Ith acetonitrile (ACN), and dried in a vacuum centrifuge. After reduction (10 mM dithiothreitol in 100 mM NH4HCO3) and alkylation (10 iodoacetamide in 100 mM NH4HCO3), dried gel slices were incubated on ice for 15?0 minutes with Trypsin gold (12.5 ng/mL) in digestion buffer (50 mM NH4HCO3, 5 mM CaCl2). Excess buffer was removed and 20?0 mL of digestion buffer without Trypsin Gold was added to the gel slices followed by incubation at 37uC overnight. PeptidesIn-Vitro Translation with Unnatural Amino Acidswere extracted from the gel slices by washing once with 25 mM NH4HCO3, ACN and 1 formic acid (FA). The samples were then dried in a vacuum centrifuge. The extracted peptides were purified and concentrated using ZipTip pipette tips (Millipore), following the manufacturer’s instruction. ESI-MS/MS analysis was performed using reverse phase nanoLC (Agilent Technology) connected directly to the LTQ XL Orbitrap EDT mass spectrometer (Thermo Electron, Wien, Title Loaded From File Austria) at the Analytical Research Services Instrumentation Unit, BGU. The peptides were eluted with an increasing ACN gradient (Solvent A, 0.1 FA, 5 ACN; Solvent B, 0.1 FA, 80 ACN) over a period of 70 min. MS/MS spectra were acquired in a data-dependent fashion. Instrument control was performed using the Xcalibur software package (Thermo Electron). Theoretical monoisotopic masses for the peptides generated by trypsin digestion of WT GFP were predicted with PeptideMass (http://web.expasy.org/peptide_mass/), while fragmentation of the FSVSGEGEGDATYGK peptide and theoretical molecular masses of the peptide species were calculated with the MS-Product software at the ProteinProspector web service (http://prospector. ucsf.edu/prospector/cgi-bin/msform.cgi?form = msproduct). Theoretical molecular masses for peptides containing UAA were adjusted manually.the WT expression level was achieved at MjtRNACUA concentration of 600 mg/mL and of a tRNACUAOpt concentration of 480 mg/mL, respectively. This experiment revealed that the nature of suppressor tRNA significantly affects the efficiency of TAG nonsense suppression in recombinant proteins, while application of tRNACUAOpt allows one to reach at least similar protein yields as that of WT protein.The Effect of the Title Loaded From File Nucleotide following the Stop Codon on the Expression of UAA-containing ProteinsAs it is mentioned above, the TAG stop codon specifying the desired position for UAA incorporation into a recombinant protein could be recognized by either RF1 or by the cognate suppressor tRNA. It has been shown that the identity of the nucleotide following nonsense codon impinge on the selection rate of RF1 [12], i.e. a low rate of stop signal recognition by RF1 means that mRNA interaction with near-cognate aminoacyltRNA or frame-shifting occurs faster than does RF1 binding to the ribosomal A-site [12]. Based on the literature screened [17,19,22,25,26], we suggested that the forth nucleotide in tetranucleotide stop signal could affect the rate of nonsense suppression [12,13]. To verify this notion, we selected several amino acids in two different GFP b-sheets and their adjacent loop that were substituted to TAG, the location was selected in a way that afforded that the immediate nucleotide downstream from the stop codon differed from one location to another. Thus, we constructed plasmids encoding GFP Y39TAG, K41TAG, L42TAG and K45TAG mutants, where the amber codon was followed by a guanine (G), a cytosine (C), an adenine (A) and a thymine (T), respectivel.Ith acetonitrile (ACN), and dried in a vacuum centrifuge. After reduction (10 mM dithiothreitol in 100 mM NH4HCO3) and alkylation (10 iodoacetamide in 100 mM NH4HCO3), dried gel slices were incubated on ice for 15?0 minutes with Trypsin gold (12.5 ng/mL) in digestion buffer (50 mM NH4HCO3, 5 mM CaCl2). Excess buffer was removed and 20?0 mL of digestion buffer without Trypsin Gold was added to the gel slices followed by incubation at 37uC overnight. PeptidesIn-Vitro Translation with Unnatural Amino Acidswere extracted from the gel slices by washing once with 25 mM NH4HCO3, ACN and 1 formic acid (FA). The samples were then dried in a vacuum centrifuge. The extracted peptides were purified and concentrated using ZipTip pipette tips (Millipore), following the manufacturer’s instruction. ESI-MS/MS analysis was performed using reverse phase nanoLC (Agilent Technology) connected directly to the LTQ XL Orbitrap EDT mass spectrometer (Thermo Electron, Wien, Austria) at the Analytical Research Services Instrumentation Unit, BGU. The peptides were eluted with an increasing ACN gradient (Solvent A, 0.1 FA, 5 ACN; Solvent B, 0.1 FA, 80 ACN) over a period of 70 min. MS/MS spectra were acquired in a data-dependent fashion. Instrument control was performed using the Xcalibur software package (Thermo Electron). Theoretical monoisotopic masses for the peptides generated by trypsin digestion of WT GFP were predicted with PeptideMass (http://web.expasy.org/peptide_mass/), while fragmentation of the FSVSGEGEGDATYGK peptide and theoretical molecular masses of the peptide species were calculated with the MS-Product software at the ProteinProspector web service (http://prospector. ucsf.edu/prospector/cgi-bin/msform.cgi?form = msproduct). Theoretical molecular masses for peptides containing UAA were adjusted manually.the WT expression level was achieved at MjtRNACUA concentration of 600 mg/mL and of a tRNACUAOpt concentration of 480 mg/mL, respectively. This experiment revealed that the nature of suppressor tRNA significantly affects the efficiency of TAG nonsense suppression in recombinant proteins, while application of tRNACUAOpt allows one to reach at least similar protein yields as that of WT protein.The Effect of the Nucleotide following the Stop Codon on the Expression of UAA-containing ProteinsAs it is mentioned above, the TAG stop codon specifying the desired position for UAA incorporation into a recombinant protein could be recognized by either RF1 or by the cognate suppressor tRNA. It has been shown that the identity of the nucleotide following nonsense codon impinge on the selection rate of RF1 [12], i.e. a low rate of stop signal recognition by RF1 means that mRNA interaction with near-cognate aminoacyltRNA or frame-shifting occurs faster than does RF1 binding to the ribosomal A-site [12]. Based on the literature screened [17,19,22,25,26], we suggested that the forth nucleotide in tetranucleotide stop signal could affect the rate of nonsense suppression [12,13]. To verify this notion, we selected several amino acids in two different GFP b-sheets and their adjacent loop that were substituted to TAG, the location was selected in a way that afforded that the immediate nucleotide downstream from the stop codon differed from one location to another. Thus, we constructed plasmids encoding GFP Y39TAG, K41TAG, L42TAG and K45TAG mutants, where the amber codon was followed by a guanine (G), a cytosine (C), an adenine (A) and a thymine (T), respectivel.
