The stability of enzymes is critical for their application in industrial processes, which generally require different conditions from the natural enzyme environment. Both rational and random protein engineering approaches have been used to increase stability, with the latter requiring extensive experimental effort for the screening of variants. Moreover, some general rules addressing the molecular origin of protein thermostability have been established. Herein, we demonstrate the use of molecular dynamics simulations to gain molecular level understanding of protein thermostability and to engineer stabilizing mutations. Carbonic anhydrase (CA) is an enzyme with a high potential for biotechnological carbon capture applications, provided it can be engineered to withstand the high temperature process environments, inevitable in most gas treatment units. In this study, we used molecular dynamics simulations at 343, 353, and 363 K to study the relationship between structure flexibility and thermostability in bacterial α-CAs and applied this knowledge to the design of mutants with increased stability. The most thermostable α-CA known, TaCA from Thermovibrio ammonificans, had the most rigid structure during molecular dynamics simulations, but also showed regions with high flexibility. The most flexible amino acids in these regions were identified from root mean square fluctuation (RMSF) studies, and stabilizing point mutations were predicted based on their capacity to improve the calculated free energy of unfolding. Disulfide bonds were also designed at sites with suitable geometries and selected based on their location at flexible sites, assessed by B-factor calculation. Molecular dynamics simulations allowed the identification of five mutants with lower RMSF of the overall structure at 400 K, compared to wild-type TaCA. Comparison of free-energy landscapes between wild-type TaCA and the most promising mutants, Pro165Cys-Gln170Cys and Asn140Gly, showed an increased conformational stability of the mutants at 400 K.
Palm oil mill effluent (POME) is a highly contaminating wastewater due to its high chemical oxygen demand (COD) and biochemical oxygen demand (BOD). Conventional treatment methods require longer residence time (10-15 days) and higher operating cost. Owing to this, finding a suitable and efficient method for the treatment of POME is crucial. In this investigation, ultrasound cavitation technology has been used as an alternative technique to treat POME. Cavitation is the phenomenon of formation, growth and collapse of bubbles in a liquid. The end process of collapse leads to intense conditions of temperature and pressure and shock waves which assist various physical and chemical transformations. Two different ultrasound systems i.e. ultrasonic bath (37 kHz) and a hexagonal triple frequency ultrasonic reactor (28, 40 and 70 kHz) of 15 L have been used. The results showed a fluctuating COD pattern (in between 45,000 and 60,000 mg/L) while using ultrasound bath alone, whereas a non-fluctuating COD pattern with a final COD of 27,000 mg/L was achieved when hydrogen peroxide was introduced. Similarly for the triple frequency ultrasound reactor, coupling all the three frequencies resulted into a final COD of 41,300 mg/L compared to any other individual or combination of two frequencies. With the possibility of larger and continuous ultrasonic cavitational reactors, it is believed that this could be a promising and a fruitful green process engineering technique for the treatment of POME.