Near-Native Protein Loop Sampling Using Nonparametric Density Estimation Accommodating Sparcity

Unlike the core structural elements of a protein like regular secondary structure, template based modeling (TBM) has difficulty with loop regions due to their variability in sequence and structure as well as the sparse sampling from a limited number of homologous templates. We present a novel, knowledge-based method for loop sampling that leverages homologous torsion angle information to estimate a continuous joint backbone dihedral angle density at each loop position. The φ,ψ distributions are estimated via a Dirichlet process mixture of hidden Markov models (DPM-HMM). Models are quickly generated based on samples from these distributions and were enriched using an end-to-end distance filter. The performance of the DPM-HMM method was evaluated against a diverse test set in a leave-one-out approach. Candidates as low as 0.45 Å RMSD and with a worst case of 3.66 Å were produced. For the canonical loops like the immunoglobulin complementarity-determining regions (mean RMSD <2.0 Å), the DPM-HMM method performs as well or better than the best templates, demonstrating that our automated method recaptures these canonical loops without inclusion of any IgG specific terms or manual intervention. In cases with poor or few good templates (mean RMSD >7.0 Å), this sampling method produces a population of loop structures to around 3.66 Å for loops up to 17 residues. In a direct test of sampling to the Loopy algorithm, our method demonstrates the ability to sample nearer native structures for both the canonical CDRH1 and non-canonical CDRH3 loops. Lastly, in the realistic test conditions of the CASP9 experiment, successful application of DPM-HMM for 90 loops from 45 TBM targets shows the general applicability of our sampling method in loop modeling problem. These results demonstrate that our DPM-HMM produces an advantage by consistently sampling near native loop structure. The software used in this analysis is available for download at http://www.stat.tamu.edu/~dahl/software/cortorgles/

Characteristics of Different Systems for the Solar Drying of Crops

Solar dryers are used to enable the preservation of agricultural crops, food processing industries for dehydration of fruits and vegetables, fish and meat drying, dairy industries for production of milk powder, seasoning of wood and timber, textile industries for drying of textile materials. The fundamental concepts and contexts of their use to dry crops is discussed in the chapter. It is shown that solar drying is the outcome of complex interactions particular between the intensity and duration of solar energy, the prevailing ambient relative humidity and temperature, the characteristics of the particular crop and its pre-preparation and the design and operation of the solar dryer

Evaluation of nutritional composition and antioxidant activity of Borage (Echium amoenum) and Valerian (Valerian officinalis)

The nutritional composition and antioxidant activity (in aqueose and solvent extracts) of two medicinal plants of Iranian origin Borage (Echium amoenum) and Valerian (Valerian officinalis) used as tea were determined. Samples were analyzed for antioxidant components viz. polyphenols, vitamin C, β carotene, flavonoids, anthocyanins and tannins. Antioxidant assays such as free radical scavenging activity, reducing power and total antioxidant activity were carried out for ethanol, methanol, acetone, 80% methanol and 80% ethanolic extracts. In borage highest and least activity was observed in water and acetone extract respectively in all assays. In Valerian, 80% methanolic extract showed highest activity in reducing power and free radical scavenging activity assay. Total polyphenols in borage and valerian were 1,220 and 500 mg in ethanolic extracts and 25 and 130 mg in acetonic extracts respectively. Total carotenoids and vitamin C contents were 31.6 and 133.69 mg and 51.2 and 44.87 mg for borage and valerian respectively. Highest amount of tannins were extracted in 80% methanolic extract. It can be concluded that borage and valerian exhibited antioxidant activity in all extracts. The antioxidant activity could be attributed to their polyphenol and tannin and flavonoids contents. In all assays borage showed higher activity than valerian

Synthetic and structural routes for the rational conversion of peptides into small molecules

The demand for modified peptides with improved stability profiles and pharmacokinetic properties is driving extensive research effort in this field. The conversion of peptides into organic molecules, as traditional drugs, is a long and puzzled way. Many and versatile approaches have been described for designing peptide mimetics: the substitution of natural residues with modified amino acids and the rigidification and modification of the backbone are the main structural and chemical routes walked in medicinal chemistry. All of these strategies have been successfully applied to obtain active new compounds in molecular biology, drug discovery and design. Here we propose a panoramic review of the most common methods for the preparation of modified peptides and the most interesting findings of the last decade