| Summary: | Protein misfolding diseases represent a large burden to human health for which only symptomatic
treatment is generally available. These diseases, such as Creutzfeldt-Jakob disease, amyotrophic
lateral sclerosis, and the systemic amyloidoses, are characterized by conversion of globular, nativelyfolded
proteins into pathologic β-sheet rich protein aggregates deposited in affected tissues. Understanding
the thermodynamic and kinetic details of protein misfolding on a molecular level depends
on accurately appraising the free energies of the folded, partially unfolded intermediate,
and misfolded protein conformers. There are multiple energetic and entropic contributions to the
total free energy, including nonpolar, electrostatic, solvation, and configurational terms. To accurately
assess the electrostatic contribution, a method to calculate the spatially-varying dielectric
constant in a protein/water system was developed using a generalization of Kirkwood Frohlich theory
along with brief all-atom molecular dynamics simulations. This method was combined with
previously validated models for nonpolar solvation and configurational entropy in an algorithm to
calculate the free energy change on partial unfolding of contiguous protein subsequences. Results
were compared with those from a minimal, topologically-based Gō model and direct calculation
of free energies by steered all-atom molecular dynamics simulations. This algorithm was applied
to understand the early steps in the misfolding mechanism for β₂-microglobulin, prion protein,
and superoxide dismutase 1 (SOD1). It was hypothesized that SOD1 misfolding may follow a
template-directed mechanism like that discovered previously for prion protein, so misfolding of
SOD1 was induced in cell culture by transfection with mutant SOD1 constructs and observed to
stably propagate intracellularly and intercellularly much like an infectious prion. A defined minimal
assay with recombinant SOD protein demonstrated the sufficiency of mutant SOD1 alone
to trigger wtSOD1 misfolding, reminiscent of the “protein-only” hypothesis of prion spread. Finally,
protein misfolding as a feature of disease may extend beyond neurodegeneration and amyloid
formation to cancer, in which derangement of protein folding quality control may lead to antibodyrecognizable
misfolded protein present selectively on cancer cell surfaces. The evidence for this
hypothesis and possible therapeutic targets are discussed as a future direction.
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