3,470 research outputs found
A novel iterative strategy for protein design
We propose and discuss a novel strategy for protein design. The method is
based on recent theoretical advancements which showed the importance to treat
carefully the conformational free energy of designed sequences. In this work we
show how computational cost can be kept to a minimum by encompassing negative
design features, i.e. isolating a small number of structures that compete
significantly with the target one for being occupied at low temperature. The
method is succesfully tested on minimalist protein models and using a variety
of amino acid interaction potentials.Comment: 9 pages, 8 figure
A multiplicity result for double singularly perturbed elliptic systems
We show that the number of low energy solutions of a double singularly
perturbed Schroedinger Maxwell system type on a smooth 3 dimensional manifold
(M,g) depends on the topological properties of the manifold. The result is
obtained via Lusternik Schnirelmann category theory
Elucidation of the disulfide folding pathway of hirudin by a topology-based approach
A theoretical model for the folding of proteins containing disulfide bonds is
introduced. The model exploits the knowledge of the native state to favour the
progressive establishment of native interactions. At variance with traditional
approaches based on native topology, not all native bonds are treated in the
same way; in particular, a suitable energy term is introduced to account for
the special strength of disulfide bonds (irrespective of whether they are
native or not) as well as their ability to undergo intra-molecular reshuffling.
The model thus possesses the minimal ingredients necessary to investigated the
much debated issue of whether the re-folding process occurs through partially
structured intermediates with native or non-native disulfide bonds. This
strategy is applied to a context of particular interest, the re-folding process
of Hirudin, a thrombin-specific protease inhibitor, for which conflicting
folding pathways have been proposed. We show that the only two parameters in
the model (temperature and disulfide strength) can be tuned to reproduce well a
set of experimental transitions between species with different number of formed
disulfide. This model is then used to provide a characterisation of the folding
process and a detailed description of the species involved in the rate-limiting
step of Hirudin refolding.Comment: 14 pages, 9 figure
Topological jamming of spontaneously knotted polyelectrolyte chains driven through a nanopore
The advent of solid state nanodevices allows for interrogating the
physico-chemical properties of a polyelectrolyte chain by electrophoretically
driving it through a nanopore. Salient dynamical aspects of the translocation
process have been recently characterized by theoretical and computational
studies of model polymer chains free from self-entanglement. However,
sufficiently long equilibrated chains are necessarily knotted. The impact of
such topological "defects" on the translocation process is largely unexplored,
and is addressed in this study. By using Brownian dynamics simulations on a
coarse-grained polyelectrolyte model we show that knots, despite being trapped
at the pore entrance, do not "per se" cause the translocation process to jam.
Rather, knots introduce an effective friction that increases with the applied
force, and practically halts the translocation above a threshold force. The
predicted dynamical crossover, which is experimentally verifiable, is of
relevance in applicative contexts, such as DNA nanopore sequencing.Comment: 6 pages; 7 figure
Multiscale entanglement in ring polymers under spherical confinement
The interplay of geometrical and topological entanglement in semiflexible
knotted polymer rings confined inside a spherical cavity is investigated using
advanced numerical methods. By using stringent and robust algorithms for
locating knots, we characterize how the knot length lk depends on the ring
contour length, Lc and the radius of the confining sphere, Rc . In the no- and
strong- confinement cases we observe weak knot localization and complete knot
delocalization, respectively. We show that the complex interplay of lk, Lc and
Rc that seamlessly bridges these two limits can be encompassed by a simple
scaling argument based on deflection theory. The same argument is used to
rationalize the multiscale character of the entanglement that emerges with
increasing confinement.Comment: 9 pages 9 figure
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