Baolin Liu

Predict the glass transition temperature of glycerol–water binary cryoprotectant by molecular dynamic simulation☆

Vitrification is proposed to be the best way for the cryopreservation of organs. The glass transition temperature (T(g)) of vitrification solutions is a critical parameter of fundamental importance for cryopreservation by vitrification. The instruments that can detect the thermodynamic, mechanical and dielectric changes of a substance may be used to determine the glass transition temperature. T(g) is usually measured by using differential scanning calorimetry (DSC). In this study, the T(g) of the glycerol-aqueous solution (60%, wt/%) was determined by isothermal-isobaric molecular dynamic simulation (NPT-MD). The software package Discover in Material Studio with the Polymer Consortium Force Field (PCFF) was used for the simulation. The state parameters of heat capacity at constant pressure (C(p)), density (rho), amorphous cell volume (V(cell)) and specific volume (V(specific)) and radial distribution function (rdf) were obtained by NPT-MD in the temperature range of 90-270K. These parameters showed a discontinuity at a specific temperature in the plot of state parameter versus temperature. The temperature at the discontinuity is taken as the simulated T(g) value for glycerol-water binary solution. The T(g) values determined by simulation method were compared with the values in the literatures. The simulation values of T(g) (160.06-167.51K) agree well with the DSC results (163.60-167.10K) and the DMA results (159.00K). We drew the conclusion that molecular dynamic simulation (MDS) is a potential method for investigating the glass transition temperature (T(g)) of glycerol-water binary cryoprotectants and may be used for other vitrification solutions.

Molecular simulation of β-cyclodextrin inclusion complex with 2-phenylethyl alcohol

The structures of β-cyclodextrin inclusion complexes with 2-phenylethyl alcohol in vacuum and aqueous solution have been investigated by using molecular dynamics simulation. The inclusion structures and the physicochemical stability of the complexes were also analysed, discussed and validated by ultraviolet spectrums and thermodynamic properties. The results of molecular dynamics simulation indicate that the A-type β-cyclodextrin inclusion complex with 2-phenylethyl alcohol in both vacuum and aqueous solution have better physical stability, and its chemical stability also has obvious promotion than that of free one. Therefore, the β-cyclodextrin can be used to control and regulate the release of the 2-phenylethyl in food.

A molecular simulation study of the protection of insulin bioactive structure by trehalose

AbstractBiopharmaceuticals are proteins with a crucial role in the treatment of many diseases. However, these protein medicines are often thermally labile and therefore unsuitable for long-term application and storage, as they tend to lose their activity under ambient conditions. Desiccation is one approach to improving protein stability, but the drying process itself can cause irreversible damage. In the current study, insulin was chosen as an example of a thermally sensitive biopharmaceutical to investigate whether the disaccharide, trehalose, can prevent loss of structural integrity due to drying. The experiment was performed using replica exchange molecular simulation and Gromacs software with a Gromos96 (53a6) force field. The results indicate that trehalose preserves the bioactive structure of insulin during drying, consistent with the use of trehalose as a protectant for thermally sensitive biopharmaceuticals. For instance, at the water content of 1.77xa0%, insulin without any protectants yields the highest RMSD value as 0.451xa0nm, then the RMSD of insulin in presence of trehalose only ca. 0.100xa0nm.n Graphical AbstractProtection of insulin bioactive structure by trehalose: Native crystal structure of insulin (A, PDBID: 3inc), structure of dried insulin without any protectant (B), structure of dried insulin with trehalose (C), all of them are shown in the solid ribbon style with helices in red, turns in green and coils in gray. In contrast, insulin structures are completely reserved in the presence of trehalose. The tertiary structure of dried insulin with trehalose is remarkably similar to the native structure. These results indicate that, as trehalose maintains insulin structure in the dry state, it should also prevent the protein from losing its bioactivity.

A novel method to predict the glass transition of 70% glycerol aqueous solution

Vitrification has been used to successfully cryopreserve cells and tissues for over 60 years. Glass transition temperature (T g) of the vitrification is a critical parameter, which has been investigated experimentally. In this study, an isothermal–isobaric molecular simulation (NPT-MD) is proposed to investigate the glass transition and T g of such vitrification solution. The cohesive energy density, solubility parameter (δ) and bulk modulus of the solution during the process of the glass transition are investigated as well. The results indicate that these properties as functions of temperature can give a definite inflexion; thus, these properties can be used to predict T g more accurately than the heat capacity (C p ), density (ρ), volume (V) and radial distribution function (rdf). At the same time, the predicted values of T g agree well with the experimental results. Therefore, molecular dynamics simulation is a potential method for investigating the glass transition and T g of the vitrification solutions.

The binding affinity of human serum albumin and paclitaxel through MMPBSA based on docked complex

Abstract The distribution, free concentration and metabolism of drugs can be significantly altered as a result of binding to albumin. At the same time, the conformational of serum albumin was also changed by interaction with low molecular weight drugs. In present work, we first equilibrated HSA in aqueous solution to obtain the solvated-HSA model. Further solvated-HSA was performed molecular docking with paclitaxel to find the binding sites. The two docking HSA-paclitaxel complexes were obtained and further equilibrated by a 12 ns MD simulation. Then, MMPBSA method was used to investigate the binding free energy of them. Finally, we correlated the fluctuations of residues with corresponding changes in the secondary structure by dssp method. Two binding sites of paclitaxel were found on HSA having considered the solvation effect. More hydrogen bonds were formed at site I respected to site II. A larger binding energy for primary binding also indicated that paclitaxel showed higher binding affinity mainly due to the stronger hydrogen bonding interactions. There was a significant difference between the two complexes on structure according to the dssp results. Moreover, structure of the binding sites exhibited more fluctuations after binding paclitaxel compared with other regions. Paclitaxel binding also induced distinct conformational changes in drug binding site even when it was empty and have contributed to a reduced binding capacity of HSA towards adriamycin.

Effect of Solvent Water Molecules on Human Serum Albumin Complex-Docked Paclitaxel by MM-PBSA Method.

Molecular modeling on solvation effect and interaction mechanism of the water molecules in the active site of protein affect significantly the interaction between protein and ligand. Detailed influence of water molecules in the active site of human serum albumin (HSA) on its paclitaxel complex as well as their interaction is essential for clinical studies. Molecular docking of both crystal-HSA and solvated-HSA with paclitaxel was performed in the present work. The docking result shows that paclitaxel is inserted more deeply in the binding pocket of crystal-HSA than in the same site of solvated-HSA, and more intermolecular H-bonds are formed in the shrunken binding site of solvated-HSA. The favorable docking energies also reflect that solvated-HSA model is more tightly integrated with paclitaxel than crystal-HSA. According to the MD results of solvated-HSA-paclitaxel, six intermolecular H-bonds have formed at the binding site, two of them linking with the water molecules. It proves that water molecules in the binding site have affected the interaction between protein and ligand significantly. The MD results for the two complexes also suggest that the solvated protein model will lead to a rather different binding complex.

Investigation and optimisation of the drying of reduced glutathione by steered molecular dynamics simulation

The drying of reduced glutathione from a series of aqueous–ethanol binary solutions at 300 K (below human body temperature) and 330 K (above human body temperature) was investigated in detail by steered molecular simulation and an umbrella sampling method with the Gromacs software package and Gromos96(53a6) united atomic force field. The results show that electrostatic interactions between glutathione and solvent represent the main resistance to drying. When the aqueous solution was gradually changed to pure ethanol, the energy of electrostatic interaction between glutathione and solvent molecules increased by 445.088 kJ/mol, and the drying potential of mean force (PMF) free energy also fell by 253.040 kJ/mol. However, an increase in temperature from 300 to 330 K in the aqueous solution only results in an increase of 23.013 kJ/mol in electrostatic interaction energy and a decrease of 34.956 kJ/mol in drying PMF free energy. Furthermore, we show that hydrogen bonding is the major form of electrostatic interaction involved, and directly affects the drying of glutathione. Therefore, choosing water-miscible solvents that minimise hydrogen-bond formation with glutathione will enhance its drying rate, and this is likely to be more efficient than increasing the temperature of the process. Thus, a power-saving technology can be used to produce the high bioactivity medicines.

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.

Thermal Properties of PVP Cryoprotectants With Nanoparticles

Vitrification is an effective way for the cryopreservation of cells and tissues. The critical cooling rates for vitrification solution are relatively high. It is reported that nanoparticles can improve the heat tranfer properties of solutions. To increase the heat transfer coefficient of aqueous cryoprotectant solutions, HA nanoparticles were added into PVP solutions (50%, 55%, 60%, w/w). The glass transition temperature, devitrification temperature and specific heat of PVP aqueous solutions with/without HA nanoparticles (0.1%, 0.5% and 1%, w/w) were measured by differential scanning calorimeter (DSC) at the cooling rate of 20°C/min and warming rate of 10°C/min. The change of density of above solutions with temperature was determined by using a straw that can reveal the volume change of solutions. The thermal conductivity was calculated based on the experimental data. A device that can be used to measure the thermal conductivity of vitrification solutions with/without nanoparticles was developed in this study. The results showed that the glass transition temperature, devitrification temperature and specific heat of PVP aqueous solutions with HA nanoparticles are larger than that without HA nanoparticles. The thermal conductivity of solutions with HA nanoparticles is larger than that without HA nanoparticles at a specific temperature. The lower the temperature, the smaller the difference of thermal conductivity between solutions with and without HA nanoparticles. The calculated thermal conductivity meets the measured data well.Copyright