Adsorption and desorption surface dynamics of gaseous adsorbate on silicate-1 by molecular dynamics simulation

The dynamics of adsorption and desorption of gaseous molecules on the external surface of a crystal and a membrane of zeolite silicate-1 is investigated by molecular dynamics simulation. The gases are argon and three hydrocarbons, n-heptane, n-butane and ethylene. The sticking coefficient and the desorption coefficient are calculated for different coverages. The results clearly show that the desorption coefficients increase with the coverage contrary to the sticking coefficients. To have a better insight in the process, the desorption and adsorption time are computed, they are very similar and they show an increase with the coverage except for n-heptane which exhibit a specific decreasing behaviour at high loading.     

Interaction mechanism of insulin with ZnO nanoparticles by replica exchange molecular dynamics simulation

The interaction of ZnO nanoparticles with biological molecules such as proteins is one of the most important and challenging problems in molecular biology. Molecular dynamics (MD) simulations are useful technique for understating the mechanism of various interactions of proteins and nanoparticles. In the present work, the interaction mechanism of insulin with ZnO nanoparticles was studied. Simulation methods including MD and replica exchange molecular dynamics (REMD) and their conditions were surveyed. According to the results obtained by REMD simulation, it was found that insulin interacts with ZnO nanoparticle surface via its polar and charged amino acids. Unfolding insulin at ZnO nanoparticle surface, the terminal parts of its chains play the main role. Due to the linkage between chain of insulin and chain of disulfide bonds, opposite directional movements of N terminal part of chain A (toward nanoparticle surface) and N termini of chain B (toward solution) make insulin unfolding. In unfolding of insulin at this condition, its helix structures convert to random coils at terminal parts chains.     

A molecular dynamics investigation of buckling behaviour of hydrogenated graphene

Molecular dynamics simulations have been performed to characterise the stability behaviour of graphene nanoribbons having different hydrogen coverage, subject to a uniaxial compressive load. The temperature is set at a very low value to circumvent the contribution of thermal agitations. The results show that hydrogen coverage promotes to a rapid drop in the strain of buckling onset due to the effects of easy rotation of newly unsupported sp³ bonds. Furthermore, we have also found a critical value of the hydrogen adsorption above which the declining trend in the stability behaviour of hydrogenated graphene nanoribbons is reversed.     

Assessment of the chitosan-functionalized graphene oxide as a carrier for loading thioguanine,an antitumor drug and effect of urea on adsorption process: Combination of DFT computational and molecular dynamics simulation studies

In this study, the interaction thioguanine (TG) anticancer drug with the functionalized graphene oxide (GO) nanosheet surface is theoretically studied in both gas phase and separately in physiological media using the density functional theory (DFT) calculations. DFT calculations indicated the adsorption and solvation energies are negative for f-GONS/TG complexes which propose the adsorption process of TG molecule onto the f-GONS surface is possible from the energetic viewpoint. QTAIM calculations confirm the nature of partially covalent-partially electrostatic between drug and nanosheet. These results are sorely relevant that an approach for loading of TG molecule is the chemical modification of GO using covalent functionalization which can serve as a nanocarrier to load drug molecules. Moreover, to understand the effect of urea on the nature of the interaction between TG and f-GONS, molecular dynamics (MD) simulation was employed. The results indicated that in the presence of urea the adsorption process gets affected and leads to instability of system, while the affinity of the TG for adsorption onto GO surface is increased in pure water.

Communicated by Ramaswamy H. Sarma     

Different dynamics and pathway of disulfide bonds reduction of two human defensins,a molecular dynamics simulation study

Human defensins are a class of antimicrobial peptides that are crucial components of the innate immune system. Both human α defensin type 5 (HD5) and human β defensin type 3 (hBD‐3) have 6 cysteine residues which form 3 pairs of disulfide bonds in oxidizing condition. Disulfide bond linking is important to the protein structure stabilization, and the disulfide bond linking and breaking order have been shown to influence protein function. In this project, microsecond long molecular dynamics simulations were performed to study the structure and dynamics of HD5 and hBD‐3 wildtype and analogs which have all 3 disulfide bonds released in reducing condition. The structure of hBD‐3 was found to be more dynamic and flexible than HD5, based on RMSD, RMSF, and radius of gyration calculations. The disulfide bridge breaking order of HD5 and hBD‐3 in reducing condition was predicted by two kinds of methods, which gave consistent results. It was found that the disulfide bonds breaking pathways for HD5 and hBD‐3 are very different. The breaking of disulfide bonds can influence the dimer interface by making the dimer structure less stable for both kinds of defensin. In order to understand the difference in dynamics and disulfide bond breaking pathway, hydrophilic and hydrophobic accessible surface areas (ASA), buried surface area between cysteine pairs, entropy of cysteine pairs, and internal energy were calculated. Comparing to the wildtype, hBD‐3 analog is more hydrophobic, while HD5 is more hydrophilic. For hBD‐3, the disulfide breaking is mainly entropy driven, while other factors such as the solvation effects may take the major role in controlling HD5 disulfide breaking pathway. Proteins 2017; 85:665–681. © 2016 Wiley Periodicals, Inc.     

Dynamic injection behaviour of carbon monoxide nano-jets: analysis based on molecular dynamics simulation

Molecular dynamics simulation was used to characterise the dynamical injection behaviour of CO through a gold nano-injector with a Gr coating. We also varied the nozzle outlet size, system temperature, and extrusion velocity to elucidate their influence on the flow patterns, injection pressure, and flow rate of the CO nano-jets. Simulation results revealed the following important findings. (1) At 100?K, the liquefaction of a CO jet led to a wider spray angle (ø_s?=?84～96°) and allowed molecules to attach to the Gr layer, resulting in agglomeration at the orifice. (2) At 500?K and 55.824?m/s, the nebulisation of the CO nano-jet was induced, which produced a narrower spray angle (ø_s?=?47°). (3) The flow rate of CO molecules was essentially linear under the following conditions: low extrusion velocity (≤13.956?m/s), large orifice (d?=?1.5?nm), and high system temperature (≥300?K). (4) Due to the compressibility of CO molecules, the pressure inside the chamber under a high extrusion speed (≥27.912?m/s) presented a sharp increase in the middle and final extrusion stages. A delay in the pressure increase enabled the liquefaction of the extruded CO molecules, resulting in an unstable flow rate.     

Distal mutation modulates the heme sliding in mouse neuroglobin investigated by molecular dynamics simulation

Neuroglobin (Ngb), a hexa‐coordinated hemoprotein primarily expressed in the brain and retina, is thought to be involved in neuroprotection and signal transduction. Ngb can reversibly bind small ligands such as O₂ and CO to the heme iron by replacing the distal histidine which is bound to the iron as the endogenous ligand. In this work, molecular dynamics (MD) simulations were performed to investigate the functionally related structural properties and dynamical characteristics in carboxy mouse neuroglobin and three distal mutants including single mutants H64V, K67T and double mutant H64V/K67T. MD simulations suggest that the heme sliding motion induced by the binding of exogenous ligand is affected by the distal mutation obviously. Accompanying changes in loop flexibility and internal cavities imply the structural rearrangement of Ngb. Moreover, the solvent accessibility of heme and some crucial residues are influenced revealing an interactive network on the distal side. The work elucidates that the key residues K67 at E10 and H64 at E7 are significant in modulating the heme sliding and hence the structural and physiological function of Ngb. Proteins 2010. © 2010 Wiley‐Liss, Inc.     

Investigation on bioactive protection of LEA protein to insulin by molecular simulation

Nowadays various protein medicines are increasingly playing a key role on treatment of many diseases, while the bioactivity of such kinds of protein medicines is unstable because of their heat sensitivity. In order to explore a protective method and to explain the protective mechanism of protein medicines, the bioactive protection of the late embryogenesis abundant (LEA) protein to insulin was researched by molecular dynamics simulation. The results suggest that LEA proteins preserve the native structure of the insulin well. Compared with the desiccated insulin without any protection, the structure of insulin protected by LEA protein have smaller values, more centralised configurational space, lower free energies and structural cluster more closer to the native structure. All the above results prove that the LEA protein does protect the bioactivity of insulin during desiccation. The LEA protein is a perfect bioactive protectant for heat-sensitive protein medicines. Such LEA proteins can match the shape of insulin and form multisite binding interaction with insulin.     

Investigation on bioactive protection of the amino acids derived from LEA protein on insulin by molecular simulation

Nowadays heat-sensitive protein medicines are increasingly showing their importance in the treatment of various diseases. Their popularisation and application are meeting a great challenge because of their heat lability. In this study, human insulin as a heat-sensitive protein medicine and 66 amino acids derived from a Group 3 late embryogenesis abundant protein fragment as a complex bioactive protectant, were chosen to be investigated to determine whether these amino acids can be used to protect the insulin from denaturation due to drying. The experiments were carried out by using a replica exchange molecular dynamics (REMD) simulation and GROMACS software with Gromos96 (53a6) force field. The REMD results indicate that those amino acids can effectively prevent the reversal between hydrophilic and hydrophobic surface. Both the configurations and secondary structures of the protected insulin were preserved very well. The H-bonding and electrostatic interactions between the insulin and the protectant play key roles in the bioactive protection of insulin. These results agree well with the water replacement hypothesis. All the results prove that these amino acids are a perfect bioactive protectant for heat-sensitive protein medicines.     

Adsorption behaviors of hydrogen sulphide on Au(110) nanoslit array surfaces using molecular dynamics simulations

The adsorption behaviour of gas molecules on detector surfaces has a profound influence on the sensitivity of the detector. For this reason, this study used molecular dynamics simulation to explore the dynamic adsorption behaviour of hydrogen sulphide (H₂S) molecules on various types of Au surfaces, including a planar Au(1?1?0) structure and three types of slit array structures. The influence of system temperature, adsorbate concentration and the slit width of nanoarrays on diffusivity, average adsorption energy and static adsorption amount were systematically examined. Simulation results indicate that the self-diffusivity of the adsorbate molecules increases with temperature but decreases with adsorbate concentration. At low concentrations (~3 mol/L), each type of Au(1?1?0) surface structure shows good capacity to adsorb all H₂S molecules. With increasing concentration at 6.5 mol/L, the high concentration leads to adsorption saturation and many free H₂S molecules in the planar Au(1?1?0) structure. Moreover, desorption also begins to appear on the planar structures at a temperature of 300 K (at 6.5 mol/L). The simulation results indicate that the columnar array structures with a slit width ≥5.76 Å allow molecules to swiftly spread into the slits and provide more stable adsorption sites (i.e. with a higher adsorption energy), which can effectively address the issues of high-temperature desorption and adsorption saturation. Particularly at low temperatures (≤100 K), slit structures presented a level of static adsorption of H₂S that was 30% to 35 higher than that of planar structures.     

Exploring single-domain antibody thermostability by molecular dynamics simulation

Abstract

Single-domain antibodies also known as nanobodies are recombinant antigen-binding domains that correspond to the heavy-chain variable region of camelid antibodies. Previous experimental studies showed that the nanobodies have stable and active structures at high temperatures. In this study, the thermal stability and dynamics of nanobodies have been studied by employing molecular dynamics simulation at different temperatures. Variations in root mean square deviation, native contacts, and solvent-accessible surface area of the nanobodies during the simulation were calculated to analyze the effect of different temperatures on the overall conformation of the nanobody. Then, the thermostability mechanism of this protein was studied through calculation of dynamic cross-correlation matrix, principal component analyses, native contact analyses, and root mean square fluctuation. Our results manifest that the side chain conformation of some residues in the complementarity-determining region 3 (CDR3) and also the interaction between α-helix region of CDR3 and framework2 play a critical role to stabilize the protein at a high temperature.

Communicated by Ramaswamy H. Sarma     

Effect of chirality,length and diameter of carbon nanotubes on the adsorption of 20 amino acids: a molecular dynamics simulation study

We carried out molecular dynamics simulations to study the adsorption of all the 20 amino acids (AAs; aromatic, polar and non-polar) on the surface of chiral, zigzag and armchair single-walled carbon nanotubes. The adsorption was occurring in all systems. In the aromatic AAs, the π–π stacking and the semi-hydrogen bond formation cause a strong interaction with the carbon nanotubes (CNTs). We also investigated the chirality, length and diameter dependencies on adsorption energies. We found that all AAs have more tendency to adsorption on the chiral and zigzag CNTs over the armchair. The results show that increasing both the diameter and the length causes the enhancement of the adsorption energy. But, the effect of the length is more than of the diameter. For example, the adsorption energy of Trp on the surface of CNT (4,1), with 2 nm length, is 20.4 kcal/mol. When the length of CNT becomes twice, the adsorption energy increases by 24 ± 0.3%. But by doubling the diameter, the adsorption energy increased only by 9.8 ± 0.25%.     

Exploring the effect of inhibitor AKB-9778 on VE-PTP by molecular docking and molecular dynamics simulation

Diabetic macular edema, also known as diabetic eye disease, is mainly caused by the overexpression of vascular endothelial protein tyrosine phosphatase (VE-PTP) at hypoxia/ischemic. AKB-9778 is a known VE-PTP inhibitor that can effectively interact with the active site of VE-PTP to inhibit the activity of VE-PTP. However, the binding pattern of VE-PTP with AKB-9778 and the dynamic implications of AKB-9778 on VE-PTP system at the molecular level are poorly understood. Through molecular docking, it was found that the AKB-9778 was docked well in the binding pocket of VE-PTP by the interactions of hydrogen bond and Van der Waals. Furthermore, after molecular dynamic simulations on VE-PTP system and VE-PTP ^AKB-9778 system, a series of postdynamic analyses found that the flexibility and conformation of the active site undergone an obvious transition after VE-PTP binding with AKB-9778. Moreover, by constructing the RIN, it was found that the different interactions in the active site were the detailed reasons for the conformational differences between these two systems. Thus, the finding here might provide a deeper understanding of AKB-9778 as VE-PTP Inhibitor.     

Neon atoms oscillating inside carbon and boron nitride nanotubes: a fully atomistic molecular dynamics investigation

In the present work, based on extensive fully atomistic molecular dynamics simulations, we discuss the dynamics of neon atoms oscillating inside (5,5) single-walled carbon nanotubes (CNTs) and boron nitride nanotubes (BNNTs). Our results show that sustained high-frequency oscillatory regimes are possible for a large range of temperatures. Our results also show that the general features of the oscillations are quite similar to those observed in CNT and BNNT, in contrast with some speculations in previous works in the literature about the importance of broken symmetry and chirality exhibited by BNNTs.     

Discovery of promising FtsZ inhibitors by E-pharmacophore, 3D-QSAR,molecular docking study,and molecular dynamics simulation

Filamentous temperature-sensitive protein Z (FtsZ), playing a key role in bacterial cell division, is regarded as a promising target for the design of antimicrobial agent. This study is looking for potential high-efficiency FtsZ inhibitors. Ligand-based pharmacophore and E-pharmacophore, virtual screening and molecular docking were used to detect promising FtsZ inhibitors, and molecular dynamics simulation was used to study the stability of protein-ligand complexes in this paper. Sixty-three inhibitors from published literatures with pIC₅₀ ranging from 2.483 to 5.678 were collected to develop ligand-based pharmacophore model. 4DXD bound with 9PC was selected to develop the E-pharmacophore model. The pharmacophore models validated by test set method and decoy set were employed for virtual screening to exclude inactive compounds against ZINC database. After molecular docking, ADME analysis, IFD docking and MM-GBSA, 8 hits were identified as potent FtsZ inhibitors. A 50?ns molecular dynamics simulation was implemented on the compounds to assess the stability between potent inhibitors and FtsZ. The results indicated that the candidate compounds had a high docking score and were strongly combined with FtsZ by forming hydrogen bonding interactions with key amino acid residues, and van der Waals forces and hydrophobic interactions had significant contribution to the stability of the binding. Molecular dynamics simulation results showed that the protein-ligand compounds performed well in both the stability and flexibility of the simulation process.     

Prediction of chlortetracycline adsorption on the Fe3O4 nanoparticle using molecular dynamics simulation

Abstract

Molecular dynamics (MD) simulation was applied to investigate the adsorption mechanism of chlortetracycline (CTC) antibiotic molecule as the aqueous pollutant on the Fe₃O₄ nanoparticle (NP). Two different NP sizes with a diameter of about 1.4?nm and 3.5?nm were selected. Initially, the stability of both NPs in water was investigated by calculating radial distribution function curves of NP atoms. Simulation results confirmed the stable crystallographic structures of both NPs. However, small NP induce greater structural stabilization. Then, CTC molecules were adsorbed on NPs surface in various pollutant concentrations. Electrostatic and hydrogen bond were the major types of interactions between CTC molecules and the adsorbent surface. CTC molecules formed a complex with NP surface from their amine side chains; while they were parallel to each other in their aromatic rings and π-π bond between two CTC molecules was formed. Diffusion rate of CTC molecules could predict the adsorption mechanism. At lower concentration of CTC, CTC molecules tend to adsorb on the NP surface. At these concentrations, the diffusion rate of CTC was high. By increasing the CTC concentration, the pollutant agglomeration was enhanced which decreased the diffusion rate. At this time, the surface of NP was saturated. In addition, the results of isotherm curves showed that CTC adsorption on small NPs could be defined with both Langmuir and Freundlich isotherm models, while Freundlich isotherm model was more appropriate for larger NPs. In conclusion, observations confirmed that MD simulation could successfully predict the behavior of CTC adsorption on the Fe₃O₄ NP surface.

Communicated by Ramaswamy H. Sarma     

Effect of hydrogen coverage on the buckling of penta-graphene by molecular dynamics simulation

By employing a series of MD simulations, buckling behaviour of penta-graphene and functionalised penta-graphene having different hydrogen (H) coverage is presented in this study. To this end, the buckling onset strain is determined for different systems. The results reveal that the new allotrope is slightly stiffer than graphene. Moreover, the effect of H adatoms in the range 0–56% on buckling behaviour is investigated. Finally it is shown that the H coverage has an influence on stability, and ripple-type destortion of the penta-graphene under compression.