Chairperson, Graduate Committee: Brian BothnerRayaprolu, VamseedharBenjamin M. Manning, Trevor Douglas and Brian Bothner were co-authors of the article, 'Virus particles as active nanomaterials that can rapidly change their viscoelastic properties in response to dilute solutions' in the journal 'RSC softmatter' which is contained within this thesis.Shannon Kruse, Navid Movahed, Tim Potter, Balasubramanian Venkatakrishnan, Bridget Lins, Antonette Bennett, Robert McKenna, Mavis Agbandje-McKenna and Brian Bothner were co-authors of the article, 'Comparative analysis of adeno associated virus capsid stability and dynamics' submitted to the journal 'Journal of virology' which is contained within this thesis.Navid Movahed, Ravikant Chaudhary, Geoff Blatter, Alec Skuntz, Sue Brumfield, Jonathan K. Hilmer, Mark J. Young, Trevor Douglas and Brian Bothner were co-authors of the article, 'Learning new tricks from an old dog; studies of CCMV capsid swelling' submitted to the journal 'Journal of virology' which is contained within this thesis.2015-01-132015-01-132013https://scholarworks.montana.edu/handle/1/8762Viruses are the most abundant form of life on the planet. Many forms are pathogenic and represent a major threat to human health, but viruses recently have been used as nanoscale tools for gene therapy, drug delivery and enzyme nanoreactors. Viruses have historically been viewed as static and rigid delivery vehicles, but over the last few decades they have been recognized as flexible structures. Their structural dynamics are a crucial element of their functionality. Characterizing the biophysical properties of these viruses is both challenging and exciting. We have developed and used a multidimensional approach to tackle this task. Our techniques include Differential Scanning Fluorimetry, which probes the melting temperatures of virus capsids by the use of a fluorescent dye and Hydrogen-Deuterium Mass Spectrometry, which investigates the flexibility of the virus capsid protein by following the change in mass when Hydrogen is exchanged with Deuterium. Flexible regions exchange more. The above techniques are well complemented by the use of size-exclusion chromatography, which differentiates virus capsids based on their hydrodynamic radius and Limited proteolysis which again probes dynamic regions of the capsids up to the amino acid level. We have studied two different systems, Cowpea chlorotic mottle virus (CCMV) and Adeno-associated virus (AAV) using these methodologies. The sum result of these assays indicate that, in case of CCMV, capsids can undergo structural transitions due to very subtle pH and cation concentrations and the capsid protein is capable of rigid body transitions which affect the stability, while maintaining most of the secondary structure. In the case of AAV, the inherent sequence differences explains only partially the differences in stability and proteolytic susceptibility.enVirusesMorphologyBiophysicsStructural dynamicsDissertationCopyright 2013 by Vamseedhar Rayaprolu