Energy landscape for DNA rotation and sliding through a phage portal

Biophysical Journal

Volumn 96, Issue 4, 2009, Pages

  Nummela, Jeremiah ^a   Andricioaei, Ioan ^a  

^a UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

OSTEOPONTIN; VIRUS DNA;

ARTICLE; BACTERIOPHAGE; CRYOELECTRON MICROSCOPY; CRYSTAL STRUCTURE; DNA PACKAGING; ENERGY; MOLECULAR DYNAMICS; MOLECULAR MODEL; NONHUMAN; PROTEIN DNA BINDING; TEMPERATURE DEPENDENCE; VALIDATION PROCESS; BACILLUS PHAGE; BACILLUS SUBTILIS; CHEMICAL STRUCTURE; CHEMISTRY; COMPUTER SIMULATION; LETTER; METABOLISM; PHYSIOLOGY; ROTATION; VIRION;

BACILLUS PHAGES; BACILLUS SUBTILIS; COMPUTER SIMULATION; DNA, VIRAL; MODELS, MOLECULAR; ROTATION; VIRION;

EID: 62649121513     PISSN: 00063495     EISSN: 15420086     Source Type: Journal    
DOI: 10.1016/j.bpj.2008.12.3761     Document Type: Article

References (16)

1. Moore, S. D., and P. E. Prevelige Jr. 2002. DNA packaging: a new class of molecular motors. Curr. Biol. 12:R96-R98.
2. Johnson, J. E., and W. Chiu. 2007. DNA packaging and delivery machines in tailed bacteriophages. Curr. Opin. Struct. Biol. 17:237-243. (Pubitemid 46575256)
3. Smith, D. E., S. J. Tans, S. B. Smith, S. Grimes, D. L. Anderson, et al. 2001. The bacteriophage φ29 portal motor can package DNA against a large internal force. Nature. 413:748-752.
4. Rickgauer, J. P., D. N. Fuller, S. Grimes, P. J. Jardine, D. L. Anderson, et al. 2008. Portal motor velocity and internal force resisting viral DNA packaging in bacteriophage φ29. Biophys. J. 94:159-167.
5. Fuller, D. N., D. M. Raymer, V. I. Kottadiel, V. B. Rao, and D. E. Smith. 2007. Single phage T4 DNA packaging motors exhibit large force generation, high velocity, and dynamic variability. Proc. Natl. Acad. Sci. USA. 104:16868-16873.
6. Hendrix, R. W. 1978. Symmetry mismatch and DNA packaging in large bacteriophages. Proc. Natl. Acad. Sci. USA. 75:4779-4783. (Pubitemid 9048617)
7. Lebedev, A. A., M. H. Krause, A. L. Isidro, A. A. Vagin, E. V. Orlova, et al. 2007. Structural framework for DNA translocation via the viral portal protein. EMBO J. 26:1984-1994.
8. Chemla, Y. R., K. Aathavan, J. Michaelis, S. Grimes, P. J. Jardine, et al. 2005. Mechanism of force generation of a viral DNA packaging motor. Cell. 122:683-692.
9. Dube, P., P. Tavares, R. Lurz, and M. van Heel. 1993. The portal protein of bacteriophage SPP1: a DNA pump with 13-fold symmetry. EMBO J. 12:1303-1309.
10. Simpson, A. A., Y. Tao, P. G. Leiman, M. O. Badasso, Y. He, et al. 2000. Structure of the bacteriophage φ29 DNA packaging motor. Nature. 408:745-750.
11. Hugel, T., J. Michaelis, C. L. Hetherington, P. J. Jardine, S. Grimes, et al. 2007. Experimental test of connector rotation during DNA packaging into bacteriophage φ29 capsids. PLoS Biol. 5:e59.
12. Oliveira, L., A. O. Henriques, and P. Tavares. 2006. Modulation of the viral ATPase activity by the portal protein correlates with DNA packaging efficiency. J. Biol. Chem. 281:21914-21923. (Pubitemid 44181895)
13. Cuervo, A., M. C. Vaney, A. A. Antson, P. Tavares, and L. Oliveira. 2007. Structural rearrangements between portal protein subunits are essential for viral DNA translocation. J. Biol. Chem. 282:18907-18913. (Pubitemid 47100132)
14. Orlova, E. V., B. Gowen, A. Dröge, A. Stiege, F. Weise, et al. 2003. Structure of a viral DNA gatekeeper at 10 Å resolution by cryo-electron microscopy. EMBO J. 22:1255-1262.
15. Tama, F., O. Miyashita, and C. L. Brooks III. 2004. Normal mode based flexible fitting of high-resolution structure into low-resolution experimental data from cryo-EM. J. Struct. Biol. 147:315-326. (Pubitemid 39140738)
16. Raspaud, E., T. Forth, C. Saõ-José, P. Tavares, and M. de Frutos. 2007. A kinetic analysis of DNA ejection from tailed phages revealing the prerequisite activation energy. Biophys. J. 93:3999-4005. (Pubitemid 350223815)