Skip to main content
×
Home
    • Aa
    • Aa
  • Get access
    Check if you have access via personal or institutional login
  • Cited by 20
  • Cited by
    This article has been cited by the following publications. This list is generated based on data provided by CrossRef.

    Podgornik, Rudolf Aksoyoglu, M. Alphan Yasar, Selcuk Svenšek, Daniel and Parsegian, V. Adrian 2016. DNA Equation of State: In Vitro vs In Viro. The Journal of Physical Chemistry B, Vol. 120, Issue. 26, p. 6051.


    Anany, H. Brovko, L.Y. El-Arabi, T. and Griffiths, M.W. 2015. Handbook of Natural Antimicrobials for Food Safety and Quality.


    Yang, Teng-Chieh Ortiz, David Nosaka, Lyn’Al Lander, Gabriel C. and Catalano, Carlos Enrique 2015. Thermodynamic Interrogation of the Assembly of a Viral Genome Packaging Motor Complex. Biophysical Journal, Vol. 109, Issue. 8, p. 1663.


    Mutsafi, Yael Fridmann-Sirkis, Yael Milrot, Elad Hevroni, Liron and Minsky, Abraham 2014. Infection cycles of large DNA viruses: Emerging themes and underlying questions. Virology, Vol. 466-467, p. 3.


    Andrews, B. T. and Catalano, C. E. 2013. Strong subunit coordination drives a powerful viral DNA packaging motor. Proceedings of the National Academy of Sciences, Vol. 110, Issue. 15, p. 5909.


    Chowdhury, Debashish 2013. Stochastic mechano-chemical kinetics of molecular motors: A multidisciplinary enterprise from a physicist’s perspective. Physics Reports, Vol. 529, Issue. 1, p. 1.


    DeRouchey, Jason Hoover, Brandon and Rau, Donald C. 2013. A Comparison of DNA Compaction by Arginine and Lysine Peptides: A Physical Basis for Arginine Rich Protamines. Biochemistry, Vol. 52, Issue. 17, p. 3000.


    Singh, Pragya Nakatani, Eri Goodlett, David R. and Catalano, Carlos Enrique 2013. A Pseudo-Atomic Model for the Capsid Shell of Bacteriophage Lambda Using Chemical Cross-Linking/Mass Spectrometry and Molecular Modeling. Journal of Molecular Biology, Vol. 425, Issue. 18, p. 3378.


    Hetherington, C.L. Moffitt, J.R. Jardine, P.J. and Bustamante, C. 2012. Comprehensive Biophysics.


    Leclercq, Sébastien Gilbert, Clément and Cordaux, Richard 2012. Cargo capacity of phages and plasmids and other factors influencing horizontal transfers of prokaryote transposable elements. Mobile Genetic Elements, Vol. 2, Issue. 2, p. 115.


    Medina, Elizabeth Nakatani, Eri Kruse, Shannon and Catalano, Carlos Enrique 2012. Thermodynamic Characterization of Viral Procapsid Expansion into a Functional Capsid Shell. Journal of Molecular Biology, Vol. 418, Issue. 3-4, p. 167.


    Qiu, Xiangyun Rau, Donald C. Parsegian, V. Adrian Fang, Li Tai Knobler, Charles M. and Gelbart, William M. 2011. Salt-Dependent DNA-DNA Spacings in Intact BacteriophageλReflect Relative Importance of DNA Self-Repulsion and Bending Energies. Physical Review Letters, Vol. 106, Issue. 2,


    Baclayon, M. Wuite, G. J. L. and Roos, W. H. 2010. Imaging and manipulation of single viruses by atomic force microscopy. Soft Matter, Vol. 6, Issue. 21, p. 5273.


    Chirico, N. Vianelli, A. and Belshaw, R. 2010. Why genes overlap in viruses. Proceedings of the Royal Society B: Biological Sciences, Vol. 277, Issue. 1701, p. 3809.


    Jeembaeva, Meerim Jönsson, Bengt Castelnovo, Martin and Evilevitch, Alex 2010. DNA Heats Up: Energetics of Genome Ejection from Phage Revealed by Isothermal Titration Calorimetry. Journal of Molecular Biology, Vol. 395, Issue. 5, p. 1079.


    Medina, Elizabeth Wieczorek, Doug Medina, Eva Margarita Yang, Qin Feiss, Michael and Catalano, Carlos Enrique 2010. Assembly and Maturation of the Bacteriophage Lambda Procapsid: gpC Is the Viral Protease. Journal of Molecular Biology, Vol. 401, Issue. 5, p. 813.


    Kennedy, Michael A and Parks, Robin J 2009. Adenovirus Virion Stability and the Viral Genome: Size Matters. Molecular Therapy, Vol. 17, Issue. 10, p. 1664.


    Levandovsky, Artem and Zandi, Roya 2009. Nonequilibirum Assembly, Retroviruses, and Conical Structures. Physical Review Letters, Vol. 102, Issue. 19,


    Ru, C. Q. 2009. Buckling of empty spherical viruses under external pressure. Journal of Applied Physics, Vol. 105, Issue. 12, p. 124701.


    Yang, Qin Maluf, Nasib Karl and Catalano, Carlos Enrique 2008. Packaging of a Unit-Length Viral Genome: The Role of Nucleotides and the gpD Decoration Protein in Stable Nucleocapsid Assembly in Bacteriophage λ. Journal of Molecular Biology, Vol. 383, Issue. 5, p. 1037.


    ×

Biophysics of viral infectivity: matching genome length with capsid size

  • Elmar Nurmemmedov (a1), Martin Castelnovo (a2), Carlos Enrique Catalano (a3) and Alex Evilevitch (a1)
  • DOI: http://dx.doi.org/10.1017/S0033583508004666
  • Published online: 01 April 2008
Abstract
Abstract

In this review, we discuss recent advances in biophysical virology, presenting experimental and theoretical studies on the physical properties of viruses. We focus on the double-stranded (ds) DNA bacteriophages as model systems for all of the dsDNA viruses both prokaryotic and eukaryotic. Recent studies demonstrate that the DNA packaged into a viral capsid is highly pressurized, which provides a force for the first step of passive injection of viral DNA into a bacterial cell. Moreover, specific studies on capsid strength show a strong correlation between genome length, and capsid size and robustness. The implications of these newly appreciated physical properties of a viral particle with respect to the infection process are discussed.

Copyright
Corresponding author
*Author for correspondence: Dr A. Evilevitch, Department of Biochemistry, Center for Chemistry and Chemical Engineering, Lund University, Box 124, S-221 00, Lund, Sweden.  Tel.: +46 46 222 3291; Fax: +46 46 222 4116; Email: Alex.Evilevitch@biochemistry.lu.se
Linked references
Hide All

This list contains references from the content that can be linked to their source. For a full set of references and notes please see the PDF or HTML where available.

M. Alcorlo , V. Gonzalez-Huici , J. M. Hermoso , W. J. Meijer & M. Salas (2007). The phage phi29 membrane protein p16·7, involved in DNA replication, is required for efficient ejection of the viral genome. Journal of Bacteriology 189, 55425549.

I. Ali , D. Marenduzzo & J. M. Yeomans (2006). Polymer packaging and ejection in viral capsids: shape matters. Physical Review Letters 96, 208102.

A. Amalfitano & R. J. Parks (2002). Separating fact from fiction: assessing the potential of modified adenovirus vectors for use in human gene therapy. Current Gene Therapy 2, 111133.

D. L. Anderson & S. Grimes (2005). The phi29 DNA packaging motor: seeking the mechanism. In Viral Genome Packaging Machines: Genetics, Structure and Mechanism (ed. C. E. Catalano ), pp. 102113. Georgetown, TX: Landes Bioscience/Eurekah.com.

P. G. Arscott , A. Z. Li & V. A. Bloomfield (1990). Condensation of DNA by trivalent cations. 1. Effects of DNA length and topology on the size and shape of condensed particles. Biopolymers 30, 619630.

J. D. Baines & S. K. Weller (2005). Cleavage and packaging of herpes simplex virus 1 DNA. In Viral Genome Packaging Machines: Genetics, Structure and Mechanism (ed. C. E. Catalano ), pp. 135150. Georgetown, TX, USA: Landes Bioscience/Eurekah.com.

J. B. Bancroft , E. Hiebert , M. W. Rees & R. Markham (1968a). Properties of cowpea chlorotic mottle virus, its protein and nucleic acid. Virology 34, 224239.

J. B. Bancroft , G. W. Wagner & C. E. Bracker (1968b). The self-assembly of a nucleic-acid free pseudo-top component for a small spherical virus. Virology 36, 146149.

R. G. Baumann , J. Mullaney & L. W. Black (2006). Portal fusion protein constraints on function in DNA packaging of bacteriophage T4. Molecular Microbiology 61, 1632.

A. Becker , H. Murialdo & M. Gold (1977). Studies on an in vitro system for the packaging and maturation of phage lambda DNA. Virology 78, 277290.

L. W. Black (1989). DNA packaging in dsDNA bacteriophages. Annual Review of Microbiology 43, 267292.

L. W. Black , W. W. Newcomb , J. W. Boring & J. C. Brown (1985). Ion etching bacteriophage T4: support for a spiral-fold model of packaged DNA. Proceedings of the National Academy of Sciences USA 82, 79607964.

V. A. Bloomfield (1991). Condensation of DNA by multivalent cations: considerations on mechanism. Biopolymers 31, 14711481.

V. A. Bloomfield (1997). DNA condensation by multivalent cations. Biopolymers 44, 269282.

P. Boulanger , M. Le Maire , M. Bonhivers , S. Dubois , M. Desmadril & L. Letellier (1996). Purification and structural and functional characterization of FhuA, a transporter of the Escherichia coli outer membrane. Biochemistry 35, 1421614224.

D. Brockmann , L. Hufnagel & T. Geisel (2006). The scaling laws of human travel. Nature 439, 462465.

M. Buenemann & P. Lenz (2007). Mechanical limits of viral capsids. Proceedings of the National Academy of Sciences USA 104, 99259930.

G. Cardone , D. C. Winkler , B. L. Trus , N. Cheng , J. E. Heuser , W. W. Newcomb , J. C. Brown & A. C. Steven (2007). Visualization of the herpes simplex virus portal in situ by cryo-electron tomography. Virology 361, 426434.

C. Carrasco , A. Carreira , I. A. Schaap , P. A. Serena , J. Gomez-Herrero , M. G. Mateu & P. J. De Pablo (2006). DNA-mediated anisotropic mechanical reinforcement of a virus. Proceedings of the National Academy of Sciences USA 103, 1370613711.

S. Casjens & P. Weigele (2005). DNA packaging by bacteriophage P22. In Viral Genome Packaging Machines: Genetics, Structure and Mechanism (ed. C. E. Catalano ), pp. 8088. Georgetown, TX, USA: Landes Bioscience/Eurekah.com.

D. L. Caspar & A. Klug (1962). Physical principles in the construction of regular viruses. Cold Spring Harbor Symposium on Quantitative Biology 27, 124.

M. Castelnovo , R. K. Bowles , H. Reiss & W. M. Gelbart (2003). Osmotic force resisting chain insertion in a colloidal suspension. European Physical Journal E. Soft Matter 10, 191197.

M. Castelnovo & A. Evilevitch (2007). DNA ejection from bacteriophage: towards a general behavior for osmotic-suppression experiments. European Physical Journal E. Soft Matter 24, 918.

C. E. Catalano (2005b). Viral Genome Packaging Machines: Genetics, Structure and Mechanism. Georgetown, TX, USA: Landes Bioscience/Eurekah.com. New York, NY, USA: Kluwer Academic/Plenum Publishers.

M. E. Cerritelli , N. Cheng , A. H. Rosenberg , C. E. McPherson , F. P. Booy & A. C. Steven (1997). Encapsidated conformation of bacteriophage T7 DNA. Cell 91, 271280.

S. Chai , R. Lurz & J. C. Alonso (1995). The small subunit of the terminase enzyme of Bacillus subtilis bacteriophage SPP1 forms a specialized nucleoprotein complex with the packaging initiation region. Journal of Molecular Biology 252, 386398.

J. F. Conway , N. Cheng , P. D. Ross , R. W. Hendrix , R. L. Duda & A. C. Steven (2007). A thermally induced phase transition in a viral capsid transforms the hexamers, leaving the pentamers unchanged. Journal of Structural Biology 158, 224232.

A. Cordova , M. Deserno , W. M. Gelbart & A. Ben-Shaul (2003). Osmotic shock and the strength of viral capsids. Biophysical Journal 85, 7074.

M. De Frutos , S. Brasiles , P. Tavares & E. Raspaud (2005a). Effect of spermine and DNase on DNA release from bacteriophage T5. European Physical Journal E. Soft Matter 17, 429434.

M. De Frutos , L. Letellier & E. Raspaud (2005b). DNA ejection from bacteriophage T5: analysis of the kinetics and energetics. Biophysical Journal 88, 13641370.

M. De Paepe & F. Taddei (2006). Viruses' life history: towards a mechanistic basis of a trade-off between survival and reproduction among phages. PLoS Biology 4, e193.

T. Dokland (1999). Scaffolding proteins and their role in viral assembly. Cellular and Molecular Life Sciences 56, 580603.

T. Dokland & H. Murialdo (1993). Structural transitions during maturation of bacteriophage lambda capsids. Journal of Molecular Biology 233, 682694.

A. Droge & P. Tavares (2000). In vitro packaging of DNA of the Bacillus subtilis bacteriophage SPP1. Journal of Molecular Biology 296, 103115.

A. Droge & P. Tavares (2005). Bacteriophage SPP1 DNA packaging. In Viral Genome Packaging Machines: Genetics, Structure and Mechanism (ed. C. E. Catalano ), pp. 89101. Georgetown, TX, USA: Landes Bioscience/Eurekah.com.

R. L. Duda (1998). Protein chainmail: catenated protein in viral capsids. Cell 94, 5560.

W. Earnshaw , S. Casjens & S. C. Harrison (1976). Assembly of the head of bacteriophage P22: x-ray diffraction from heads, proheads and related structures. Journal of Molecular Biology 104, 387410.

W. C. Earnshaw & S. R. Casjens (1980). DNA packaging by the double-stranded DNA bacteriophages. Cell 21, 319331.

W. C. Earnshaw & S. C. Harrison (1977). DNA arrangement in isometric phage heads. Nature 268, 598602.

W. C. Earnshaw , J. King , S. C. Harrison & F. A. Eiserling (1978). The structural organization of DNA packaged within the heads of T4 wild-type, isometric and giant bacteriophages. Cell 14, 559568.

E. J. Enemark & L. Joshua-Tor (2006). Mechanism of DNA translocation in a replicative hexameric helicase. Nature 442, 270275.

A. Evilevitch (2006). Effects of condensing agent and nuclease on the extent of ejection from phage lambda. Journal of Physical Chemistry B, 110, 2226122265.

A. Evilevitch , M. Castelnovo , C. M. Knobler & W. M. Gelbart (2004). Measuring the force ejecting DNA from phage. Journal of Physical Chemistry B 108, 68386843.

A. Evilevitch , L. T. Fang , A. M. Yoffe , M. Castelnovo , D. C. Rau , V. A. Parsegian , W. M. Gelbart & C. M. Knobler (2008). Effects of salt concentrations and bending energy on the extent of ejection of phage genomes. Biophysical Journal 94, 11101120.

A. Evilevitch , J. W. Gober , M. Phillips , C. M. Knobler & W. M. Gelbart (2005). Measurements of DNA lengths remaining in a viral capsid after osmotically suppressed partial ejection. Biophysical Journal 88, 751756.

A. Evilevitch , L. Lavelle , C. M. Knobler , E. Raspaud & W. M. Gelbart (2003). Osmotic pressure inhibition of DNA ejection from phage. Proceedings of the National Academy of Sciences USA 100, 92929295.

M. Feiss & C. E. Catalano (2005). Bacteriophage lambda terminase and the mechanism of viral DNA packaging. In Viral Genome Packaging Machines: Genetics, Structure, and Mechanism (ed. C. E. Catalano ), pp. 539. New York, NY, USA: Landes Bioscience/Eurekah.com.

M. Feiss , R. A. Fisher , M. A. Crayton & C. Egner (1977). Packaging of the bacteriophage lambda chromosome: effect of chromosome length. Virology 77, 281293.

J. T. Finch & J. B. Bancroft (1968). Structure of the reaggregted protein shells of 2 spherical viruses. Nature 220, 815816.

C. Forrey & M. Muthukumar (2006). Langevin dynamics simulations of genome packing in bacteriophage. Biophysical Journal 91, 2541.

H. Fujisawa & M. Morita (1997). Phage DNA packaging. Genes Cells 2, 537545.

D. N. Fuller , D. M. Raymer , V. I. Kottadiel , V. B. Rao & D. E. Smith (2007a). Single phage T4 DNA packaging motors exhibit large force generation, high velocity, and dynamic variability. Proceedings of the National Academy of Sciences USA 104, 1686816873.

D. N. Fuller , D. M. Raymer , J. P. Rickgauer , R. M. Robertson , C. E. Catalano , D. L. Anderson , S. Grimes & D. E. Smith (2007b). Measurements of single DNA molecule packaging dynamics in bacteriophage lambda reveal high forces, high motor processivity, and capsid transformations. Journal of Molecular Biology 373, 11131122.

I. S. Gabashvili & A. Grosberg (1992). Dynamics of double stranded DNA reptation from bacteriophage. Journal of Biomolcular Structure and Dynamics 9, 911920.

L. Gan , J. F. Conway , B. A. Firek , N. Cheng , R. W. Hendrix , A. C. Steven , J. E. Johnson & R. L. Duda (2004). Control of crosslinking by quaternary structure changes during bacteriophage HK97 maturation. Molecular Cell 14, 559569.

L. Gan , J. A. Speir , J. F. Conway , G. Lander , N. Cheng , B. A. Firek , R. W. Hendrix , R. L. Duda , L. Liljas & J. E. Johnson (2006). Capsid conformational sampling in HK97 maturation visualized by X-ray crystallography and cryo-EM. Structure 14, 16551665.

H. Gaussier , Q. Yang & C. E. Catalano (2006). Building a virus from scratch: assembly of an infectious virus using purified components in a rigorously defined biochemical assay system. Journal of Molecular Biology 357, 11541166.

M. M. Gibbons & W. S. Klug (2007a). Mechanical modeling of viral capsids. Journal of Materials Science 42, 89959004.

M. M. Gibbons & W. S. Klug (2007b). Nonlinear finite-element analysis of nanoindentation of viral capsids. Physical Review E 75, 031901.

V. Gonzalez-Huici , M. Salas & J. M. Hermoso (2004). The push-pull mechanism of bacteriophage O29 DNA injection. Molecular Microbiology 52, 529540.

P. Grayson , A. Evilevitch , M. M. Inamdar , P. K. Purohit , W. M. Gelbart , C. M. Knobler & R. Phillips (2006). The effect of genome length on ejection forces in bacteriophage lambda. Virology 348, 430436.

P. Grayson , L. Han , T. Winther & R. Phillips (2007). Real-time observations of single bacteriophage lambda DNA ejections in vitro. Proceedings of the National Academy of Sciences USA 104, 1465214657.

P. Guo , S. Grimes & D. Anderson (1986). A defined system for in vitro packaging of DNA-gp3 of the Bacillus subtilis bacteriophage phi 29. Proceedings of the National Academy of Sciences USA 83, 35053509.

K. Hamada , H. Fujisawa & T. Minagawa (1986). A defined in vitro system for packaging of bacteriophage T3 DNA. Virology 151, 119123.

D. P. Harrison & V. C. Bode (1975). Putrescine and certain polyamines can inhibit DNA injection from bacteriophage lambda. Journal of Molecular Biology 96, 461470.

S. C. Harrison (1983). Packaging of DNA into bacteriophage heads: a model. Journal of Molecular Biology 171, 577580.

R. W. Hendrix (1978). Symmetry mismatch and DNA packaging in large bacteriophages. Proceedings of the National Academy of Sciences USA 75, 47794783.

R. X. Hendrix , J. W. Roberts , F. W. Stahl & R. A. Weisberg (1983). Lambda II. New York: Cold Spring Harbor Laboratory.

A. D. Hershey & M. Chase (1952). Independent functions of viral protein and nucleic acid in growth of bacteriophage. Journal of General Physiology 36, 3956.

E. Hiebert , J. B. Bancroft & C. E. Bracker (1968). The assembly in vitro of some small spherical viruses, hybrid viruses, and other nucleoproteins. Virology 34, 492508.

Y. Hwang & M. Feiss (1995). A defined system for in vitro lambda DNA packaging. Virology 211, 367376.

M. M. Inamdar , W. M. Gelbart & R. Phillips (2006). Dynamics of DNA ejection from bacteriophage. Biophysical Journal 91, 411420.

I. Ivanovska , G. Wuite , B. Jonsson & A. Evilevitch (2007). Internal DNA pressure modifies stability of WT phage. Proceedings of the National Academy of Sciences USA 104, 96039608.

I. L. Ivanovska , P. J. De Pablo , B. Ibarra , G. Sgalari , F. C. Mackintosh , J. L. Carrascosa , C. F. Schmidt & G. J. Wuite (2004). Bacteriophage capsids: tough nanoshells with complex elastic properties. Proceedings of the National Academy of Sciences USA 101, 76007605.

D. Jeruzalmi , M. O'Donnell & J. Kuriyan (2002). Clamp loaders and sliding clamps. Current Opinion in Structural Biology 12, 217224.

D. E. Kainov , E. J. Mancini , J. Telenius , J. Lisal , J. M. Grimes , D. H. Bamford , D. I. Stuart & R. Tuma (2008). Structural basis of mechanochemical coupling in a hexameric molecular motor. Journal of Biological Chemistry 283, 36073617.

W. K. Kegel & P. van der Schoot (2004). Competing hydrophobic and screened-coulomb interactions in hepatitis B virus capsid assembly. Biophysical Journal 86, 39053913.

P. Kemp , M. Gupta & I. J. Molineux (2004). Bacteriophage T7 DNA ejection into cells is initiated by an enzyme-like mechanism. Molecular Microbiology 53, 12511265.

J. Kindt , S. Tzlil , A. Ben-Shaul & W. M. Gelbart (2001). DNA packaging and ejection forces in bacteriophage. Proceedings of the National Academy of Sciences USA 98, 1367113674.

W. S. Klug , R. F. Bruinsma , J. P. Michel , C. M. Knobler , I. L. Ivanovska , C. F. Schmidt & G. J. Wuite (2006). Failure of viral shells. Physical Review Letters 97, 228101.

W. S. Klug & M. Ortiz (2003). A director field model of DNA packaging in viral capsids. Journal of the Mechanics and Physics of Solids 51, 18151847.

N. Kol , M. Gladnikoff , D. Barlam , R. Z. Shneck , A. Rein & I. Rousso (2006). Mechanical properties of murine leukemia virus particles: effect of maturation. Biophysical Journal 91, 767774.

N. Kol , Y. Shi , M. Tsvitov , D. Barlam , R. Z. Shneck , M. S. Kay & I. Rousso (2007). A stiffness switch in human immunodeficiency virus. Biophysical Journal 92, 17771783.

J. C. Lamarque , T. V. Le & S. C. Harvey (2004). Packaging double-helical DNA into viral capsids. Biopolymers 73, 348355.

G. C. Lander , L. Tang , S. R. Casjens , E. B. Gilcrease , P. Prevelige , A. Poliakov , C. S. Potter , B. Carragher & J. E. Johnson (2006). The structure of an infectious P22 virion shows the signal for headful DNA packaging. Science 312, 17911795.

R. Lata , J. F. Conway , N. Cheng , R. L. Duda , R. W. Hendrix , W. R. Wikoff , J. E. Johnson , H. Tsuruta & A. C. Steven (2000). Maturation dynamics of a viral capsid: visualization of transitional intermediate states. Cell 100, 253263.

K. K. Lee , L. Gan , H. Tsuruta , R. W. Hendrix , R. L. Duda & J. E. Johnson (2004). Evidence that a local refolding event triggers maturation of HK97 bacteriophage capsid. Journal of Molecular Biology 340, 419433.

J. Lidmar , L. Mirny & D. R. Nelson (2003). Virus shapes and buckling transitions in spherical shells. Physical Review E 68, 051910.

H. Lin , M. N. Simon & L. W. Black (1997). Purification and characterization of the small subunit of phage T4 terminase, gp16, required for DNA packaging. Journal of Biological Chemistry 272, 34953501.

C. R. Locker & S. C. Harvey (2006). A model for viral genome packing. Multiscale Modeling and Simulation 5, 12641279.

D. Lof , K. Schillen , B. Jonsson & A. Evilevitch (2007a). Dynamic and static light scattering analysis of DNA ejection from the phage lambda. Physical Review E. Statistical, Nonlinear and Soft Matter Physics 76, 011914.

D. Lof , K. Schillen , B. Jonsson & A. Evilevitch (2007b). Forces controlling the rate of DNA ejection from phage lambda. Journal of Molecular Biology 368, 5565.

N. K. Maluf , H. Gaussier , E. Bogner , M. Feiss & C. E. Catalano (2006). Assembly of bacteriophage lambda terminase into a viral DNA maturation and packaging machine. Biochemistry 45, 1525915268.

S. Mangenot , M. Hochrein , J. Radler & L. Letellier (2005). Real-time imaging of DNA ejection from single phage particles. Current Biology 15, 430435.

J. P. Michel , I. L. Ivanovska , M. M. Gibbons , W. S. Klug , C. M. Knobler , G. J. Wuite & C. F. Schmidt (2006). Nanoindentation studies of full and empty viral capsids and the effects of capsid protein mutations on elasticity and strength. Proceedings of the National Academy of Sciences USA 103, 61846189.

M. S. Mitchell , S. Matsuzaki , S. Imai & V. B. Rao (2002). Sequence analysis of bacteriophage T4 DNA packaging/terminase genes 16 and 17 reveals a common ATPase center in the large subunit of viral terminases. Nucleic Acids Research 30, 40094021.

I. J. Molineux (2001). No syringes please, ejection of phage T7 DNA from the virion is enzyme driven. Molecular Microbiology 40, 18.

M. C. Morais , Y. Tao , N. H. Olson , S. Grimes , P. J. Jardine , D. L. Anderson , T. S. Baker & M. G. Rossmann (2001). Cryoelectron-microscopy image reconstruction of symmetry mismatches in bacteriophage phi29. Journal of Structural Biology 135, 3846.

W. W. Newcomb , F. P. Booy & J. C. Brown (2007). Uncoating the herpes simplex virus genome. Journal of Molecular Biology 370, 633642.

T. T. Nguyen , R. F. Bruinsma & W. M. Gelbart (2005). Elasticity theory and shape transitions of viral shells. Physical Review E 72, 051923.

T. Odijk (1998). Hexagonally packed DNA within bacteriophage T7 stabilized by curvature stress. Biophysical Journal 75, 12231227.

P. M. Ojala , B. Sodeik , M. W. Ebersold , U. Kutay & A. Helenius (2000). Herpes simplex virus type 1 entry into host cells: reconstitution of capsid binding and uncoating at the nuclear pore complex in vitro. Molecular Cell Biology 20, 49224931.

L. Oliveira , J. C. Alonso & P. Tavares (2005). A defined in vitro system for DNA packaging by the bacteriophage SPP1: insights into the headful packaging mechanism. Journal of Molecular Biology 353, 529539.

A. Oppenheim & A. Peleg (1989). Helpers for efficient encapsidation of SV40 pseudovirions. Gene 77, 7986.

V. A. Parsegian , R. P. Rand , N. L. Fuller & D. C. Rau (1986). Osmotic stress for the direct measurement of intermolecular forces. Methods in Enzymology 127, 400416.

S. S. Patel & I. Donmez (2006). Mechanisms of helicases. Journal of Biological Chemistry 281, 1826518268.

A. S. Petrov , M. B. Boz & S. C. Harvey (2007a). The conformation of double-stranded DNA inside bacteriophages depends on capsid size and shape. Journal of Structural Biology 160, 241248.

A. S. Petrov , K. Lim-Hing & S. C. Harvey (2007b). Packaging of DNA by bacteriophage epsilon15: structure, forces, and thermodynamics. Structure 15, 807812.

P. K. Purohit , M. M. Inamdar , P. D. Grayson , T. M. Squires , J. Kondev & R. Phillips (2005). Forces during bacteriophage DNA packaging and ejection. Biophysical Journal 88, 851866.

P. K. Purohit , J. Kondev & M. Phillips (2003a). Force steps during viral DNA packaging? Journal of the Mechanics and Physics of Solids 51, 22392257.

P. K. Purohit , J. Kondev & R. Phillips (2003b). Mechanics of DNA packaging in viruses. Proceedings of the National Academy of Sciences USA 100, 31733178.

V. B. Rao , V. Thaker & L. W. Black (1992). A phage T4 in vitro packaging system for cloning long DNA molecules. Gene 113, 2533.

E. Raspaud , D. Durand & F. Livolant (2005). Interhelical spacing in liquid crystalline spermine and spermidine-DNA precipitates. Biophysical Journal 88, 392403.

E. Raspaud , M. Olvera De La Cruz , J. L. Sikorav & F. Livolant (1998). Precipitation of DNA by polyamines: a polyelectrolyte behavior. Biophysical Journal 74, 381393.

D. C. Rau & V. A. Parsegian (1992). Direct measurement of the intermolecular forces between counterion-condensed DNA double helices. Evidence for long range attractive hydration forces. Biophysical Journal 61, 246259.

F. J. Rentas & V. B. Rao (2003). Defining the bacteriophage T4 DNA packaging machine: evidence for a C-terminal DNA cleavage domain in the large terminase/packaging protein gp17. Journal of Molecular Biology 334, 3752.

K. E. Richards , R. C. Williams & R. Calendar (1973). Mode of DNA packing within bacteriophage heads. Journal of Molecular Biology 78, 255259.

J. P. Rickgauer , D. N. Fuller , S. Grimes , P. J. Jardine , D. L. Anderson & D. E. Smith (2008). Portal motor velocity and internal force resisting viral DNA packaging in bacteriophage ϕ29. Biophysical Journal 94, 159167.

S. C. Riemer & V. A. Bloomfield (1978). Packaging of DNA in bacteriophage heads: some considerations on energetics. Biopolymers 17, 785794.

M. Roa & D. Scandella (1976). Multiple steps during the interaction between coliphage lambda and its receptor protein in vitro. Virology 72, 182194.

P. D. Ross , N. Cheng , J. F. Conway , B. A. Firek , R. W. Hendrix , R. L. Duda & A. C. Steven (2005). Crosslinking renders bacteriophage HK97 capsid maturation irreversible and effects an essential stabilization. EMBO Journal 24, 13521363.

P. D. Ross , J. F. Conway , N. Cheng , L. Dierkes , B. A. Firek , R. W. Hendrix , A. C. Steven & R. L. Duda (2006). A free energy cascade with locks drives assembly and maturation of bacteriophage HK97 capsid. Journal of Molecular Biology 364, 512525.

C. Sao-Jose , S. Lhuillier , R. Lurz , R. Melki , J. Lepault , M. A. Santos & P. Tavares (2006). The ectodomain of the viral receptor YueB forms a fiber that triggers ejection of bacteriophage SPP1 DNA. Journal of Biological Chemistry 281, 1146411470.

J. A. Schellman & N. Parthasarathy (1984). X-ray diffraction studies on cation-collapsed DNA. Journal of Molecular Biology 175, 313329.

P. Serwer (1986). Arrangement of double-stranded DNA packaged in bacteriophage capsids. An alternative model. Journal of Molecular Biology 190, 509512.

H. Shibata , H. Fujisawa & T. Minagawa (1987). Early events in DNA packaging in a defined in vitro system of bacteriophage T3. Virology 159, 250258.

J. L. Sikorav , J. Pelta & F. Livolant (1994). A liquid crystalline phase in spermidine-condensed DNA. Biophysical Journal 67, 13871392.

D. E. Smith , S. J. Tans , S. B. Smith , S. Grimes , D. L. Anderson & C. Bustamante (2001). The bacteriophage straight phi29 portal motor can package DNA against a large internal force. Nature 413, 748752.

A. J. Spakowitz & Z. G. Wang (2005). DNA packaging in bacteriophage: is twist important? Biophysical Journal 88, 39123923.

N. Sternberg & R. Weisberg (1977). Packaging of coliphage lambda DNA. II. The role of the gene D protein. Journal of Molecular Biology 117, 733759.

R. M. Story , H. Li & J. N. Abelson (2001). Crystal structure of a DEAD box protein from the hyperthermophile Methanococcus jannaschii. Proceedings of the National Academy of Sciences USA 98, 14651470.

H. H. Strey , R. Podgornik , D. C. Rau & V. A. Parsegian (1998). DNA–DNA interactions. Current Opinion in Structural Biology 8, 309313.

M. Sun , D. Louie & P. Serwer (1999). Single-event analysis of the packaging of bacteriophage T7 DNA concatemers in vitro. Biophysical Journal 77, 16271637.

S. Sun , K. Kondabagil , P. M. Gentz , M. G. Rossmann & V. B. Rao (2007). The structure of the ATPase that powers DNA packaging into bacteriophage T4 procapsids. Molecular Cell 25, 943949.

M. Suwalsky , W. Traub , U. Shmueli & J. A. Subirana (1969). An X-ray study of the interaction of DNA with spermine. Journal of Molecular Biology 42, 363373.

F. Tama & C. L. Brooks 3rd. (2005). Diversity and identity of mechanical properties of icosahedral viral capsids studied with elastic network normal mode analysis. Journal of Molecular Biology 345, 299314.

W. E. Thomas , E. Trintchina , M. Forero , V. Vogel & E. V. Sokurenko (2002). Bacterial adhesion to target cells enhanced by shear force. Cell 109, 913923.

S. Tristram-Nagle & J. F. Nagle (2007). HIV-1 fusion peptide decreases bending energy and promotes curved fusion intermediates. Biophysical Journal 93, 20482055.

S. Tzlil , J. T. Kindt , W. M. Gelbart & A. Ben-Shaul (2003). Forces and pressures in DNA packaging and release from viral capsids. Biophysical Journal 84, 16161627.

G. W. Wagner & J. B. Bancroft (1968). The self-assembly of spherical viruses with mixed coat proteins. Virology 34, 748756.

M. Widom , J. Lidmar & D. R. Nelson (2007). Soft modes near the buckling transition of icosahedral shells. Physical Review E 76, 031911.

W. R. Wikoff , Z. Che , R. L. Duda , R. W. Hendrix & J. E. Johnson (2003). Crystallization and preliminary analysis of a dsDNA bacteriophage capsid intermediate: Prohead II of HK97. Acta Crystallographica D. Biological Crystallography 59, 20602064.

W. R. Wikoff , J. F. Conway , J. Tang , K. K. Lee , L. Gan , N. Cheng , R. L. Duda , R. W. Hendrix , A. C. Steven & J. E. Johnson (2006). Time-resolved molecular dynamics of bacteriophage HK97 capsid maturation interpreted by electron cryo-microscopy and X-ray crystallography. Journal of Structural Biology 153, 300306.

W. R. Wikoff , R. L. Duda , R. W. Hendrix & J. E. Johnson (1998). Crystallization and preliminary X-ray analysis of the dsDNA bacteriophage HK97 mature empty capsid. Virology 243, 113118.

W. R. Wikoff , R. L. Duda , R. W. Hendrix & J. E. Johnson (1999). Crystallographic analysis of the dsDNA bacteriophage HK97 mature empty capsid. Acta Crystallographica D. Biological Crystallography 55, 763771.

W. R. Wikoff , L. Liljas , R. L. Duda , H. Tsuruta , R. W. Hendrix & J. E. Johnson (2000). Topologically linked protein rings in the bacteriophage HK97 capsid. Science 289, 21292133.

Q. Yang & C. E. Catalano (2003). Biochemical characterization of bacteriophage lambda genome packaging in vitro. Virology 305, 276287.

H. Zheng , A. S. Olia , M. Gonen , S. Andrews , G. Cingolani & T. Gonen (2008). A conformational switch in bacteriophage p22 portal protein primes genome injection. Molecular Cell 29, 376383.

S. B. Zimmerman (1993). Macromolecular crowding effects on macromolecular interactions: some implications for genome structure and function. Biochimica et Biophysica Acta 1216, 175185.

Recommend this journal

Email your librarian or administrator to recommend adding this journal to your organisation's collection.

Quarterly Reviews of Biophysics
  • ISSN: 0033-5835
  • EISSN: 1469-8994
  • URL: /core/journals/quarterly-reviews-of-biophysics
Please enter your name
Please enter a valid email address
Who would you like to send this to? *
×