Molecular Dynamics Simulation for Mechanism Elucidation of Food Processing and Safety: State of the Art

Abstract

Molecular dynamics (MD) simulation is a useful technique to study the interaction between molecules and how they are affected by various processes and processing conditions. This review summarizes the application of MD simulations in food processing and safety, with an emphasis on the effects that emerging nonthermal technologies (for example, high hydrostatic pressure, pulsed electric field) have on the molecular and structural characteristics of foods and biomaterials. The advances and potential projection of MD simulations in the science and engineering aspects of food materials are discussed and focused on research work conducted to study the effects of emerging technologies on food components. It is expected by showing key case studies that it will stir novel developments as a valuable tool to study the effects of emerging food technologies on biomaterials. This review is useful to food researchers and the food industry, as well as researchers and practitioners working on flavor and nutraceutical encapsulations, dietary carbohydrate product developments, modified starches, protein engineering, and other novel food applications.

Interactions between cell wall polysaccharides and polyphenols: Effect of molecular internal structure

“…For the more complex model simulation of oenin, catechin, and pectin, the distance between the catechin atom and the pectin molecule to the C 2 atom of oenin was about 3.0 Å, which prevented the entrance of solvent molecules and interaction with oenin; this explained the more stable state of the ternary complex (A. Fernandes et al., 2016). The combination of MD simulation with other simulation methods (e.g., molecular docking, Brownian motion, and Monte Carlo simulation) may expand its applications to the elucidation of interactions between biological macromolecules (Chen, Huang, Miao, Feng, & Campanella, 2019).…”

“…Fernandes et al, 2016). The combination of MD simulation with other simulation methods (e.g., molecular docking, Brownian motion, and Monte Carlo simulation) may expand its applications to the elucidation of interactions between biological macromolecules (Chen, Huang, Miao, Feng, & Campanella, 2019).…”

Mechanism of binding interactions between young apple polyphenols and porcine pancreatic α-amylase

“…The molecular docking was performed by Accelrys Discovery Studio 3.5 software (Accelrys Inc., San Diego, CA) with PPA (PDB:1PIF) as the model protein, according to one previously-described method with some modifications (Miao, Jiang, Jiang, Zhang, & Li, 2015;Chen, Huang, Miao, Feng, & Campanella, 2018). The structures of the ligands tested, including TA, CHA, CA and EC were generated and energy optimized using the Chem3D Ultra 6.0 software.…”

“…The structures of the ligands tested, including TA, CHA, CA and EC were generated and energy optimized using the Chem3D Ultra 6.0 software. All the docking studies were conducted using the CHARMM force field (Chen et al, 2018). The binding affinity was estimated using the docking score and the binding energy, E b .…”

Heat-Stable Hazelnut Profilin: Molecular Dynamics Simulations and Immunoinformatics Analysis

“…This behavior can be attributed to hydrogen bonding, salt bridges, van der Waals’ interactions, hydrophobic internal packing, improved electrostatic interactions, and others [ 21 , 22 ]. Currently, molecular dynamics simulation techniques allow us to understand the behavior of many proteins submitted to high temperatures, and to enable us to predict their behavior [ 23 , 24 , 25 , 26 ]. For example, the soy allergen has been analyzed by molecular dynamics simulations methods to understand the structural conformation for the development of antiallergenic drugs [ 27 , 28 ].…”