Magnetic fluid hyperthermia is a promising cancer therapy in which magnetic nanoparticles are acted upon by a high-frequency oscillating magnetic field. While the accepted mechanism is localized hyperthermia, it is plausible that shear stresses due to nanoparticles rotating near a cell membrane may induce rupture, enhancing the effectiveness of the treatment. With the goal of understanding this further, molecular dynamics simulations were carried out on a model cell membrane. A bilayer composed of dipalmitoylphosphatidylcholine lipids was subjected to an incremental tension as well as an incremental shear stress. In both cases, it was found that the bilayer could withstand a surface tension of approximately 90 mN/m prior to rupture. Under tension, the bilayer ruptured at double its initial area, whereas under shear, the bilayer ruptured at 1.8 times its initial area. The results show that both incremental tension and incremental shearing are able to produce bilayer rupture, with shear being more injurious, yielding a larger surface tension for a smaller deformation. This information allows for comparison between the estimated energy required to rupture a cell membrane and the energy that a magnetic nanoparticle would be able to generate while rotating in a cellular environment. Our estimates indicate that magnetically blocked nanoparticles with diameters larger than 50 nm may result in rupture due to shear.

Atherogenesis, the uncontrolled deposition of modified lipoproteins in inflamed arteries, serves as a focal trigger of cardiovascular disease (CVD). Polymeric biomaterials have been envisioned to counteract atherogenesis based on their ability to repress scavenger mediated uptake of oxidized lipoprotein (oxLDL) in macrophages. Following the conceptualization in our laboratories of a new library of amphiphilic macromolecules (AMs), assembled from sugar backbones, aliphatic chains and poly(-ethylene glycol) tails, a more rational approach is necessary to parse the diverse features such as charge, hydrophobicity, sugar composition and stereochemistry. In this study, we advance a computational biomaterials design approach to screen and elucidate anti-atherogenic biomaterials with high efficacy. AMs were quantified in terms of not only 1D (molecular formula) and 2D (molecular connectivity) descriptors, but also new 3D (molecular geometry) descriptors of AMs modeled by coarse-grained molecular dynamics (MD) followed by all-atom MD simulations. Quantitative structure-activity relationship (QSAR) models for anti-atherogenic activity were then constructed by screening a total of 1164 descriptors against the corresponding, experimentally measured potency of AM inhibition of oxLDL uptake in human monocyte-derived macrophages. Five key descriptors were identified to provide a strong linear correlation between the predicted and observed anti-atherogenic activity values, and were then used to correctly forecast the efficacy of three newly designed AMs. Thus, a new ligand-based drug design framework was successfully adapted to computationally screen and design biomaterials with cardiovascular therapeutic properties.

In fibrolamellar hepatocellular carcinoma a single genetic deletion results in the fusion of the first exon of the heat shock protein 40, DNAJB1, which encodes the J domain, with exons 2–10 of the catalytic subunit of protein kinase A, PRKACA. This produces an enzymatically active chimeric protein J-PKAcα. We used molecular dynamics simulations and NMR to analyze the conformational landscape of native and chimeric kinase, and found an ensemble of conformations. These ranged from having the J-domain tucked under the large lobe of the kinase, similar to what was reported in the crystal structure, to others where the J-domain was dislodged from the core of the kinase and swinging free in solution. These simulated dislodged states were experimentally captured by NMR. Modeling of the different conformations revealed no obvious steric interactions of the J-domain with the rest of the RIIβ holoenzyme.

Fibrolamellar hepatocellular carcinoma (FLHCC) is driven by J-PKAca, a kinase fusion chimera of the J domain of DnaJB1 with PKAca, the catalytic subunit of protein kinase A (PKA). Here we report the crystal structures of the chimeric fusion RIa 2 :J-PKAca 2 holoenzyme formed by J-PKAca and the PKA regulatory (R) subunit RIa, and the wild-type (WT) RIa 2 : PKAca 2 holoenzyme. The chimeric and WT RIa holoenzymes have quaternary structures different from the previously solved WT RIb and RIIb holoenzymes. The WT RIa holoenzyme showed the same configuration as the chimeric RIa 2 :J-PKAca 2 holoenzyme and a distinct second conformation. The J domains are positioned away from the symmetrical interface between the two RIa:J-PKAca heterodimers in the chimeric fusion holoenzyme and are highly dynamic. The structural and dynamic features of these holoenzymes enhance our understanding of the fusion chimera protein J-PKAca that drives FLHCC as well as the isoform specificity of PKA. ACKNOWLEDGMENTSWe thank Drs. Alexandr Kornev, Di Xia, and Kylie Walters for critical reading of the manuscript and helpful discussions.