Improvement of 3D protein models using multiple templates guided by single-template model quality assessment

Motivation: Modelling the 3D structures of proteins can often be enhanced if more than one fold template is used during the modelling process. However, in many cases, this may also result in poorer model quality for a given target or alignment method. There is a need for modelling protocols that can both consistently and significantly improve 3D models and provide an indication of when models might not benefit from the use of multiple target-template alignments. Here, we investigate the use of both global and local model quality prediction scores produced by ModFOLDclust2, to improve the selection of target-template alignments for the construction of multiple-template models. Additionally, we evaluate clustering the resulting population of multi- and single-template models for the improvement of our IntFOLD-TS tertiary structure prediction method. Results: We find that using accurate local model quality scores to guide alignment selection is the most consistent way to significantly improve models for each of the sequence to structure alignment methods tested. In addition, using accurate global model quality for re-ranking alignments, prior to selection, further improves the majority of multi-template modelling methods tested. Furthermore, subsequent clustering of the resulting population of multiple-template models significantly improves the quality of selected models compared with the previous version of our tertiary structure prediction method, IntFOLD-TS.

Insights into dietary flavonoids as molecular templates for the design of anti-platelet drugs

Flavonoids are low-molecular weight, aromatic compounds derived from fruits, vegetables, and other plant components. The consumption of these phytochemicals has been reported to be associated with reduced cardiovascular disease (CVD) risk, attributed to their anti-inflammatory, anti-proliferative, and anti-thrombotic actions. Flavonoids exert these effects by a number of mechanisms which include attenuation of kinase activity mediated at the cell-receptor level and/or within cells, and are characterized as broad-spectrum kinase inhibitors. Therefore, flavonoid therapy for CVD is potentially complex; the use of these compounds as molecular templates for the design of selective and potent small-molecule inhibitors may be a simpler approach to treat this condition. Flavonoids as templates for drug design are, however, poorly exploited despite the development of analogues based on the flavonol, isoflavonone, and isoflavanone subgroups. Further exploitation of this family of compounds is warranted due to a structural diversity that presents great scope for creating novel kinase inhibitors. The use of computational methodologies to define the flavonoid pharmacophore together with biological investigations of their effects on kinase activity, in appropriate cellular systems, is the current approach to characterize key structural features that will inform drug design. This focussed review highlights the potential of flavonoids to guide the design of clinically safer, more selective, and potent small-molecule inhibitors of cell signalling, applicable to anti-platelet therapy.

Investigating flavonoids as molecular templates for the design of small-molecule inhibitors of cell signaling

Epidemiological and clinical trials reveal compelling evidence for the ability of dietary flavonoids to lower cardiovascular disease risk. The mechanisms of action of these polyphenolic compounds are diverse, and of particular interest is their ability to function as protein and lipid kinase inhibitors. We have previously described structure-activity studies that reinforce the possibility for using flavonoid structures as templates for drug design. In the present study, we aim to begin constructing rational screening strategies for exploiting these compounds as templates for the design of clinically relevant, antiplatelet agents. We used the platelet as a model system to dissect the structural influence of flavonoids, stilbenes, anthocyanidins, and phenolic acids on inhibition of cell signaling and function. Functional groups identified as relevant for potent inhibition of platelet function included at least 2 benzene rings, a hydroxylated B ring, a planar C ring, a C ring ketone group, and a C-2 positioned B ring. Hydroxylation of the B ring with either a catechol group or a single C-4' hydroxyl may be required for efficient inhibition of collagen-stimulated tyrosine phosphorylated proteins of 125 to 130 kDa, but may not be necessary for that of phosphotyrosine proteins at approximately 29 kDa. The removal of the C ring C-3 hydroxyl together with a hydroxylated B ring (apigenin) may confer selectivity for 37 to 38 kDa phosphotyrosine proteins. We conclude that this study may form the basis for construction of maps of flavonoid inhibitory activity on kinase targets that may allow a multitargeted therapeutic approach with analogue counterparts and parent compounds.

New self-assembling multifunctional templates for the biofabrication and controlled self-release of cultured tissue

The need to source live human tissues for research and clinical applications has been a major driving force for the development of new biomaterials. Ideally, these should elicit the formation of scaffold-free tissues with native-like structure and composition. In this study, we describe a biologically interactive coating that combines the fabrication and subsequent self-release of live purposeful tissues using template–cell–environment feedback. This smart coating was formed from a self-assembling peptide amphiphile comprising a proteasecleavable sequence contiguous with a cell attachment and signaling motif. This multifunctional material was subsequently used not only to instruct human corneal or skin fibroblasts to adhere and deposit discreet multiple layers of native extracellular matrix but also to govern their own self-directed release from the template solely through the action of endogenous metalloproteases. Tissues recovered through this physiologically relevant process were carrier-free and structurally and phenotypically equivalent to their natural counterparts. This technology contributes to a new paradigm in regenerative medicine, whereby materials are able to actively direct and respond to cell behavior. The novel application of such materials as a coating capable of directing the formation and detachment of complex tissues solely under physiological conditions can have broad use for fundamental research and in future cell and tissue therapies.

Bio-fabrication and physiological self-release of tissue equivalents using smart peptide amphiphile templates

In this study we applied a smart biomaterial formed from a self-assembling, multi-functional synthetic peptide amphiphile (PA) to coat substrates with various surface chemistries. The combination of PA coating and alignment-inducing functionalised substrates provided a template to instruct human corneal stromal fibroblasts to adhere, become aligned and then bio-fabricate a highlyordered, multi-layered, three-dimensional tissue by depositing an aligned, native-like extracellular matrix. The newly-formed corneal tissue equivalent was subsequently able to eliminate the adhesive properties of the template and govern its own complete release via the action of endogenous proteases. Tissues recovered through this method were structurally stable, easily handled, and carrier-free. Furthermore, topographical and mechanical analysis by atomic force microscopy showed that tissue equivalents formed on the alignment-inducing PA template had highly-ordered, compact collagen deposition, with a two-fold higher elastic modulus compared to the less compact tissues produced on the non-alignment template, the PA-coated glass. We suggest that this technology represents a new paradigm in tissue engineering and regenerative medicine, whereby all processes for the biofabrication and subsequent self-release of natural, bioprosthetic human tissues depend solely on simple templatetissue feedback interactions.

Aligned platinum nanowire networks from surface-oriented lipid cubic phase templates

Mesoporous metal structures featuring a bicontinuous cubic morphology have a wide range of potential applications and novel opto-electronic properties, often orientation-dependent. We describe the production of nanostructured metal films 1–2 microns thick featuring 3D-periodic ‘single diamond’ morphology that show high out-of-plane alignment, with the (111) plane oriented parallel to the substrate. These are produced by electrodeposition of platinum through a lipid cubic phase (QII) template. Further investigation into the mechanism for the orientation revealed the surprising result that the QII template, which is tens of microns thick, is polydomain with no overall orientation. When thicker platinum films are grown, they also show increased orientational disorder. These results suggest that polydomain QII samples display a region of uniaxial orientation at the lipid/substrate interface up to approximately 2.8 ± 0.3 μm away from the solid surface. Our approach gives previously unavailable information on the arrangement of cubic phases at solid interfaces, which is important for many applications of QII phases. Most significantly, we have produced a previously unreported class of oriented nanomaterial, with potential applications including metamaterials and lithographic masks.

Using Polycarbonate Membranes as Templates for the Preparation of Au Nanostructures for Surface-Enhanced Raman Scattering

Polycarbonate membranes (PCM) of various pores sizes (400, 200, 100 and 50 nm) were used as templates for gold deposition. The electrodeposition from gold ions resulted in the formation of gold nanotubes when large pores size PCMs (400 and 200 nm) were used. On the other hand, gold nanowires were predominant for the PCMs with smaller pores size (100 and 50 nm). Surface-enhanced Raman scattering (SERS) from the probe molecule 4-mercaptopyridine (4-MPy) was obtained from all these nanostructures. The SERS efficiency of the substrates produced using the PC M templates were compared to two commonly used SERS platforms: a roughened gold electrode and gold nanostructures electrodeposited through organized polystyrene spheres (PSS). The SERS signal of the probe molecule increased as the pore diameter of the PCM template decreased. Moreover, the SERS efficiency from the nanostructures produced using 50 nm PCM templates was four and two times better than the signal from the roughened gold electrode and the PSS template, respectively. The SERS substrates prepared using PCM templates were more homogenous over a larger area (ca. 1 cm(2)), presented better spatial and sample to sample reproducibility than the other substrates. These results show that SERS substrates prepared using PCM templates are promising for the fabrication of planar SERS platforms for analytical/bioanalytical applications.

IFTrace: Video segmentation of deformable objects using the Image Foresting Transform

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

Continuously deformable topological structure

Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)

Nonpolynomial potentials with deformable topological structures

Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)

Synthesis of manganese porphyrinosilica imprinted with templates using the sol-gel process

The optimized conditions for the preparation of a new manganese porphyrinosilica-template material are reported. The manganese porphyrinosilica-template was prepared by the sol-gel process, by the reaction of -SO2Cl groups present in the phenyl rings of MnTDC(SO2Cl)PPCl with 3-aminopropyltriethoxysilane. The reaction produces a precursor porphyrinopropylsilyl species, which were then polymerized with tetraethoxysilane. The presence of manganese porphyrin on xerogel is confirmed by ultraviolet visible absorption spectroscopy and thermogravimetric analysis (TGA). The prepared materials have surface areas between 19 and 674 m2 g-1. Electron spectroscopy imaging of the materials show that manganese distribution in the xerogel is uniform. Both manganese(III) porphyrinosilica-template and a similar iron(III) porphyrinosilica-template can catalyze the epoxidation of cyclooctene using iodozylbenzene as oxygen donor. The metalloporphyrinosilica-template presents catalytic activity similar to that of metaloporphyrin in solution. © 2000 Elsevier Science B.V. All rights reserved.

Vocal folds vibrations with a three-dimensional deformable model

In this work a computational method is presented to simulate the movements of vocal folds in three dimensions. The proposed model consists of a mesh free structure where each vertex is connected its neighbor through a group spring-damper. Forced oscillations were studied by time varying surface forces. The preliminary results using this model are similar with the literature and with the experimental stroboscopic observations of larynx. © 2006 IEEE.

Liquid foam templates associated with the sol-gel process for production of zirconia ceramic foams

The unique properties of ceramic foams enable their use in a variety of applications. This work investigated the effects of different parameters on the production of zirconia ceramic foam using the sol-gel process associated with liquid foam templates. Evaluation was made of the influence of the thermal treatment temperature on the porous and crystalline characteristics of foams manufactured using different amounts of sodium dodecylsulfate (SDS) surfactant. A maximum pore volume, with high porosity (94%) and a bimodal pore size distribution, was observed for the ceramic foam produced with 10% SDS. Macropores, with an average size of around 30 μm, were obtained irrespective of the SDS amount, while the average size of the supermesopores increased systematically as the SDS amount was increased up to 10%, after which it decreased. X-ray diffraction analyses showed that the sample treated at 500 °C was amorphous, while crystallization into a tetragonal metastable phase occurred at 600 °C due to the presence of sulfate groups in the zirconia structure. At 800 and 1000 °C the monoclinic phase was observed, which is thermodynamically stable at these temperatures. © 2013 by the authors; licensee MDPI, Basel, Switzerland.

Syntheses of bismuth titanate templates obtained by the molten salt method

Bismuth titanate templates (Bi4Ti3O12) were synthesized by the molten salt method in Na2SO4 and K2SO4 fluxes, using an amorphous Bi4Ti 3O12 precursor and a mechanically mixed Bi 2O3+TiO2 mixture as the starting materials. The templates were characterized by means of X-Ray Diffraction, FT-IR, FT-Raman, FEG-SEM and TEM. The templates are free of secondary phases and present orthorhombic structure with orientation in the c-plane. FT-IR suggests no traces of sulfate groups revealing that the molten salt synthesis was beneficial for elimination of inorganic species and for the arrangement of individual nanocrystals into ordered lattices. FEG-SEM analyses of BIT templates revealed that most of the grains were homogeneous with a length of 3.1 μm and a width of 0.3 μm and had plate-like morphology. TEM investigations show that the c-axis of the perovskite units is parallel to the thickness direction of the grains and no liquid-phase was formed during BIT phase formation. © 2013 Elsevier Ltd and Techna Group S.r.l.