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  • The discovery of proteases that are active in organic

    2019-07-11

    The discovery of proteases that are active in organic solvent media has greatly extended their ability in the synthesis of useful products. Microbial proteases which are able be catalyse in non-aqueous solvents present new expectation in enzyme applications. This kind of enzymes gives a major contribution in bioremediation industries because most of the environment pollutants can be classified as hydrophobic solvents and degradation of these solvents can be done by microorganisms [8]. Inactivation of the enzyme by organic solvents caused by various factors and possibilities including conformation change of proteins, decreased conformational flexibility, loss of crucial water, thermodynamic stabilization of the substrate ground state and interfacial inactivation [9]. The main cause for loss of enzyme activity is the loss of crucial water molecules that can restrain protein conformation mobility, disrupt hydrogen bond formation, and reduced enzyme substrate interactions [10]. Studies on the enzymes that are stable in the presence of organic solvents become an essential area in enzymology. Protein conformation in organic solvent media is critical to elucidate on the mechanism of the enzymes. Thus, the employments of X-ray crystallography and in silico study are definitely the perfect method to describe the behaviour of the enzyme. Having a three-dimensional structure of a protein at atomic level is important for several reasons such as enable to gather information about how protein works in biology; the function and the structure of a protein dictate what that protein is capable of doing. MD simulation of protein in the presence of organic solvents has provided various advantages such as analyses, based on stability and flexibility of the protein [11,12]. Some of information such as how active site of the enzyme respond to the interfacial activation also derive from the MD simulation where the lid of the enzyme can be seen in open or close confirmation [11]. The residue that play an important role in thermal 2-Cl-IB-MECA molecular or organic solvent tolerant (hydrophilic residue) also been reported by using in silico study [11,13,14]. The recombinant elastase from Pseudomonas aeruginosa strain K has demonstrated a stability and enhancement of the activity in hydrophilic organics solvents such as DMSO, methanol, ethanol and 1-propanol [15]. In order to discern its structural features as an organic solvent–stable enzyme and to see in silico interaction of the enzyme in organic solvent environment. The crystal structure of recombinant elastase strain K was successfully elucidated [16] and MD simulation was attempted. In this report, we present a structure refinement, elucidation and MD simulation of elastase strain K. Information obtained from the structural features and MD simulation of this enzyme would provide useful insight for rational design of enzymes suitable for future industrial application particularly involving biocatalysts in organic media.
    Experimental section
    Results and discussion
    Conclusion In this research, a crystal structure of elastase from P.aeruginosa strain K was solved and MD simulation was performed using the crystal structure, in order to study the properties of organic solvent tolerant enzyme. Crystal structure reveals that elastase from P.aeruginosa strain K is a zinc metalloproteinase enzyme by having a His-140, His-144 and Glu-164 served as a ligand for zinc ion. The crystal structure also shows that a conserve catalytic triad which are Glu-141, Tyr-155 and His-223. MD simulation of elastase from P.aeruginosa strain K with organic solvents showed a mixture of structural stability and flexibility. Elastase from P.aeruginosa strain K flexible conformation allows the enzyme to work in organic solvents. The active site of the enzymes remains unaffected make the zinc binding site and catalytic site for proteolytic activity available even in the presence of organic solvents. Increased in the helical strand and decreased in beta strand could promote the enzyme activity in organic solvents. Amino acid residues located at the surface such as Asp-48, Arg-108, Tyr-257, Pro-298 and disulfide bridge in Cys-30 to Cys-58 were responsible for enzyme stability in organic solvents. Stability and flexibility of elastase from P.aeruginosa strain K in organic solvents can provide various advantages in the industry that include promoting the synthesis of peptide bonds.