potential energy surface of single-strand dinucleotides in the conformational space of duplex DNA. 33, pp. 5749-5762.
    • (2005) , vol.33 , pp. 5749-5762
    • ElSawy, K.M.1    Hodgson, M.K.2    Caves, L.S.D.3
  • 8
    • 0035997081 scopus 로고    scopus 로고
    • Model-based analysis of assembly kinetics for virus capsids or other spherical polymers
    • Endres, D. and Zlotnick, A. (2002) Model-based analysis of assembly kinetics for virus capsids or other spherical polymers. 83, pp. 1217-1230.
    • (2002) , vol.83 , pp. 1217-1230
    • Endres, D.1    Zlotnick, A.2
  • 9
    • 48549096940 scopus 로고    scopus 로고
    • Biologic constraint on modelling virus assembly
    • Garcea, R. L. (2008) Biologic constraint on modelling virus assembly. pp. 257-264.
    • (2008) , pp. 257-264
    • Garcea, R.L.1
  • 10
    • 0040321024 scopus 로고    scopus 로고
    • Experimental measurement of the effective dielectric in the hydrophobic core of a protein
    • Garcia-Moreno, B., Dwyer, J. J., Gittis, A. G., Lattman, E. E., Spencer, D. S. and Stites, W. E. (1997) Experimental measurement of the effective dielectric in the hydrophobic core of a protein. 64, pp. 211-224.
    • (1997) , vol.64 , pp. 211-224
    • Garcia-Moreno, B.1    Dwyer, J.J.2    Gittis, A.G.3    Lattman, E.E.4    Spencer, D.S.5    Stites, W.E.6
  • 11
    • 34247261990 scopus 로고    scopus 로고
    • Free energy landscape of a biomolecule in dihedral principal component space: Sampling convergence and correspondence between structures and minima
    • Gia, G. and Maisuradze, D. M. L. (2007) Free energy landscape of a biomolecule in dihedral principal component space: Sampling convergence and correspondence between structures and minima. 67, pp. 569-578.
    • (2007) , vol.67 , pp. 569-578
    • Gia, G.1    Maisuradze, D.M.L.2
  • 12
    • 0347602124 scopus 로고    scopus 로고
    • Converging free energy estimates: MM-PB(GB)SA studies on the protein-protein complex Ras-Raf
    • Gohlke, H. and Case, D. A. (2004) Converging free energy estimates: MM-PB(GB)SA studies on the protein-protein complex Ras-Raf. 25, pp. 238-250.
    • (2004) , vol.25 , pp. 238-250
    • Gohlke, H.1    Case, D.A.2
  • 13
    • 33745787907 scopus 로고    scopus 로고
    • Dynamic pathways for viral capsid assembly
    • Hagan, M. F. and Chandler, D. (2006) Dynamic pathways for viral capsid assembly. 91, pp. 42-54.
    • (2006) , vol.91 , pp. 42-54
    • Hagan, M.F.1    Chandler, D.2
  • 14
    • 33646132744 scopus 로고    scopus 로고
    • Stochastic kinetics of viral capsid assembly based on detailed protein structures
    • Hemberg, M., Yaliraki, S. N. and Barahona, M. (2006) Stochastic kinetics of viral capsid assembly based on detailed protein structures. 90, pp. 3029-3042.
    • (2006) , vol.90 , pp. 3029-3042
    • Hemberg, M.1    Yaliraki, S.N.2    Barahona, M.3
  • 15
    • 28644432877 scopus 로고    scopus 로고
    • Very fast empirical prediction and rationalization of protein pKa values
    • Hui, Li, Robertson, A. D. and Jensen, J. H. (2005) Very fast empirical prediction and rationalization of protein pKa values. 61, pp. 704-721.
    • (2005) , vol.61 , pp. 704-721
    • Hui, Li.1    Robertson, A.D.2    Jensen, J.H.3
  • 16
    • 0034749345 scopus 로고    scopus 로고
    • Roles of disulfide linkage and calcium ion-mediated interactions in assembly and disassembly of virus-like particles composed of simian virus 40 VP1 capsid protein
    • Ishizu, K. I., Watanabe, H., Han, S. I., Kanesashi, S. N., Hoque, M., Yajima, H., Kataoka, K. and Handa, H. (2001) Roles of disulfide linkage and calcium ion-mediated interactions in assembly and disassembly of virus-like particles composed of simian virus 40 VP1 capsid protein. 75, pp. 61-72.
    • (2001) , vol.75 , pp. 61-72
    • Ishizu, K.I.1    Watanabe, H.2    Han, S.I.3    Kanesashi, S.N.4    Hoque, M.5    Yajima, H.6    Kataoka, K.7    Handa, H.8
  • 17
    • 0032817445 scopus 로고    scopus 로고
    • Cys9, Cys104 and Cys207 of simian virus 40 Vp1 are essential for inter-pentamer disulfide-linkage and stabilization in cell-free lysates
    • Jao, C. C., Weidman, M. K., Perez, A. R. and Gharakhanian, E. (1999) Cys9, Cys104 and Cys207 of simian virus 40 Vp1 are essential for inter-pentamer disulfide-linkage and stabilization in cell-free lysates. 80, pp. 2481-2489.
    • (1999) , vol.80 , pp. 2481-2489
    • Jao, C.C.1    Weidman, M.K.2    Perez, A.R.3    Gharakhanian, E.4
  • 19
    • 21844471075 scopus 로고    scopus 로고
    • Assembly models for Papovaviridae based on tiling theory
    • Keef, T., Taormina, A. and Twarock, R. (2005) Assembly models for Papovaviridae based on tiling theory. 2, pp. 175-188.
    • (2005) , vol.2 , pp. 175-188
    • Keef, T.1    Taormina, A.2    Twarock, R.3
  • 20
    • 33645287743 scopus 로고    scopus 로고
    • Classification of capped tubular viral particles in the family of Papovaviridae
    • Keef, T., Taormina, A. and Twarock, R. (2006) Classification of capped tubular viral particles in the family of Papovaviridae. 18, p. S375.
    • (2006) , vol.18
    • Keef, T.1    Taormina, A.2    Twarock, R.3
  • 21
    • 48549089362 scopus 로고    scopus 로고
    • Blueprints for viral capsids in the family of Papovaviridae
    • Keef, T., Twarock, R. and Elsawy, K. M. (2008) Blueprints for viral capsids in the family of Papovaviridae.
    • (2008)
    • Keef, T.1    Twarock, R.2    Elsawy, K.M.3
  • 22
    • 0029984841 scopus 로고    scopus 로고
    • Purification and characterization of virus-like particles and pentamers produced by the expression of SV40 capsid proteins in insect cells
    • Kosukegawa, A., Arisaka, F., Takayama, M., Yajima, H., Kaidow, A. and Handa, H. (1996) Purification and characterization of virus-like particles and pentamers produced by the expression of SV40 capsid proteins in insect cells. 1290, pp. 37-45.
    • (1996) , vol.1290 , pp. 37-45
    • Kosukegawa, A.1    Arisaka, F.2    Takayama, M.3    Yajima, H.4    Kaidow, A.5    Handa, H.6
  • 24
    • 33847712647 scopus 로고    scopus 로고
    • Deciphering the kinetic mechanism of spontaneous self-assembly of icosahedral capsids
    • Nguyen, H. D., Reddy, V. S. and Brooks III, C. L. (2007) Deciphering the kinetic mechanism of spontaneous self-assembly of icosahedral capsids. 7, pp. 338-344.
    • (2007) , vol.7 , pp. 338-344
    • Nguyen, H.D.1    Reddy, V.S.2    Brooks III, C.L.3
  • 25
    • 0042115213 scopus 로고    scopus 로고
    • A new paradigm for parallel adaptive meshing algorithms
    • Randolph, E. B. and Michael, H. (2000) A new paradigm for parallel adaptive meshing algorithms. 22, pp. 1411-1443.
    • (2000) , vol.22 , pp. 1411-1443
    • Randolph, E.B.1    Michael, H.2
  • 26
    • 38349040438 scopus 로고    scopus 로고
    • Self-assembly of polyhedral shells: A molecular dynamics study
    • Rapaport, D. C. (2004) Self-assembly of polyhedral shells: A molecular dynamics study. 70, p. 51905.
    • (2004) , vol.70 , pp. 51905
    • Rapaport, D.C.1
  • 27
    • 0020031457 scopus 로고
    • Polyoma virus capsid structure at 22.5 Å resolution
    • Rayment, I., Baker, T. S., Caspar, D. L. D. and Murakami, W. T. (1982) Polyoma virus capsid structure at 22.5 Å resolution. 295, pp. 110-115.
    • (1982) , vol.295 , pp. 110-115
    • Rayment, I.1    Baker, T.S.2    Caspar, D.L.D.3    Murakami, W.T.4
  • 28
    • 0022549499 scopus 로고
    • Self-assembly of purified polyomavirus capsid protein VP1
    • Salunke, D. M., Caspar, D. L. and Garcea, R. L. (1986) Self-assembly of purified polyomavirus capsid protein VP1. 46, pp. 895-904.
    • (1986) , vol.46 , pp. 895-904
    • Salunke, D.M.1    Caspar, D.L.2    Garcea, R.L.3
  • 29
    • 0024761528 scopus 로고
    • Polymorphism in the assembly of polyomavirus capsid protein VP1
    • Salunke, D. M., Caspar, D. L. and Garcea, R. L. (1989) Polymorphism in the assembly of polyomavirus capsid protein VP1. 56, pp. 887-900.
    • (1989) , vol.56 , pp. 887-900
    • Salunke, D.M.1    Caspar, D.L.2    Garcea, R.L.3
  • 30
    • 0141634366 scopus 로고    scopus 로고
    • The physical basis of microtubule structure and stability
    • Sept, D., Baker, N. A. and McCammon, J. A. (2003) The physical basis of microtubule structure and stability. 12, pp. 2257-2261.
    • (2003) , vol.12 , pp. 2257-2261
    • Sept, D.1    Baker, N.A.2    McCammon, J.A.3
  • 31
    • 32844457567 scopus 로고
    • Accurate calculation of hydration free energies using macroscopic solvent models
    • Sitkoff, D., Sharp, K. A. and Honig, B. (1994) Accurate calculation of hydration free energies using macroscopic solvent models. 98, pp. 1978-1988.
    • (1994) , vol.98 , pp. 1978-1988
    • Sitkoff, D.1    Sharp, K.A.2    Honig, B.3
  • 32
    • 0030584124 scopus 로고    scopus 로고
    • The structure of simian virus 40 refined at 3.1 Å resolution
    • Stehle, T., Gamblin, S. J., Yan, Y. and Harrison, S. C. (1996) The structure of simian virus 40 refined at 3.1 Å resolution. 4, pp. 165-182.
    • (1996) , vol.4 , pp. 165-182
    • Stehle, T.1    Gamblin, S.J.2    Yan, Y.3    Harrison, S.C.4
  • 33
    • 0347949637 scopus 로고    scopus 로고
    • Revisiting free energy calculations: A theoretical connection to MM/PBSA and direct calculation of the association free energy
    • Swanson, J. M., Henchman, R. H. and McCammon, J. A. (2004) Revisiting free energy calculations: A theoretical connection to MM/PBSA and direct calculation of the association free energy. 86, pp. 67-74.
    • (2004) , vol.86 , pp. 67-74
    • Swanson, J.M.1    Henchman, R.H.2    McCammon, J.A.3
  • 34
    • 48549097723 scopus 로고
    • Disulphide bonds and protein stability
    • Thomas, E. C. (1988) Disulphide bonds and protein stability. 8, pp. 57-63.
    • (1988) , vol.8 , pp. 57-63
    • Thomas, E.C.1
  • 35
    • 21444443790 scopus 로고    scopus 로고
    • Mathematical models for tubular structures in the family of Papovaviridae
    • Twarock, R. (2005) Mathematical models for tubular structures in the family of Papovaviridae. 67, pp. 973-987.
    • (2005) , vol.67 , pp. 973-987
    • Twarock, R.1
  • 36
    • 33845629453 scopus 로고    scopus 로고
    • Mathematical virology: A novel approach to the structure and assembly of viruses
    • Twarock, R. (2006) Mathematical virology: A novel approach to the structure and assembly of viruses. 364, pp. 3357-3373.
    • (2006) , vol.364 , pp. 3357-3373
    • Twarock, R.1
  • 37
    • 8144227214 scopus 로고    scopus 로고
    • Origin of icosahedral symmetry in viruses
    • Zandi, R., Reguera, D., Bruinsma, R. F., Gelbart, W. M. and Rudnick, J. (2004) Origin of icosahedral symmetry in viruses. 101, pp. 15556-15560.
    • (2004) , vol.101 , pp. 15556-15560
    • Zandi, R.1    Reguera, D.2    Bruinsma, R.F.3    Gelbart, W.M.4    Rudnick, J.5
  • 38
    • 0034715825 scopus 로고    scopus 로고
    • Mechanism of capsid assembly for an icosahedral plant virus
    • Zlotnick, A., Aldrich, R., Johnson, J. M., Ceres, P. and Young, M. J. (2000) Mechanism of capsid assembly for an icosahedral plant virus. 277, pp. 450-456.
    • (2000) , vol.277 , pp. 450-456
    • Zlotnick, A.1    Aldrich, R.2    Johnson, J.M.3    Ceres, P.4    Young, M.J.5


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.