D mutations identified in this study are in blue. `*’ denotes residues that are identical in all sequences, `:’ denotes conserved substations and `.’ indicates semi-conserved substitutions. doi:10.1371/journal.pone.0067197.gFigure 3. Activity assay for ADPN hydrolysis. The reactions were performed at 35uC 150 rpm, for 30 min. 0.1 g/L purified nitrilase and 50 mM ADPN were added to 10 mL potassium phosphate (50 mM, pH 7.5). Error bars represent the standard deviation from three separate trials. doi:10.1371/journal.pone.0067197.gScreen and Application of Recombinant NitrilasesFigure 4. Comparison of wild-type nitrilases for IDAN hydrolytic activity in 50 mM potassium phosphate (pH 7.5) at 35uC for 2 h. The concentration of IDAN was 105 mM. The activity was assayed according to the standard methods. Error bars represent the standard deviation from three separate trials. doi:10.1371/journal.pone.0067197.g20 h and harvested by centrifugation (9,000 rpm, 20 min). Cells were washed twice with 0.9 (w/v) NaCl [23].Enzyme PurificationCell pellets were resuspended in 30 mL 50 mM potassium phosphate (pH 7.5) and lysed by Lycerol, and centrifugation at 12000g for 15 minutes before ultracentrifugation at 33000 rpm sonication. Lysate was clarified by centrifugation at 9,000 rpm for 20 min at 4uC and the supernatant was retained for purification. The soluble fraction was loaded onto a 10 mL Ni-NTA superflow Title Loaded From File column pre-equilibrated with 20 mM potassium phosphate, 300 mM sodium chloride (pH 8.0). The column was washed with 20 mM potassium phosphate, 300 mM sodium chloride, and 50 mM imidazole (pH 8.0) to remove any non-specifically bound proteins. The proteins were eluted with 20 mM potassium phosphate, 300 mM sodium chloride, and 500 mM imidazole (pH 8.0). All of these steps are under a constant flow rate of 1 mL/min at 4uC. Protein purification of the eluted fraction was assessed by sodium dodecyl sulfate polyacrylamide (SDS-PAGE) analysis, proteins bands were visualized with Coomassie brilliant blue R-250 [24].Figure 5. Structural analysis of AcN A) overlay of AcN (grey) overlay of PaN (red) with active site residues rendered as stick revealing nearly identical structural similarity. The non-overlapping regions are highlighted in yellow. B) Docking analysis of AcN with IDAN, dashed lines represent H-bonds (red), carbon atoms (green), hydrogen atoms (grey), nitrogen atoms (blue), oxygen atoms (red), and sulfur atoms (orange). C) Docking analysis of AcN with CCA, dashed lines represent H-bonds (red), carbon atoms (green), hydrogen atoms (grey), nitrogen atoms (blue), oxygen atoms (red), and sulfur atoms (orange). doi:10.1371/journal.pone.0067197.gCircular Dichroism (CD) MeasurementsCD spectra were recorded on a JASCO J-815 Spectropolarimeter (JASCO Corporation, Tokyo, Japan) using Spectra Manager 228 software with sensitivity of standard digital integration time (D.I.T) of 2 second, bandwidth of 3.00 nm. Far-UV scans were performed at 0.5 mM protein in 50 mM potassium phosphate (pH 7.5) in a 10-mm cuvette. The spectra were recorded from 200 nm to 250 nm with a scan speed of 100 nm/min at 25uC. Data were expressed as mean residue ellipticity ([h]mrw,l) (in degNcm2Ndmol21) as described previously [25]. Thermal denaturation of enzymes was followed as a function of temperature by continuously monitoring ellipticity changes at 222 nm using a step size of 0.4uC. The melting temperature (Tm) was calculated by taking the first order derivative of the sigmoidal curve obtained from the melting curve [26].at 150 r/min. ADPN was assayed using Agilent 6890.D mutations identified in this study are in blue. `*’ denotes residues that are identical in all sequences, `:’ denotes conserved substations and `.’ indicates semi-conserved substitutions. doi:10.1371/journal.pone.0067197.gFigure 3. Activity assay for ADPN hydrolysis. The reactions were performed at 35uC 150 rpm, for 30 min. 0.1 g/L purified nitrilase and 50 mM ADPN were added to 10 mL potassium phosphate (50 mM, pH 7.5). Error bars represent the standard deviation from three separate trials. doi:10.1371/journal.pone.0067197.gScreen and Application of Recombinant NitrilasesFigure 4. Comparison of wild-type nitrilases for IDAN hydrolytic activity in 50 mM potassium phosphate (pH 7.5) at 35uC for 2 h. The concentration of IDAN was 105 mM. The activity was assayed according to the standard methods. Error bars represent the standard deviation from three separate trials. doi:10.1371/journal.pone.0067197.g20 h and harvested by centrifugation (9,000 rpm, 20 min). Cells were washed twice with 0.9 (w/v) NaCl [23].Enzyme PurificationCell pellets were resuspended in 30 mL 50 mM potassium phosphate (pH 7.5) and lysed by sonication. Lysate was clarified by centrifugation at 9,000 rpm for 20 min at 4uC and the supernatant was retained for purification. The soluble fraction was loaded onto a 10 mL Ni-NTA superflow column pre-equilibrated with 20 mM potassium phosphate, 300 mM sodium chloride (pH 8.0). The column was washed with 20 mM potassium phosphate, 300 mM sodium chloride, and 50 mM imidazole (pH 8.0) to remove any non-specifically bound proteins. The proteins were eluted with 20 mM potassium phosphate, 300 mM sodium chloride, and 500 mM imidazole (pH 8.0). All of these steps are under a constant flow rate of 1 mL/min at 4uC. Protein purification of the eluted fraction was assessed by sodium dodecyl sulfate polyacrylamide (SDS-PAGE) analysis, proteins bands were visualized with Coomassie brilliant blue R-250 [24].Figure 5. Structural analysis of AcN A) overlay of AcN (grey) overlay of PaN (red) with active site residues rendered as stick revealing nearly identical structural similarity. The non-overlapping regions are highlighted in yellow. B) Docking analysis of AcN with IDAN, dashed lines represent H-bonds (red), carbon atoms (green), hydrogen atoms (grey), nitrogen atoms (blue), oxygen atoms (red), and sulfur atoms (orange). C) Docking analysis of AcN with CCA, dashed lines represent H-bonds (red), carbon atoms (green), hydrogen atoms (grey), nitrogen atoms (blue), oxygen atoms (red), and sulfur atoms (orange). doi:10.1371/journal.pone.0067197.gCircular Dichroism (CD) MeasurementsCD spectra were recorded on a JASCO J-815 Spectropolarimeter (JASCO Corporation, Tokyo, Japan) using Spectra Manager 228 software with sensitivity of standard digital integration time (D.I.T) of 2 second, bandwidth of 3.00 nm. Far-UV scans were performed at 0.5 mM protein in 50 mM potassium phosphate (pH 7.5) in a 10-mm cuvette. The spectra were recorded from 200 nm to 250 nm with a scan speed of 100 nm/min at 25uC. Data were expressed as mean residue ellipticity ([h]mrw,l) (in degNcm2Ndmol21) as described previously [25]. Thermal denaturation of enzymes was followed as a function of temperature by continuously monitoring ellipticity changes at 222 nm using a step size of 0.4uC. The melting temperature (Tm) was calculated by taking the first order derivative of the sigmoidal curve obtained from the melting curve [26].at 150 r/min. ADPN was assayed using Agilent 6890.
