Application of molecular dynamics simulation in food carbohydrate research—a review

Application of the molecular dynamics simulation GROMACS in food science

Food comprises proteins, lipids, sugars and various other molecules that constitute a multicomponent biological system. It is challenging to investigate microscopic changes in food systems solely by performing conventional experiments. Molecular dynamics (MD) simulation serves as a crucial bridge in addressing this research gap. The Groningen Machine for Chemical Simulations (GROMACS) is an open-source, high-performing molecular dynamics simulation software that plays a significant role in food science research owing to its high flexibility and powerful functionality; it has been used to explore the molecular conformations and the mechanisms of interaction between food molecules at the microcosmic level and to analyze their properties and functions. This review presents the workflow of the GROMACS software and emphasizes the recent developments and achievements in its applications in food science research, thus providing important theoretical guidance and technical support for obtaining an in-depth understanding of the properties and functions of food.

Analysis of the relationship between starch molecular conformation and enzymatic hydrolysis efficiency

Resistant starch (RS) is important in controlling diabetes. The primary objective of this study is to examine the impact of molecular conformation on the enzymatic hydrolysis efficiency of starch by α-amylase. And the interactions between starch molecules with different conformations and α-amylase were analysed by using molecule dynamics simulation and molecular docking. It was found, the natural conformational starch molecule was hydrolysed from the middle of the starch chain by α-amylase, producing polysaccharides. The bent PS-conformational starch molecules with multiple O2-O3 intramolecular hydrogen bonds produced by high-pressure was hydrolysed from the head of the starch chain to produce glucose, which is not conducive to RS formation. The stretched H-conformation without intramolecular hydrogen bonds produced by heat treatment was not hydrolysed by α-amylase. However, it occupied the active groove and formed strong interactions with α-amylase, which prevented other starch molecules from binding to α-amylase, thus reducing hydrolysis efficiency. Moreover, the total interaction energies between the three starch molecules and α-amylase were approximately 78 kJ/mol. And several hydrogen bonds were formed between the starch molecules and α-amylase, which provides evidence for the continuous sliding hydrolysis hypothesis of α-amylase. Moreover, these results provide an important reference for elucidating the mechanism of RS formation.

Investigation of the formation mechanism of the pepper starch-piperine complex

In this study, a new carrier for loading piperine was prepared using pepper starch, and its interaction mechanism was investigated. The porous pepper starch-piperine complex (PPS-PIP) showed higher loading efficiency (76.15 %) compared to the porous corn starch-piperine complex (PCS-PIP (52.34 %)). This may be ascribed to the hemispherical shell structure of porous pepper starch (PPS) compared to the porous structure of porous corn starch (PCS) based on the SEM result. PPS-PIP had smaller particle size (10.53 μm), higher relative crystallinity (38.95 %), and better thermal stability (87.45 °C) than PCS-PIP (17.37 μm, 32.17 %, 74.35 °C). Fourier transform infrared spectroscopy (FTIR) results implied that piperine not only forms a complex with amylose but may also be physically present in porous starch. This was demonstrated by the short-range order and X-ray type. Molecular dynamics simulations confirmed that hydrogen bonding is the primary interaction between amylose and piperine. Besides the formation of the amylose-piperine complex, some of the piperine is also present in physical form.

Glycans modulate lipid binding in Lili-Mip lipocalin protein: insights from molecular simulations and protein network analyses

The unique viviparous Pacific Beetle cockroaches provide nutrition to their embryo by secreting milk proteins Lili-Mip, a lipid-binding glycoprotein that crystallises in-vivo. The resolved in-vivo crystal structure of variably glycosylated Lili-Mip shows a classical Lipocalin fold with an eight-stranded antiparallel beta-barrel enclosing a fatty acid. The availability of physiologically unaltered glycoprotein structure makes Lili-Mip a very attractive model system to investigate the role of glycans on protein structure, dynamics, and function. Towards that end, we have employed all-atom molecular dynamics simulations on various glycosylated stages of a bound and free Lili-Mip protein and characterised the impact of glycans and the bound lipid on the dynamics of this glycoconjugate. Our work provides important molecular-level mechanistic insights into the role of glycans in the nutrient storage function of the Lili-Mip protein. Our analyses show that the glycans stabilise spatially proximal residues and regulate the low amplitude opening motions of the residues at the entrance of the binding pocket. Glycans also preserve the native orientation and conformational flexibility of the ligand. However, we find that either deglycosylation or glycosylation with high-mannose and paucimannose on the core glycans, which better mimic the natural insect glycosylation state, significantly affects the conformation and dynamics. A simple but effective distance- and correlation-based network analysis of the protein also reveals the key residues regulating the barrel's architecture and ligand binding characteristics in response to glycosylation.

More simple, efficient and accurate food research promoted by intermolecular interaction approaches: A review

The investigation of intermolecular interactions has become increasingly important in many studies, mainly by combining different analytical approaches to reveal the molecular mechanisms behind specific experimental phenomena. From spectroscopic analysis to sophisticated molecular simulation techniques like molecular docking, molecular dynamics (MD) simulation, and quantum chemical calculations (QCC), the mechanisms of intermolecular interactions are gradually being characterized more clearly and accurately, leading to revolutionary advances. This article aims to review the progression in the main techniques involving intermolecular interactions in food research and the corresponding experimental results. Finally, we discuss the significant impact that cutting-edge molecular simulation technologies may have on the future of conducting deeper exploration. Applications of molecular simulation technology may revolutionize the food research, making it possible to design new future foods with precise nutrition and desired properties.

Multiscale structure and precipitation mechanism of debranched starch precipitated by different alcohols

Alcohol solution is a cheap, simple, and effective precipitating solvent frequently used for separating debranched starch (DBS), yet little is known about the precipitation mechanism of DBS by different alcohols. This study precipitated DBS from pullulanase-hydrolyzed starch using ethanol, n-butanol, and isopentanol. The multiscale structures of DBS were characterized, including chain length, single/double helix, and crystalline. The chain conformation and precipitation mechanism of DBS in different alcohols was investigated using molecular dynamics (MD) simulation. DBS precipitated by n-butanol contained the largest proportion of short chain (DP6-24, 83.2 %), the highest V-type crystallinity (21.1 %), and the largest single-helix content (24.7 %). A single helix conformation of DBS chain was determined in alcohols, where alcohol molecules entered the helix cavity. Intra/inter-molecular hydrogen bonds stabilized the helix, with a large number of hydrogen bonds leading to strong molecular interaction and stable helical structure. The solvent accessible surface area of DBS chain decreased by 7.88-19.32 % in alcohols, and the radial distribution function revealed that the first solvent layer of DBS chain at 0.29 nm was closely related to hydrogen bonding. This study provides a basis for the choice of precipitation solvent for preparing DBS with different chain lengths and physicochemical properties.

Application of molecular dynamics simulation for exploring the roles of plant biomolecules in promoting environmental health

Understanding the dynamic changes of plant biomolecules is vital for exploring their mechanisms in the environment. Molecular dynamics (MD) simulation has been widely used to study structural evolution and corresponding properties of plant biomolecules at the microscopic scale. Here, this review (i) outlines structural properties of plant biomolecules, and the crucial role of MD simulation in advancing studies of the biomolecules; (ii) describes the development of MD simulation in plant biomolecules, determinants of simulation, and analysis parameters; (iii) introduces the applications of MD simulation in plant biomolecules, including the response of the biomolecules to multiple stresses, their roles in corrosive environments, and their contributions in improving environmental health; (iv) reviews techniques integrated with MD simulation, such as molecular biology, quantum mechanics, molecular docking, and machine learning modeling, which bridge gaps in MD simulation. Finally, we make suggestions on determination of force field types, investigation of plant biomolecule mechanisms, and use of MD simulation in combination with other techniques. This review provides comprehensive summaries of the mechanisms of plant biomolecules in the environment revealed by MD simulation and validates it as an applicable tool for bridging gaps between macroscopic and microscopic behavior, providing insights into the wide application of MD simulation in plant biomolecules.

Discovery of aromatic 2-(3-(methylcarbamoyl) guanidino)-N-aylacetamides as highly potent chitinase inhibitors

Chitinases are important glycoside hydrolases that are closely related to bacterial pathogenesis, fungal cell wall remodelling, and insect moulting. Consequently, chitinases have become attractive targets for therapeutic drugs and pesticides. In this study, we designed and synthesised a series of novel chitinase inhibitors based on the N-methylcarbamoylguanidinyl group of the natural product argifin. The most active compound 8h showed strong inhibitory activity against the group I chitinases HsChit1, SmChiB, and OfChi-h, with IC₅₀ values of 0.19 µM, 4.2 nM, and 25 nM, respectively. Binding mode studies revealed that the compound 8h formed π-π stacking/hydrophobic interactions at +1 or +2 subsite of chitinases. In addition, a key hydrogen bond net was formed between the pharmacophore N-methylcarbamoylguanidinyl and key residues at the -1 subsite. Together, the findings of this study provide novel insights into the development of potent small-molecule chitinase inhibitors using a combination of planar structures and N-methylcarbamoylguanidinyl.

Mechanisms Underlying the Formation of Amylose- Lauric Acid-β-Lactoglobulin Complexes: Experimental and Molecular Dynamics Studies

The aim of the present study was to reveal the mechanisms underlying the formation of ternary complexes with a model system of amylose (AM), lauric acid (LA), and β-lactoglobulin (βLG) using experimental studies and molecular dynamics (MD) simulations. Experimental analyses showed that hydrophobic interactions and hydrogen bonds contributed more than electrostatic forces to the formation of the AM-LA-βLG complex. MD simulations indicated that interactions between AM and βLG through electrostatic forces and hydrogen bonds, and to a less extent van der Waals forces, and interactions between AM and LA through van der Waals forces, were mostly responsible for complex formation. The combination of experimental results and MD simulations has provided new mechanistic insights and led us to conclude that hydrophobic interactions, van der Waals forces between AM and LA, and van der Waals forces and hydrogen bonds between AM and βLG were the main driving forces for the formation of the AM-LA-βLG complex.

Exploration of the process and mechanism of magnesium chloride induced starch gelatinization

As a new starch gelatinization method, salt induced gelatinization can not only reduce energy consumption but also impart special physicochemical properties to starch gel. In this study, the process and mechanism of MgCl₂ induced starch gelatinization were explored. The results showed that, potato starch could be gelatinized after a treatment of 4 mol/L MgCl₂ for 3 h. The gelatinization started with the slight damage of outer shells, then the internal molecules leached out through the cracks or holes to form gel, finally the outer shells disintegrated. During the gelatinization process, the viscosity and granule size gradually increased after 0.5 h, while the original crystallinity disappeared rapidly in 0.5 h. Besides, MgCl₂ significantly increased the electrostatic interaction, then made starch molecules closer to each other and become denser, which may have close relationship with the appearance of the cracks and the disappearance of crystallization. Moreover, MgCl₂ enhanced the hydration and increased the binding free energy of starch molecules, then promoted starch gelatinization and accelerated the destruction of starch structure, which may be the critical factors of the starch gelatinization induced by MgCl₂. The results will provide reference for the research and application of salt induced gelatinization.

Heat-induced conversion of multiscale molecular structure of natural food nutrients: A review

Thermal process is the most important way of treating foods. Heat energy inputted into the natural food system induces the depolymerization of multi-scale structures of matrix, and causes the intramolecular and intermolecular interactions of different nutrients. It attacks and breaks the original polymeric molecule structures and the functional properties of macronutrients such as carbohydrates, proteins and lipids. Micronutrients such as vitamins and other novel functional ingredients are also thermally converted. The heat-induced conversions of nutrients are slightly or totally with discrepancy in simple-, simulated- and real-food systems, respectively. Thus, this review aims to extensively summarize the heat-induced structural characteristics, thermal conversion pathways and pyrolysis mechanism of nutrients both in simple and complex food matrices. The structural change of each nutrient and its thermal reaction kinetics depend on the molecule structure and polymeric characteristic of the unit substances in the system.

Online analysis of D-glucose and D-mannose aqueous mixtures using Raman spectroscopy: an in silico and experimental approach

Raman spectroscopy was applied to an aqueous solution containing D-mannose and D-glucose at a fixed dry matter content. The Raman measurement apparatus was adapted online at the industrial scale to monitor a bioprocess including an epimerization reaction. Online Raman spectroscopy and deconvolution techniques were successfully applied to monitor in real time the D-mannose and D-glucose concentrations using the Raman shifts at 960 cm-1 and 974 cm-1 respectively. The two anomeric forms, α and β of D-mannose in the pyranose conformation were quantified. In silico analysis of vibrational frequencies and Raman intensities of hydrated structure of D-mannose and D-glucose in the pyranose form for α and β anomers were carried out using a two-step procedure. First molecular dynamics was used to generate the theoretical carbohydrates' structures keeping the experimental dry matter content, then quantum mechanics was used to compute the Raman frequencies and intensities. Computed vibrational frequencies are in satisfactory agreement with the experimental spectra considering a hydration shell approach. Raman intensities are qualitatively in accordance with the experimental data. The interpretation of Raman frequencies and intensities led to acceptable results regarding the current possible structures of D-mannose and D-glucose in aqueous solution. Online Raman spectroscopy coupled with in silico approaches such as quantum mechanics and molecular dynamics methodology is proved to be a valuable tool to quantify the carbohydrates and stereoisomers content in complex aqueous mixtures. This methodology offers a new way to monitor any bioprocesses that encounter aqueous mixtures of D-glucose and D-mannose.

Molecular dynamic simulation: Structural insights of multi-stranded curdlan in aqueous solution

In this work, by using molecular dynamic simulation we provide microscale structure information which helps to reveal the molecular mechanisms concerning the multi-chain conformational behavior of short curdlan. Through simulations starting with different conformations of curldan dodecasaccharides, it is found that the right-handed triple helix is thermodynamically the most stable conformation in aqueous solutions, which is well maintained and stabilized by an inter-strand hydrogen bonding network of the C₂ hydroxyls. Unlike any predicted forms, the inter-strand hydrogen bonds exhibit a left-handed double helix pattern with preferred global orientations. Temperature REMD results suggest that the formation of triple helix is temperature sensitive, but the already formed triple helix is not. Investigation of curdlan with numbers of repeating units from 3 to 12 captures a critical value of 6, which in a way elucidates the relationship between the formation of triple helix and the chain length.

Atomistic Modeling of Peptide Aggregation and β-Sheet Structuring in Corn Zein for Viscoelasticity

The structure-function relationships of plant-based proteins that give rise to desirable texture attributes in order to mimic meat products are generally unknown. In particular, it is not clear how to engineer viscoelasticity to impart cohesiveness and proper mouthfeel; however, it is known that intermolecular β-sheet structures have the potential to enhance the viscoelastic property. Here, we investigated the propensity of selected peptide segments within common corn α-zein variants to maintain stable aggregates and β-sheet structures. Simulations on dimer systems showed that stability was influenced by the initial orientation and the presence of contiguous small hydrophobic residues. Simulations using eight-peptide β-sheet oligomers revealed that peptide sequences without proline had higher levels of β-sheet structuring. Additionally, we identified that sequences with a dimer hydrogen-bonding density of >22% tended to have a larger percent β-sheet conformation. These results contribute to understanding how the viscoelasticity of zein can be increased for use in plant-based meat analogues.

Molecular dynamics simulation of lentinan and its interaction with the innate receptor dectin-1

Lentinan, a β-1,3-D-glucan, is clinically used as an immune enhancement drug for tumor therapy. Dectin-1 is a cell-surface immune receptor, which plays an important role in immunological defense against fungal pathogens and β-glucan-mediated immune modulation. Herein we attempted to study the advanced structure of lentinan and how lentinan interacts with dectin-1 for its immune enhancement effect. We firstly used MD simulation and rigid macromolecule docking, combining some spectral techniques, to uncover the complex 3D conformation of a typical polysaccharide - lentinan, and the detailed interaction mode of lentinan with dectin-1. We proved by computational simulation that lentinan can maintain its triple-helix through hydrogen network and disclosed some structural properties of lentinan. We also characterized the affinity of lentinan to dectin-1 by LSPR and binding free energy calculation, and we found out that hydrogen bonds and CH-π interaction are the major contributors for lentinan's binding to dectin-1. Besides, after bound with lentinan, dectin-1 might surprisingly go through a conformational change. In summary, our work provided insights into lentinan's advanced structure and β-glucan recognition by dectin-1.

Diversity of the Hydrogen Bond Network and Its Impact on NMR Parameters of Amylose B Polymorph: A Study Using Molecular Dynamics and DFT Calculations Within Periodic Boundary Conditions

Classical molecular dynamics simulations have been combined with quantum (DFT) calculations of ¹³C NMR parameters in order to relate the experimental spectrum of the double-helix form of the amylose B-polymorph in highly crystalline conditions not only to its 3D structure but also to the arrangement of atoms in the crystal lattice. Structures obtained from these simulations or from geometry optimization procedures at the DFT level have shown the presence of hydrogen bond networks between sugars of the same helix or between residues of the two chains of the double helix. ¹³C NMR parameter calculations have revealed the impact of such a network on the chemical shifts of carbon atoms. In addition, DFT calculations using periodic boundary conditions were compulsory to highlight the presence of two types of sugar within the crystal sample. It allows us to confirm, theoretically, the experimental hypothesis that the existence of two distinct sugar types in the NMR spectrum is a consequence of crystal packing.

Analysis of the complexation process between starch molecules and trilinolenin

Starch is a basic biomacromolecule, and an in-depth understanding of the process and mechanism of starch-lipid complexation has great significance for starch based food and pharmaceutical. In this study, molecular dynamics simulation was used to explore the complexation details between starch molecules and trilinolenin, such as complexation process, interaction forces, conformation changes and stability changes, which are difficult to be verified by using other characterization methods. The results show that, firstly, starch residues of one turn helix (8 residues) are enough to bind a trilinolenin molecule firmly. Secondly, the complex is maintained by Van der Waals and electrostatic interaction. Thirdly, the residues complexed with trilinolenin become more stable than the former or the free residues. In brief, the complexation process, interaction forces, conformation changes and stability changes of the starch-trilinolenin complex were clarified in this study. The results may create new insights for the research about the interaction of starch and lipid, then provide theoretical guidance for the research on starch based food and pharmaceutical.

Three-Dimensional Structures of Carbohydrates and Where to Find Them

Analysis and systematization of accumulated data on carbohydrate structural diversity is a subject of great interest for structural glycobiology. Despite being a challenging task, development of computational methods for efficient treatment and management of spatial (3D) structural features of carbohydrates breaks new ground in modern glycoscience. This review is dedicated to approaches of chemo- and glyco-informatics towards 3D structural data generation, deposition and processing in regard to carbohydrates and their derivatives. Databases, molecular modeling and experimental data validation services, and structure visualization facilities developed for last five years are reviewed.

Interactions in saccharide/cation/water systems: Insights from density functional theory

Interactions between saccharides and ions in aqueous solutions are of great importance in many fields (chemistry, physico-chemistry, biology, food industries). Thus, this work proposes to develop a methodology dealing with the characterization and the understanding of interactions between saccharides and cations in presence of water molecules, by a quantum mechanics approach. In the first part, the saccharide hydration properties (xylose, glucose, sucrose) in pure water are determined. Results show that the saccharide coordination numbers, as well as the saccharides hydration enthalpy, increase with the saccharide hydrophilic group number. In the second part, the influence of cations on saccharides hydration properties, and inversely, is evaluated. In saccharide/cation/water systems, the decrease in hydration enthalpy of cations and saccharides shows that both species are dehydrated and that saccharide dehydration depends on the nature of the cation. The dehydration sequence of saccharides was explained from the study of saccharide/cation interactions.

Coarse-grained molecular dynamics simulations of α-1,3-glucan

In this paper we present a computational study of aggregation in aqueous solutions of α-1,3-glucan captured using a coarse-grained (CG) model that can be extended to other polysaccharides. This CG model captures atomistic geometry (i.e., relative placement of the hydrogen bonding donors and acceptors within the monomer) of the α-1,3-glucan monomer, the directional interactions due to the donor-acceptor hydrogen bonds, and their effect on aggregation of multiple α-1,3-glucan chains without the extensive computational resources needed for simulations with atomistic models. Using this CG model, we conduct molecular dynamics simulations to assess the effect of varying α-1,3-glucan chain length and hydrogen bond interaction strengths on the aggregation of multiple chains at finite concentrations in implicit solvent. We quantify the hydrogen bonding strength needed for multiple chains to aggregate, the distribution of inter- and intra-chain hydrogen bonds within the aggregate and in some cases, the shapes of the aggregate. We also explore the effect of substitution/silencing of some randomly selected or specific hydrogen bonding sites in the chain on the aggregation and aggregate structure. In the unmodified α-1,3-glucan solution, the inter-chain hydrogen bonds cause the chains to aggregate into sheets. Random silencing of hydrogen bonding donor sites only increases the hydrogen bond strength needed for aggregation but retains the same aggregate structure as the unmodified chains. Specific silencing of the hydrogen-bonding site on the C6 carbon leads to the chains aggregating into planar sheets that then fold over to form hollow cylinders at intermediate hydrogen bond strength - 4.7 to 5.3 kcal mol-1. These cylindrical aggregates assemble end-to-end to form larger aggregates at higher hydrogen bond strengths.

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

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.

Sequential molecule-triggered-release system based on acetylated amylose helix aggregates

We developed a molecule-triggered-release system based on acetylated amylose helix aggregates, in which the triggered conditions and duration time can be adjusted. The system could even be customized to meet specific demands.