Proteins and their interacting partners: an introduction to protein–ligand binding site prediction methods

Elucidating the biological and biochemical roles of proteins, and subsequently determining their interacting partners, can be difficult and time consuming using in vitro and/or in vivo methods, and consequently the majority of newly sequenced proteins will have unknown structures and functions. However, in silico methods for predicting protein–ligand binding sites and protein biochemical functions offer an alternative practical solution. The characterisation of protein–ligand binding sites is essential for investigating new functional roles, which can impact the major biological research spheres of health, food, and energy security. In this review we discuss the role in silico methods play in 3D modelling of protein–ligand binding sites, along with their role in predicting biochemical functionality. In addition, we describe in detail some of the key alternative in silico prediction approaches that are available, as well as discussing the Critical Assessment of Techniques for Protein Structure Prediction (CASP) and the Continuous Automated Model EvaluatiOn (CAMEO) projects, and their impact on developments in the field. Furthermore, we discuss the importance of protein function prediction methods for tackling 21st century problems.

Rainfastness of poly(vinyl alcohol) deposits on Vicia faba leaf surfaces: from laboratory-scale washing to simulated rain

Rainfastness is the ability of agrochemical deposits to resist wash-off by rain and other related environmental phenomena. This work reports laboratory-scale and raintower studies of the rainfastness of fluorescently labeled poly(vinyl alcohol) (PVA) using fluorescent microscopy combined with image analysis. Samples of hydrolyzed PVA exhibit improved rainfastness over a threshold molecular weight, which correlates with PVA film dissolution, swelling, and crystalline properties. It was also established that the rainfastness of PVA scaled with the molecular weight over this threshold. These PVA samples were further characterized in order to determine the effect of the crystallinity on rainfastness. The quantification of rainfastness is of great interest to the field of agrochemical formulation development in order to improve the efficacy of pesticides and their adjuvants.

Histomorphometric Evaluation of Bioceramic Molecular Impregnated and Dual Acid-Etched Implant Surfaces in the Human Posterior Maxilla

Background: Physical and bioceramic incorporation surface treatments at the nanometer scale showed higher means of bone-to-implant contact (BIC) and torque values compared with surface topography at the micrometer scale; however, the literature concerning the effect of nanometer scale parameters is sparse. Purpose: The aim of this study was to evaluate the influence of two different implant surfaces on the percentage bone-to-implant contact (BIC%) and bone osteocyte density in the human posterior maxilla after 2 months of unloaded healing. Materials and Methods: The implants utilized presented dual acid-etched (DAE) surface and a bioceramic molecular impregnated treatment (Ossean(R), Intra-Lock International, Boca Raton, FL, USA) serving as control and test, respectively. Ten subjects (59 1 9 years of age) received two implants (one of each surface) during conventional implant surgery in the posterior maxilla. After the non-loaded period of 2 months, the implants and the surrounding tissue were removed by means of a trephine and were non-decalcified processed for ground sectioning and analysis of BIC%, bone density in threaded area (BA%), and osteocyte index (Oi). Results: Two DAE implants were found to be clinically unstable at time of retrieval. Histometric evaluation showed significantly higher BIC% and Oi for the test compared to the control surface (p < .05), and that BA% was not significantly different between groups. Wilcoxon matched pairs test was used to compare the differences of histomorphometric variables between implant surfaces. The significance test was conducted at a 5% level of significance. Conclusion: The histological data suggest that the bioceramic molecular impregnated surface-treated implants positively modulated bone healing at early implantation times compared to the DAE surface.

A molecular phylogeny of the stingless bee genus Melipona (Hymenoptera: Apidae)

Stingless bees (Meliponini) constitute a diverse group of highly eusocial insects that occur throughout tropical regions around the world. The meliponine genus Melipona is restricted to the New World tropics and has over 50 described species. Melipona, like Apis, possesses the remarkable ability to use representational communication to indicate the location of foraging patches. Although Melipona has been the subject of numerous behavioral, ecological, and genetic studies, the evolutionary history of this genus remains largely unexplored. Here, we implement a multigene phylogenetic approach based on nuclear, mitochondrial, and ribosomal loci, coupled with molecular clock methods, to elucidate the phylogenetic relationships and antiquity of subgenera and species of Melipona. Our phylogenetic analysis resolves the relationship among subgenera and tends to agree with morphology-based classification hypotheses. Our molecular clock analysis indicates that the genus Melipona shared a most recent common ancestor at least similar to 14-17 million years (My) ago. These results provide the groundwork for future comparative analyses aimed at understanding the evolution of complex communication mechanisms in eusocial Apidae. (C) 2010 Elsevier Inc. All rights reserved.

The genus Coleodactylus (Sphaerodactylinae, Gekkota) revisited: A molecular phylogenetic perspective

Nucleotide sequence data from a mitochondrial gene (16S) and two nuclear genes (c-mos, RAG-1) were used to evaluate the monophyly of the genus Coleodactylus, to provide the first phylogenetic hypothesis of relationships among its species in a cladistic framework, and to estimate the relative timing, of species divergences. Maximum Parsimony, Maximum Likelihood and Bayesian analyses of the combined data sets retrieved Coleodactylus as a monophyletic genus, although weakly Supported. Species were recovered as two genetically and morphological distinct clades, with C. amazonicus populations forming the sister taxon to the meridionalis group (C. brachystoma, C. meridionalis, C. natalensis, and C. septentrionalis). Within this group, C. septentrionalis was placed as the sister taxon to a clade comprising the rest of the species, C. meridionalis was recovered as the sister species to C. brachystoma, and C natalensis was found nested within C. meridionalis. Divergence time estimates based on penalized likelihood and Bayesian dating methods do not Support the previous hypothesis based on the Quaternary rain forest fragmentation model proposed to explain the diversification of the genus. The basal cladogenic event between major lineages of Coleodactylus was estimated to have occurred in the late Cretaceous (72.6 +/- 1.77 Mya), approximately at the same point in time than the other genera of Sphaerodactylinae diverged from each other. Within the meridionalis group, the split between C. septentrionalis and C. brachystoma + C. meridionalis was placed in the Eocene (46.4 +/- 4.22 Mya), and the divergence between C. brachystoma and C. meridionalis was estimated to have occurred in the Oligocene (29.3 +/- 4.33 Mya). Most intraspecific cladogenesis occurred through Miocene to Pliocene, and only for two conspecific samples and for C. natalensis could a Quaternary differentiation be assumed (1.9 +/- 1.3 Mya). (C) 2008 Elsevier Inc. All rights reserved.

Evolutionary history of Ramphastos toucans: Molecular phylogenetics, temporal diversification, and biogeography

The toucan genus Ramphastos (Piciformes: Ramphastidae) has been a model in the formulation of Neotropical paleobiogeographic hypotheses. Weckstein (2005) reported on the phylogenetic history of this genus based on three mitochondrial genes, but some relationships were weakly supported and one of the subspecies of R. vitellinus (citreolaemus) was unsampled. This study expands on Weckstein (2005) by adding more DNA sequence data (including a nuclear marker) and more samples, including R v. citreolaemus. Maximum parsimony, maximum likelihood, and Bayesian methods recovered similar trees, with nodes showing high support. A monophyletic R. vitellinus complex was strongly supported as the sister-group to R. brevis. The results also confirmed that the southeastern and northern populations of R. vitellinus ariel are paraphyletic. X v. citreolaemus is sister to the Amazonian subspecies of the vitellinus complex. Using three protein-coding genes (COI, cytochrome-b and ND2) and interval-calibrated nodes under a Bayesian relaxed-clock framework, we infer that ramphastid genera originated in the middle Miocene to early Pliocene, Ramphastos species originated between late Miocene and early Pleistocene, and intra-specific divergences took place throughout the Pleistocene. Parsimony-based reconstruction of ancestral areas indicated that evolution of the four trans-Andean Ramphastos taxa (R. v. citreolaemus, R. a. swainsonii, R. brevis and R. sulfuratus) was associated with four independent dispersals from the cis-Andean region. The last pulse of Andean uplift may have been important for the evolution of R. sulfuratus, whereas the origin of the other trans-Andean Ramphastos taxa is consistent with vicariance due to drying events in the lowland forests north of the Andes. Estimated rates of molecular evolution were higher than the ""standard"" bird rate of 2% substitutions/site/million years for two of the three genes analyzed (cytochrome-b and ND2). (C) 2009 Elsevier Inc. All rights reserved.

Molecular characterization and fumonisin production by Fusarium verticillioides isolated from corn grains of different geographic origins in Brazil

Gibberella moniliformis is most commonly associated with maize worldwide and produces high levels of fumonisins, some of the most agriculturally important mycotoxins. Studies demonstrate that molecular methods can be helpful for a rapid identification of Fusarium species and their levels of toxin production. The purpose of this research was to apply molecular methods (AFLP, TEF-1 alpha partial gene sequencing and PCR based on MAT alleles) for the identification of Fusarium species isolated from Brazilian corn and to verify if real time RT-PCR technique based on FUM1 and FUM19 genes is appropriated to estimate fumonisins B(1) and B(2) production levels. Among the isolated strains, 96 were identified as Fusarium verricillioides, and four as other Fusarium species. Concordant phylogenies were obtained by AFLP and TEF-1 alpha sequencing, permitting the classification of the different species into distinct clades. Concerning MAT alleles, 70% of the F. verricillioides isolates carried the MAT-1 and 30% MAT-2. A significant correlation was observed between the expression of the genes and toxin production r=0.95 and r=0.79 (correlation of FUM1 with FB(1) and FB(2), respectively, P < 0.0001): r=0.93 and r =0.78 (correlation of FUM19 with FB(1) and FB(2). respectively, P < 0.0001). Molecular methods used in this study were found to be useful for the rapid identification of Fusarium species. The high and significant correlation between FUM1 and FUM19 expression and fumonisins production suggests that real time RT-PCR is suitable for studies considering the influence of abiotic and biotic factors on expression of these genes. This is the first report concerning the expression of fumonisin biosynthetic genes in Fusarium strains isolated from Brazilian agricultural commodity. (c) 2010 Elsevier B.V. All rights reserved.

Correlation Between Etest (R), Disk Diffusion, and Microdilution Methods for Antifungal Susceptibility Testing of Candida Species From Infection and Colonization

The correlation between the microdilution (MD), Etest (R) (ET), and disk diffusion (DD) methods was determined for amphotericin B, itraconazole and fluconazole. The minimal inhibitory concentration (MIC) of those antifungal agents was established for a total of 70 Candida spp. isolates from colonization and infection. The species distribution was: Candida albicans (n = 27), C. tropicalis (n = 17), C. glabrata (n = 16), C. parapsilosis (n = 8), and C. lusitaniae (n = 2). Non-Candida albicans Candida species showed higher MICs for the three antifungal agents when compared with C. albicans isolates. The overall concordance (based on the MIC value obtained within two dilutions) between the ET and the MD method was 83% for amphotericin B, 63% for itraconazole, and 64% for fluconazole. Considering the breakpoint, the agreement between the DD and MD methods was 71% for itraconazole and 67% for fluconazole. The DD zone diameters are highly reproducible and correlate well with the MD method, making agar-based methods a viable alternative to MD for susceptibility testing. However, data on agar-based tests for itraconazole and amphotericin B are yet scarce. Thus, further research must still be carded out to ensure the standardization to other antifungal agents. J. Clin. Lab. Anal. 23:324-330, 2009. (C) 2009 Wiley-Liss, Inc.

Investigation by Combined Solid-State NMR and SAXS Methods of the Morphology and Domain Size in Polystyrene-b-Polyethylene Oxide-b-Polystyrene Triblock Copolymers

The microphase structure of a series of polystyrene-b-polyethylene oxide-b-polystyrene (SEOS) triblock copolymers with different compositions and molecular weights has been studied by solid-state NMR, DSC, wide and small angle X-ray scattering (WAXS and SAXS). WAXS and DSC measurements were used to detect the presence of crystalline domains of polyethyleneoxide (PEO) blocks at room temperature as a function of the copolymer chemical composition. Furthermore, DSC experiments allowed the determination of the melting temperatures of the crystalline part of the PEO blocks. SAXS measurements, performed above and below the melting temperature of the PEO blocks, revealed the formation of periodic structures, but the absence or the weakness of high order reflections peaks did not allow a clear assessment of the morphological structure of the copolymers. This information was inferred by combining the results obtained by SAXS and (1)H NMR spin diffusion experiments, which also provided an estimation of the size of the dispersed phases of the nanostructured copolymers. (C) 2009 Wiley Periodicals, Inc. J Polym Sci Part B: Polym Phys 48:55-64,2010

Structural effects and hydrogen bonds on N,N `-di(methoxycarbonylsulfenyl)urea, [CH(3)OC(O)SNH](2)CO, studied by experimental and theoretical methods

Pure N,N`-di(methoxycarbonylsulfenyl)urea, [CH(3)OC(O)SNH](2)CO, is quantitatively prepared by the hydrolysis reaction of CH(3)OC(O)SNCO and characterized by (1)H NMR, GC-MS and FTIR spectroscopy techniques. Structural and conformational properties are analyzed using a combined approach with data obtained from X-ray diffraction, vibrational spectra and theoretical calculation methods. The IR and Raman spectra for normal and deuterated species are reported. The crystal structure of [CH(3)OC(O)SNH](2)CO was determined by X-ray diffraction methods. The substance crystallizes in the orthorhombic P2(1)2(1)2 space group with a = 9.524(2), b = 12.003(1), c = 4.481 (1) angstrom, and Z = 2 moieties in the unit cell. The molecule is sited on a twofold crystallographic axis (C(2)) parallel to c and shows the anti-anti conformation (S-N single bonds antiperiplanar with respect to the opposite C-N single bonds in sulfenyl-urea-sic group). Neighboring molecules are arranged in a chain motif that extends along the C(2)-axis and is held by bifurcated NH center dot center dot center dot O center dot center dot center dot HN intermolecular bonds. A local planar symmetry is observed in the crystal for the central -SN(H)C(O)N(H)S- skeleton. Experimental and calculated data allow to trace this structural feature to the occurrence of N-H center dot center dot center dot O=C hydrogen bonding interactions. Calculated vibrational and structural properties are in good agreement with the experimentally determined features. (C) 2008 Elsevier B.V. All rights reserved.

Sugarcane Phosphoribosyl Pyrophosphate Synthetase: Molecular Characterization of a Phosphate-independent PRS

Phosphoribosyl pyrophosphate synthetase (PRS-EC:2.7.6.1) is an important enzyme present in several metabolic pathways, thus forming a complex family of isoenzymes. However, plant PRS enzymes have not been extensively investigated. In this study, a sugarcane prs gene has been characterized from the Sugar Cane Expressed Sequence Tag Genome Project. This gene contains a 984-bp open reading frame encoding a 328-amino acid protein. The predicted amino acid sequence has 77% and 78% amino acid sequence identity to Arabidopsis thaliana and Spinacia oleracea PRS4, respectively. The assignment of sugarcane PRS as a phosphate-independent PRS isoenzyme (Class II PRS) is verified following enzyme assay and phylogenetic reconstruction of PRS homologues. To gain further insight into the structural framework of the phosphate independence of sugarcane PRS, a molecular model is described. This model reveals the formation of two conserved domains elucidating the structural features involved in sugarcane PRS phosphate independence. The recombinant PRS retains secondary structure elements and a quaternary arrangement consistent with known PRS homologues, based on circular dichroism measurements.