3,138 research outputs found
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
The surgical treatment of Parkinson's disease cryothalamectomy
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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
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
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