An Overview of Molecular Dynamics Simulation for Food Products and Processes

Abstract

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.

Effect of Structural Targeted Modifications on the Potential Allergenicity of Peanut Allergen Ara h 2

“…Groningen Machine for Chemical Simulations (GROMACS) (Stockholm Center for Biomembrane Research, Stockholm, Sweden) was used to run the relevant MD simulations. 23 The tertiary structure of Ara h 2 was modeled using SWISS-MODEL. The amino acid sequences and protein names of Ara h 2 and its mutants were entered separately, and the highest-scoring protein [Protein Data Bank (PDB) entry 3OB4] was selected as the template for modeling, whereby the PDB file was obtained and used as the initial file for the GROMACS simulation.…”

“…With the refinement of research, molecular dynamics (MD) simulation has been widely used to analyze the structure of biological macromolecules. 23 Offermann and colleagues 24 used MD simulations to provide insight into the conformational changes of Cor a 8 upon ligand binding. Vanga et al 25 used the molecular modeling concept to understand the influence of food processing on protein and the changes in structure.…”

“…With the refinement of research, molecular dynamics (MD) simulation has been widely used to analyze the structure of biological macromolecules . Offermann and colleagues used MD simulations to provide insight into the conformational changes of Cor a 8 upon ligand binding.…”

Surface functionalization of graphene nanosheet with poly (l-histidine) and its application in drug delivery: covalent vs non-covalent approaches

“…A 1.4 nm cut-off is adopted for van der Waals interactions, while the long-range electrostatic interactions are examined based on the Particle-mesh Ewald Method 45 . The visual molecular dynamics package is utilized to view the entire simulation process 46 .…”

“…Radial distribution function (RDF). The RDF is calculated by Rog and Martinez-Seara's methodology to examine the distributions of drug molecules around the carrier 46 . Indeed, the analysis of RDF data shows how the particles in a system are arranged radially.…”