One of the critical steps in the life cycle of a virus is the packaging of the genome. This research is aimed at understanding the structural, kinetic and thermodynamic aspects of viral packaging in two simple, but very different, systems. Lambdoid bacteriophage use an ATP-driven motor to insert a double-stranded DNA (ds-DNA) genome into a preformed capsid. Nodaviruses assemble the protein capsid around a genome containing two single-stranded RNAs through an orchestrated series of protein-RNA and protein-protein binding events. We will use a variety of tools to develop a series of increasingly detailed three-dimensional molecular models for bacteriophage P4; and for two RNA viruses, satellite tobacco mosaic virus (STMV) and pariacoto virus (PaV). PaV is a well-characterized member of the Nodaviridae family. This research is aimed at rationalizing a wide variety of experimental data, and at developing hypotheses that will motivate future experimental work. The work on ds-DNA bacteriophage is motivated, in part, by the hypothesis that this system is ideal for the development of tools for the more accurate treatment of electrostatic effects, which is critical for further advances in our understanding of structural and thermodynamic issues in nucleic acids. The work on STMV and PaV will test the hypothesis that RNA selection in packaging is not driven by the recognition of a particular RNA sequence or small local structural motif, but by the viral RNA's ability to adopt secondary structures compatible with constraints imposed by viral symmetry.

Agency
National Institute of Health (NIH)
Institute
National Institute of General Medical Sciences (NIGMS)
Type
Research Project (R01)
Project #
5R01GM070785-03
Application #
7061334
Study Section
Molecular and Cellular Biophysics Study Section (BBCA)
Program Officer
Basavappa, Ravi
Project Start
2004-05-01
Project End
2008-04-30
Budget Start
2006-05-01
Budget End
2007-04-30
Support Year
3
Fiscal Year
2006
Total Cost
$239,258
Indirect Cost
Name
Georgia Institute of Technology
Department
Biology
Type
Schools of Arts and Sciences
DUNS #
097394084
City
Atlanta
State
GA
Country
United States
Zip Code
30332
Waters, James T; Kim, Harold D; Gumbart, James C et al. (2016) DNA Scrunching in the Packaging of Viral Genomes. J Phys Chem B 120:6200-7
Garmann, Rees F; Gopal, Ajaykumar; Athavale, Shreyas S et al. (2015) Visualizing the global secondary structure of a viral RNA genome with cryo-electron microscopy. RNA 21:877-86
Harvey, Stephen C (2015) The scrunchworm hypothesis: transitions between A-DNA and B-DNA provide the driving force for genome packaging in double-stranded DNA bacteriophages. J Struct Biol 189:1-8
Harvey, Stephen C (2014) Comment on the letter by A. Ben-Shaul: ""entropy, energy, and bending of DNA in viral capsids"". Biophys J 106:489-92
Harvey, Stephen C; Zeng, Yingying; Heitsch, Christine E (2013) The icosahedral RNA virus as a grotto: organizing the genome into stalagmites and stalactites. J Biol Phys 39:163-72
Horowitz, Eric D; Rahman, K Shefaet; Bower, Brian D et al. (2013) Biophysical and ultrastructural characterization of adeno-associated virus capsid uncoating and genome release. J Virol 87:2994-3002
Petrov, Anton S; Douglas, Scott S; Harvey, Stephen C (2013) Effects of pulling forces, osmotic pressure, condensing agents and viscosity on the thermodynamics and kinetics of DNA ejection from bacteriophages to bacterial cells: a computational study. J Phys Condens Matter 25:115101
Athavale, Shreyas S; Gossett, J Jared; Bowman, Jessica C et al. (2013) In vitro secondary structure of the genomic RNA of satellite tobacco mosaic virus. PLoS One 8:e54384
Zeng, Yingying; Larson, Steven B; Heitsch, Christine E et al. (2012) A model for the structure of satellite tobacco mosaic virus. J Struct Biol 180:110-6
Smyda, Mark R; Harvey, Stephen C (2012) The entropic cost of polymer confinement. J Phys Chem B 116:10928-34

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