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1.
Prog Mol Biol Transl Sci ; 174: 79-103, 2020.
Artículo en Inglés | MEDLINE | ID: mdl-32828471

RESUMEN

We provide a brief overview of the topological features found in structured proteins and of the dynamical processes that involve knots. We then discuss the knotted states that arise in the intrinsically disordered polyglutamine and α-synuclein. We argue that the existence of the knotted conformations stalls degradation by proteases and thus enhances aggregation. This mechanism works if the length of a peptide chain exceeds a threshold, as in the Huntington disease. We also study the cavities that form within the conformations of the disordered proteins. The volume of the cavities varies in time in a way that is different than that of the radius of gyration or the end-to-end distance. In addition, we study the traffic between the conformational basins and identify patterns associated with the deep and shallow knots. The results are obtained by molecular dynamics simulations that use coarse-grained and all-atom models (with and without the explicit solvent).


Asunto(s)
Proteínas Intrínsecamente Desordenadas/química , Degeneración Nerviosa/patología , Animales , Humanos , Modelos Moleculares , Péptidos/química , Conformación Proteica , Proteolisis
2.
Phys Chem Chem Phys ; 21(18): 9285-9295, 2019 May 08.
Artículo en Inglés | MEDLINE | ID: mdl-30931451

RESUMEN

When confined between graphene layers, water behaves differently from the bulk and exhibits unusual properties such as fast water flow and ordering into a crystal. The hydrogen-bonded network is affected by the limited space and by the characteristics of the confining walls. The presence of an extraordinary number of hydronium and hydroxide ions in narrow channels has the following effects: (i) they affect water permeation through the channel, (ii) they may interact with functional groups on the graphene oxide surface and on the edges, and (iii) they change the thermochemistry of water, which are fundamentally important to understand, especially when confined water is subjected to an external electric field. Here we study the physical properties of water when confined between two graphene sheets and containing hydronium and hydroxide. We found that: (i) there is a disruption in the solvation structure of the ions, which is also affected by the layered structure of confined water, (ii) hydronium and hydroxide occupy specific regions inside the nanochannel, with a prevalence of hydronium (hydroxide) ions at the edges (interior), and (iii) ions recombine more slowly in confined systems than in bulk water, with the recombination process depending on the channel height and commensurability between the size of the molecules and the nanochannel height - a decay of 20% (40%) in the number of ions in 8 ps is observed for a channel height of h = 7 Å (bulk water). Our work reveals distinctive properties of water confined in a nanocapillary in the presence of additional hydronium and hydroxide ions.

3.
Sci Rep ; 7(1): 13481, 2017 10 18.
Artículo en Inglés | MEDLINE | ID: mdl-29044124

RESUMEN

We show that a carbon nanotube decorated with different types of charged metallic nanoparticles exhibits unusual two-dimensional vibrations when actuated by applied electric field. Such vibrations and diverse possible trajectories are not only fundamentally important but also have minimum two characteristic frequencies that can be directly linked back to the properties of the constituents in the considered nanoresonator. Namely, those frequencies and the maximal deflection during vibrations are very distinctively dependent on the geometry of the nanotube, the shape, element, mass and charge of the nanoparticle, and are vastly tunable by the applied electric field, revealing the unique sensing ability of devices made of molecular filaments and metallic nanoparticles.

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