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1.
Sci Rep ; 9(1): 7481, 2019 May 16.
Artigo em Inglês | MEDLINE | ID: mdl-31097749

RESUMO

Ataxin-7 (Atx7) is a disease-related protein associated with the pathogenesis of spinocerebellar ataxia 7, while its polyglutamine (polyQ) tract in N-terminus is the causative source of aggregation and proteinopathy. We investigated the structure, dynamics and aggregation properties of the N-terminal 62-residue fragment of Atx7 (Atx7-N) by biochemical and biophysical approaches. The results showed that the normal Atx7-N with a tract of 10 glutamines (10Q) overall adopts a flexible and disordered structure, but it may contain a short or small population of helical structure in solution. PolyQ expansion increases the α-helical propensity of the polyQ tract and consequently enhances its transformation into ß-sheet structures during amyloid aggregation. An alanine-rich region (ARR) just ahead of the polyQ tract forms a local and relatively stable α-helix. The ARR α-helix can initiate and stabilize helical formation of the following polyQ tract, but it may suppress aggregation of the polyQ-expanded Atx7-N both in vitro and in cell. Thus, the preceding ARR segment in Atx7-N may influence the dynamic structure and aggregation property of the polyQ tract and even determine the threshold of the pathogenic polyQ lengths. This study may gain structural and dynamic insights into amyloid aggregation of Atx7 and help us further understand the Atx7 proteinopathy based on polyQ expansion.

2.
Langmuir ; 34(38): 11442-11448, 2018 09 25.
Artigo em Inglês | MEDLINE | ID: mdl-30184425

RESUMO

In this study, we prepared biocompatible superhydrophilic and underwater superoleophobic tannic acid (TA)/polyvinylpyrrolidone (PVP)-coated stainless-steel meshes that mediated extremely efficient separations of mixtures of oil and water. These TA/PVP-coated stainless-steel meshes displayed excellent antifouling properties and could be used to separate oil/water mixtures continuously for up to 24 h. Moreover, a funnel-like TA/PVP-coated stainless-steel mesh device could be used for underwater oil transportation and collection. In conjunction with our continuous oil removal system, this device allowed for the continuous collection and removal of oil pollutants from underwater environments. The high performance of these TA/PVP-coated stainless-steel meshes and their green, low-energy, cost-effective preparation suggests great potential for practical applications.

3.
J Biol Chem ; 285(5): 3053-63, 2010 Jan 29.
Artigo em Inglês | MEDLINE | ID: mdl-19996093

RESUMO

ATP binding cassette transporters are integral membrane proteins that use the energy released from ATP hydrolysis at the two nucleotide binding domains (NBDs) to translocate a wide variety of substrates through a channel at the two transmembrane domains (TMDs) across the cell membranes. MsbA from Gram-negative bacteria is a lipid and multidrug resistance ATP binding cassette exporter that can undergo large scale conformational changes between the outward-facing and the inward-facing conformations revealed by crystal structures in different states. Here, we use targeted molecular dynamics simulation methods to explore the atomic details of the conformational transition from the outward-facing to the inward-facing states of MsbA. The molecular dynamics trajectories revealed a clear spatiotemporal order of the conformational movements. The disruption of the nucleotide binding sites at the NBD dimer interface is the very first event that initiates the following conformational changes, verifying the assumption that the conformational conversion is triggered by ATP hydrolysis. The conserved x-loops of the NBDs were identified to participate in the interaction network that stabilizes the cytoplasmic tetrahelix bundle of the TMDs and play an important role in mediating the cross-talk between the NBD and TMD. The movement of the NBD dimer is transmitted through x-loops to break the tetrahelix bundle, inducing the packing rearrangements of the transmembrane helices at the cytoplasmic side and the periplasmic side sequentially. The packing rearrangement within each periplasmic wing of TMD that results in exposure of the substrate binding sites occurred at the end stage of the trajectory, preventing the wrong timing of the binding site accessibility.


Assuntos
Transportadores de Cassetes de Ligação de ATP/metabolismo , Proteínas de Bactérias/química , Salmonella typhimurium/metabolismo , Transportadores de Cassetes de Ligação de ATP/química , Trifosfato de Adenosina/química , Sítio Alostérico , Proteínas de Bactérias/metabolismo , Membrana Celular/metabolismo , Simulação por Computador , Citoplasma/metabolismo , Dimerização , Hidrólise , Bicamadas Lipídicas/química , Conformação Molecular , Conformação Proteica , Estrutura Secundária de Proteína , Eletricidade Estática
4.
J Phys Chem A ; 111(46): 11894-903, 2007 Nov 22.
Artigo em Inglês | MEDLINE | ID: mdl-17966997

RESUMO

This work aims to investigate the reaction mechanism of lanthanum atom with formaldehyde in the gas phase using density functional theory and coupled cluster calculations. The results indicate that the minimum energy pathway, similar to the reactions of its neighboring yttrium with formaldehyde, is the formation of the eta2-formaldehyde-metal complex followed by two C-H insertions which leads to metal dihydrides and carbon monoxide. The competing pathway producing a metal-carbonyl compound and hydrogen molecule favors a high-spin state and thus involves a spin conversion from doublet state to quartet state. The crossing region of the doublet and quartet potential energy surfaces (PES) has been estimated by a simple approach as proposed by Yoshizawa et al. Less favorable pathways leading to metal monoxide and carbene radical by C-O insertion as well as formyllanthanum by single C-H insertion are also studied. Compared with the CCSD(T) method, the BP86 method tends to overestimate the binding energies of the d-rich compounds, though the two methods qualitatively agree well on the reaction mechanism. Finally, the (n - 1)d1ns2 to (n - 1)d2ns1 promotion effect is proposed to account for the difference in the formation mechanism of the metal-carbonyl compounds LaCO and YCO, which may also extend to the reactions of formaldehyde with other "general" group III rare earth elements including Sc, Ce, Gd, and Lu.

5.
J Phys Chem A ; 110(40): 11537-42, 2006 Oct 12.
Artigo em Inglês | MEDLINE | ID: mdl-17020267

RESUMO

Small neutral, anionic, and cationic silver cluster hydrides AgnH and anionic HAgnH (n=1-7) have been studied using the PW91PW91 density functional method. It was found that the most stable structure of the AgnH complex (neutral or charged) does not always come from that of the lowest energy bare silver cluster plus an attached H atom. Among various possible adsorption sites, the bridge site is energetically preferred for the cationic and most cases of neutral Agn. For anionic Agn, the top site is preferred for smaller Agn within n

6.
J Am Chem Soc ; 128(34): 11114-23, 2006 Aug 30.
Artigo em Inglês | MEDLINE | ID: mdl-16925429

RESUMO

The oxidative dehydrogenation (ODH) of propane on single-crystal V(2)O(5)(001) is studied by periodic density functional theory (DFT) calculations. The energetics and pathways for the propane to propene conversion are determined. We show that (i) the C-H bond of propane can be activated by both the terminal and the bridging lattice O atoms on the surface with similar activation energies. At the terminal O site both the radical and the oxo-insertion pathways are likely for the C-H bond activation, while only the oxo-insertion mechanism is feasible at the bridging O site. (ii) Compared to that at the terminal O site, the propene production from the propoxide at the bridging O site is much easier due to the weaker binding of propoxide at the bridging O. It is concluded that single-crystal V(2)O(5)(001) is not a good catalyst due to the terminal O being too active to release propene. It is expected that an efficient catalyst for the ODH reaction has to make a compromise between the ability to activate the C-H bond and the ability to release propene.

7.
J Phys Chem A ; 110(22): 7167-72, 2006 Jun 08.
Artigo em Inglês | MEDLINE | ID: mdl-16737267

RESUMO

CO adsorption on small neutral, anionic, and cationic silver clusters Ag(n) (n = 1-7) has been studied with use of the PW91PW91 density functional theory (DFT) method. The adsorption of CO on-top site, among various possible sites, is energetically preferred irrespective of the charge state of the silver cluster. The cationic silver clusters generally have a greater tendency to adsorb CO than the anionic and neutral silver ones, except for n = 3 and 4, and the binding energies reach a local minimum at n = 5. The binding energies on the neutral clusters, instead, reach a local maximum at n = 3, which is about 0.87 eV, probably large enough to be captured in the experiments. Binding of CO to the silver clusters is generally weaker than that to the copper and gold counterparts at the same size and charge state. This is due to the weaker orbital interaction between silver and CO, which is caused by the larger atomic radius of the silver atom. In contrast, Au atoms with a larger nuclear charge but a similar atomic radius to silver owing to the lanthanide contraction are able to have a stronger interaction with CO.

8.
J Chem Phys ; 124(18): 184102, 2006 May 14.
Artigo em Inglês | MEDLINE | ID: mdl-16709092

RESUMO

Twenty-three density functional theory (DFT) methods, including the second- and the third-generation functionals, are tested in conjunction with two basis sets (LANL2DZ and SDD) for studying the properties of neutral and ionic silver clusters. We find that DFT methods incorporating the uniform electron gas limit in the correlation functional, namely, those with Perdew's correlation functionals (PW91, PBE, P86, and TPSS), Becke's B95, and the Van Voorhis-Scuseria functional VSXC, generally perform better than the other group of functionals, e.g., those incorporating the LYP correlation functional and variations of the B97 functional. Strikingly, these two groups of functionals can produce qualitatively different results for the Ag3 and Ag4 clusters. The energetic properties and vibrational frequencies of Ag(n) are also evaluated by the different functionals. The present study shows that the choice of DFT methods for heavy metals may be critical. It is found that the exact-exchange-incorporated PBE functional (PBE1PBE) is among the best for predicting the range of properties.

9.
J Chem Phys ; 122(14): 144701, 2005 Apr 08.
Artigo em Inglês | MEDLINE | ID: mdl-15847547

RESUMO

Chlorine adsorption on small neutral, anionic, and cationic silver clusters Ag(n) (n=2-7) has been studied using the PW91PW91 density functional method. It was found that the adsorption of chlorine on the lowest-energy bare clusters does not always produce the lowest-energy complexes. In addition, the binding of chlorine can greatly change the geometries of the silver clusters in some cases. Among various possible adsorption sites, bridge site is energetically preferred for the neutral Ag(n) while top site is energetically more preferred for the anionic Ag(n) with n< or =6. For cationic clusters, adsorptions on bridge and face sites have similar binding energies, which are much larger than those on top sites. Natural bond orbital analyses show that irrespective of charge state, electrons always transfer from silver atoms to adsorbate and silver acts like alkali metals in the interaction with chlorine atom. Significant odd-even alternation patterns in the properties of the complexes have been observed: Even-electron clusters often have higher ionization energies, lower electron affinities, and higher dissociation energies than their odd-electron neighbors. It was also found that chlorine atoms bind more strongly with odd-electron bare clusters than with even-electron bare clusters. These patterns reveal that even-electron clusters are more stable than odd-electron clusters.

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