Difference between revisions of "20.109(S23):M1D8"

Introduction

Protocols

Part 1: Identify common features in SMM hits

One method for assessing protein-small molecule binding is to visually inspect known small molecule binders for common features / structures. To do this you will carefully examine the hits and identify any common features / structures. As in the image below, it is possible that multiple features will be present within the same small molecule.

Review the hits that were identified in the SMM screen completed for TDP43-RRM12. To see the chemical structures, translate the SMILES strings using one of the methods described in the text below the table. It may be easier to copy / paste the small molecule images into a powerpoint file so you can readily see all of the structures. Also, it may be helpful to use a color-coding system (like the one in the image provided above) to highlight features / structures that are common to the hits.

These online resources may be helpful to learning more about the hits identified in the SMM:

• Cloud version of ChemDraw here.
  • Copy and paste the small molecule smiles into the work space to get a chemical structure
• Platform to transform the smiles information into a PubChem ID here.
  • Copy and paste the smiles into the input ID search to determine the ID number.
• PubChem database of chemical information here.
  • Includes small molecule molecular weight and other useful information.

In your laboratory notebook, complete the following:

• How many features did you identify that are present in two or more of the small molecules that putatively bind TDP43-RRM12? Are there more or less than you expected?
• Is there a feature present in all of the identified small molecules? What might this suggest about the binding site(s) and / or binding ability of TDP43-RRM12?
• Can you assign the identified small molecules to sub-groups based on the common features that are present?
• What might the different features represent? More specifically, consider whether each subgroup has a unique binding site on the target protein or if each subgroup represents different solutions for interacting with the same binding site.
• How might you make modifications to the small molecules / features to probe binding? As a hint, consider how different functional groups could be positioned at a given site without altering qualitative binding in the SMM assay to translate that into some testable ideas.

Part 2: Outline Data summary and divide workload accordingly

In science publications it is uncommon to find single-author papers. Most science is done in collaboration with peers and colleagues, and this is true for your Data summary assignment. You will work with your partner to prepare a draft and revision that describes the work you completed in Module 1. To ensure the work is distributed evenly you will first assess what needs to be done to complete the assignment and then decide who will be responsible for which parts.

Assess what needs to be done

Prepare an outline for your Data summary that highlights the components that should be included (i.e. "Background & Motivation" and "Results, Figure 1"). For each component, list what has been done (for example, "prompts regarding information for Background & Motivation section from due M1D2 homework") and what needs to be completed (for example, "use due M1D2 answers to write bullets for Background & Motivation section").

Distribute what needs to be done between partners

With your partner, decide who will tackle which components of the assignment. Discuss what work needs to be completed such that you are both in agreement on what is expected. Then discuss who will be responsible for that work. Remember that the assignment is graded as a whole and both partners will receive a score based on the whole and not their individual contributions. In this, it is important that both partners are involved in all components...either as the primary writer or as a reviewer. Next, coordinate times that you can meet to discuss the progress of the work and / or to review the work. It is also helpful to set deadlines for when certain work should be done so both partners are able to stay on track and be accountable.

Questions to guide your discussion:

1. What needs to be done for the assignment?
2. What components should each person complete (because of prior knowledge or interest or because of homework assignments)?
3. What are reasonable deadlines by which each component can be completed?

In your laboratory notebook, complete the following:

• Based on your discussion with your laboratory partner, record the following:
  • What has been done?
  • What needs to be done?
  • Who will complete which components?
  • When will you meet to discuss progress and review the completed components?

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