Atomevo: a web server combining protein modelling, docking, molecular dynamic simulation and MMPBSA analysis of Candida antarctica lipase B (CalB) fusion protein.

Although current computational biology software is available and has prompted the development of enzyme-substrates simulation, they are difficult to install and inconvenient to use. This makes the time-consuming and error-prone process. By far there is still a lack of a complete tool which can provide a one-stop service for the enzyme-substrates simulation process. Hence, in this study, several computational biology software was extended development and integrated as a website toolbox named Atomevo. The Atomevo is a free web server providing a user-friendly interface for enzyme-substrates simulation: (1) protein homologous modeling; (2) parallel docking module of Autodock Vina 1.2; (3) automatic modeling builder for Gromacs molecular dynamics simulation package; and (4) Molecular Mechanics/Poisson-Boltzmann Surface Area (MMPBSA) analysis module for receptor-ligand binding affinity analysis. We officially launched the web server and provided instructions through a case for the design and simulation of Candida antarctica lipase B (CalB) fusion protein called Maltose Binding Protein-Thioredoxin A-Candida antarctica lipase B (MBP-TrxA-CalB).

Molecular Dynamic Simulation of the Porcine Pancreatic Lipase in Non-aqueous Organic Solvents.

This paper investigates the conformational stability of porcine pancreatic lipase (PPL) in three non-aqueous organic solvents, including dimethyl sulfoxide (DMSO), propylene glycol (PRG), and ethanol (EtOH) through molecular dynamic (MD) simulation. The root mean square deviations (RMSDs), radius of gyration (Rg), solution accessible surface area (SASA), radial distribution function (RDF), hydrogen bond (H-bond), Ramachandran plot analysis, secondary structure, and enzyme substrate affinity of the PPL in the various organic solvents were comparatively investigated. The results showed that the backbone and active pocket RMSD, and hydrophilic ASA of PPL in three solvents increase with the increase in the solvent LogP, while the Rg, hydrophobic ASA, and H-bond between the solvent and PPL decrease. Among the three organic solvents, DMSO acts as a better solvent, in which the PPL can be loose and extended, and retains its native backbone in DMSO compared to PRG and EtOH. Moreover, Ramachandran plot analysis indicated that the PPL structure quality in DMSO was higher than that in PRG and EtOH. Also, the molecular docking results showed that PPL in DMSO exhibited the highest enzyme-substrate affinity.

Operation of a vertical algal biofilm enhanced raceway pond for nutrient removal and microalgae-based byproducts production under different wastewater loadings.

In this study, a vertical-algal-biofilm-enhanced raceway pond (VAB-enhanced raceway pond) was designed and assessed for wastewater treatment and algal biomass production under different nutrient loading rates. Results indicated that the maximum removal capacity of the system was accordingly 7.52, 6.76 and 0.11 g·m-2·day-1 for COD, TN and TP, under which the wastewater effluent concentration could be respectively reduced from 106.00, 92.71 and 1.48 mg/L to 43.5, 11.03 and 0.46 mg/L in continuous mode. Meanwhile, about 7.47-10.10 t·ha-1·year-1 of lipid, 14.85-23.01 t·ha-1·year-1 of protein and 10.69-14.20 t·ha-1·year-1 of carbohydrate could be produced from the algae by the system in large scale. The corresponding estimated stoichiometric-methane-potential and biodiesel production of the harvested biomass was 21,471-29,136 m3·ha-1·year-1 and 0.57-1.15 t·ha-1·year-1, respectively. The findings of this study demonstrate the feasibility of using VAB-enhanced raceway pond for economically and cost-effectively recovery of nutrients from the wastewater via algal-based byproducts production.