Secondary Binding Site of Trypsin: Revealed by Crystal Structure of Trypsin-Peptide Complex

ARCTIC-3D: automatic retrieval and clustering of interfaces in complexes from 3D structural information

The formation of a stable complex between proteins lies at the core of a wide variety of biological processes and has been the focus of countless experiments. The huge amount of information contained in the protein structural interactome in the Protein Data Bank can now be used to characterise and classify the existing biological interfaces. We here introduce ARCTIC-3D, a fast and user-friendly data mining and clustering software to retrieve data and rationalise the interface information associated with the protein input data. We demonstrate its use by various examples ranging from showing the increased interaction complexity of eukaryotic proteins, 20% of which on average have more than 3 different interfaces compared to only 10% for prokaryotes, to associating different functions to different interfaces. In the context of modelling biomolecular assemblies, we introduce the concept of "recognition entropy", related to the number of possible interfaces of the components of a protein-protein complex, which we demonstrate to correlate with the modelling difficulty in classical docking approaches. The identified interface clusters can also be used to generate various combinations of interface-specific restraints for integrative modelling. The ARCTIC-3D software is freely available at github.com/haddocking/arctic3d and can be accessed as a web-service at wenmr.science.uu.nl/arctic3d.

Inhibitory effect of lignin from Canna edulis Ker residues on trypsin: kinetics and molecular docking studies

BACKGROUND

Lignin extracted from Canna edulis Ker residues shows a strong inhibitory effect on α-glucosidase and a promoting effect on α-amylase. Protease activity inhibition may play a key role in disease processes, such as metastasis, tumor invasion and bacterial colonization. Hence, in the present study, the inhibitory mechanism of lignin on trypsin was examined, including the interaction type, thermodynamic parameters, structure, reaction site and molecular docking.

RESULTS

The isolated lignin presented an inhibitory effect on trypsin activity with an IC₅₀ value of 1.35 μmol L^-1 . This inhibition was a mixed linear type with a constant K_i of 3.92 μmol L^-1 . The lignin could bind with the key amino acid residue Ser195 on the active site of the trypsin molecule to inhibit its activity, and the phenolic hydroxyl group and -OH on the β-O-4 structure of the lignin molecule were the major groups bound with trypsin.

CONCLUSION

These results illustrate the inhibitory effects of Canna edulis residue lignin on protease, which helps with respect to understanding the possible application of lignin in the food industry in functional foods. © 2020 Society of Chemical Industry.

A Comparative Analysis of Different Grades of Silica Particles and Temperature Variants of Food-Grade Silica Nanoparticles for Their Physicochemical Properties and Effect on Trypsin

While silica particles are used extensively in food products, different grades and temperature variants of silica particles have not been compared for their physiochemical and biological properties. Different grades of silica (food-grade nanoparticles (FG-NPs), nonfood-grade nanoparticles (NFG-NPs), and food-grade micron particles (FG-MPs)) and the temperature variants generated by exposing FG-NPs to wet heating, dry heating, and refrigeration were compared for their physicochemical properties and interaction with trypsin. FG-NPs were similar to NFG-NPs and FG-MPs in their elemental composition and amorphous nature but had relatively less branched and ring siloxane groups than the latter ones. There were subtle but noticeable changes in the agglomeration behavior and relative abundance of different silica groups in FG-NPs exposed to food-handling temperatures. Secondary structure and function of trypsin were negatively impacted by FG-NPs and their temperature variants. Silica particles showed a "mixed-type inhibition" of trypsin resulting in partial digestion of bovine serum albumin. In conclusion, our studies showed differences in the surface chemistry of different grades of silica particles and temperature variants of FG-NPs and their negative impact on the structure and function of trypsin.

Trypsin inhibition by a peptide hormone: crystal structure of trypsin-vasopressin complex

The large variety of serine protease inhibitors, available from various sources such as tissues, microorganisms, plants, etc., play an important role in regulating the proteolytic enzymes. The analysis of protease-inhibitor complexes helps in understanding the mechanism of action, as well as in designing inhibitors. Vasopressin, an anti-diuretic nonapeptide hormone, is found to be an effective inhibitor of trypsin, with a K(i) value of 5 nM. The crystal structure of the trypsin-vasopressin complex revealed that vasopressin fulfils all the important interactions for an inhibitor, without any break in the scissile peptide bond. The cyclic nature due to a disulfide bridge between Cys1 and Cys6 of vasopressin provides structural rigidity to the peptide hormone. The trypsin-binding site is located at the C terminus, while the neurophysin-binding site is at the N terminus of vasopressin. This study will assist in designing new peptide inhibitors. This study suggests that vasopressin inhibition of trypsin may have unexplored biological implications.