A bioinformatics approach was developed to classify peptides selected by in vivo techniques according to their inorganic solid-binding properties. Our approach performs all-against-all comparisons of experimentally selected peptides with short amino acid sequences that were categorized for their binding affinity and scores the alignments using sequence similarity scoring matrices. We generated novel scoring matrices that optimize the similarities within the strong-binding peptide sequences and the differences between the strong- and weak-binding peptide sequences. Using the scoring matrices thus generated, a given peptide is classified based on the sequence similarity to a set of experimentally selected peptides. We demonstrate the new approach by classifying experimentally characterized quartz-binding peptides and computationally designing new sequences with specific affinities. Experimental verifications of binding of these computationally designed peptides confirm our predictions with high accuracy. We further show that our approach is a general one and can be used to design new sequences that bind to a given inorganic solid with predictable and enhanced affinity.

Binding kinetics of platinum-, silica-, and gold-binding peptides were investigated using a modified surface plasmon resonance spectroscopy (SPR). Platinum binding septa-peptides, quartz-binding dodecapeptides, and gold-binding 14-aa peptides were originally selected using phage or cell surface display libraries using the mineral or pure forms of these materials. All of the peptides were synthesized singly to investigate their binding kinetics and to assess quantitatively the specific affinity of each to its material of selection. The peptides were also postselection engineered to contain multiple copies of the same original sequences to quantify the effects of repeating units. SPR spectroscopy, normally using gold surfaces, was modified to contain a thin film (a few nm thick) of the material of interest (silica or platinum) on gold to allow the quantitative study of the adsorption kinetics of specific solid-binding peptides. The SPR experiments, carried out at different concentrations, on all three materials substrates, resulted in Langmuir behavior that allowed the determination of the kinetic parameters, including adsorption, desorption, and equilibrium binding constants for each of the solids as well as free energy of adsorption. Furthermore, we also tested multiple repeats of the peptide sequences, specifically three repeats, to see if there is a general trend of increased binding with increased number of binding domains. There was no general trend in the binding strength of the peptides with the increase of the repeat units from one to three, possibly because of the conformational changes between the single and multiple repeat polypeptides. In all cases, however, the binding was strong enough to suggest that these inorganic binding peptides could potentially be used as specific molecular linkers to bind molecular entities to specific solid substrates due to their surface recognition characteristics.

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Some novel 4,5-disubstituted-2,4-dihydro-3H-1,2,4-triazol-3-one (3, 6, 8, 9) derivatives and or 3-(4-methylphenyl)[1,2,4]triazolo[3,4-b][1,3]benzoxazole (5) were synthesized from the reaction of various ester ethoxycarbonylhydrazones (1a-e) with several primary amines. The synthesis of 4-amino-5-(4-chlorophenyl)-2-[(5-mercapto-1,3,4-oxadiazol-2-yl)methyl]-2,4-dihydro-3H-1,2,4-triazol-3-one (13) was performed starting from 4-Amino-5-(4-chlorophenyl)-2,4-dihydro-3H-1,2,4-triazol-3-one (2) by four steps; then 13 was converted to the corresponding Schiff base (14) by using 4-methoxybenzaldehyde. Finally, two Mannich base derivatives of 14 were obtained by using morpholine or methyl piperazine as amine component. All newly synthesized compounds were screened for their antimicrobial activities and some of which were found to possess good or moderate activities against the test microorganisms.

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Schizochytrium species is one of the most studied microalgae for production of docosahexaenoic acid (DHA) which is an omega-3 fatty acid with positive effects for human health. However, high cost and low yield in production phase makes optimization of cultivation process inevitable. We focus on the optimization of DHA production using Schizochytrium sp. using different media supplements; glucose, fructose and glycerol as carbon variants, proteose peptone and tryptone as nitrogen variants. The highest biomass (5.61 g/L) and total fatty acid yield (1.74 g/L) were obtained in proteose peptone medium which was used as the alternative nitrogen source instead of yeast extract. The highest DHA yield (0.40 g/L) was achieved with glycerol as the carbon source although it had the second lowest biomass production after ethanol containing medium. Ethanol, as an alternative carbon source and a precursor for acetyl-CoA, increased DHA percentage in total lipid content from 29.94 to 40.04% but decreasing the biomass drastically. Considering different carbon and nitrogen sources during cultivation of Schizochytrium sp. will improve DHA production. Combination of proteose peptone and glycerol as nitrogen and carbon sources, respectively, and addition of ethanol with a proper timing will be useful to have higher DHA yield.Electronic supplementary materialThe online version of this article (10.1186/s13568-018-0540-4) contains supplementary material, which is available to authorized users.

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