The formation of mature viruses is an important research area, not only because of what we learn about the viruses themselves, but because viruses are simple model systems for elucidating the fundamental principles behind the assembly of large macromolecular complexes. This proposal presents a combined modeling and experimental approach to the investigation of two kinds of small, unenveloped, icosahedral viruses. Bacteriophages package their double-stranded DNA genomes into preformed protein capsids, using an ATP-driven motor to overcome the electrostatic, elastic and entropic forces that oppose packaging. In contrast, single-stranded RNA viruses assemble spontaneously, with the protein capsid forming around the outside of the RNA genome without the expenditure of energy. We will continue our investigations of the structural and thermodynamic aspects of DNA packaging in bacteriophage, focusing our efforts on DNA-DNA and DNA-capsid interactions, and on DNA kinking. We will also undertake an investigation of the forces opposing the compaction of DNA to high density in non-viral systems. The principles learned from these efforts will have implications for the understanding of genome structures and the regulation of gene expression in both prokaryotic and eukaryotic cells. Our investigations on RNA viruses will include the develop of improved three-dimensional models for satellite tobacco mosaic virus (STMV) and pariacoto virus (PaV); the development of methods for modeling assembly of RNA viruses; and experimental investigations of the condensation of RNA by polycations, particularly basic polypeptides. The work on RNA viruses is based on the hypothesis that assembly is initiated by strong but nonspecific interactions between positively charged polypeptides and the negatively charged RNA, leading to a collapsed aggregate resembling condensed DNA, followed by the formation of the mature virus. If correct, this hypothesis could provide the basis for new drug design strategies. The results might well apply to the formation of other large RNA-protein assemblies as well. ? ?

Public Health Relevance

Viruses cause many human diseases. An understanding of how they are assembled would offer important opportunities for the development of new antiviral drugs. In addition, bacteriophage (viruses that infect bacteria) have been used occasionally in the past to treat bacterial infections in humans. Knowledge about bacteriophage assembly could prove useful in the design of new antibacterial agents. ? ? ?

Agency
National Institute of Health (NIH)
Institute
National Institute of General Medical Sciences (NIGMS)
Type
Research Project (R01)
Project #
2R01GM070785-05
Application #
7528903
Study Section
Macromolecular Structure and Function D Study Section (MSFD)
Program Officer
Basavappa, Ravi
Project Start
2004-05-01
Project End
2012-04-30
Budget Start
2008-07-01
Budget End
2009-04-30
Support Year
5
Fiscal Year
2008
Total Cost
$296,874
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
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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
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 (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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