Hydrogen bonding in molecular recognition by HIV-1 protease

Microstructure and digestive behaviors of inner, middle, and outer layers of pork during heating

To investigate the effects of heat treatment on the microstructure and digestive behaviors of pork, meat samples were subjected to a 100 °C water bath for 26 min. The inner, medium, and outer layers were assigned and analyzed according to the temperature gradient. Compared to the raw samples, significant changes were observed in the microscopic structure of pork. As the temperature increased, the myofibrillar structure of pork underwent increasingly severe damage and the moisture content decreased significantly (P < 0.05). Moreover, differential peptides were identified in digested products of the inner, middle, and outer layers of cooked pork, which are mainly derived from the structural proteins of pork. The outcomes of molecular docking indicated that a greater number of hydrogen bonds were formed between myosin and the digestive enzyme in the inner layer, rather than other parts, contributing to the transformation of digestive behaviors.

Effects of temperature and pH on the structure of a metalloprotease from Lactobacillus fermentum R6 isolated from Harbin dry sausages and molecular docking between protease and meat protein

BACKGROUND

Microbial protease can interact with meat protein in fermented meat products at a certain pH and temperature. To investigate the effects of various pH values and temperatures on the structural characteristics of Lactobacillus fermentum R6 protease, which was isolated from Harbin dry sausages, spectroscopy techniques and molecular dynamics were utilized to evaluate structural changes.

RESULTS

The protease exhibited a stable spatial structure at pH 7 and 40 °C, and the extension of the protease structure was also promoted. Although the structure of the protease could be changed or destroyed by pH 8 and 70 °C, it was mainly determined by the changes of secondary and tertiary structures such as α-helix, β-sheet, β-turn and random coil. In addition, carbonyl vibration, -NH vibration, C-H stretching vibration and disulphide bonds were present in L. fermentum R6 protease under various pH and temperature conditions. Molecular docking showed that the protease can interact with myosin light chain, myosin heavy chain, actin and myoglobin.

CONCLUSION

The protease can maintain stable structure and interact with meat protein, which reflected certain application prospects in the fermentation of Harbin dry sausages. © 2021 Society of Chemical Industry.

Design, synthesis and biological evaluation of HIV-1 protease inhibitors with morpholine derivatives as P2 ligands in combination with cyclopropyl as P1' ligand

A series of novel HIV-1 protease inhibitors has been designed and synthesized, which contained morpholine derivatives as the P2 ligands and hydrophobic cyclopropyl as the P1' ligand at the meantime in this study, with the aim of improving the interactions between the active sites of HIV-1 protease and the inhibitors. Twenty-eight compounds were synthesized and assessed, among which inhibitors m18 and m1 exhibited excellent inhibitory effect on the activity of HIV-1 protease with IC₅₀ value of 47 nM and 53 nM, respectively. The molecular modeling of m1 revealed possible hydrogen bondings or van der Waals between the inhibitor and the protease, worthy of in-depth study.

Explicit Hydrogen-Bond Potentials and Their Application to NMR Scalar Couplings in Proteins

Hydrogen bonds (H bonds) are fundamental for the stability, structure, and dynamics of chemically and biologically relevant systems. One of the direct means to detect H bonds in proteins is NMR spectroscopy. As H bonds are dynamic in nature, atomistic simulations offer a meaningful way to characterize and analyze properties of hydrogen bonds, provided a sufficiently accurate interaction potential is available. Here, we use explicit H-bond potentials to investigate scalar coupling constants (h3)JNC' and characterize the conformational ensemble for increasingly accurate intermolecular potentials. By considering a range of proteins with different overall topology a general procedure to improve the hydrogen-bonding potential ("morphing potentials") based on experimental information is derived. The robustness of this approach is established through explicit simulations in full solvation and comparison with experimental results. The H-bond potentials used here lead to more directional H bonds than conventional electrostatic representations employed in molecular mechanics potentials. It is found that the optimized potentials lead to H-bond geometries in remarkable agreement with previous ab initio and knowledge-based approaches to H bonds in model systems and in proteins. This suggests that, by combining theory, computation, and experimental data, H-bonding potentials can be improved and are potentially useful to better study coupling, energy transfer, and allosteric communication in proteins.