Molecular dynamics simulation of methane hydrate dissociation by depressurisation

Methane (CH₄) hydrate dissociation and the mechanism by depressurisation are investigated by molecular dynamics (MD) simulation. The hydrate decomposition processes are studied by the ‘vacuum removal method’ and the normal method. It is found that the hydrate decomposition is promoted by depressurisation. The quasi-liquid layer is formed in the hydrate surface layer. The driving force of dissociation is found to be controlled by the concentration gradient between the H₂O molecules of the hydrate surface layer and the H₂O molecules of the hydrate inner layer. The clathrates collapse gradually, and the hydrate decomposes layer by layer. Relative to our previous MD simulation results, this study shows that the rate of the hydrate dissociation by depressurisation is slower than that by the thermal stimulation and the inhibitor injection. This study illustrated that MD simulation can play a significant role in investigating the hydrate decomposition mechanisms.     

Dissociation mechanism of gas hydrates (I,II, H) of alkane molecules: a comparative molecular dynamics simulation

Employing NPT molecular dynamics method with consistent valence force field, the dissociation processes of sI, sII and sH gas hydrates are simulated at different temperatures and at a constant pressure of 100 MPa. The dissociation mechanisms of gas hydrates are revealed by analysing the structural snapshots, radial distribution functions and diffusion coefficients at different temperatures. As temperature increases, the diffusion rates of water molecules and guest molecules increase; thus the clathrate skeleton formed by water molecules with hydrogen bonds distorts and breaks down; meanwhile the guest molecules encapsulated in the water cavities are released. The size of guest molecules affects the dissociation behaviour of gas hydrate. In addition, the dissociation behaviour also relies on the structural phase of gas hydrates.     

Molecular dynamics simulation of replacement of methane hydrate with carbon dioxide

Molecular dynamics simulation was performed to analyse the phenomena of replacement of methane hydrate with carbon dioxide (CO₂) at 270 K and 5.0 MPa for 5300 ps. The methane hydrate phase was constructed with 16 unit cells of hydrate. Every cage in the hydrate was occupied by one methane molecule. The methane hydrate phase was sandwiched between two CO₂ phases. During the simulation the hydrate partially melted and liquid water phase appeared, and CO₂ dissolved in the liquid water phase. The replacements were observed three times at the hydrate–liquid water interface during the simulation. In the first case, the replacement occurred at a S-cage without changing the structure. In the second case, an M-cage of methane hydrate partially collapsed, and methane and CO₂ molecules exchanged. After the exchange, the cage occupied by CO₂ remained in the M-cage structure. In the third case, a S-cage of methane hydrate partially collapsed, and methane and CO₂ molecules exchanged. After the exchange, the cage occupied by CO₂ changed to an M-cage-like structure.     

Calculation of diffusion coefficient for supercritical carbon dioxide and carbon dioxide+naphthalene system by molecular dynamics simulation using EPM2 model

NVT ensemble molecular dynamics (MD) simulation has been applied to calculate the self-diffusion coefficients of carbon dioxide and the tracer diffusion coefficients of naphthalene in supercritical carbon dioxide. The simulation was carried out in the pressure range from 8 to 40 MPa. The elementary physical model proposed by Harris and Yung was adopted for carbon dioxide and some approximation models were used for naphthalene. The systems of MD simulation for carbon dioxide consist of 256 particles. One naphthalene molecule was added for carbon dioxide+naphthalene system. The system can be assumed to be an infinite dilution condition for carbon dioxide+naphthalene system and the mutual diffusion coefficients are equal to the tracer diffusion coefficients of naphthalene. The self-diffusion coefficients of carbon dioxide and the tracer diffusion coefficients of naphthalene in supercritical carbon dioxide can be calculated by mean square displacement. The calculated results of diffusion coefficients showed good agreement with the experimental data without adjustable parameters.     

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     

Dynamic properties of methane,water and methane hydrates using computational simulations

In this study, the vibrational spectrum of methane hydrates is calculated through dynamic molecular simulations based on two different methods. The spectra obtained using the proposed procedure allow the differentiation of the contributions of different inter- and intramolecular motion types in the spectrum, which cannot be produced with the traditional method based on atomic velocities. Simulations were carried out at different composition, pressure and temperature conditions to observe the effect of these variables on the vibrational spectrum. The proposed method allowed the observation of a difference in the frequencies for the C–H stretching vibrations between small and large cavities, which agrees with reported experimental values.     

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.     

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.     

Replica-exchange molecular dynamics simulation for understanding the initial process of amyloid peptide aggregation

We applied replica-exchange molecular dynamics simulation to five fragments of amyloid-β peptide in order to study the mechanism of amyloid fibril formation. In this study, we calculated the free energy by focusing on how to form the β-structures to obtain the dominant structures. We classify the obtained β-structures and elucidate the order of β-structure assembly.     

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.     

Implicit solvent models for flexible protein-protein docking by molecular dynamics simulation

The suitability of three implicit solvent models for flexible protein-protein docking by procedures using molecular dynamics simulation is investigated. The three models are (i) the generalized Born (GB) model implemented in the program AMBER6.0; (ii) a distance-dependent dielectric (DDD) model; and (iii) a surface area-dependent model that we have parameterized and call the NPSA model. This is a distance-dependent dielectric model modified by neutralizing the ionizable side-chains and adding a surface area-dependent solvation term. These solvent models were first tested in molecular dynamics simulations at 300 K of the native structures of barnase, barstar, segment B1 of protein G, and three WW domains. These protein structures display a range of secondary structure contents and stabilities. Then, to investigate the performance of the implicit solvent models in protein docking, molecular dynamics simulations of barnase/barstar complexation, as well as PIN1 WW domain/peptide complexation, were conducted, starting from separated unbound structures. The simulations show that the NPSA model has significant advantages over the DDD and GB models in maintaining the native structures of the proteins and providing more accurate docked complexes.     

Targeted molecular dynamics simulation studies of binding and conformational changes in E. coli MurD

Enzymes involved in the biosynthesis of bacterial peptidoglycan, an essential cell wall polymer unique to prokaryotic cells, represent a highly interesting target for antibacterial drug design. Structural studies of E. coli MurD, a three-domain ATP hydrolysis driven muramyl ligase revealed two inactive open conformations of the enzyme with a distinct C-terminal domain position. It was hypothesized that the rigid body rotation of this domain brings the enzyme to its closed active conformation, a structure, which was also determined experimentally. Targeted molecular dynamics 1 ns-length simulations were performed in order to examine the substrate binding process and gain insight into structural changes in the enzyme that occur during the conformational transitions into the active conformation. The key interactions essential for the conformational transitions and substrate binding were identified. The results of such studies provide an important step toward more powerful exploitation of experimental protein structures in structure-based inhibitor design.     

The mechanism for the complexation and dissociation between siRNA and PMAL: a molecular dynamics simulation study based on a coarse-grained model

Abstract

The capacity of silencing genes makes small interfering RNA (siRNA) becomes potential candidates for curing many fatal diseases. Due to the low stability and delivery efficiency of siRNA, the design of amphiphilic carrier for siRNA delivery is vital for the practical gene therapy. In the present work, we explored how the complexation and dissociation of siRNA with poly (maleic anhydride-alt-1-decene) substituted with 3-(dimethylamino) propylamine (PMAL), which is a recent synthesised amphiphilic polymer and can be used in delivery of siRNAs and proteins, using traditional molecular dynamics simulations, together with steered molecular dynamics simulations. It was shown that the complexation of siRNA with PMALs can spontaneously occur, no matter what unit number of PMAL is. PMALs of different unit numbers form micelle-like structures and interact with siRNA surface. With the increase of unit number, PMAL becomes more flexible and interacts with siRNA from attachment to entanglement. The dissociation of PMAL from siRNA is an energy-consuming process. The free energy difference increases with the unit number of PMAL. The free energy for dissociation involves both the stretch of PMAL and the separation of PMAL from siRNA. Therefore, an optimal unit number of PMAL is critical for the delivery efficiency of siRNA when PMAL is used as carrier. In present work, when the radius of gyration of PMAL approaches to that of siRNA, PMAL gives a favoured both complexation and dissociation between siRNA and PMAL. Finally, we propose the mechanism of complexation and dissociation of PMAL with siRNA. The above simulation established a molecular insight of the interaction between siRNA and PMAL and was helpful for the design and applications of new PMAL-based polymers as siRNA delivery carriers.     

Ab initio DFT study of structural and mechanical properties of methane and carbon dioxide hydrates

The structural and mechanical properties of methane and carbon dioxide hydrates were investigated using density functional theory simulations. Well-established equations of state of solids and exchange-correlation functionals were used for fitting the unit lattice total energy as a function of volume, and the full second-order elastic constants of these two gas hydrates were determined by energy–strain analyses. The polycrystalline elastic properties were also calculated from the unit lattice results. The final results for methane hydrate agree well with available experimental data and with other theoretical results. The two gas hydrates were found to be highly elastically isotropic, but they differed significantly in shear properties. The presented results for carbon dioxide hydrates are the first complete set reported so far. The results are a significant contribution to the ab initio material characterisation of gas hydrates required for ongoing fundamental studies and technological applications.     

Understanding interaction and dynamics of water molecules in the epoxy via molecular dynamics simulation

The robust structural integrity of the epoxy plays an important role in ensuring the long-term service life of its applications, which is affected by the absorbed moisture. In order to understand the mechanism of the moisture effect, the knowledge of the interaction and dynamics of the water molecules inside the epoxy is of great interest. Molecular dynamics simulation is used in this work to investigate the structure and bonding behaviour of the water molecules in the highly cross-linked epoxy network. When the moisture concentration is low, the water molecules are well dispersed in the cross-linked structure and located in the vicinity of the epoxy functional groups, which predominantly form the hydrogen bond (H-bond) with the epoxy network, resulting in the low water mobility in the epoxy. At the high concentration, the water favourably forms the large cluster due to the predominant water–water H-bond interaction, and the water molecules diffuse primarily inside the cluster, which leads to the high water mobility and the accelerated H-bond dynamics. The variation of the bonding behaviour and dynamics of the water molecules reported here could be exploited to understand the material change and predict the long-term performance of the epoxy-based products during the intended service life.     

A steered molecular dynamics method with direction optimization and its applications on ligand molecule dissociation

In this paper, a steered molecular dynamics method with pulling direction optimization is proposed to dissociate ligand molecule from receptor. A multi-population genetic algorithm based on the information entropy is developed to search the optimal pulling direction. By imposing an optimization phase in the conventional steered molecular dynamics simulation, a better substrate-exit channel for the buried active site can be found. The novel simulation method has been used to dissociate the substrate-bound complex structure of cytochrome P450 3A4-metyrapone. The results show that the new pathway obtained by the proposed method has advantages such as lower energy barrier, less dissociation time and shorter motion trajectory than that by the conventional steered molecular dynamics.     

Investigation of the role of disulphide bond in modulating internal motions of BmK AGAP protein by molecular dynamics simulation

Elucidating structural determinants in the functional regions of toxins can provide useful knowledge for designing novel analgesic peptides. A series of 100 ns MD simulations were performed on the scorpion toxin BmK AGAP in native and disulphide bond broken states. The comparison of disulphide bond broken states with the native state showed the α-helix was found to be the key to the analgesic activity. Furthermore, our results revealed disulphide bonds have considerable influence on the functionally important essential modes of motions and the correlations between the motions of the Core domain and the C-terminal region which are involved in the analgesic activity. Therefore, we can conclude that disulphide bonds have a crucial role in modulating the function via adjusting the dynamics of scorpion toxin BmK AGAP molecule.     

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.     

On using time-averaging restraints in molecular dynamics simulation

Introducing experimental values as restraints into molecular dynamics (MD) simulations to bias the values of particular molecular properties, such as nuclear Overhauser effect intensities or distances, 3J coupling constants, chemical shifts or crystallographic structure factors, towards experimental values is a widely used structure refinement method. To account for the averaging of experimentally derived quantities inherent in the experimental techniques, time-averaging restraining methods may be used. In the case of structure refinement using 3J coupling constants from NMR experiments, time-averaging methods previously proposed can suffer from large artificially induced structural fluctuations. A modified time-averaged restraining potential energy function is proposed which overcomes this problem. The different possible approaches are compared using stochastic dynamics simulations of antamanide, a cyclic peptide of ten residues.