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20.109(F22): Laboratory Fundamentals of Biological Engineering

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Fall 2022 schedule        FYI        Assignments        Homework        Class data        Communication        Accessibility

       M1: Genomic instability        M2: Drug discovery        M3: Project design       


Today you will analyze the data for the DSF experiment. These results will be the focus of your major writing assignment for this module, the Research article.

As a reminder DSF is a functional assay used to probe the interaction between a single protein of interest and a putative small molecule binder. In this assay, the melting temperature (Tm) of the protein is measured using a fluorescent dye and a change in the melting temperature (ΔTm) when the small molecule is present in the reaction is indicative of binding.

The DSF assay is one method used to validate 'hits' identified using a high-throughput approach, such as the SMM. Though an SMM was not used as part of this module, it was discussed to highlight how a researcher can easily screen through tens-of-thousands of compounds to generate a curated list of small molecules that can be further tested using a functional assay. For this module, we started with a short list of compounds based on known binders of our protein of interest. In either case, the workflow of this type of project is 1) identify putative binders using a screen or other method to generate a curated list of hits, 2) validate hits using a functional assay, 3) measure parameters such as specificity and affinity that exist between the protein of interest and validated hits.

Fa22 M2D6 workflow.png


Part 1: Examine binding shifts

You will receive two XML files containing raw data from each well of a 384 well plate over the specified range of temperatures. These files can be opened by dragging onto an open Excel window. The XML sheet with "Melt" in the file name will contain raw fluorescence intensity data, while the other sheet with "Tm" in its name will have the values for the first derivative of the melt curve. The leftmost column gives you the identity of the well. Refer back to your notes to determine what samples were loading in which wells. The “X” column denotes the temperature and the “Y” column denotes the fluorescence value for that well at that temperature.

One basic way to determine the "melting temperature," or Tm of the protein is to determine temperature at the inflection point of the melting curve. This inflection point would occur at the maximum value of the first derivative. The BioRad CFX machine we use actually exports the negative of the first derivative in the Excel file, so we will find the minimum value in the first derivative Excel file, and take the corresponding temperature to be the Tm in each condition.

  1. Open the Excel file corresponding to the first derivative data
  2. Copy over the column with the well identifier in a separate worksheet under column A, Copy over the temperature data in celsius in column B, and copy over the fluorescence data in column C
  3. At a row on the bottom of column C, type in the following command: =INDEX($B$FirstRow:$B$LastRow, MATCH(MIN(CFirstRow:CLastRow),CFirstRow:CLastRow,0)), where FirstRow corresponds to the row number of the first row containing data, and LastRow contains the row number of the last row containing data.
  4. Press enter, and double check that the listed temperature occurs at the minimum value of the first derivative.
  5. Then, drag the bottom left corner of the cell across all relevant columns to apply the formula to those columns of interest.
  6. Plot the columns relevant to your data set by making a scatter plot ("straight marked scatter"), having the temperature (values in column B) on the x-axis, and the first derivative values on the y-axis.
  7. Double check by eye that the values you calculated to be the melting temperatures correspond to the minimum values on the curves. (See example plot in the introduction section of the M2D5 wiki page)
  8. Next, you may also check to see what the melting curves look like in terms of raw fluorescence by plotting fluorescence intensity vs. temperature in the "Melt Curve RFU Results" file. Again, validate the results you found by eye to see if the Tm values correspond to the inflection point of the raw fluorescence melt curves.
  9. To determine whether ligand bound to either FKBP12 or FKBP35, plot the corresponding curves on the same plot as your DMSO control per compound tested. Quantify the shifts.
  10. Record the Tm values calculated for the small molecules you tested on the Class data page of the wiki.

In your laboratory notebook, complete the following:

  • Record the Tm values.
  • Attach the graphs generated as part of the analysis.

Part 2: Organize figures and outline results text for your Research article

The goal for today is to focus on how you will communicate the results you are gathering and analyzing in the Research article.

Currently, you have partial drafts and outlines for each of the sections (with Instructor feedback!) that will be included in the Research article. Today you will organize and write a detailed outline for the data that you collected for this module. Use the skills you learned when you completed the figure homework and apply them to the remaining figures for your Research article.

To get started on this process, complete the following:

  1. Make a list of all of the schematics / data figures / tables that will be included.
  2. Organize the figures such that the data tell a coherent story that answers your research question.
  3. Complete the following steps for each figure:
    • Write a conclusive figure title that relays the main take-home message for the data shown.
    • Write a results subsection title that mimics the figure title.
    • Outline the text that will be included in the results subsection using the prompts included in the Results section of Research article page.

In your laboratory notebook, complete the following:

  • Include the list of schematics / data figures / tables.
  • For each schematic / data figure / table, provide a brief summary of the information that will included in the text of the results section.

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