This work was funded by the National Council for Scientific and Technological Development (CNPq, Brazil) [grant numbers 428048/2018-8 and 402556/2022-4] and the University of Brasilia (Brazil).&#160;The author thanks Dr. Duarte Nuno Carvalho and Dr. Evelyn Santos (i3s, Porto, Portugal) for providing access to their smartphones used in this research.

1. Preparation of the Bradford protein assay reagent
<ol>
	<li>Dissolve 100 mg of Coomassie Brilliant Blue G in 50 mL 95% (w/v) ethanol. Mix until Coomassie Brilliant Blue G is completely dissolved. 
	CAUTION: Ethanol is flammable and causes eye irritation. Avoid flames and use goggles.</li>
	<li>To the previous solution, add 100 mL of 85% (w/v) phosphoric acid carefully. 
	CAUTION: Phosphoric acid is corrosive to metals and causes skin corrosion, serious eye damage, and acute oral toxicity. Wear gloves and goggles.</li>
	<li>Add the solution containing Coomassie Brilliant Blue G, ethanol, and phosphoric acid slowly to 600 mL of deionized water.</li>
	<li>Dilute the solution to a final volume of 1,000 mL. Scale up or down according to the number of samples to be analyzed. As described in the original method7, final concentrations in the working Bradford reagent should be 0.01% (w/v) Coomassie Brilliant Blue G, 4.7% (w/v) ethanol, and 8.5% (w/v) phosphoric acid.</li>
	<li>Remove any insoluble material filtering through filter paper (Whatman #1 paper or equivalent).</li>
	<li>The reagent is stable for several weeks when stored at room temperature (RT) and protected from light. Filter as necessary since precipitates may form over time. 
	&#8203;NOTE: Alternatively, ready to dilute and use Bradford reagents are commercially available. Follow the manufacturer&#39;s instructions for preparing the reagent and proceed to the next step.</li>
</ol>
2. Preparation of protein standard solutions
<ol>
	<li>Prepare a stock solution (refer to step 2.4) of an isolated protein to be used as standard. An affordable and commonly used protein is bovine serum albumin (BSA). Other options are ovalbumin and bovine gamma globulin.</li>
	<li>If the molar absorptivity of the protein used as standard is known, check the concentration of the stock solution in a spectrophotometer.</li>
	<li>For BSA, a commonly used formula is BSA (mg/mL) = (A280/6.6)&#160;&#215; 10, where A280 is the absorbance at 280 nm with a path length of 1 cm read against an appropriate blank (i.e., &#949;2801% = 6.6)7. For example, 0.8 mg/mL BSA has an absorbance of 0.528 at 280 nm.</li>
	<li>To generate the standard curve, prepare several dilutions of BSA within 0.025 mg/mL and 1.0 mg/mL. These will result in 0.25-10 &#181;g of BSA per well after adding a sample volume of 10 &#181;L per well. 
	NOTE: Protein standard solutions should be prepared in a medium with the same composition (final concentration) of the medium used to prepare samples.</li>
</ol>
3. Assay
<ol>
	<li>Dilute the samples to achieve a protein concentration within the standard curve range of 0.025-1.0 mg/mL. Have several (at least 3) sample dilutions within the range. 
	NOTE: Samples can be diluted with phosphate-buffered saline (PBS) or any other medium/buffer composition compatible with the Bradford reagent. The final concentration of medium components should not differ between standard and samples.</li>
	<li>Add 10 &#181;L of each protein standard solution to three wells (i.e., in triplicate) of a 96-well microplate. For the 0 (zero) protein point, add 10 &#181;L of the buffer/medium used to prepare the standard solutions and sample dilutions.</li>
	<li>To another set of wells, add 10 &#181;L of each sample dilution to three wells (i.e., in triplicate) of the same 96-well microplate. One approach is to add different volumes of a sample and complete with a medium of up to 10 &#181;L per well (e.g., 0.5 &#181;L, 1 &#181;L, 2 &#181;L, 4 &#181;L, and 8 &#181;L of the sample plus 9.5 &#181;L, 9 &#181;L, 8 &#181;L, 6 &#181;L, and 2 &#181;L of medium).</li>
	<li>Add 250 &#181;L of Bradford protein assay reagent to all wells. A typical microplate setup is shown in Figure 2. In this example, a set of blank wells containing 260 &#181;L (the final volume per well) water was included to serve as blank in a microplate reader (step 4.5). This is required only if absorbance data will also be collected. 
	NOTE: Prepare a standard curve in the same microplate of samples each time the assay is performed. In other words, if the number of samples requires another plate, prepare another standard curve in the second plate, and so on.</li>
	<li>Record results (section 4) within 5-15 min.</li>
</ol>
<img alt="Figure 2" class="xfigimg" src="/files/ftp_upload/65547/65547fig02v2.jpg" /> 
Figure 2: A typical plate layout for the Bradford protein assay. Blank refers to three wells containing 260 &#181;L of water to be used as blank in a microplate reader. STD refers to protein standards. S1-S6 are six different samples. SX_1-SX_4 are four different sample dilutions for each sample. <a href="https://www.jove.com/files/ftp_upload/65547/65547fig02large.jpg" target="_blank">Please click here to view a larger version of this figure.</a>
4. Recording results
<ol>
	<li>In a well-illuminated room, hold the microplate parallel to the bench against a uniform white background (e.g., a paper sheet) with one hand. Ensure accurate alignment by placing a bubble level on the plate.</li>
	<li>With the other hand, hold the smartphone parallelly (some camera applications usefully indicate the inclination of the device) to the bench and the microplate and take one or several pictures of the whole microplate (Figure 3). In iOS devices, turn on the camera level indicator in the camera settings by enabling the Grid option. In Android devices, turn on the camera level indicator in the camera settings by enabling Framing Hints.</li>
	<li>No special lighting apparatus is required, but take care to avoid shadows and reflections. For example, avoid shading the plate or the background with the smartphone and avoid shading the background with the microplate. Small reflections in the edges of the well area are not a problem; color data can be extracted from a very small area in the center of each well.</li>
	<li>Briefly check the picture for background uniformity, shadows, and reflections. Also, take a look at the angle of the wells; the center of each well should be directly visible (i.e., not behind well walls).</li>
	<li>If the comparison between microplate absorbance readings and picture color data is desired, read the microplate at 590 nm and 450 nm in a microplate reader21.</li>
</ol>
<img alt="Figure 3" class="xfigimg" src="/files/ftp_upload/65547/65547fig03v2.jpg" /> 
Figure 3: Capturing the results of the Bradford protein assay. In a well-illuminated room, the microplate is positioned parallelly to the bench against a uniform background with one hand. With the other hand, the smartphone is hold parallelly to the bench and the microplate. <a href="https://www.jove.com/files/ftp_upload/65547/65547fig03large.jpg" target="_blank">Please click here to view a larger version of this figure.</a>
5. Extracting color data-Automatically
<ol>
	<li>Download ImageJ and ReadPlate22, an ImageJ plugin is available at&#160;https://imagej.nih.gov/ij/plugins/readplate/index.html (this is a .txt file).</li>
	<li>Open ImageJ, click on Plugins &#62; Install and select the file downloaded in step 6.1.</li>
	<li>Set the measurement parameters by clicking on Analyze &#62; Set Measurements and check the following options: Area; Standard deviation; Min &#38; max gray value; Mean gray value; Modal gray value. On the bottom of the window, set Redirect to: None and Decimal places (0-9): 3.</li>
	<li>Go to File &#62; Open and select the picture of the microplate taken in step 4.</li>
	<li>Go to Plugins &#62; ReadPlate. Read the instructions and then click OK.</li>
	<li>Select the number of wells: 96.</li>
	<li>Using the Rectangular selection tool automatically loaded by the plugin, make a rectangle beginning in the center of the A1 well and ending in the center of the H12 well. Then, click OK.</li>
	<li>Select the Blue channel and click OK.</li>
	<li>Confirm the default parameters by clicking on OK.</li>
	<li>Check if the software delineated an area inside each well and if the selected areas are not covering areas with abnormal shadows or reflection. Click OK.</li>
	<li>Save the results and repeat steps 5.8-5.10 for the green channel.</li>
	<li>Calculate the blue-to-green ratio using the mode for each color. 
	&#8203;NOTE: The calculation can be done manually or using the software of the reader preferences, such as R, Microsoft Excel, or GraphPad Prism.</li>
</ol>
6. Extracting color data-Manually
<ol>
	<li>Download Inkscape, a free and open-source graphics editor. 
	NOTE: Any software with the color picker tool (usually depicted as an eye dropper) can be used to identify the color and extract RGB data.</li>
	<li>Open Inkscape, go to File &#62; Open. Select the picture of the microplate taken in Step 4.</li>
	<li>Pick the Select and Transform Objects (S) tool, which is depicted as an arrow on the top-left side, and click on the picture. A dashed line border will indicate the selection.</li>
	<li>Select the Pick Colors from Image (D) tool, which is depicted as an eye dropper on the left side.</li>
	<li>Click in the center of a well. The color on the bottom panel (&#34;Fill:&#34;) will change accordingly. Click on the color and a Fill and Stroke tab will pop up on the right side.</li>
	<li>Change the Flat Color dropdown menu to RGB. Record the values shown for the blue and green channels for each well.</li>
	<li>Calculate the blue-to-green ratio using the recorded values. 
	&#8203;NOTE: The calculation can be done manually or using the software of the reader preferences, such as R, Microsoft Excel, or GraphPad Prism.</li>
</ol>
7. Building standard curves and extrapolating unknowns
<ol>
	<li>Plot the average green-to-blue intensity ratio as a function of protein standard concentration. 
	NOTE: Plot the data manually or using the software of the reader preferences, such as R, Microsoft Excel, or GraphPad Prism.</li>
	<li>Calculate the average green-to-blue intensity ratio for each sample and dilution.</li>
	<li>Check if the signal obtained for the sample lies within the linear range of the protein standard.</li>
	<li>Ignore any value below or above the minimum or maximum values of the standard curve.</li>
	<li>Use the linear equation describing the standard curve to extrapolate the amount of protein in the sample. Multiply the calculated values by the dilution factor accordingly.</li>
</ol>

Smartphone as an Analytical Device to Quantify Protein Using Bradford Assay

<ol>
	<li>Zaguri, M., Kandel, S., Rinehart, S. A., Torsekar, V. R., Hawlena, D. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Protein+quantification+in+ecological+studies:+A+literature+review+and+empirical+comparisons+of+standard+methodologies.">Protein quantification in ecological studies: A literature review and empirical comparisons of standard methodologies.</a> Methods in Ecology and Evolution. 12 (7), 1240-1251 (2021).</li><li>Koga, T., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Mild+electrical+stimulation+and+heat+shock+ameliorates+progressive+proteinuria+and+renal+inflammation+in+mouse+model+of+Alport+syndrome.">Mild electrical stimulation and heat shock ameliorates progressive proteinuria and renal inflammation in mouse model of Alport syndrome.</a> PLoS One. 7 (8), e43852 (2012).</li><li>Peterson, G. L. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Determination+of+total+protein.">Determination of total protein.</a> Methods in Enzymology. 91, 95-119 (1983).</li><li>Goldfarb, A. R., Saidel, L. J., Mosovich, E. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=The+ultraviolet+absorption+spectra+of+proteins.">The ultraviolet absorption spectra of proteins.</a> The Journal of Biological Chemistry. 193 (1), 397-404 (1951).</li><li>Lowry, O. H., Rosebrough, N. J., Farr, A. L., Randall, R. J. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Protein+measurement+with+the+Folin+phenol+reagent.">Protein measurement with the Folin phenol reagent.</a> The Journal of Biological Chemistry. 193 (1), 265-275 (1951).</li><li>Smith, P. K., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Measurement+of+protein+using+bicinchoninic+acid.">Measurement of protein using bicinchoninic acid.</a> Analytical Biochemistry. 150 (1), 76-85 (1985).</li><li>Bradford, M. M. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=A+rapid+and+sensitive+method+for+the+quantitation+of+microgram+quantities+of+protein+utilizing+the+principle+of+protein-dye+binding.">A rapid and sensitive method for the quantitation of microgram quantities of protein utilizing the principle of protein-dye binding.</a> Analytical Biochemistry. 72 (1-2), 248-254 (1976).</li><li>Datki, Z., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Application+of+BisANS+fluorescent+dye+for+developing+a+novel+protein+assay.">Application of BisANS fluorescent dye for developing a novel protein assay.</a> PLoS One. 14 (4), e0215863 (2019).</li><li>Van Noorden, R., Maher, B., Nuzzo, R. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=The+top+100+papers.">The top 100 papers.</a> Nature. 514 (7524), 550-553 (2014).</li><li>. Scopus Available from: <a target="_blank" href="https://www.scopus.com/">https://www.scopus.com/</a> (2022)</li><li>Compton, S. J., Jones, C. G. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Mechanism+of+dye+response+and+interference+in+the+Bradford+protein+assay.">Mechanism of dye response and interference in the Bradford protein assay.</a> Analytical Biochemistry. 151 (2), 369-374 (1985).</li><li>Chial, H. J., Thompson, H. B., Splittgerber, A. G. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=A+spectral+study+of+the+charge+forms+of+Coomassie+Blue+G.">A spectral study of the charge forms of Coomassie Blue G.</a> Analytical Biochemistry. 209 (2), 258-266 (1993).</li><li>Pande, S. V., Murthy, M. S. R. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=A+modified+micro-Bradford+procedure+for+elimination+of+interference+from+sodium+dodecyl+sulfate,+other+detergents,+and+lipids.">A modified micro-Bradford procedure for elimination of interference from sodium dodecyl sulfate, other detergents, and lipids.</a> Analytical Biochemistry. 220 (2), 424-426 (1994).</li><li>Gogstad, G. O., Krutnes, M. -. B. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Measurement+of+protein+in+cell+suspensions+using+the+Commassie+brilliant+blue+dye-binding+assay.">Measurement of protein in cell suspensions using the Commassie brilliant blue dye-binding assay.</a> Analytical Biochemistry. 126 (2), 355-359 (1982).</li><li>Friedenauer, S., Berlet, H. H. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Sensitivity+and+variability+of+the+Bradford+protein+assay+in+the+presence+of+detergents.">Sensitivity and variability of the Bradford protein assay in the presence of detergents.</a> Analytical Biochemistry. 178 (2), 263-268 (1989).</li><li>Stoscheck, C. M. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Increased+uniformity+in+the+response+of+the+Coomassie+blue+G+protein+assay+to+different+proteins.">Increased uniformity in the response of the Coomassie blue G protein assay to different proteins.</a> Analytical Biochemistry. 184 (1), 111-116 (1990).</li><li>Zor, T., Selinger, Z. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Linearization+of+the+Bradford+protein+assay+increases+its+sensitivity:+Theoretical+and+experimental+studies.">Linearization of the Bradford protein assay increases its sensitivity: Theoretical and experimental studies.</a> Analytical Biochemistry. 236 (2), 302-308 (1996).</li><li>Gee, C. T., Kehoe, E., Pomerantz, W. C. K., Penn, R. L. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Quantifying+protein+concentrations+using+smartphone+colorimetry:+A+new+method+for+an+established+test.">Quantifying protein concentrations using smartphone colorimetry: A new method for an established test.</a> Journal of Chemical Education. 94 (7), 941-945 (2017).</li><li>de Camargo, C., Vicentini, M., Gobbi, A., Martinez, D., Lima, R. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Smartphone+for+point-of-care+quantification+of+protein+by+Bradford+assay.">Smartphone for point-of-care quantification of protein by Bradford assay.</a> Journal of the Brazilian Chemical Society. 28 (4), 689-693 (2016).</li><li>Moreira, D. C. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=RGBradford:+Accurate+measurement+of+protein+concentration+using+a+smartphone+camera+and+the+blue+to+green+intensity+ratio.">RGBradford: Accurate measurement of protein concentration using a smartphone camera and the blue to green intensity ratio.</a> Analytical Biochemistry. 655, 114839 (2022).</li><li>Ernst, O., Zor, T. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Linearization+of+the+Bradford+Protein+Assay.">Linearization of the Bradford Protein Assay.</a> Journal of Visualized Experiments. (38), 1918 (2010).</li><li>Angelani, C. R., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=A+metabolic+control+analysis+approach+to+introduce+the+study+of+systems+in+biochemistry:+the+glycolytic+pathway+in+the+red+blood+cell:+Metabolic+control+analysis+and+the+glycolytic+pathway.">A metabolic control analysis approach to introduce the study of systems in biochemistry: the glycolytic pathway in the red blood cell: Metabolic control analysis and the glycolytic pathway.</a> Biochemistry and Molecular Biology Education. 46 (5), 502-515 (2018).</li></ol>

The author has no conflicts of interest to declare.

This paper describes RGBradford, a method that uses a smartphone camera to record data from a Bradford protein assay, extract color data, and accurately quantify protein levels in biological samples as originally described recently20. One difference from the original RGBradford method is that here a procedure for obtaining color data automatically with an ImageJ plugin22 was used. The main novelty of the RGBradford method is the use of RGB data as analytical signals; thus, ...

Regardless of the downstream use (e.g., ELISA, enzyme kinetics, western blotting, protein purification, and mass spectrometry), protein quantification is crucial for accurate analysis in life sciences laboratories. In addition to their use as secondary readouts (i.e., to calculate relative levels of analytes per mass of protein), protein levels in a sample can also be the desired output itself. For example, one can be interested in protein levels in food resources1 or in urine2. There are many methods available to measure protein concentration in samples3, including direct UV absorbance readings4, protein-copper chelation5,6, protein-dye binding colorimetric assays7, and protein-dye binding fluorescent assays8. The relevance of protein quantitation is evidenced by the presence of two papers describing protein measurement methods5,7 in the top-3 of the most cited literature9,10. Despite the fact that many authors neglect their actual citation by citing non-primary references or not citing anything at all, the original papers describing the Lowry protein assay and the Bradford protein assay amount &#62;200,000 citations each10.
The popularity of the Bradford assay stems from its affordability, simplicity, speed, and sensitivity. The assay is based on the interaction between proteins and the dye Coomassie Brilliant Blue G under acidic conditions. Under the conditions of the assay (i.e., low pH), the dye exists in three forms: a red cationic form with &#955;max at 470 nm; a green neutral form with &#955;max at 650 nm; and a blue anionic form with &#955;max at 590 nm11,12 (Figure 1). The cationic form predominates in the absence of proteins. As proteins interact with the dye, they stabilize the blue anionic form, causing a noticeable change in the color of the solution, from brownish to blue. Usually, the change in the concentration of the blue form of the dye is quantified spectrophotometrically, whose absorbance at 590-595 nm is proportional to the quantity of protein in the assay.
<img alt="Figure 1" class="xfigimg" src="/files/ftp_upload/65547/65547fig01v2.jpg" /> 
Figure 1: Coomassie brilliant blue G absorption spectra under the conditions of the Bradford assay. The three main peaks are marked with arrows indicating the &#955;max of the red (470 nm), green (650 nm), and blue (590 nm) forms of the dye. Spectra were recorded in the absence of protein (yellow line) and in the presence of 3 &#181;g (gray line) and 10 &#181;g (blue line) of bovine serum albumin. <a href="https://www.jove.com/files/ftp_upload/65547/65547fig01large.jpg" target="_blank">Please click here to view a larger version of this figure.</a>
The widespread use of the Bradford assay has led to the identification of several limitations (e.g., variable responses to different proteins11, and interference by lipids13 and detergents7) and the development of modifications to improve its performance (e.g., the addition of detergents14,15, alkalinization14,16 and use of the ratio of absorbances17). In addition to modifications in the assay itself, the use of alternative devices, such as smartphones or cameras, to capture analytical signals have also been described18,19,20. Indeed, the development of methods that make use of smartphones as portable chemical analyzers has been an active area of research. The motivation for the use of smartphones stems from the affordability, portability, ease of use, and widespread availability of these devices.
This paper provides a protocol for protein quantification using the RGBradford assay20, which uses a smartphone as an analytical device. In contrast to the original RGBradford publication20, here, a procedure that streamlines the color extraction process has been introduced. It involves the utilization of a freely available software application to extract color information from each well of a microplate picture automatically, saving significant time and effort. This is an alternative to the previous method of manually acquiring color data from each well one by one using a graphics editor software application20. Ultimately, protein levels in samples can be quantified using color data extracted from a picture of a microplate taken with a smartphone.

<table border="1" fo:keep-together.within-page="1" fo:keep-with-next.within-page="always">
	<tbody>
		<tr>
			<td>96-well flat-bottom polystyrene microtiter plates&#160;</td>
			<td>Jet Biofil, Guangzhou, China</td>
			<td>TCP011096</td>
			<td>Any flat-bottom microplate compativle with optical reading will suffice.&#160;</td>
		</tr>
		<tr>
			<td>Bovine serum albumin</td>
			<td>Sigma-Aldrich, St. Louis, MO</td>
			<td>A2153</td>
			<td></td>
		</tr>
		<tr>
			<td>Coomassie Brilliant Blue G</td>
			<td>Sigma-Aldrich, St. Louis, MO</td>
			<td>B0770</td>
			<td></td>
		</tr>
		<tr>
			<td>Ethyl alcohol</td>
			<td></td>
			<td></td>
			<td></td>
		</tr>
		<tr>
			<td>iPhone 11</td>
			<td>Apple</td>
			<td>MWM02BR/A</td>
			<td>Can be substituted with other smartphone equiped with a camera</td>
		</tr>
		<tr>
			<td>iPhone 14 Pro</td>
			<td>Apple</td>
			<td>N/A</td>
			<td></td>
		</tr>
		<tr>
			<td>Phosphoric acid</td>
			<td>Sigma-Aldrich, St. Louis, MO</td>
			<td>695017</td>
			<td></td>
		</tr>
		<tr>
			<td>Redmi Note 9 Pro</td>
			<td>XIAOMI&#160;</td>
			<td>N/A</td>
			<td></td>
		</tr>
		<tr>
			<td>S22 Ultra</td>
			<td>Samsung&#160;</td>
			<td>N/A</td>
			<td></td>
		</tr>
		<tr>
			<td>SpectraMax 384 Plus. Microplate reader.</td>
			<td>Molecular Devices, San Jose, CA</td>
			<td>PLUS 384</td>
			<td>Any microplate reader capable of reading at 450 nm and 590 nm will work. This is optional. The method was actually created to dismiss the need of a microplate reader.</td>
		</tr>
	</tbody>
</table>

rgbradford: protein quantitation with a smartphone camera

Protein quantitation is an essential procedure in life sciences research. Amongst several other methods, the Bradford assay is one of the most used. Because of its widespread, the limitations and advantages of the Bradford assay have been exhaustively reported, including several modifications of the original method to improve its performance. One of the alterations of the original method is the use of a smartphone camera as an analytical instrument. Taking advantage of the three forms of the Coomassie Brilliant Blue dye that exist in the conditions of the Bradford assay, this paper describes how to accurately quantify protein in samples using color data extracted from a single picture of a microplate. After performing the assay in a microplate, a picture is taken using a smartphone camera, and RGB color data is extracted from the picture using a free and open-source image analysis software application. Then, the ratio of blue to green intensity (in the RGB scale) of samples with unknown concentrations of protein is used to calculate the protein content based on a standard curve. No significant difference is observed between values calculated using RGB color data and those calculated using conventional absorbance data.

Figure 4&#160;is a picture of a microplate from which color data was extracted, and absorbance at 450 nm and 590 nm was recorded. The RGB color data reported here as representative were obtained automatically as described in section 5. A typical pattern of color data is an increase in the blue values and a decrease in the red and green values (Figure 5). Note that despite the evident reflection in all wells and a not perfectly aligned microplate (<strong class="...

Watch this Scientific Journal Video about An Alternative Approach to Protein Quantification by Bradford Assay Using a Smartphone at JoVE.com

Author Spotlight: An Alternative Approach to Protein Quantification by Bradford Assay Using a Smartphone 

This paper provides a protocol for protein quantification using the Bradford assay and a smartphone as an analytical device. Protein levels in samples can be quantified using color data extracted from a picture of a microplate taken with a smartphone.

RGBradford: Protein Quantitation with a Smartphone Camera

Protein quantitation is an essential procedure in life sciences research. Amongst several other methods, the Bradford assay is one of the most used. ...

rgbradford-protein-quantitation-with-a-smartphone-camera

Research

JoVE Journal

Biochemistry

2.7K Views.  University of Brasilia. This paper provides a protocol for protein quantification using the Bradford assay and a smartphone as an analytical device. Protein levels in samples can be quantified using color data extracted from a picture of a microplate taken with a smartphone.

Video: Author Spotlight: An Alternative Approach to Protein Quantification by Bradford Assay Using a Smartphone 

Fluorescence Anisotropy as a Tool to Study Protein-protein Interactions

Protein-protein interactions play an essential role in the function of a living organism. Once an interaction has been identified and validated it is necessary to characterize it at the structural and mechanistic level. Several biochemical and biophysical methods exist for such purpose. Among them, fluorescence anisotropy is a powerful technique particularly used when the fluorescence intensity of a fluorophore-labeled protein remains constant upon protein-protein interaction. In this technique, a fluorophore-labeled protein is excited with vertically polarized light of an appropriate wavelength that selectively excites a subset of the fluorophores according to their relative orientation with the incoming beam. The resulting emission also has a directionality whose relationship in the vertical and horizontal planes defines anisotropy (r) as follows: r=(IVV-IVH)/(IVV+2IVH), where IVV and IVH are the fluorescence intensities of the vertical and horizontal components, respectively. Fluorescence anisotropy is sensitive to the rotational diffusion of a fluorophore, namely the apparent molecular size of a fluorophore attached to a protein, which is altered upon protein-protein interaction. In the present text, the use of fluorescence anisotropy as a tool to study protein-protein interactions was exemplified to address the binding between the protein mutated in the Shwachman-Diamond Syndrome (SBDS) and the Elongation factor like-1 GTPase (EFL1). Conventionally, labeling of a protein with a fluorophore is carried out on the thiol groups (cysteine) or in the amino groups (the N-terminal amine or lysine) of the protein. However, SBDS possesses several cysteines and lysines that did not allow site directed labeling of it. As an alternative technique, the dye 4&#39;,5&#39;-bis(1,3,2 dithioarsolan-2-yl) fluorescein was used to specifically label a tetracysteine motif, Cys-Cys-Pro-Gly-Cys-Cys, genetically engineered in the C-terminus of the recombinant SBDS protein. Fitting of the experimental data provided quantitative and mechanistic information on the binding mode between these proteins.

Protein interactions are at the heart of a cell&#39;s function. Calorimetric and spectroscopic techniques are commonly used to characterize them. Here we describe fluorescence anisotropy as a tool to study the interaction between the protein mutated in the Shwachman-Diamond Syndrome (SBDS) and the Elongation factor-like 1 GTPase (EFL1).

Protein-protein interactions play an essential role in the function of a living organism. Once an interaction has been identified and validated it is ...

Using Scaffold Liposomes to Reconstitute Lipid-proximal Protein-protein Interactions In Vitro

Studies of integral membrane proteins in vitro are frequently complicated by the presence of a hydrophobic transmembrane domain. Further complicating these studies, reincorporation of detergent-solubilized membrane proteins into liposomes is a stochastic process where protein topology is impossible to enforce. This paper offers an alternative method to these challenging techniques that utilizes a liposome-based scaffold. Protein solubility is enhanced by deletion of the transmembrane domain, and these amino acids are replaced with a tethering moiety, such as a His-tag. This tether interacts with an anchoring group (Ni2+ coordinated by nitrilotriacetic acid (NTA(Ni2+)) for His-tagged proteins), which enforces a uniform protein topology at the surface of the liposome. An example is presented wherein the interaction between Dynamin-related protein 1 (Drp1) with an integral membrane protein, Mitochondrial Fission Factor (Mff), was investigated using this scaffold liposome method. In this work, we have demonstrated the ability of Mff to efficiently recruit soluble Drp1 to the surface of liposomes, which stimulated its GTPase activity. Moreover, Drp1 was able to tubulate the Mff-decorated lipid template in the presence of specific lipids. This example demonstrates the effectiveness of scaffold liposomes using structural and functional assays and highlights the role of Mff in regulating Drp1 activity.

Using Scaffold Liposomes to Reconstitute Lipid-proximal Protein-protein Interactions In Vitro

This paper describes a method for assessing the interactions and assemblies of integral membrane proteins in vitro with various partner factors in a lipid-proximal environment.

Studies of integral membrane proteins in vitro are frequently complicated by the presence of a hydrophobic transmembrane domain. Further complicating ...

Assaying Protein Kinase Activity with Radiolabeled ATP

Protein kinases are able to govern large-scale cellular changes in response to complex arrays of stimuli, and much effort has been directed at uncovering allosteric details of their regulation. Kinases comprise signaling networks whose defects are often hallmarks of multiple forms of cancer and related diseases, making an assay platform amenable to manipulation of upstream regulatory factors and validation of reaction requirements critical in the search for improved therapeutics. Here, we describe a basic kinase assay that can be easily adapted to suit specific experimental questions including but not limited to testing the effects of biochemical and pharmacological agents, genetic manipulations such as mutation and deletion, as well as cell culture conditions and treatments to probe cell signaling mechanisms. This assay utilizes radiolabeled [&#947;-32P] ATP, which allows for quantitative comparisons and clear visualization of results, and can be modified for use with immunoprecipitated or recombinant kinase, specific or typified substrates, all over a wide range of reaction conditions.

Protein kinases are highly evolved signaling enzymes and scaffolds that are critical for inter- and intracellular signal transduction. We present a protocol for measuring kinase activity through the use of radiolabeled adenosine triphosphate ([&#947;-32P] ATP), a reliable method to aid in elucidation of cellular signaling regulation.

Protein kinases are able to govern large-scale cellular changes in response to complex arrays of stimuli, and much effort has been directed at uncovering ...

Investigating Protein Sequence-structure-dynamics Relationships with Bio3D-web

We demonstrate the usage of Bio3D-web for the interactive analysis of biomolecular structure data. The Bio3D-web application provides online functionality for: (1) The identification of related protein structure sets to user specified thresholds of similarity; (2) Their multiple alignment and structure superposition; (3) Sequence and structure conservation analysis; (4) Inter-conformer relationship mapping with principal component analysis, and (5) comparison of predicted internal dynamics via ensemble normal mode analysis. This integrated functionality provides a complete online workflow for investigating sequence-structure-dynamic relationships within protein families and superfamilies.

A protocol for the online investigation of protein sequence-structure-dynamics relationships using Bio3D-web is presented.

We demonstrate the usage of Bio3D-web for the interactive analysis of biomolecular structure data. The Bio3D-web application provides online functionality ...

Real-time Tracking of DNA Fragment Separation by Smartphone

Slab gel electrophoresis (SGE) is the most common method for the separation of DNA fragments; thus, it is broadly applied to the field of biology and others. However, the traditional SGE protocol is quite tedious, and the experiment takes a long time. Moreover, the chemical consumption in SGE experiments is very high. This work proposes a simple method for the separation of DNA fragments based on an SGE chip. The chip is made by an engraving machine. Two plastic sheets are used for the excitation and emission wavelengths of the optical signal. The fluorescence signal of the DNA bands is collected by smartphone. To validate this method, 50, 100, and 1,000 bp DNA ladders were separated. The results demonstrate that a DNA ladder smaller than 5,000 bp can be resolved within 12 min and with high resolution when using this method, indicating that it is an ideal substitute for the traditional SGE method.

Traditional slab gel electrophoresis (SGE) experiments require a complicated apparatus and high chemical consumption. This work presents a protocol that describes a low-cost method to separate DNA fragments within a short timeframe.

Slab gel electrophoresis (SGE) is the most common method for the separation of DNA fragments; thus, it is broadly applied to the field of biology and ...

A Yeast 2-Hybrid Screen in Batch to Compare Protein Interactions

Screening for protein-protein interactions using the yeast 2-hybrid assay has long been an effective tool, but its use has largely been limited to the discovery of high-affinity interactors that are highly enriched in the library of interacting candidates. In a traditional format, the yeast 2-hybrid assay can yield too many colonies to analyze when conducted at low stringency where low affinity interactors might be found. Moreover, without a comprehensive and complete interrogation of the same library against different bait plasmids, a comparative analysis cannot be achieved. Although some of these problems can be addressed using arrayed prey libraries, the cost and infrastructure required to operate such screens can be prohibitive. As an alternative, we have adapted the yeast 2-hybrid assay to simultaneously uncover dozens of transient and static protein interactions within a single screen utilizing a strategy termed DEEPN (Dynamic Enrichment for Evaluation of Protein Networks), which incorporates high-throughput DNA sequencing and computation to follow the evolution of a population of plasmids that encode interacting partners. Here, we describe customized reagents and protocols that allow a DEEPN screen to be executed easily and cost-effectively.

Batch processing of yeast 2-hybrid screens allows for direct comparison of the interaction profiles of multiple bait proteins with a highly complex set of prey fusion proteins. Here, we describe refined methods, new reagents, and how to implement their use for such screens.

Screening for protein-protein interactions using the yeast 2-hybrid assay has long been an effective tool, but its use has largely been limited to the ...

High Sensitivity Measurement of Transcription Factor-DNA Binding Affinities by Competitive Titration Using Fluorescence Microscopy

Accurate quantification of transcription factor (TF)-DNA interactions is essential for understanding the regulation of gene expression. Since existing approaches suffer from significant limitations, we have developed a new method for determining TF-DNA binding affinities with high sensitivity on a large scale. The assay relies on the established fluorescence anisotropy (FA) principle but introduces important technical improvements. First, we measure a full FA competitive titration curve in a single well by incorporating TF and a fluorescently labeled reference DNA in a porous agarose gel matrix. Unlabeled DNA oligomer is loaded on the top as a competitor and, through diffusion, forms a spatio-temporal gradient. The resulting FA gradient is then read out using a customized epifluorescence microscope setup. This improved setup greatly increases the sensitivity of FA signal detection, allowing both weak and strong binding to be reliably quantified, even for molecules of similar molecular weights. In this fashion, we can measure one titration curve per well of a multi-well plate, and through a fitting procedure, we can extract both the absolute dissociation constant (KD) and active protein concentration. By testing all single-point mutation variants of a given consensus binding sequence, we can survey the entire binding specificity landscape of a TF, typically on a single plate. The resulting position weight matrices (PWMs) outperform those derived from other methods in predicting in vivo TF occupancy. Here, we present a detailed guide for implementing HiP-FA on a conventional automated fluorescent microscope and the data analysis pipeline.

Here we present a novel method for determining binding affinities at equilibrium and in solution with high sensitivity on a large scale. This improves the quantitative analysis of transcription factor-DNA binding. The method is based on automated fluorescence anisotropy measurements in a controlled delivery system.

Accurate quantification of transcription factor (TF)-DNA interactions is essential for understanding the regulation of gene expression. Since existing ...

Analysis of Protein Folding, Transport, and Degradation in Living Cells by Radioactive Pulse Chase

Radioactive pulse-chase labeling is a powerful tool for studying the conformational maturation, the transport to their functional cellular location, and the degradation of target proteins in live cells. By using short (pulse) radiolabeling times (&lt;30 min) and tightly controlled chase times, it is possible to label only a small fraction of the total protein pool and follow its folding. When combined with nonreducing/reducing SDS-polyacrylamide gel electrophoresis (SDS-PAGE) and immunoprecipitation with (conformation-specific) antibodies, folding processes can be examined in great detail. This system has been used to analyze the folding of proteins with a huge variation in properties such as soluble proteins, single and multi-pass transmembrane proteins, heavily N- and O-glycosylated proteins, and proteins with and without extensive disulfide bonding. Pulse-chase methods are the basis of kinetic studies into a range of additional features, including co- and posttranslational modifications, oligomerization, and polymerization, essentially allowing the analysis of a protein from birth to death. Pulse-chase studies on protein folding are complementary with other biochemical and biophysical methods for studying proteins in vitro by providing increased temporal resolution and physiological information. The methods as described within this paper are adapted easily to study the folding of almost any protein that can be expressed in mammalian or insect-cell systems.

Here we describe a protocol for a general pulse-chase method that allows the kinetic analysis of folding, transport, and degradation of proteins to be followed in live cells.

Radioactive pulse-chase labeling is a powerful tool for studying the conformational maturation, the transport to their functional cellular location, and ...

Detection of Protein Ubiquitination Sites by Peptide Enrichment and Mass Spectrometry

The posttranslational modification of proteins by the small protein ubiquitin is involved in many cellular events. After tryptic digestion of ubiquitinated proteins, peptides with a diglycine remnant conjugated to the epsilon amino group of lysine (&#39;K-&#949;-diglycine&#39; or simply &#39;diGly&#39;) can be used to track back the original modification site. Efficient immunopurification of diGly peptides combined with sensitive detection by mass spectrometry has resulted in a huge increase in the number of ubiquitination sites identified up to date. We have made several improvements to this workflow, including offline high pH reverse-phase fractionation of peptides prior to the enrichment procedure, and the inclusion of more advanced peptide fragmentation settings in the ion routing multipole. Also, more efficient cleanup of the sample using a filter-based plug in order to retain the antibody beads results in a greater specificity for diGly peptides. These improvements result in the routine detection of more than 23,000 diGly peptides from human cervical cancer cells (HeLa) cell lysates upon proteasome inhibition in the cell. We show the efficacy of this strategy for in-depth analysis of the ubiquitinome profiles of several different cell types and of in vivo samples, such as brain tissue. This study presents an original addition to the toolbox for protein ubiquitination analysis to uncover the deep cellular ubiquitinome.

We present a method for the purification, detection, and identification of diGly peptides that originate from ubiquitinated proteins from complex biological samples. The presented method is reproducible, robust, and outperforms published methods with respect to the level of depth of the ubiquitinome analysis.

The posttranslational modification of proteins by the small protein ubiquitin is involved in many cellular events. After tryptic digestion of ...

Creating Highly Specific Chemically Induced Protein Dimerization Systems by Stepwise Phage Selection of a Combinatorial Single-Domain Antibody Library

Protein dimerization events that occur only in the presence of a small-molecule ligand enable the development of small-molecule biosensors for the dissection and manipulation of biological pathways. Currently, only a limited number of chemically induced dimerization (CID) systems exist and engineering new ones with desired sensitivity and selectivity for specific small-molecule ligands remains a challenge in the field of protein engineering. We here describe a high throughput screening method, combinatorial binders-enabled selection of CID (COMBINES-CID), for the de novo engineering of CID systems applicable to a large variety of ligands. This method uses the two-step selection of a phage-displayed combinatorial nanobody library to obtain 1) &#34;anchor binders&#34; that first bind to a ligand of interest and then 2) &#34;dimerization binders&#34; that only bind to anchor binder-ligand complexes. To select anchor binders, a combinatorial library of over 109 complementarity-determining region (CDR)-randomized nanobodies is screened with a biotinylated ligand and hits are validated with the unlabeled ligand by bio-layer interferometry (BLI). To obtain dimerization binders, the nanobody library is screened with anchor binder-ligand complexes as targets for positive screening and the unbound anchor binders for negative screening. COMBINES-CID is broadly applicable to select CID binders with other immunoglobulin, non-immunoglobulin, or computationally designed scaffolds to create biosensors for in vitro and in vivo detection of drugs, metabolites, signaling molecules, etc.

Creating chemically induced protein dimerization systems with desired affinity and specificity for any given small molecule ligand would have many biological sensing and actuation applications. Here, we describe an efficient, generalizable method for de novo engineering of chemically induced dimerization systems via the stepwise selection of a phage-displayed combinatorial single-domain antibody library.