Molecular models of NS3 protease variants of the Hepatitis C virus

Background: Hepatitis C virus (HCV) currently infects approximately three percent of the world population. In view of the lack of vaccines against HCV, there is an urgent need for an efficient treatment of the disease by an effective antiviral drug. Rational drug design has not been the primary way for discovering major therapeutics. Nevertheless, there are reports of success in the development of inhibitor using a structure-based approach. One of the possible targets for drug development against HCV is the NS3 protease variants. Based on the three-dimensional structure of these variants we expect to identify new NS3 protease inhibitors. In order to speed up the modeling process all NS3 protease variant models were generated in a Beowulf cluster. The potential of the structural bioinformatics for development of new antiviral drugs is discussed.Results: the atomic coordinates of crystallographic structure 1CU1 and 1DY9 were used as starting model for modeling of the NS3 protease variant structures. The NS3 protease variant structures are composed of six subdomains, which occur in sequence along the polypeptide chain. The protease domain exhibits the dual beta-barrel fold that is common among members of the chymotrypsin serine protease family. The helicase domain contains two structurally related beta-alpha-beta subdomains and a third subdomain of seven helices and three short beta strands. The latter domain is usually referred to as the helicase alpha-helical subdomain. The rmsd value of bond lengths and bond angles, the average G-factor and Verify 3D values are presented for NS3 protease variant structures.Conclusions: This project increases the certainty that homology modeling is an useful tool in structural biology and that it can be very valuable in annotating genome sequence information and contributing to structural and functional genomics from virus. The structural models will be used to guide future efforts in the structure-based drug design of a new generation of NS3 protease variants inhibitors. All models in the database are publicly accessible via our interactive website, providing us with large amount of structural models for use in protein-ligand docking analysis.

SrBi2Ta2O9 ferroelectric thick films prepared by electrophoretic deposition using aqueous suspension

SrBi2Ta2O9 ferroelectric thick films were prepared by electrophoretic deposition (EPD). For that, ceramic powders were prepared by chemical method in order to obtain compounds with chemical homogeneity. The polymeric precursor method was used for the synthesis of the SrBi2Ta2O9 powder. The crystallographic structure of the powder was examined by X-ray diffraction, and the surface area was determined by single point BET adsorption. The 0.03 vol.% suspension was formed by dispersing the powder in water using two different polymers as dispersants: an ester polyphosphate (C213) and an ammonium polyacrilate (Darvan 821-A). It was investigated the influence of the different dispersants in the surface properties of the powder by zeta potential measurements. The films were deposited on platinum-coated alumina and Pt/Ti/SiO2/Si substrates by a 4 mA constant current, for 10 min, using two parallel electrodes placed at a separation distance of 3 min in the suspension. Several cycles of deposition-drying of the deposit were carried out until reaching the desired thickness. After thermal treatment at temperatures ranging from 700 to 1000 degreesC, the films were characterized by X-ray diffraction and scanning electron microscopy for the microstructure observation. (C) 2003 Elsevier Ltd. All rights reserved.

Molecular models of cyclin-dependent kinase 1 complexed with inhibitors

Roscovitine and flavopiridol have been shown to potently inhibit cyclin-dependent kinase 1 and 2 (CDK1 and 2). The structures of CDK2 complexed with roscovitine and deschoroflavopiridol have been reported, however no crystallographic structure is available for complexes of CDK1 with inhibitors. The present work describes two molecular models for the binary complexes CDK1:roscovitine and CDK1:flavopiridol. These structural models indicate that both inhibitors strongly bind to the ATP-binding pocket of CDKI and structural comparison of the CDK complexes correlates the structures with differences in inhibition of these CDKs by flavopiridol and roscovitine. This article explains the structural basis for the observed differences in activity of these inhibitors. (C) 2004 Elsevier B.V. All rights reserved.

Magnetic doping in Zn7-xMxSb2O12 spinels (M = Ni and Co)

In this article we present a concise report on our studies on the magnetic behavior and structural arrangements of the inverse spinel Zn7-xMxSb2O12 system (M = Ni, Co). Studies on the temperature dependence of the magnetization (M) of several samples in this system showed the occurrence of a spin-glass-like state in temperatures around 10 K. The capability of this system to hold magnetic ions in either octahedral and/or tetrahedral positions is responsible for the occurrence of competing ferromagnetic and antiferromagnetic interactions. This condition is likely to cause the appearance of the observed spin-glass-like behavior. (C) 2002 Elsevier B.V. B.V. All rights reserved.

Preparation of SrBi2Ta2O9 ferroelectric thick films by electrophoretic deposition using aqueous suspensions

SrBi2Ta2O9 ferroelectric thick films were prepared by electrophoretic deposition (EPD). For that, ceramic powders were prepared by chemical method in order to obtain compounds with chemical homogeneity. The polymeric precursor method was used for the synthesis of the SrBi2Ta2O9 powder. The crystallographic structure of the powder was examined by X-ray diffraction, and the surface area was determined by single point BET adsorption. The 0.03 vol% suspension was formed by dispersing the powder in water using two different polymers as dispersants: an ester polyphosphate (C213) and an ammonium polyacrilate (Darvan 821-A). The influence of the different dispersants on the powder surface properties were investigated by zeta potential measurements. The films were deposited on platinum-coated alumina and Pt/Ti/SiO2/Si substrates by electrophoretic deposition using a 4 mA constant current, for 10 min, with two parallel electrodes placed at a separation distance of 3 min in the suspension. Several cycles of deposition-drying of the deposit was carried out until the desired thickness was obtained. After thermal treatment at temperatures ranging from 700 to 1000degreesC, the films were characterized by X-ray diffraction and scanning electron microscopy.

Disulfide Biochemistry in 2-Cys Peroxiredoxin: Requirement of Glu50 and Arg146 for the Reduction of Yeast Tsa1 by Thioredoxin

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

Intrinsic magnetic properties of BixCo2-xMnO 4 spinels obtained by short-time etching

We report the structural and magnetic properties of Co2MnO 4, partially substituted by Bi at the octahedral site. Bismuth enhances ferromagnetism due to a decrease of the Co2+-Co2+ antiferromagnetic interactions and an increase of the Mn3+-Mn 4+ exchanges. Spurious phases (magnetic and/or nonmagnetic oxides) can easily form because of the large differences between the ionic radii of Bi3+ and Co3+, hiding or altering the intrinsic physical properties of the main BixCo2-xMnO4 phase. An easy way to eliminate the secondary phases is using acid reagents. Short-time etching of Bi0.1Co1.9MnO4 using nitric acid was successfully used, keeping most of the properties of the initial compound, with no alteration of the crystallographic structure. Final stoichiometry was respected (∼Bi0.08Co1.82MnO4), meaning that the material after etching definitely contains bismuth elements in its structure and the observed properties are intrinsic to the oxide spinel. Additional experiments were performed as a function of the synthesis conditions, showing that an optimal pH value of 7 allowed the best magnetic response of the non-doped material. © 2013 Elsevier B.V. All rights reserved.

Tribocorrosion behaviour of anodic treated titanium surfaces intended for dental implants

Tribocorrosion plays an important role in the lifetime of metallic implants. Once implanted, biomaterials are subjected to micro-movements in aggressive biological fluids. Titanium is widely used as an implant material because it spontaneously forms a compact and protective nanometric thick oxide layer, mainly TiO2, in ambient air. That layer provides good corrosion resistance, and very low toxicity, but its low wear resistance is a concern. In this work, an anodizing treatment was performed on commercial pure titanium to form a homogeneous thick oxide surface layer in order to provide bioactivity and improve the biological, chemical and mechanical properties. Anodizing was performed in an electrolyte containing β-glycerophosphate and calcium acetate. The influence of the calcium acetate content on the tribocorrosion behaviour of the anodized material was studied. The concentration of calcium acetate in the electrolyte was found to largely affect the crystallographic structure of the resulting oxide layer. Better tribocorrosion behaviour was noticed on increasing the calcium acetate concentration. © 2013 IOP Publishing Ltd.

Docking e análise do modo de ligação de três moléculas pequenas, um benzimidazol e dois compostos de crômio, nos sulcos do DNA 5'-CGCGAATTCGCG-3

Pós-graduação em Ciência e Tecnologia de Materiais - FC

Estudos estruturais com fosfolipases A2 homólogas de veneno botrópicos em presença de íons com importância funcional

Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)

Complexos contendo o ligante 2 - Mercaptopiridina derivados da série '[RUCL IND. 3(NO)(P-P)]'

Pós-graduação em Química - IQ

Desenvolvimento de biocidas inorgânicos a base de óxidos de titânio e silício com prata para desinfecção de águas contaminadas com microrganismo

Pós-graduação em Ciência e Tecnologia de Materiais - FC

Nanopartículas aciculares metálicas de 'Fe', 'Fe''Co', 'Fe''TR' e 'Fe''Co''TR'('TR'='La'-'Tb') para tecnologia avançada de gravação magnética

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

Estudos estruturais com miotoxinas do tipo fosfolipases A2 homólogas do veneno de serpentes do gênero Bothrops: avanços no entendimento da relação estrutura-função

Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)

Function inferences from a molecular structural model of bacterial ParE toxin

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)