Simulated cytoskeletal collapse via tau degradation.

We present a coarse-grained two dimensional mechanical model for the microtubule-tau bundles in neuronal axons in which we remove taus, as can happen in various neurodegenerative conditions such as Alzheimers disease, tauopathies, and chronic traumatic encephalopathy. Our simplified model includes (i) taus modeled as entropic springs between microtubules, (ii) removal of taus from the bundles due to phosphorylation, and (iii) a possible depletion force between microtubules due to these dissociated phosphorylated taus. We equilibrate upon tau removal using steepest descent relaxation. In the absence of the depletion force, the transverse rigidity to radial compression of the bundles falls to zero at about 60% tau occupancy, in agreement with standard percolation theory results. However, with the attractive depletion force, spring removal leads to a first order collapse of the bundles over a wide range of tau occupancies for physiologically realizable conditions. While our simplest calculations assume a constant concentration of microtubule intercalants to mediate the depletion force, including a dependence that is linear in the detached taus yields the same collapse. Applying percolation theory to removal of taus at microtubule tips, which are likely to be the protective sites against dynamic instability, we argue that the microtubule instability can only obtain at low tau occupancy, from 0.06-0.30 depending upon the tau coordination at the microtubule tips. Hence, the collapse we discover is likely to be more robust over a wide range of tau occupancies than the dynamic instability. We suggest in vitro tests of our predicted collapse.

Vindication of Yb2Ti2O7 as a model exchange quantum spin ice.

We use numerical linked-cluster expansions to compute the specific heat C(T) and entropy S(T) of a quantum spin ice Hamiltonian for Yb2Ti2O7 using anisotropic exchange interactions, recently determined from inelastic neutron scattering measurements, and find good agreement with experimental calorimetric data. This vindicates Yb2Ti2O7 as a model quantum spin ice. We find that in the perturbative weak quantum regime, such a system has a ferrimagnetic ordered ground state, with two peaks in C(T): a Schottky anomaly signaling the paramagnetic to spin ice crossover, followed at a lower temperature by a sharp peak accompanying a first-order phase transition to the ordered state. We suggest that the two C(T) features observed in Yb2Ti2O7 are associated with the same physics. Spin excitations in this regime consist of weakly confined spinon-antispinon pairs. We anticipate that the conventional ground state with exotic quantum dynamics will prove a prevalent characteristic of many real quantum spin ice materials.

Massive conformation change in the prion protein: Using dual-basin structure-based models to find misfolding pathways.

We employ all-atom structure-based models with a force field with multiple energetic basins for the C-terminal (residues 166-226) of the mammalian prion protein. One basin represents the known alpha-helical (αH) structure while the other represents the same residues in a left-handed beta-helical (LHBH) conformation. The LHBH structure has been proposed to help describe one class of in vitro grown fibrils, as well as possibly self-templating the conversion of normal cellular prion protein to the infectious form. Yet, it is unclear how the protein may make this global rearrangement. Our results demonstrate that the conformation changes are not strongly limited by large-scale geometry modification and that there may exist an overall preference for the LHBH conformation. Furthermore, our model presents novel intermediate trapping conformations with twisted LHBH structure.

Evaluating force field accuracy with long-time simulations of a ß-hairpin tryptophan zipper peptide.

We have combined graphics processing unit-accelerated all-atom molecular dynamics with parallel tempering to explore the folding properties of small peptides in implicit solvent on the time scale of microseconds. We applied this methodology to the synthetic ß-hairpin, trpzip2, and one of its sequence variants, W2W9. Each simulation consisted of over 8 µs of aggregated virtual time. Several measures of folding behavior showed good convergence, allowing comparison with experimental equilibrium properties. Our simulations suggest that the intramolecular interactions of tryptophan side chains are responsible for much of the stability of the native fold. We conclude that the ff99 force field combined with ff96 φ and ψ dihedral energies and an implicit solvent can reproduce plausible folding behavior in both trpzip2 and W2W9.

Overexpression and overactivation of Akt in thyroid carcinoma.

Enhanced activation of Akt occurs in Cowden's disease, an inherited syndrome of follicular thyroid, breast, colon, and skin tumors, via inactivation of its regulatory protein, PTEN. Whereas PTEN inactivation is uncommon in sporadic thyroid cancer, activation of growth factor pathways that signal through Akt is frequently identified. We hypothesized that Akt overactivation could be a common finding in sporadic thyroid cancer and might be important in thyroid cancer biology. We examined thyroid cancer cells lines and benign and malignant thyroid tissue for total Akt activation and isoform-specific Akt expression. In thyroid cancer cells, Akt 1, 2, and 3 proteins were expressed, total Akt was activated by insulin phosphatidylinositol 3'-kinase, and inhibition of phosphatidylinositol 3'-kinase reduced cell viability. In human thyroid tissue, increased levels of phosphorylated total Akt were identified in follicular but not papillary cancers compared with normal tissue. Levels of Akt 1 and 2 proteins and Akt 2 RNA were elevated only in the follicular cancers. In paired samples, Akt 1, 2, 3, and phospho-Akt levels were higher in five of six cancers, including three of three follicular cancers. These data suggest that Akt activation may play a role in the pathogenesis or progression of sporadic thyroid cancer.

Cytotoxic activity of 2',2'-difluorodeoxycytidine (gemcitabine) in poorly differentiated thyroid carcinoma cells.

Poorly differentiated and anaplastic thyroid cancers are aggressive and usually fatal neoplasms, despite aggressive treatment. We performed an in vitro study to assess the activity of gemcitabine (2',2' difluorodeoxycytidine), a new fluorinated nucleoside analogue, against three poorly differentiated human thyroid carcinoma cell lines (ARO, WRO, and NPA). Each cell line was exposed to increasing concentrations of gemcitabine (0.0003 to 3000 mumol/L) for 24, 48, and 72 hours. Maximal reduction in cell viability was seen after 72 hours of gemcitabine for all three cell lines as measured by 3-(4,5-dimethyl thiazolyl-2)-2,5-diphenyl tetrazolium bromide (MTT) assay. NPA cells were more sensitive than the other two lines after 24 and 48 hours of exposure, but all cell lines were similarly sensitive at 72 hours. A cytotoxic effect was confirmed by DNA assay of adherent cells. IC50 concentrations for reduction in cell viability ranged from 0.731 and 0.986 mumol/L for each cell line after 72 hours of exposure. These concentrations are lower than serum levels in phase 1 clinical trials of gemcitabine for other malignancies. In summary, gemcitabine has activity against poorly differentiated thyroid cancer cell lines in vitro. In vivo studies using xenograft models are warranted to confirm these promising observations.