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The properties of infectious prions and the pathology of the diseases they cause are dependent upon the unique conformation of each prion strain. How the pathology of prion disease correlates with different strains and genetic backgrounds has been investigated via in vivo assays, but how interactions between specific prion strains and cell types contribute to the pathology of prion disease has been dissected more effectively using in vitro cell lines. Observations made through in vivo and in vitro assays have informed each other with regard to not only how genetic variation influences prion properties, but also how infectious prions are taken up by cells, modified by cellular processes and propagated, and the cellular components they rely on for persistent infection. These studies suggest that persistent cellular infection results from a balance between prion propagation and degradation. This balance may be shifted depending upon how different cell lines process infectious prions, potentially altering prion stability, and how fast they can be transported to the lysosome. Thus, in vitro studies have given us a deeper understanding of the interactions between different prions and cell types and how they may influence prion disease phenotypes in vivo.

Accumulation of insoluble aggregates of infectious, partially protease-resistant prion protein (PrPD) generated via the misfolding of protease sensitive prion protein (PrPC) into the same infectious conformer, is a hallmark of prion diseases. Aggregated PrPD is taken up and degraded by cells, a process likely involving changes in aggregate structure that can be monitored by accessibility of the N-terminus of full-length PrPD to cellular proteases. We therefore tracked the protease sensitivity of full-length PrPD before and after cellular uptake for two murine prion strains, 22L and 87V. For both strains, PrPD aggregates were less stable following cellular uptake with increased accessibility of the N-terminus to cellular proteases across most aggregate sizes. However, a limited size range of aggregates was able to better protect the N-termini of full-length PrPD, with the N-terminus of 22L-derived PrPD more protected than that of 87V. Interestingly, changes in aggregate structure were associated with minimal changes to the protease-resistant core of PrPD. Our data show that cells destabilize the aggregate quaternary structure protecting PrPD from proteases in a strain-dependent manner, with structural changes exposing protease sensitive PrPD having little effect on the protease-resistant core, and thus conformation, of aggregated PrPD.

The formation and disassembly of macromolecular particles is a ubiquitous and essential feature of virtually all living organisms. Additionally, diseases are often associated with the accumulation and propagation of biologically active nanoparticles, like the formation of toxic protein aggregates in protein misfolding diseases and the growth of infectious viral particles. The heterogeneous and dynamic nature of biologically active particles can make them exceedingly challenging to study. The single-particle fluorescence technique known as burst analysis spectroscopy (BAS) was developed to facilitate real-time measurement of macromolecular particle distributions in the submicron range in a minimally perturbing, free-solution environment. Here, we develop a multicolor version of BAS and employ it to examine two problems in macromolecular assembly: 1) the extent of DNA packing heterogeneity in bacteriophage viral particles and 2) growth models of non-native protein aggregates. We show that multicolor BAS provides a powerful and flexible approach to studying hidden properties of important biological particles like viruses and protein aggregates.

A key constraint on the growth of most organisms is the slow and inefficient folding of many essential proteins. To deal with this problem, several diverse families of protein folding machines, known collectively as molecular chaperones, developed early in evolutionary history. The functional role and operational steps of these remarkably complex nanomachines remain subjects of active debate. Here we present evidence that, for the GroEL-GroES chaperonin system, the non-native substrate protein enters the folding cycle on the trans ring of the double-ring GroEL-ATP-GroES complex rather than the ADP-bound complex. The properties of this ATP complex are designed to ensure that non-native substrate protein binds first, followed by ATP and finally GroES. This binding order ensures efficient occupancy of the open GroEL ring and allows for disruption of misfolded structures through two phases of multiaxis unfolding. In this model, repeated cycles of partial unfolding, followed by confinement within the GroEL-GroES chamber, provide the most effective overall mechanism for facilitating the folding of the most stringently dependent GroEL substrate proteins. Background: Chaperonins like the GroEL-GroES complex facilitate protein folding in the cell. Results: Substrate proteins are captured by the open, trans ring of the GroEL-ATP-GroES complex and are partially unfolded. Conclusion: Maximally efficient folding requires repeated cycles of substrate protein unfolding by the GroEL-GroES complex. Significance: Establishing how substrate proteins are processed by chaperonins is essential for understanding how proteins fold inside cells.

The concentrated and complex interior of a cell presents a difficult challenge to folding of many essential proteins. Partially structured folding intermediates, populated during biosynthesis or upon environmental stress, are prone to assemble into large, non-functional aggregates. A network of specialized molecular chaperones evolved to deal with this problem. How aggregate disassembly is accomplished, its impact on disease progression, and how disaggregation is coupled to productive folding is not well understood. We have therefore initiated an effort to establish the enzyme RuBisCo as a model substrate for studying GroEL-dependent protein folding. We have engineered the sequence of RuBisCo so that exogenous fluorescent probes can be coupled to designed surface cysteine residues in a highly specific manner. We are applying fluorescence based techniques to the study of RuBisCO aggregate formation and disassembly by the DnaK-ClpB bi-chaperone system. Our preliminary studies with acid and urea denatured RuBisCo have shown that this protein populates at least two general aggregate assembly pathways, distinguishable by their distinctly different types of aggregate growth. We have also found that the DnaK system (DnaK/DnaJ/GrpE) is capable of altering the progression of RuBisCo aggregation on its own, without either fully arresting aggregation or fully disassembling RuBisCo aggregates. using both light scattering and fluorescence resonance energy transfer (FRET), we find that RuBisCo aggregates are good substrates for the full DnaK-ClpB system.