Interaction between β-lactoglobulin and EGCG under high-pressure by molecular dynamics simulation

Fabrication and characterization of curcumin-loaded composite nanoparticles based on high-hydrostatic-pressure-treated zein and pectin: Interaction mechanism, stability, and bioaccessibility

We successfully designed curcumin (Cur)-loaded composite nanoparticles consisting of high-hydrostatic-pressure-treated (HHP-treated) zein and pectin with a pressure of 150 MPa (zein-150 MPa-P-Cur), showing nano-spherical structure with high zeta-potential (-36.72 ± 1.14 mV) and encapsulation efficiency (95.64 ± 1.23 %). We investigated the interaction mechanism of the components in zein-150 MPa-P-Cur using fluorescence spectroscopy, molecular dynamics simulation, Fourier-transform infrared spectrometry and scanning electron microscopy techniques. Compared with zein-P-Cur, the binding sites and binding energy (-53.68 kcal/mol vs. - 44.22 kcal/mol) of HHP-treated zein and Cur were increased. Meanwhile, the interaction force among HHP-treated zein, pectin, and Cur was significantly enhanced, which formed a tighter and more stable particle structure to further improve package performance. Additionally, Cur showed the best chemical stability in zein-150 MPa-P-Cur. And the bioavailability of Cur was increased to 65.53 ± 1.70 %. Collectively, composite nanoparticles based on HHP-treated zein and pectin could be used as a promising Cur delivery system.

Structural dynamics insights into the M306L, M306V, and D1024N mutations in Mycobacterium tuberculosis inducing resistance to ethambutol

Resistance to anti-tuberculosis drugs, especially ethambutol (EMB), has been widely reported worldwide. EMB resistance is caused by mutations in the embB gene, which encodes the arabinosyl transferase enzyme. This study aimed to detect mutations in the embB gene of Mycobacterium tuberculosis from Papua and to evaluate their impact on the effectiveness of EMB. We analyzed 20 samples of M. tuberculosis culture that had undergone whole-genome sequencing, of which 19 samples were of sufficient quality for further bioinformatics analysis. Mutation analysis was performed using TBProfiler, which identified M306L, M306V, D1024N, and E378A mutations. In sample TB035, the M306L mutation was present along with E378A. The binding affinity of EMB to arabinosyl transferase was calculated using AutoDock Vina. The molecular docking results revealed that all mutants demonstrated an increased binding affinity to EMB compared to the native protein (-0.948 kcal/mol). The presence of the M306L mutation, when coexisting with E378A, resulted in a slight increase in binding affinity compared to the M306L mutation alone. The molecular dynamics simulation results indicated that the M306L, M306L + E378A, M306V, and E378A mutants decreased protein stability. Conversely, the D1024N mutant exhibited stability comparable to the native protein. In conclusion, this study suggests that the M306L, M306L + E378A, M306V, and E378A mutations may contribute to EMB resistance, while the D1024N mutation may be consistent with continued susceptibility to EMB.

Unraveling the effects of low protein-phenol binding affinity on the structural properties of beta-lactoglobulin

Non-covalent interactions of phenolics with proteins cannot always be readily identified, often leading to contradictory results described in the literature. This results in uncertainties as to what extent phenolics can be added to protein solutions (for example for bioactivity studies) without affecting the protein structure. Here, we clarify which tea phenolics (epigallocatechin gallate (EGCG), epicatechin and gallic acid) interact with the whey protein β-lactoglobulin by combining various state-of-the-art-methods. STD-NMR revealed that all rings of EGCG can interact with native β-lactoglobulin, indicating multidentate binding, as confirmed by the small angle X-ray scattering experiments. For epicatechin, unspecific interactions were found only at higher protein:epicatechin molar ratios and only with ¹H NMR shift perturbation and FTIR. For gallic acid, none of the methods found evidence for an interaction with β-lactoglobulin. Thus, gallic acid and epicatechin can be added to native BLG, for example as antioxidants without causing modification within wide concentration ranges.

New molecular insights for 4H-1,2,4-triazole derivatives as inhibitors of tankyrase and Wnt-signaling antagonist: a molecular dynamics simulation study

Tankyrase (TNKS) enzymes remained central biotargets to treat Wnt-driven colorectal cancers. The success of Olaparib posited the druggability of PARP family enzymes depending on their role in tumor proliferation. In this work, an MD-simulation-based comparative assessment of the protein-ligand interactions using the best-docked poses of three selected compounds (two of the designed and previously synthesized molecules obtained through molecular docking and one reported TNKS inhibitor) was performed for a 500 ns period. The PDB:ID-7KKP and 3U9H were selected for TNKS1 and TNKS2, respectively. The Molecular Mechanics Generalized Born Surface Area (MM-GBSA) based binding energy data exhibited stronger binding of compound-15 (average values of -102.92 and -104.32 kcal/mol for TNKS1 and TNKS2, respectively) as compared to compound-22 (average values of -82.99 and -85.68 kcal/mol for TNKS1 and TNKS2, respectively) and the reported compound-32 (average values of -81.89 and -74.43 kcal/mol for TNKS1 and TNKS2, respectively). Compound-15 and compound-22 exhibited comparable or superior binding to both receptors forming stable complexes when compared to that of compound-32 upon examining their MD trajectories. The key contributors were hydrophobic stacking and optimum hydrogen bonding allowing these molecules to occupy the adenosine pocket by interfacing D-loop residues. The results of bond distance analysis, radius of gyration, root mean square deviation, root mean square fluctuation, snapshots at different time intervals, LUMO-HUMO energy differences, electrostatic potential calculations, and binding free energy suggested better binding efficiency for compound-15 to TNKS enzymes. The computed physicochemical and ADMET properties of compound-15 were encouraging and could be explored further for drug development.Communicated by Ramaswamy H. Sarma.

An Overview of Molecular Dynamics Simulation for Food Products and Processes

Molecular dynamics (MD) simulation is a particularly useful technique in food processing. Normally, food processing techniques can be optimized to favor the creation of higher-quality, safer, more functional, and more nutritionally valuable food products. Modeling food processes through the application of MD simulations, namely, the Groningen Machine for Chemical Simulations (GROMACS) software package, is helpful in achieving a better understanding of the structural changes occurring at the molecular level to the biomolecules present in food products during processing. MD simulations can be applied to define the optimal processing conditions required for a given food product to achieve a desired function or state. This review presents the development history of MD simulations, provides an in-depth explanation of the concept and mechanisms employed through the running of a GROMACS simulation, and outlines certain recent applications of GROMACS MD simulations in the food industry for the modeling of proteins in food products, including peanuts, hazelnuts, cow’s milk, soybeans, egg whites, PSE chicken breast, and kiwifruit.