Electrostatics in the Stability and Misfolding of the Prion Protein: Salt Bridges, Self-Energy, and Solvation

Using a recently developed mesoscopic theory of protein dielectrics, we have calculated the salt bridge energies, total residue electrostatic potential energies, and transfer energies into a low dielectric amyloid-like phase for 12 species and mutants of the prion protein. Salt bridges and self energies play key roles in stabilizing secondary and tertiary structural elements of the prion protein. The total electrostatic potential energy of each residue was found to be invariably stabilizing. Residues frequently found to be mutated in familial prion disease were among those with the largest electrostatic energies. The large barrier to charged group desolvation imposes regional constraints on involvement of the prion protein in an amyloid aggregate, resulting in an electrostatic amyloid recruitment profile that favours regions of sequence between alpha helix 1 and beta strand 2, the middles of helices 2 and 3, and the region N-terminal to alpha helix 1. We found that the stabilization due to salt bridges is minimal among the proteins studied for disease-susceptible human mutants of prion protein

Influx of pwm-modulation upon torque harmonics of induction machines

Influx of pwm-modulation upon torque harmonics of induction machines

Minimal distance transformations between links and polymers: Principles and examples

The calculation of Euclidean distance between points is generalized to one-dimensional objects such as strings or polymers. Necessary and sufficient conditions for the minimal transformation between two polymer configurations are derived. Transformations consist of piecewise rotations and translations subject to Weierstrass-Erdmann corner conditions. Numerous examples are given for the special cases of one and two links. The transition to a large number of links is investigated, where the distance converges to the polymer length times the mean root square distance (MRSD) between polymer configurations, assuming curvature and non-crossing constraints can be neglected. Applications of this metric to protein folding are investigated. Potential applications are also discussed for structural alignment problems such as pharmacophore identification, and inverse kinematic problems in motor learning and control.Comment: Submitted to J. Phys.:Condens. Matte

β-arrestin/connexin 43 complex anchors ERKs outside the nucleus: a pre-requisite for bisphosphonate anti-apoptotic effect mediated by CX43/ERK in osteocytes

Bisphosphonates (BPs) anti-fracture ef cacy may be due in part to inhibition of osteocyte apoptosis. This effect requires opening of con- nexin (Cx) 43 hemichannels and phosphoryla- tion of the extracellular signal regulated kinases (ERKs). However, unlike ERK activation by other stimuli, the Cx43/ERK pathway activated by BPs does not result in nuclear ERK accumulation. In- stead, the anti-apoptotic effect of BPs depends on phosphorylation of cytoplasmic ERK targets and is abolished by forced nuclear retention of ERKs. We now report that ERKs and the scaf- folding protein β-arrestin co-immuno-precipitate with Cx43 in MLO-Y4 osteocytic cells and that the BP alendronate increases this association. Moreover, ERK2 fused to red uorescent pro- tein (ERK2-RFP) co-localizes with Cx43 fused to green uorescent protein outside the nucleus in cells untreated or treated with alendronate. Alendronate does not induce ERK nuclear ac- cumulation in cells transfected with wild type β-arrestin (wtARR) or vector control, whereas it does in cells expressing a dominant nega- tive β-arrestin mutant (dnARR) consisting of the β-arrestin-clathrin binding domain that com- petes with endogenous β-arrestin for binding to clathrin. Alendronate activates ERKs in dnARR- transfected cells as effectively as in cells trans- fected with wtARR, demonstrating that dnARR only interferes with subcellular localization but not with activation of ERKs by BPs. Further, whereas alendronate inhibits apoptosis in cells expressing wtARR or vector control, it is inef- fective in cells expressing dnARR. Thus, BPs induce the formation of a complex comprising Cx43, β-arrestin, and clathrin, which directs ERKs outside the nucleus and is indispensable for osteocyte survival induced by BPs

Protein folding rates correlate with heterogeneity of folding mechanism

By observing trends in the folding kinetics of experimental 2-state proteins at their transition midpoints, and by observing trends in the barrier heights of numerous simulations of coarse grained, C-alpha model, Go proteins, we show that folding rates correlate with the degree of heterogeneity in the formation of native contacts. Statistically significant correlations are observed between folding rates and measures of heterogeneity inherent in the native topology, as well as between rates and the variance in the distribution of either experimentally measured or simulated phi-values.Comment: 11 pages, 3 figures, 1 tabl

Evaluating the performance of model transformation styles in Maude

Rule-based programming has been shown to be very successful in many application areas. Two prominent examples are the specification of model transformations in model driven development approaches and the definition of structured operational semantics of formal languages. General rewriting frameworks such as Maude are flexible enough to allow the programmer to adopt and mix various rule styles. The choice between styles can be biased by the programmer’s background. For instance, experts in visual formalisms might prefer graph-rewriting styles, while experts in semantics might prefer structurally inductive rules. This paper evaluates the performance of different rule styles on a significant benchmark taken from the literature on model transformation. Depending on the actual transformation being carried out, our results show that different rule styles can offer drastically different performances. We point out the situations from which each rule style benefits to offer a valuable set of hints for choosing one style over the other