AmHI Epigenetic Reader Domain cloning. Mutation of Zarvin yielding a D72C mutant was performed using a Quik-ChangeH kit (Stratagene). The respective primers used for mutation were forward 59 GGCAGCATGACCTGTCTGCTGAGC 39 and reverse 59 GCTCAGCAGACAGGTCATGCTGCC 39. Recombinant Zarvin was expressed as GST fusion protein. Expression was performed in E. coli BL21(DE3)T1r cells. For that, after cells were grown up to OD 0.6 in 26 YT medium at 37uC protein expression was induced with 0.2 mM IPTG. Expression was performed for another 5 h at 29uC. Bacteria pellets were suspended in 20 mM Tris, 50 mM NaCl, pH 10457188 7.4 and cells were cracked via lysozyme treatment for 1 h at 4uC following sonication at room temperature. The supernatant of subsequent ultracentrifugation was bound to a 20 ml GSTrap column (GE Healthcare) using a BioRad FPLC at 4uC. Bound protein was washed with three buffers to remove unwanted components. First, a high saltAnalytical GelfiltrationGelfiltration experiments were performed using a Superdex 75 10/300 GL or a Superdex 75 16/26 column (GE Healthcare) and a BioRad FPLC at 4uC. For Autophagy calibrating the column AlphaAmylase (porcine pancreas), Ovalbumin (Sigma), GAPDH from rabbit muscle (Sigma), Chymotrypsinogen A from bovine pancreas and Lysozyme (Fluka) were used. Runs were performed at 0.5 ml/ min in 20 mM Tris, 500 mM NaCl, pH 7.4 and 20 mM Tris, 200 mM NaCl, 3 M guanidine hydrochloride, pH 7.4.Protein Concentration DeterminationProtein concentrations of stock solutions were determined by measuring the absorbance of the solution at 280 nm or 258 nm, respectively, using a NanoDrop ND 1000 (peqlab). 1315463 Absorbance was measured at least three times and averaged following concentration determination using an extinction coefficient of 1490 M21cm21 for Zarvin as well as for the Z domain and 217315 M21cm21 for Cetuximab. Parvalbumin concentrations were determined by measuring the absorbance at 258 nm and using an extinction coefficient of 1512 M21cm21, which is the sum of the absorbances of eight phenylalanine residues. It was calculated with an absorbance of 189 M21cm21 at 258 nm for one phenylalanine [29]. Exact protein concentrations of samples where CD spectra were recorded from were measured using a Cary 100 UV/Vis spectrophotometer.Modular Contrast AgentCD SpectroscopyCD spectroscopy was performed using a JASCO J815 CD spectrometer. For recording of spectra Zarvin was diluted in 20 mM Natrium phosphate buffer, pH 7.4 at a final concentration of approximately 0.15 mg/ml and using a 1 mm cuvette. CD spectra were recorded from 200?60 nm. Further parameters were data pitch: 0.2 nm, scanning mode: continuous, scanning speed: 100 nm/min, response time: 0.5 s, bandwidth: 2 nm. 15 scans were averaged for each spectrum. Spectra were recorded at room temperature. Data processing was performed by separately shifting the blank and the protein spectrum to zero for the wavelengths 250?60 nm and subsequent subtraction of the blank spectrum from the protein spectrum. Afterwards, the mdeg units of the spectrum were transformed to De MRW units using a mean residue weight (MRW) of 107.091 Da for Zarvin and the spectroscopically determined concentration of the protein in mg/ml units. These data processing steps were performed using unpublished software (Steve Martin, NIMR London). Secondary structure contents of Zarvin were calculated using the programs CDSSTR, Contin ll and Selcon 3. The complete range of secondary structure contents calculated by the three programs is displayed i.AmHI cloning. Mutation of Zarvin yielding a D72C mutant was performed using a Quik-ChangeH kit (Stratagene). The respective primers used for mutation were forward 59 GGCAGCATGACCTGTCTGCTGAGC 39 and reverse 59 GCTCAGCAGACAGGTCATGCTGCC 39. Recombinant Zarvin was expressed as GST fusion protein. Expression was performed in E. coli BL21(DE3)T1r cells. For that, after cells were grown up to OD 0.6 in 26 YT medium at 37uC protein expression was induced with 0.2 mM IPTG. Expression was performed for another 5 h at 29uC. Bacteria pellets were suspended in 20 mM Tris, 50 mM NaCl, pH 10457188 7.4 and cells were cracked via lysozyme treatment for 1 h at 4uC following sonication at room temperature. The supernatant of subsequent ultracentrifugation was bound to a 20 ml GSTrap column (GE Healthcare) using a BioRad FPLC at 4uC. Bound protein was washed with three buffers to remove unwanted components. First, a high saltAnalytical GelfiltrationGelfiltration experiments were performed using a Superdex 75 10/300 GL or a Superdex 75 16/26 column (GE Healthcare) and a BioRad FPLC at 4uC. For calibrating the column AlphaAmylase (porcine pancreas), Ovalbumin (Sigma), GAPDH from rabbit muscle (Sigma), Chymotrypsinogen A from bovine pancreas and Lysozyme (Fluka) were used. Runs were performed at 0.5 ml/ min in 20 mM Tris, 500 mM NaCl, pH 7.4 and 20 mM Tris, 200 mM NaCl, 3 M guanidine hydrochloride, pH 7.4.Protein Concentration DeterminationProtein concentrations of stock solutions were determined by measuring the absorbance of the solution at 280 nm or 258 nm, respectively, using a NanoDrop ND 1000 (peqlab). 1315463 Absorbance was measured at least three times and averaged following concentration determination using an extinction coefficient of 1490 M21cm21 for Zarvin as well as for the Z domain and 217315 M21cm21 for Cetuximab. Parvalbumin concentrations were determined by measuring the absorbance at 258 nm and using an extinction coefficient of 1512 M21cm21, which is the sum of the absorbances of eight phenylalanine residues. It was calculated with an absorbance of 189 M21cm21 at 258 nm for one phenylalanine [29]. Exact protein concentrations of samples where CD spectra were recorded from were measured using a Cary 100 UV/Vis spectrophotometer.Modular Contrast AgentCD SpectroscopyCD spectroscopy was performed using a JASCO J815 CD spectrometer. For recording of spectra Zarvin was diluted in 20 mM Natrium phosphate buffer, pH 7.4 at a final concentration of approximately 0.15 mg/ml and using a 1 mm cuvette. CD spectra were recorded from 200?60 nm. Further parameters were data pitch: 0.2 nm, scanning mode: continuous, scanning speed: 100 nm/min, response time: 0.5 s, bandwidth: 2 nm. 15 scans were averaged for each spectrum. Spectra were recorded at room temperature. Data processing was performed by separately shifting the blank and the protein spectrum to zero for the wavelengths 250?60 nm and subsequent subtraction of the blank spectrum from the protein spectrum. Afterwards, the mdeg units of the spectrum were transformed to De MRW units using a mean residue weight (MRW) of 107.091 Da for Zarvin and the spectroscopically determined concentration of the protein in mg/ml units. These data processing steps were performed using unpublished software (Steve Martin, NIMR London). Secondary structure contents of Zarvin were calculated using the programs CDSSTR, Contin ll and Selcon 3. The complete range of secondary structure contents calculated by the three programs is displayed i.
