We describe a conceptual framework for understanding the way large RNA molecules fold based on the notion that their free-energy landscape is rugged. A key prediction of our theory is that RNA folding can be described by the kinetic partitioning mechanism (KPM). According to KPM a small fraction of molecules folds rapidly to the native state whereas the remaining fraction is kinetically trapped in a low free-energy non-native state. This model provides a unified description of the way RNA and proteins fold. Single-molecule experiments on Tetrahymena ribozyme, which directly validate our theory, are analyzed using KPM. We also describe the earliest events that occur on microsecond time scales in RNA folding. These must involve collapse of RNA molecules that are mediated by counterion-condensation. Estimates of time scales for the initial events in RNA folding are provided for the Tetrahymena ribozyme.

Although initially responsive to androgen signaling inhibitors (ASIs), metastatic castration-resistant prostate cancer (mCRPC) inevitably develops and is incurable. In addition to adenocarcinoma (adeno), neuroendocrine prostate cancer (NEPC) emerges to confer ASI resistance. We have previously combined laser capture microdissection and phage antibody display library selection on human cancer specimens and identified novel internalizing antibodies binding to tumor cells residing in their tissue microenvironment. We identified the target antigen for one of these antibodies as CD46, a multifunctional protein that is best known for negatively regulating the innate immune system. CD46 is overexpressed in primary tumor tissue and CRPC (localized and metastatic; adeno and NEPC), but expressed at low levels on normal tissues except for placental trophoblasts and prostate epithelium. Abiraterone- and enzalutamide-treated mCRPC cells upregulate cell surface CD46 expression. Genomic analysis showed that the CD46 gene is gained in 45% abiraterone-resistant mCRPC patients. We conjugated a tubulin inhibitor to our macropinocytosing anti-CD46 antibody and showed that the resulting antibody-drug conjugate (ADC) potently and selectively kills both adeno and NEPC cell lines in vitro (sub-nM EC50) but not normal cells. CD46 ADC regressed and eliminated an mCRPC cell line xenograft in vivo in both subcutaneous and intrafemoral models. Exploratory toxicology studies of the CD46 ADC in non-human primates demonstrated an acceptable safety profile. Thus, CD46 is an excellent target for antibody-based therapy development, which has potential to be applicable to both adenocarcinoma and neuroendocrine types of mCRPC that are resistant to current treatment.

The collapse kinetics of strongly charged polyelectrolytes in poor solvents is investigated by Langevin simulations and scaling arguments. We investigate the role of valence z of counterions, solvent quality, and shape of counterions on the dynamics of collapse. On the basis of the simulations, a number of results are obtained. (1) The rate of collapse, which is measured using the time dependence of the radius of gyration of the chain, increases sharply as z increases from 1 to 4. The collapse is particularly slow for the monovalent case and is observed only when the solvent quality is sufficiently poor. (2) Although the routes to collapse depend on z and the solvent quality a general collapse mechanism emerges. Upon quenching to low temperatures, counterions condense rapidly on a diffusion-limited time scale. At intermediate times metastable pearl-necklace structures form. The clusters merge at longer times with the largest one growing at the expense of smaller ones which is reminiscent of the Lifshitz-Slyozov growth mechanism. (3) The structure of the globule is controlled by z and the solvent quality. The combined system of the collapsed chain and the condensed counterions forms a Wigner crystal when the solvent quality is not too poor provided z g 2. For very poor solvents the morphology of the collapsed structure resembles a Wigner glass. These results are used to obtain a valence dependent diagram of states for strongly charged polyelectrolytes in poor solvents. (4) For a fixed z and quality of the solvent, the efficiency of collapse decreases dramatically as the size of the counterion increases. The shape of the counterions also affects the collapse dynamics. Spherical counterions are more efficient condensing agents than an isovalent cigar-shaped counterions.