Application Of Molecular Dynamics Simulations Research Articles

The Applications of Molecular Dynamics Simulation in Studying Protein Structure and Dynamics

The Applications of Molecular Dynamics Simulation in Studying Protein Structure and Dynamics

Evaluation of the impact of two C5 genetic variants on C5-eculizumab complex stability at the molecular level

Complement C5 is the target of the monoclonal antibody eculizumab, used in complement dysregulating disorders, like the rare disease Paroxysmal Nocturnal Hemoglobinuria (PNH). PNH is an acquired hematopoietic stem cell condition characterized by aberrant destruction of erythrocytes, chronic hemolytic anemia, and thromboembolism propensity. C5 is a protein component of the complement system which is part of the immune system of the body and plays a prominent role in the destruction of red blood cells, misidentifying them as a threat. This work describes the application of molecular dynamics simulations to the study of the underlying interactions between complement C5 and eculizumab. This study also reveals the importance of single nucleotide polymorphisms on C5 protein concerning the effective inhibition of the mAB, involving the mechanistic events taking place at the interface spots of the complex. The predicted conformational change in the C5 Arg885/His/Cys mutation has implications on the protein’s interaction with eculizumab, compromising their compatibility. The acquired insights into the conformational changes, dynamics, flexibility, and interactions shed light on the knowledge of the function of this biomolecule providing answers about the poor response to the treatment in PNH patient carriers of the mutations. By investigating the intricate dynamics, significant connections between C5 and eculizumab can be uncovered. Such insights may aid in the creation of novel compounds or lead to the enhancement of eculizumab’s efficacy. Communicated by Ramaswamy H. Sarma

Exploring thermal properties of PbSnTeSe and PbSnTeS high entropy alloys with machine-learned potentials

Lattice thermal conductivity plays an important role in material science, especially significant in thermoelectric materials. Recent research has unveiled the potential of high entropy alloys (HEAs) as good candidates for thermoelectric materials due to their notably low lattice thermal conductivity. This study investigates the lattice thermal conductivities of two specific HEAs, namely PbSnTeSe and PbSnTeS, through the application of molecular dynamics simulations (MDS) with machine-learned potentials. The findings not only demonstrate substantial agreement with experimental results for PbSnTeSe but also highlight the precision and efficiency of machine-learned potentials as a powerful tool in material research. The combination of machine-learned potentials with classical MDS offers an effective solution for simulating the thermodynamic properties of complicated systems like HEAs, with accuracy comparable to first-principle calculations. Furthermore, the investigation reveals that the lattice thermal conductivities of PbSnTeS are lower than those of PbSnTeSe, indicating its potential as a promising candidate for thermoelectric materials.

Pool boiling simulation using molecular dynamics approach: Comparing the effectiveness of adding nanoparticles versus creating porous nanostructures

This paper presents the pool boiling process of argon atoms on the copper surface by employing molecular dynamics simulation. Through the application of molecular dynamics simulation, this study explores three cases: the plain surface, and adding platinum and aluminum nanoparticles to the argon fluid. The main objective is to offer a comprehensive comparative analysis to highlight the significance and innovation of this research. The investigation aims to assess the effectiveness of two methods for improving heat transfer: the addition of nanoparticles to the base fluid and the creation of porous nanostructure. By subjecting these approaches to identical simulation conditions, an enthralling evaluation unfolds. The simulation framework is first validated, and then the results are presented and compared with the case of creating porous geometry. The results reveal that while the evaporation rate has a similar impact in both cases, creating porous geometry results in a 3.68% higher argon temperature compared to adding nanoparticles. On the other hand, adding nanoparticles enhances the maximum heat flux by approximately 15% more than creating porous geometry. This research compares two approaches to offer valuable investigations and insights into enhancing heat transfer efficiency due to the growing demand for strategies that promote heat transfer.

The Progress of the Interfacial Diffusion between Virgin and Aged Asphalt Based on Molecular Dynamics Simulation: A Review

The utilization rate of reclaimed asphalt pavement is significantly low in the sustainable design process of asphalt roads. Numerous researchers have extensively investigated the recycling and utilization of reclaimed asphalt pavements from various perspectives. Molecular dynamics simulations could elucidate the diffusion phenomenon occurring at the molecular scale between virgin and aged asphalt interfaces. This review provides a comprehensive summary of the simulation methods and applications of molecular dynamics simulation in the interface diffusion problem between virgin and aged asphalt. Diffusion theory and model testing methods are discussed. The review proposes the basic steps of molecular dynamics simulation and summarizes the molecular models with the corresponding parameter settings of virgin asphalt and aged asphalt. Moreover, the current influencing factors on the interfacial diffusion problem of virgin and aged asphalt are discussed. The paper explores the validation parameters including density, viscosity, radial distribution function (RDF), glass transition temperature, and solubility parameters based on the existing research. Molecular dynamics simulation could simulate interface diffusion at a micro-scale and clarify the diffusion depth and influence range of different asphalts. The purpose of the study of molecular dynamics is to solve interface issues and advance optimization of reclaimed materials.

Application of molecular dynamic simulations in modeling the excited state behavior of confined molecules.

Relative to isotropic organic solvent medium, the structure and conformation of a reactant molecule in an organized and confining medium are often different. In addition, because of the rigidity of the immediate environment, the reacting molecule have a little freedom to undergo large changes even upon gaining energy or modifications in the electronic structure. These alterations give rise to differences in the photochemistry of a molecular and supramolecular species. In this study, one such example is presented. α-Alkyl dibenzylketones upon excitation in isotropic solvents give products via Norrish type I and type II reactions that are independent of the chain length of the alkyl substituent. On the other hand, when these molecules are enclosed within an organic capsule of volume ~ 550Å3, they give products that are strikingly dependent on the length of the α-alkyl substitution. These previously reported experimental observations are rationalized based on the structures generated by molecular modeling (docking and molecular dynamics (MD) simulations). It is shown that MD simulations that are utilized extensively in biologically important macromolecules can also be useful to understand the excited state behavior of reactive molecules that are part of supramolecular assemblies. These simulations can provide structural information of the reactant molecule and the surroundings complementing that with the one obtained from 1 and 2D NMR experiments. MD simulated structures of seven α-alkyl dibenzylketones encapsulated within the octa acid capsule provide a clear understanding of their unique behavior in this restricted medium. Because of the rigidity of the medium, these structures although generated in the ground state can rationalize the photochemical behavior of the molecules in the excited state.

Formation of degraded LDPE surfaces using mechanical cleavage and shock compression analyzed by means of molecular dynamics simulations

Low Density Polyethylene, LDPE, samples were subjected to analysis based on application of molecular dynamics simulations. The samples were composed of polymer molecules with molecular weight 30 000 amu and 2% of branched carbon atoms. The calculations were carried out using various force fields i.e. Amber pairwise additive force field and four types of many body reactive force fields like AIREBO, AIREBO-M, ReaxFF and ci-ReaxFF. For each force field the material properties of the samples were determined i.e.: Young's modulus, Poisson's ratio, yield strength and share modulus using the determined stress–strain curves. The samples were subjected to mechanical cleaving by applying an external forces in order to generate surfaces of LDPE. These surfaces were analyzed in terms of their chemical composition and number and types of radical ends formed on the surfaces. Additionally, the samples were subjected to shock compression in order to produce more deeper chemical transformations which should be more representative to naturally degraded nanoplastics. We conclude that the CHO ReaxFF force field is the most reliable for generating degraded LDPE surfaces which can be next used in standard molecular dynamics involving interaction of nanoplastic with proteins or lipid membranes, for instance.

Applications of Molecular Dynamics Simulations in Drug Discovery.

In the current drug development process, molecular dynamics (MD) simulations have proven to be very useful. This chapter provides an overview of the current applications of MD simulations in drug discovery, from detecting protein druggable sites and validating drug docking outcomes to exploring protein conformations and investigating the influence of mutations on its structure and functions. In addition, this chapter emphasizes various strategies to improve the conformational sampling efficiency in molecular dynamics simulations. With a growing computer power and developments in the production of force fields and MD techniques, the importance of MD simulations in helping the drug development process is projected to rise significantly in the future.

Application of Molecular Dynamics Simulations to Determine Interactions between Canary Seed (Phalaris canariensis L.) Bioactive Peptides and Skin-Aging Enzymes.

Food bioactive peptides are well recognized for their health benefits such as antimicrobial, antioxidant, and antihypertensive benefits, among others. Their drug-like behavior has led to their potential use in targeting skin-related aging factors like the inhibition of enzymes related with the skin-aging process. In this study, canary seed peptides (CSP) after simulated gastrointestinal digestion (<3 kDa) were fractioned by RP-HPLC and their enzyme-inhibition activity towards elastase and tyrosinase was evaluated in vitro. CSP inhibited elastase (IC50 = 6.2 mg/mL) and tyrosinase (IC50 = 6.1 mg/mL), while the hydrophobic fraction-VI (0.2 mg/mL) showed the highest inhibition towards elastase (93%) and tyrosinase (67%). The peptide fraction with the highest inhibition was further characterized by a multilevel in silico workflow, including physicochemical descriptor calculations, antioxidant activity predictions, and molecular dynamics-ensemble docking towards elastase and tyrosinase. To gain insights into the skin permeation process during molecular dynamics simulations, based on their docking scores, five peptides (GGWH, VPPH, EGLEPNHRVE, FLPH, and RPVNKYTPPQ) were identified to have favorable intermolecular interactions, such as hydrogen bonding of polar residues (W, H, and K) to lipid polar groups and 2-3 Å van der Waals close contact of hydrophobic aliphatic residues (P, V, and L). These interactions can play a critical role for the passive insertion of peptides into stratum corneum model skin-membranes, suggesting a promising application of CSP for skin-aging treatments.

Application of molecular dynamics simulations in interface interaction of clay: Current status and perspectives

AbstractTo understand the research progress of molecular dynamics (MD) method in the field of clay minerals, the application of MD in the interface interaction of clay minerals is reviewed in this paper. MD simulations have become the indispensable means to study mineral interface effects. Clay minerals are common associated minerals with hydrophilic surface, the ease of argillization, negative electricity, and the ability of forming impurities and defects. They are widely concerned in the fields of mine wastewater treatment, fine clay mineral flotation, shale oil and gas exploitation, and so forth. In addition, clay minerals are considered as natural adsorbents due to their large specific surface area, but their complex interface interactions hinder their effective utilization. Therefore, it is particularly important to reveal the interaction mechanism of clay interface at the atomic/molecular level by means of software simulation technology. In this review, our focus is on the applications of MD method in the field of clay mineral interface interaction, such as clay/gas interface, clay/water interface, agents and clay/water interface, and mineral particle and clay/water interface. Furthermore, the history and shortcomings of MD simulation are summarized. The research and effective utilization of clay interface are summarized and prospected as well.

The application of molecular dynamic simulations

Molecular dynamic(MD) simulations have been developed into a mature tool for researchers and have had a huge impact on the aspects of drug discovery, molecular biology, and prediction of specific structures and related functions of macromolecules in recent years. The aim of this article is to provide some essential knowledge about the theories and applications of this useful technology. This introduction to molecular dynamics starts from the definition of some basic concepts, including the molecular mechanics force fields and how they are applied to the motion systems of molecular dynamics simulations and their developments recently. Also, the outstanding strengths and limitations of the MD simulations are discussed, as are some possible solutions to them. This article shows the wide applications of MD simulations, including drug discovery, prediction of structure, and allostery. Due to the growing power of computational calculations and its important role in simulating the biological process between receptors and ligands like allosteric binding sites, MD simulations are thought to be more and more important in the near future.

Application of molecular dynamic simulation on evaluating toxicity mechanisms of organophosphate esters to Photobacterium phosphoreum

Organophosphate esters (OPEs) that are widely used as additives in industrial products have been monitored ubiquitously in environmental media. With the health hazards and ecological risks caused by OPEs being attracted more and more attention, screening toxicity mechanism was essential for risk assessment. In this study, Photobacterium phophorium was employed to test the acute toxicity of OPEs. Integrating toxicity test and molecular dynamics (MD) simulation, we calculated the binding affinity between OPEs and n-octanol (C8H18O)/ phospholipid bilayer (DPPC) to further explore the mechanism of toxicity. Good correlationship between the median effective concentration (EC50) of OPEs and binding affinity was found. Binding affinity of selected OPEs with the C8H18O/DPPC presented similar tendency. The mode of action (MOA) for OPEs to Photobacterium phophorium was shown that tris (1, 3-dichloro-2-propyl) phosphate (TDCP) belonged to reactive mechanism, triphenyl phosphate (TPhP) and tris (2-butoxyethyl) phosphate (TBEP) belonged to narcosis mechanism. It was proposed a creative method to quickly evaluate toxicity mechanisms of organophosphate esters by integrating the toxicity test and MD simulation, which could be an alternative methodology to obtain toxicity mechanism without using model organisms.

Molecular Mechanism of Tau Misfolding and Aggregation: Insights from Molecular Dynamics Simulation.

Tau dysfunction has a close association with many neurodegenerative diseases, which are collectively referred to as tauopathies. Neurofibrillary tangles (NFTs) formed by misfolding and aggregation of tau are the main pathological process of tauopathy. Therefore, uncovering the misfolding and aggregation mechanism of tau protein will help to reveal the pathogenic mechanism of tauopathies. Molecular dynamics (MD) simulation is well suited for studying the dynamic process of protein structure changes. It provides detailed information on protein structure changes over time at the atomic resolution. At the same time, MD simulation can also simulate various conditions conveniently. Based on these advantages, MD simulations are widely used to study conformational transition problems such as protein misfolding and aggregation. Here, we summarized the structural features of tau, the factors affecting its misfolding and aggregation, and the applications of MD simulations in the study of tau misfolding and aggregation.

Molecular Dynamics Simulation of Antimicrobial Peptide CM15 in Staphylococcus Aureus and Escherichia coli Model Bilayer Lipid.

In animals and plants, antimicrobial peptides (AMPs) are crucial components of defense mechanisms, as they play a crucial role in innate immunity, which protects hosts from pathogenic bacteria. The CM15 has attracted considerable interest as a novel antibiotic against gram-negative and positive pathogens. The aim of this study was to investigate the permeation potential of the CM15 with membrane bilayers of Staphylococcus aureus and Escherichia coli. The bilayer membranes of Escherichia coli and Staphylococcus aureus were modelled with the resemblance in lipid composition to its biological sample. This study followed Protein-Membrane Interaction (PMI) through successive applications of molecular dynamics simulation by GROMACS and CHARMM36 force field for two sets of 120-ns simulations. Significant results were obtained from analyzing the trajectory of the unsuccessful insertion of CM15 during simulation. Our data suggested that Lysine residues in CM15 and Cardiolipins in membrane leaflets play a crucial role in stability and interaction terms. The obtained results strengthen the insertion possibility through the toroidal model, which should consider for further studies on AMPs interaction.

Molecular dynamics simulation-based microstructure evolution and subsurface damage of Fe-Ni alloy grinding

PurposeMolecular dynamics is an emerging simulation technique in the field of machining in recent years. Many researchers have tried to simulate different processing methods of various materials with the theory of molecular dynamics (MD), and some preliminary conclusions have been obtained. However, the application of MD simulation is more limited compared with traditional finite element model (FEM) simulation technique due to the complex modeling approach and long computation time. Therefore, more studies on the MD simulations are required to provide a reliable theoretical basis for the nanoscale interpretation of grinding process. This study investigates the crystal structures, dislocations, force, temperature and subsurface damage (SSD) in the grinding of iron-nickel alloy using MD analysis.Design/methodology/approach In this study the simulation model is established on the basis of the workpiece and single cubic boron nitride (CBN) grit with embedded atom method and Morse potentials describing the forces and energies between different atoms. The effects of grinding parameters on the material microstructure are studied based on the simulation results.FindingsWhen CBN grit goes through one of the grains, the arrangement of atoms within the grain will be disordered, but other grains will not be easily deformed due to the protection of the grain boundaries. Higher grinding speed and larger cutting depth can cause greater impact of grit on the atoms, and more body-centered cubic (BCC) structures will be destroyed. The dislocations will appear in grain boundaries due to the rearrangement of atoms in grinding. The increase of grinding speed results in the more transformation from BCC to amorphous structures.Originality/valueThis study is aimed to study the grinding of Fe-Ni alloy (maraging steel) with single grit through MD simulation method, and to reveal the microstructure evolution within the affected range of SSD layer in the workpiece. The simulation model of polycrystalline structure of Fe-Ni maraging steel and grinding process of single CBN grit is constructed based on the Voronoi algorithm. The atomic accumulation, transformation of crystal structures, evolution of dislocations as well as the generation of SSD are discussed according to the simulation results.

Effect of hydrated shell layers on surface tension of electrolyte solutions: Insights from interpretable machine learning

To explore the effects of hydration shell layer on the surface tension of electrolytes solution and to build an effective prediction model, a machine learning based model is proposed to accurately predict and explain the surface tension of electrolytes solution. The model combines machine learning (ML) algorithms, force filed parameters of molecular dynamics simulations and radial distribution function (RDF) to accurately capture the structure feature for electrolytes solution. The prediction performed an extremely low average relative deviation. SHapleyAdditive explanation (SHAP) method is used to indicate the features order of importance from strong to weak. It noted that the second hydration shell on the influence of surface tension may beyond the first hydration shell. This work provides a method for one-step acquisition of surface tension data that not only to accurately predict physical and chemical properties of materials, but also to extend the application of molecular dynamics simulations, providing enlightening insights for detecting underlying physical mechanisms.

Study on the combined dust suppression effect of sodium alginate and sodium fatty acid methyl ester sulfonate

• In-depth study of coal dust wetting mechanism. • Application of molecular dynamics simulation in dust suppressants. • Study on the mechanism of dust suppression by combining different surfactants. To further improve the effect of dust control in coal mines and protect the health of workers, the effect of sodium alginate (SA) on the dust suppression ability of sodium methyl ester sulfonate (MES) was studied using molecular dynamics simulation. Scanning electron microscopy and X-ray photoelectron spectroscopy analyses were performed to compare the dust suppression effect of the SA/MES dust suppressant compound to MES by itself. The results show that when SA is present, the coal dust bonds together more, agglomerates into large particles, and settles. This finding is also consistent with the results of molecular dynamics simulations. In the analysis of relative concentrations and mean square displacement, the presence of SA can reduce the water diffusion on the coal surface, making it easier for coal dust to agglomerate. In addition, we analyzed the mode of action of SA through radial distribution and electrostatic potential, and determined that SA forms a unique networking chain structure to capture and retain water molecules. SA increases the probability of interaction between water and surfactant, thus increasing the amount of adsorption. This study provides a more in-depth understanding of the dust suppression mechanism of mixed dust suppressants.

Applications of Molecular Dynamics Simulation in Protein Study.

Molecular Dynamics (MD) Simulations is increasingly used as a powerful tool to study protein structure-related questions. Starting from the early simulation study on the photoisomerization in rhodopsin in 1976, MD Simulations has been used to study protein function, protein stability, protein–protein interaction, enzymatic reactions and drug–protein interactions, and membrane proteins. In this review, we provide a brief review for the history of MD Simulations application and the current status of MD Simulations applications in protein studies.

Application of molecular dynamics simulation in biomedicine

Molecular dynamics (MD) simulation has been widely used in the field of biomedicine to study the conformational transition of proteins caused by mutation or ligand binding/unbinding. It provides some perspectives those are difficult to find in traditional biochemical or pathological experiments, e.g., detailed effects of mutations on protein structure and protein-;protein/ligand interaction at the atomic level. In this review, a broad overview on conformation changes and drug discovery by MD simulation is given. We first discuss the preparation of protein structure for MD simulation, which is a key step that determines the accuracy of the simulation. Then, we summarize the applications of commonly used force fields and MD simulations in scientific research. Finally, enhanced sampling methods and common applications of these methods are introduced. In brief, MD simulation is a powerful tool and it can be used to guide experimental study. The combination of MD simulation and experimental techniques is an a priori means to solve the biomedical problems and give a deep understanding on the relationship between protein structure and function.

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.