Journal: Scientific Reports

Article Title: Human Sialidase Neu3 is S-Acylated and Behaves Like an Integral Membrane Protein

doi: 10.1038/s41598-017-04488-w

Figure Lengend Snippet: Neu3 behaves as an integral membrane protein. ( a ) Soluble (S, first lane) and membrane (P, second lane) fractions of NEU3 -transfected cells were obtained as described in Fig. 1a . The latter fraction was then incubated for 40 min on ice with Tris buffer (control) or Na 2 CO 3 at pH 11.5 in order to extract peripheral membrane proteins. After treatment, membranes were collected by ultracentrifugation, and membrane-bound (P, fourth and sixth lanes) and solubilized (S, third and fifth lanes) proteins were analyzed by Western blotting using anti-Neu3 antibody. K-Ras and Cav-1 were used as markers of an extractable and a non-extractable membrane protein, respectively. Tub was used as a marker of a soluble protein. ( b ) Intact NEU3 -transfected cells were treated with (+) or without (−) 100 µg/ml proteinase K (PK) for 30 min at 37 °C. The remaining proteins were run on a SDS-PAGE gel and Western blotted with anti-c-Myc and anti-Neu3 antibodies. Transferrin Receptor (TfR) was used as a marker of a PK-accessible protein, whereas Cav-1 and sialyltransferase ST3Gal-II were used as markers of proteins not accessible to PK. The molecular masses in kDa of the standard proteins are shown on the left. ( c ) Antibody accessibility in permeabilized and non-permeabilized cells. The signal of the indicated antibodies were analyzed after fixation in cells treated with 0.1% saponin in PBS/BSA (permeabilized) or with PBS/BSA alone (non-permeabilized). Cav-1 was used as a marker of an inner membrane protein detected only after cell permeabilization, and GPI-YFP was used as a marker of an outer membrane protein accessible by antibody without permeabilization. Cells nuclei were stained blue with Hoechst dye. ( d ) Cell surface proteins exposed to the extracellular environment of NEU3 -transfected cells were biotinylated and isolated by streptavidin agarose pull-down. Biotinylated (B) and non-biotinylated (NB) fractions were analyzed by Western blotting. Endogenous marker Cav-1 was used as control of a membrane protein not exposed to the extracellular environment. Densitometric analysis indicating the percentage of Neu3 in each fraction is shown. ( e ) Kyte-Doolittle hydrophobicity plot for Neu3 sequence using a window size of 19. The red line corresponds to a hydrophobicity score of 1.6 and designates an empirical cutoff value for α-helix transmembrane segments of ~19 amino acids long.

Article Snippet: Subcellular fractionation Cells were washed with cold PBS and harvested by scraping in 5 mM Tris/HCl pH 7.0 (buffer T) supplemented with protease inhibitor cocktail (PIC) (Sigma-Aldrich, St Louis, MO, USA).

Techniques: Transfection, Incubation, Western Blot, Marker, SDS Page, Staining, Isolation, Sequencing

Journal: mBio

Article Title: Preferential Packing of Acidic Glycosidases and Proteases into Bacteroides Outer Membrane Vesicles

doi: 10.1128/mBio.00909-14

Figure Lengend Snippet: OMV display protease activity. (A) Ten micrograms of OMV proteins was loaded on 10% Tris-glycine gel with 0.1% gelatin as the substrate. Following separation at denaturing conditions, proteins were renatured and then incubated at 37°C for 2 days to allow substrate cleavage. Colloidal Coomassie brilliant blue G-250 was used to stain the gel. Clear bands marked by the arrows indicate the digestion of gelatin by proteases. (B) Peptidase activity of B. fragilis vesicles was tested using different p -nitroanilide-linked amino acids. Ten micrograms of purified OMV proteins was incubated with different substrates for 1 h at 37°C. Activities were determined by measuring the absorbance of the released p -nitroanilide at 405 nm. All activities are represented relative to the alanine-peptidase activity. All experiments were done in triplicates.

Article Snippet: The peptidase enzyme activity was determined by incubation of 10 µg of the quantified OMV proteins in a 50 mM Tris-HCl buffer (pH 6.5), with 200 µl of 50 mM l -lysine-p -nitroanilide dihydrobromide, l -alanine-p -nitroanilide hydrochloride, l -leucine-p-nitroanilide, or pyroglutamic acid-p -nitroanilide (Sigma-Aldrich), for 1 h at 37°C.

Techniques: Activity Assay, Incubation, Staining, Purification

Journal: Acta Crystallographica. Section F, Structural Biology Communications

Article Title: Purification, crystallization and preliminary X-ray diffraction studies of UDP-glucose:tetrahydrobiopterin α-glucosyltransferase (BGluT) from Synechococcus sp. PCC 7942

doi: 10.1107/S2053230X13034298

Figure Lengend Snippet: A BGluT protein crystal obtained by the hanging-drop vapour-diffusion method. A rod-shaped single crystal formed using a well solution consisting of of 0.1 M bis-tris pH 5.5, 19%( w / v ) PEG 3350 with 4%( w / v ) d (+)-galactose as an additive.

Article Snippet: The fractions containing BGluT were pooled, concentrated and exchanged into buffer consisting of 20 m M Tris–HCl pH 8.0, 150 m M NaCl, 5 m M β-­mercaptoethanol by ultrafiltration (Centricon YM-30; Millipore, Bedford, Massachusetts, USA).

Techniques: Diffusion-based Assay

Journal: Acta Crystallographica Section F: Structural Biology and Crystallization Communications

Article Title: Purification, crystallization and preliminary X-ray diffraction analysis of the thiaminase type II from Staphylococcus aureus

doi: 10.1107/S1744309110043174

Figure Lengend Snippet: A crystal of Sa TenA (0.1 × 0.1 × 0.4 mm; the scale bar is 0.1 mm in length) obtained using 0.2 M sodium acetate, 0.1 M Tris–HCl pH 8.5 and 28%( w / v ) PEG 3350.

Article Snippet: The purified Sa TenA was dialyzed against 100 m M Tris–HCl buffer pH 8.0; it was then concentrated to 10 mg ml−1 using an Amicon Ultra centrifugal filter device (Millipore; 3 kDa molecular-weight cutoff) and used for initial screening of crystallization conditions.

Techniques:

Journal: Biomacromolecules

Article Title: Smooth Muscle Cell Phenotype Modulation and Contraction on Native and Cross-Linked Polyelectrolyte Multilayers

doi: 10.1021/bm9007309

Figure Lengend Snippet: Apparent modulus vs cross-linking time of native and cross-linked hydrated (PAH/PAA) 15 PAH multilayers in 0.15 M NaCl, 25 mM Tris-HCl, pH 7.4. (○) PEMU built at pH 7.4/7.4, wet thickness was 218 nm before cross-linking; (△) PEMU built at pH 7.4/4.6, wet thickness was 343 nm before cross-linking.

Article Snippet: Hydrochloric acid solution, 1 N, and tris(hydroxymethyl)aminomethane (Tris crystallized free base, Fisher) were used to prepare 25 mM Tris-HCl buffered solutions at pH 7.4 containing 150 mM NaCl (Sigma).

Techniques:

Journal: Biomacromolecules

Article Title: Smooth Muscle Cell Phenotype Modulation and Contraction on Native and Cross-Linked Polyelectrolyte Multilayers

doi: 10.1021/bm9007309

Figure Lengend Snippet: Swelling behavior for native and cross-linked polyelectrolyte multilayers. (PAH/PAA) 15 PAH PEMU dry thickness (hatched) and wet thickness after swelling the PEMUs in a 0.15 M NaCl, 25 mM Tris-HCl, pH 7.4 solution for 30 min (gray). Thickness measurements were obtained by AFM using an AC240-TS silicon cantilever.

Article Snippet: Hydrochloric acid solution, 1 N, and tris(hydroxymethyl)aminomethane (Tris crystallized free base, Fisher) were used to prepare 25 mM Tris-HCl buffered solutions at pH 7.4 containing 150 mM NaCl (Sigma).

Techniques:

Journal: Biomacromolecules

Article Title: Smooth Muscle Cell Phenotype Modulation and Contraction on Native and Cross-Linked Polyelectrolyte Multilayers

doi: 10.1021/bm9007309

Figure Lengend Snippet: Layer by layer buildup for (◻) (PAH/PAA) x PAH built at pH 7.4/4.6 in 0.15 M NaCl, 25 mM Tris-HCl, and (○) (PAH/PAA) x PAH built at pH 7.4/7.4 in 0.15 M NaCl, 25 mM Tris-HCl.

Article Snippet: Hydrochloric acid solution, 1 N, and tris(hydroxymethyl)aminomethane (Tris crystallized free base, Fisher) were used to prepare 25 mM Tris-HCl buffered solutions at pH 7.4 containing 150 mM NaCl (Sigma).

Techniques:

Journal: Sensors (Basel, Switzerland)

Article Title: Combining Electrochemical Impedance Spectroscopy and Surface Plasmon Resonance into one Simultaneous Read-Out System for the Detection of Surface Interactions

doi: 10.3390/s131114650

Figure Lengend Snippet: Alternating the media 10 mM Tris-HCl and 1× PBS buffer for three consecutive runs. ( A ) Shows the minimum shift when exchanging the media. ( B ) Illustrates the changes in amplitude and its phase at a frequency of 251 Hz, when exchanging the media. Comparing the signals, when plotted in the same graph, reveals that the read-out systems detected the media exchange simultaneously, without influencing each other ( C ).

Article Snippet: The results have shown that these media changes could be detected both by EIS and SPR and when changing the medium from 10 mM Tris-HCl to 1× PBS and then back to 10 mM Tris-HCl, no shift in minimum or impedance occurs.

Techniques: