SHAKE34 was performed on all bonds including hydrogen with the AMBER default tolerance of 10−5 Å for NVT and 10−6 Å for NVE. Non-bonded interactions were calculated directly up to 8 Å. Beyond 8 Å, electrostatic interactions were treated with cubic spline switching and the particle-mesh Ewald approximation35 in explicit solvent, with direct sum tolerances of 10−5 for NVT or 10−6 for NVE. A continuum model correction for energy and pressure was applied to long-range van der Waals interactions. The production timesteps were 2 fs for NVT and 1 fs for NVE.
Buffers
They are essential in biological research, ensuring optimal conditions for enzymes, proteins, and other biomolecules to function properly.
Buffers can be composed of various chemical compounds, such as phosphates, acetates, and tris, and their selection is crucial in experimental design.
Understanding the properties and appropriate use of buffers is key to achieving consistent and reproducabble results in a wide range of scientific applications, from cell culture to biochemical assays.
Most cited protocols related to «Buffers»
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Example 6
Compound 3 was generated from the purification process of IL-2 mutein Ala-M1 polymer prodrug 5. During separation of compound 5 on a Capto MMC ImpRes resin the later eluting peak which contains 3 was collected. The collected fraction was diluted with 10 mM succinic acid, pH 5.0 to lower the conductivity to approx. 14 mS/cm and further purified on a Äkta system equipped with a HiScreen Capto Blue column using buffer A (20 mM sodium phosphate, pH 7.5), buffer B (20 mM sodium phosphate, 1 M NaCl, pH 7.5) and a gradient from 0 to 50% buffer B in 6 column volumes. The main peak was collected and concentrated using Amicon Ultra centrifugal device (3 kDa MWCO). The concentrated solution was buffer exchanged to 10 mM Hepes, 150 mM NaCl, 3 mM EDTA, 0.05% polysorbate 20, pH 7.4 by using an Äkta system and a HiPrep 26/10 column and the concentration was adjusted to 0.25 mg/mL to give compound 3.
Example 1
The particles are synthesized by adding between about 5 mg and about 20 mg of rituximab (or non-specific IgG) to 20 mg of ABRAXANE. Saline is then added to a final volume of 2 ml for a final concentration of 10 mg/ml ABRAXANE, and the mixture is allowed to incubate at room temperature for 30 minutes to allow particle formation. Particles average about 160 nm and are termed “AR160” nanoparticles.
Optionally, the composition is divided into aliquots and frozen at −80° C. Once frozen the aliquots are optionally lyophilized overnight with the Virtis 3L benchtop lyophilizer (SP Scientific, Warmister, PA) with the refrigeration on. A lyophilized preparation is generated.
The dried aliquots are stored at room temperature. These samples are reconstituted in saline at room temperature for 30 minutes, followed by centrifugation for 7 minutes at 2000×g. The resulting sample is then resuspended in the appropriate buffer, as needed.
Example 9
NEBT7EL-pA06238 was grown on LB with 50 μg/ml kanamycin. A 600 ml culture of TBkan50 was inoculated with NEBT7EL-pA06238 and incubated overnight at 37° C. at 200 rpm. The next morning, a 10 L fermentor was prepared with 9.5 L of TB and then inoculated with 500 ml of the overnight culture. The culture was grown at 37° C. The pH was maintained at 6.2 with NaOH and the dO2 was maintained ≥20%. After 2 hours of growth, the temperature was dropped to 25° C. The culture was grown for an additional 1 hour with the OD600 around 7. IPTG was added to a final concentration of 1 mM and CoCl2 was added to 25 μM. Additional CoCl2 was added 1 and 2 hours after induction to bring the final concentration to 300 μM. The cells were grown for 20 hours at which point the fermentor was chilled to 10° C. and the cells were harvested by centrifugation. The cell pellet was stored at −80° C. until use.
The cell pellet from the fermentation was lysed by stirring in buffer with lysozyme and DNAse. Cell debris was removed by centrifugation and the supernatant was filtered through a 0.45 micron filter. Filtered supernatant was incubated with Ni-NTA agarose resin and then enzyme was eluted with imidazole. Purified FC4E pA06238 was immobilized onto 5.25 grams of ECR8204F resin using the standard published protocol from Purolite.
The immobilized enzyme was loaded into a 11×300 mm glass fixed bed reactor and run for approximately 200 h at constant temperature (60° C.) with a constant feed composition of 30 wt % fructose+70 wt % aqueous buffer solution (20 mM KPO4, 50 mM NaCl, 300 uM CoCl2). Feed rate was held constant at 140 uL/min throughout the run. The fixed bed reaction reached a maximal conversion of approximately 30% tagatose and had a half-life of −50 hours (
Example 3
Recombinant Protein Purification
Once the chimera is generated, its functionality must be assured, that is, on one hand the scFv still recognizes the CEA antigen, and on the other hand GRNLY is still cytotoxic.
Example 49
The functional activity of compounds was determined in a cell line where p70S6K is constitutively activated. Test article was dissolved in DMSO to make a 10 μM stock. PathScan® Phospho-S6 Ribosomal Protein (Ser235/236) Sandwich ELISA Kit was purchased from Cell Signaling Technology. A549 lung cancer cell line, was purchased from American Type Culture Collection. A549 cells were grown in F-12K Medium supplemented with 10% FBS. 100 μg/mL penicillin and 100 μg/mL streptomycin were added to the culture media. Cultures were maintained at 37° C. in a humidified atmosphere of 5% CO2 and 95% air. 2.0×105 cells were seeded in each well of 12-well tissue culture plates for overnight. Cells were treated with DMSO or test article (starting at 100 μM, 10-dose with 3 fold dilution) for 3 hours. The cells were washed once with ice cold PBS and lysed with 1× cell lysis buffer. Cell lysates were collected and samples were added to the appropriate wells of the ELISA plate. Plate was incubated for overnight at 4° C. 100 μL of reconstituted Phospho-S6 Ribosomal Protein (Ser235/236) Detection Antibody was added to each well and the plate was incubated at 37° C. for 1 hour. Wells were washed and 100 μl of reconstituted HRP-Linked secondary antibody was added to each well. The plate was incubated for 30 minutes at 37° C. Wash procedure was repeated and 100 μL of TMB Substrate was added to each well. The plate was incubated for 10 minutes at 37° C. 100 μL of STOP Solution was added to each well and the absorbance was read at 460 nm using Envision 2104 Multilabel Reader (PerkinElmer, Santa Clara, CA). IC50 curves were plotted and IC50 values were calculated using the GraphPad Prism 4 program based on a sigmoidal dose-response equation.
Unless otherwise noted, compounds that were tested had an IC50 of less than 50 μM in the S6K Binding assay. A=less than 0.05 μM; B=greater than 0.05 μM and less than 0.5 μM; C=greater than 0.5 μM and less than 10 μM;
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More about "Buffers"
These aqueous solutions help maintain a relatively stable pH value, resisting changes in hydrogen ion concentration upon the addition of small amounts of an acid or base.
Buffers are essential for ensuring optimal conditions for enzymes, proteins, and other biomolecules to function properly.
Buffers can be composed of various chemical compounds, such as phosphates, acetates, and tris.
The selection of the appropriate buffer is crucial in experimental design, as it can impact the performance and reproducibility of your results.
RIPA lysis buffer, for example, is a commonly used buffer for extracting proteins from cells and tissues, while the BCA protein assay kit and the Pierce BCA Protein Assay Kit are widely used for quantifying protein concentrations.
In addition to buffers, other important tools and techniques in biological research include PVDF membranes for protein transfer and detection, protease inhibitor cocktails for preserving protein integrity, and flow cytometry instruments like the FACSCalibur for analyzing cells.
Understanding the properties and appropriate use of buffers, as well as these related tools and techniques, is key to achieving consistent and reproducible results in your scientific work.
By optimizing your research protocols and enhancing reproducibility, you can unlock the true power of your research and drive scientific progress forward.