Harvey Johnson.

Graduate Student
University of California, Berkeley

B.S. Chemical Engineering, 2001
University of Delaware

hrj@uclink.berkeley.edu
Office Location: 497A Tan Hall
Office Telephone: 510-643-8340
Office Fax: 510-643-1228

Viral Capsids

The development of methods for the synthesis of conducting polymers, nanocrystalline materials, carbon nanotubes, and state-switchable molecules has yielded a wide variety of nanometer-sized components that could be incorporated into devices with unprecedented electronic and biological capabilities. However, the controlled spatial arrangement of these objects is of fundamental importance to their proper function, and thus there is a growing need for the development of methods that can organize materials with nanometer resolution. Viral protein coats represent a special class of monodispersed, functionalizable nanoparticles with utility as both nanometer-sized components and organizers.

Most viral protein coats, or capsids, are icosahedra formed from identical, self-assembling, protein units. In nature, the capsid houses and transfers the genetic material to a healthy cell where the protein units dissociate and release the RNA or DNA inside. It has been observed that capsid proteins can assemble in vitro in the absence of the viral RNA.[i] If the RNA is removed, the resulting nanometer-sized spherical particles can be used to template a variety of well-defined materials with interesting properties, including: nanobeads with catalytic and chromatographic function, molecular containers that can serve as crystallizers or transport devices, nanoporous materials resembling zeolites and lattice scaffolds.[ii]

Given the plethora of exciting potential applications for these materials, there are tremendous multidisciplinary research opportunities associated with both the development of a chemical toolkit for selective capsid modification and specific practical material science and engineering applications (protein engineering, interaction measurements, system optimization, control and scale-up). It is our aim to employ a multidisciplinary approach that combines the strengths of two research groups (Matt Francis Group: Bioorganic Material Chemistry and Clark Group: Biochemical Engineering) to explore the following specific question: “How can we employ the satellite panicium mosaic virus (SPMV) as a nanospherical template for the formation of dense, monodispersed, polymer beads?”

The solution to this problem highlights a number of the benefits of capsids (the possibility of stepwise chemistry, simplified separations and controlled product size and geometry). The bifocal emphasis of this research will be to demonstrate the power of the capsid as a nanomaterial and to accumulate a storehouse of general knowledge critically important to this bourgeoning field. The following vital questions will be addressed: “How will the addition of functional groups (metal catalysts, synthetic polymers, etc.) to the inner face of a capsid protein affect the capsid assembly? Can modified viral capsids be exploited as nanospherical templates for polymerization? How will an organic solvent partition in an aqueous-capsid system, and will capsid association be accelerated and/or stabilized? What is the correct description of the fluid mechanics and mass transfer for a packed bed reactor with nanocatalytic beads (i.e. is the system approaching the limit of the continuum approximation used in most fluid models)?” In order to answer these questions, we will design experiments to probe them in parallel.

Our experimental design will begin by developing site selective methods that can independently add desired functionality to either the inside or outside surface of the capsid. For example, the SPMV possesses a single tyrosine residue that is exposed on the outside of the capsid after assembly. This residue can be selectively functionalized using diazonium salts, resulting in the introduction of a wide variety of functional groups in specific locations on the capsid exterior. The interior surface possesses a single cystine residue that can be modified with iodoacetamides. Both of these reactions exhibit a wide range of functional-group tolerance, and will be used to create a lattice of covalently linked viruses (external modification) and introduce a variety of catalysts, inorganic nanocrystals, polymers and small molecules in aqueous solution (internal modification). All of these protein conjugates will be extensively characterized using MALDI MS, gel electrophoresis and other techniques. After the functionality has been achieved, solvent phase separations problems will be studied.

A variety of experiments will be conducted to determine the activity of the capsid as a catalytic device and the local capsid environment in a variety of solution conditions. Organic solvent partitioning into the virus will be determined by measuring the concentration of lipophilic probes using fluorescence microscopy. An electron spin resonance probe will be dually employed to characterize the local chamber environment (the order of constrained water molecules and the polarity of the solvent blend) and to catalyze a living polymerization.

[i] Chiu, W.; Burnett, R.M.; Garcea, R.L. Structural Biology of Viruses pp 3-38, Oxford University Press: New York, 1997.

[ii] Douglas, T. and Young, M. “Host-guest Encapsulation of Materials by Assembled Virus Protein Cages”, Nature 393 (6681), 152-155 (1998).