The largest database of trusted experimental protocols

8 protocols using ppsq 21

1

Protein Sequencing Using Edman Degradation

Check if the same lab product or an alternative is used in the 5 most similar protocols
Edman degradation for the N-terminal and enzyme digests of SOR was carried out using automated gas phase protein sequencer PPSQ-21 (Shimadzu). A sample of semi-pure SOR was separated on a SDS-PAGE, blotted to PVDF membrane, and then the membrane was stained with Ponceau S solution. The membrane with a band at 120 kDa was cut and subjected to N-terminal sequence analysis. For internal amino acid sequence analysis, the 120 kDa band on the membrane was reduced by dithiothreitol and then treated with iodoacetic acid and 1 M NaOH (10 µL) for 20 min. The membrane was thoroughly washed with water then with acetonitrile (2%), and finally immersed in a buffer (20 mM Tris HCl with acetonitrile 70%). Finally Actomobacter protease I (Wako pure chemical, Tokyo, 1 µg in 50 µL buffer) was added and the mixture was stood overnight at room temperature. The digest was separated on a reversed-phase HPLC (Cadenza CD-C18, Imtakt, 0.05% TFA-acetonitrile 0.05%, gradient). Each peak (215 nm) was concentrated and dissolved in 5 µL of water and the same amount of MeOH. The enzyme digest was absorbed on a PVDF membrane for the sequence analysis.
+ Open protocol
+ Expand
2

Protein Sequence Determination by V8 Protease Digestion

Check if the same lab product or an alternative is used in the 5 most similar protocols
To determine the partial amino acid sequences of sample proteins, in-gel digestion was performed according to the method of Cleveland et al. (1977) (link) using Staphylococcus aureus V8 protease (Fujifilm Wako Pure Chemical Industries, Ltd.) as described previously (Maehashi et al., 2007 (link)). After electroblotting onto a PVDF membrane (Bio-Rad Laboratories, Hercules, CA, USA), the separated band of a proteolytic fragment was excised from the membrane and subjected to amino (N)-terminal sequence (30 cycles) analysis using a gas-phase protein sequencer (PPSQ-21; Shimadzu, Kyoto, Japan). By using the first 20 amino acid sequences data were analyzed using NCBI’s protein BLAST program.
+ Open protocol
+ Expand
3

Peptide Sequence Identification

Check if the same lab product or an alternative is used in the 5 most similar protocols
The amino acid sequences of the purified peptides were estimated by Edman degradation using a PPSQ-21 (Shimadzu). The amino acid sequences were assigned to protein using Basic Local Alignment Search Tool (BLAST).
+ Open protocol
+ Expand
4

Protein Sequence Analysis by CNBr Cleavage

Check if the same lab product or an alternative is used in the 5 most similar protocols
The purified CGL1 was reduced with tri-n-butylphosphine in 7M guanidine-HCl, 10 mM EDTA, 0.5 M Tris-HCl pH 8.5. The reduced CGL1 was pyridylethylated with 4-vinyl pyridine at 25 °C for 4 h in the dark. The reduced and pyridylethylated CGL1 was chemically cleaved at the methionyl bonds with 1% CNBr in 70% (v/v) formic acid at 25 °C for 24 h by the method of Gross28 (link)35 (link)36 (link). The peptides generated by the CNBr cleavage were separated by reverse-phase high-performance liquid chromatography (RP-HPLC) using HITACHI model L-6200 and L-4200 liquid chromatographs on a Wakosil-II 5C18 AR column (4.6 × 100 mm, Wako Pure Chemical Industries Ltd., Osaka, Japan). The column was equilibrated with solvent A (0.1% trifluoroacetic acid; TFA), and the peptides were eluted at the flow rate of 1 mL/min using a linear gradient of 0–100% solvent B (acetonitrile/water/TFA, 80:20:0.1 [v/v/v]) at room temperature. The separated fractions were collected for sequencing. Automated Edman degradation37 (link)38 39 (link)40 (link) was performed using a gas phase protein sequencer (Shimadzu model PPSQ-21).
+ Open protocol
+ Expand
5

Purification and Characterization of DAP BII

Check if the same lab product or an alternative is used in the 5 most similar protocols
DAP BII was purified from P. mexicana WO24 as described previously13 (link) and the sequence of peptides derived from the N-terminus and of internal fragments was obtained by peptide sequence analysis on a PPSQ-21 (Shimadzu). Degenerate primers were designed with which an ~800 bp fragment was amplified and used as a probe against dapb2 after labeling with [α-32 (link)P]dCTP (GE Healthcare) using a BcaBEST Labeling Kit (Takara Bio).
+ Open protocol
+ Expand
6

Immunoblotting and N-terminal Sequencing of Protein Subunits

Check if the same lab product or an alternative is used in the 5 most similar protocols
Proteins were separated by sodium dodecyl sulfate–polyacrylamide gel electrophoresis (SDS-PAGE) and stained with Quick CBB (Wako). For immunoblotting, separated proteins were transferred onto a polyvinylidene difluoride (PVDF) membrane (Immun-Blot, Bio-Rad). Antibodies against the c subunit were obtained from Agrisera, and those against the β subunit were as described in the literature (31 (link)). Chemiluminescence was detected using horseradish peroxidase–conjugated secondary antibodies and ECL Prime (Life Technologies) and visualized on a LAS 3000 mini instrument (GE Healthcare). Images were digitized using the ImageJ software. Otherwise, the separated proteins were transferred onto a membrane (Sequi-Blot PVDF Membrane, Bio-Rad). The N-terminal sequences were determined by Edman degradation on a peptide sequencer (PPSQ21, Shimadzu), based on a previous study (50 (link)).
+ Open protocol
+ Expand
7

Silk Protein Extraction and N-Terminal Sequencing

Check if the same lab product or an alternative is used in the 5 most similar protocols
The fifth instar larvae of S. marmorata were collected in the middle reaches of the Chikuma River in Nagano Prefecture, Japan. The silk glands were dissected from the larvae; the major silk proteins (P3′ fraction) were extracted from the silk glands as previously reported [5, 6] . The proteins were separated by SDS-PAGE and blotted onto a PVDF membrane. The individual bands of Smsp-2, Smsp-3, and Smsp-4 were cut out from the membrane; the N-terminal amino acid sequencing was performed on an automated protein sequencer PPSQ-21 (Shimadzu).
+ Open protocol
+ Expand
8

Recombinant Contractin A Expression

Check if the same lab product or an alternative is used in the 5 most similar protocols
The coding region of mature Contractin A was amplified by PCR using two primers (forward: 5′-AAGGAGATATACATATGTCAGTTATCAATTTTGGCTG-3′ and reverse: 5′-GTTAGCAGCCGGATCCGTGAAGATAACTCGGATTGC-3′), and inserted into a pET-3a vector at NdeI and BamHI restriction sites using the In-Fusion HD Cloning Kit. The plasmid was amplified in E. coli JM109 cells, and the protein was expressed in E. coli BL21(DE3)pLysS cells. Recombinant Contractin A expression was induced with 0.4 mM isopropylthiogalactoside, and the cells were incubated for an additional 18 h at 37°C. Because the recombinant proteins were obtained as inclusion bodies after the induction and disruption of cells, they were solubilized in solubilization buffer (50 mM Tris-HCl pH 8.0, 0.2 M NaCl, 1 mM ethylenediamine tetraacetate [EDTA], 6 M guanidine hydrochloride), and the protein was refolded in the refolding buffer (0.1 M Tris-HCl pH 8.0, 0.8 M L-arginine, 2 mM EDTA, 5 mM reduced glutathione, 0.5 mM oxidized glutathione). Next, the refolded protein was dialyzed against Tris-buffered saline (TBS; 10 mM Tris-HCl pH 7.5, 0.15 M NaCl). Protein concentrations were determined from the molar absorption coefficients at 280 nm calculated from the amino acid compositions of the proteins. The N-terminal amino acid sequence of the expressed protein was determined using a protein sequencer, PPSQ-21 (Shimadzu, Kyoto, Japan).
+ Open protocol
+ Expand

About PubCompare

Our mission is to provide scientists with the largest repository of trustworthy protocols and intelligent analytical tools, thereby offering them extensive information to design robust protocols aimed at minimizing the risk of failures.

We believe that the most crucial aspect is to grant scientists access to a wide range of reliable sources and new useful tools that surpass human capabilities.

However, we trust in allowing scientists to determine how to construct their own protocols based on this information, as they are the experts in their field.

Ready to get started?

Sign up for free.
Registration takes 20 seconds.
Available from any computer
No download required

Sign up now

Revolutionizing how scientists
search and build protocols!