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Protein-imprinted polymers have been synthesized to recognize and specifically bind selected proteins. However, protein imprinting requires substantial amounts of pure protein to efficiently obtain imprinted polymers for large scale applications, e.g. protein purification by affinity chromatography. In the absence of large quantities of a pure protein of interest, an alternative strategy was developed. In this case study, neutral metalloprotease thermolysin was selected as a commercially available surrogate for imprinting polymer beads. Phosphoramidon-assisted thermolysin-imprinted beads were synthesized. During rebinding experiments, it was shown that these beads specifically bind to thermolysin. In addition, it was shown that these beads also bind in CHO cell culture supernatant to the matrix metalloprotease-9 and -12 (MMP-9, -12). Therefore, these beads can be applied as a selective sorbent for the rare metalloproteases MMP-9 and MMP-12 to remove these proteases from CHO cell culture supernatants. The high selectivity of thermolysin-imprinted beads can be extended to other proteases of the family of metalloproteases, and is not limited to thermolysin. This innovative approach is suitable to address the challenges in the field of protease purification and isolation from biotechnologically relevant media.

An innovative approach for molecularly imprinting proteins, i.e., inhibitor-assisted imprinting was used for addressing the major challenge of protein purification from biotechnologically relevant media. Pepstatin-assisted pepsin surface-imprinted microbeads were synthesized as a selective sorbent for solid phase extraction (SPE). The amino-functionalized porous core was prepared by co-condensation and post-grafting strategies. The immobilized inhibitor pre-organizes the template pepsin with a defined orientation prior to imprinting ensuring enhanced efficiency of the imprinting process. 3-aminophenylboronic acid (APBA) was used as a functional monomer establishing organic nanoscale films comprising poly(3-aminophenylboronic acid) (pAPBA) within the pores of the beads in the presence (MIP) and absence (NIP) of pepsin. Next to a detailed characterization of these advanced functional hybrid materials it was demonstrated that such porous surface-imprinted core/shell beads feature exquisite selectivity for pepsin during individual protein rebinding studies, and more importantly, during competitive rebinding studies in protein mixtures.

The right-handed α-helix is the dominant helical fold of α-peptides, whereas the left-handed 314-helix is the dominant helical fold of β-peptides. Using molecular dynamics simulations, the properties of α-helical α-peptides and 314-helical β-peptides with different C-terminal protonation states and in the solvents water and methanol are compared. The observed energetic and entropic differences can be traced to differences in the polarity of the solvent-accessible surface area and, in particular, the solute dipole moments, suggesting different reasons for their stability.

Microarrays are routine tools for transcript profiling, and genomic tiling arrays such as the Arabidopsis AGRONOMICS1 arrays have been found to be highly suitable for such experiments because changes in genome annotation can be easily integrated at the data analysis level. In a transcript profiling experiment, RNA labeling is a critical step, most often initiated by oligo-dT-primed reverse transcription. Although this has been found to be a robust and reliable method, very long transcripts or non-polyadenylated transcripts might be labeled inefficiently. In this study, we first provide data handling methods to analyze AGRONOMICS1 tiling microarrays based on the TAIR10 genome annotation. Second, we describe methods to easily quantify antisense transcripts on such tiling arrays. Third, we test a random-primed RNA labeling method, and find that on AGRONOMICS1 arrays this method has similar general performance as the conventional oligo-dT-primed method. In contrast to the latter, however, the former works considerably better for long transcripts and for non-polyadenylated transcripts such as found in mitochondria and plastids. We propose that researchers interested in organelle function use the random-primed method to unleash the full potential of genomic tiling arrays., Plant Methods, 8, ISSN:1746-4811