image.png

Lecture (03/04)

<aside> <img src="/icons/slide_green.svg" alt="/icons/slide_green.svg" width="40px" /> Lecture slides will be shared here after the class!

</aside>

<aside> <img src="/icons/video-camera_yellow.svg" alt="/icons/video-camera_yellow.svg" width="40px" /> Lecture recording

</aside>

Recitation (03/05)

<aside> <img src="/icons/slide_green.svg" alt="/icons/slide_green.svg" width="40px" /> Recitation slides Part 1:

MS2-Phage_homeworkdiscussion (1).pptx

</aside>

<aside> <img src="/icons/video-camera_yellow.svg" alt="/icons/video-camera_yellow.svg" width="40px" /> Recitation recording

</aside>

Homework

<aside> ⚠️ Please read through the full assignment before you get started. This assignment is mandatory for MIT/Harvard students and Committed Listeners. Due March 11 before lecture

</aside>

<aside> <img src="/icons/push-pin_green.svg" alt="/icons/push-pin_green.svg" width="40px" /> Key Links: http://docs.google.com/spreadsheets/d/1AsYRLlrRLd6I8abxNHfuz1OtFTSqYZ87_kefBMsxhMo/edit?gid=0#gid=0

</aside>

Part A (From Pranam)

<aside> ⚠️ Optional for MIT/Harvard Students, mandatory for Committed Listeners. Due at the start of class March 11

</aside>

  1. Sign up for HuggingFace (we will be using PepMLM: https://huggingface.co/ChatterjeeLab/PepMLM-650M)

    1. Once you login, go to the page (https://huggingface.co/settings/tokens). Click +Create new token.
    2. Make sure you type the full name ChatterjeeLab/PepMLM-650M when searching for repos. Click save token and you will see the newly token (copy that).

    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

    1. Go to the page (https://huggingface.co/ChatterjeeLab/PepMLM-650M) and find their Colab Notebook (link).
    2. Make a copy to your Google Drive, choose T4 GPU and run each block.
    3. When running into the block Input HF token , a pop-up will show Enter your token (input will not be visible):. Paste your token and Add token as git credential? (Y/n) choose n.

  2. Find the amino acid sequence for SOD1 in UniProt (ID: P00441), a protein when mutated, can cause Amyotrophic lateral sclerosis (ALS). In fact, the A4(5)V (when you change position 4 from Alanine to Valine) causes the most aggressive form of ALS, so make that change in the sequence

Should be position 5 https://www.ncbi.nlm.nih.gov/snp/rs121912442

MATKAVCVLKGDGPVQGIINFEQKESNGPVKVWGSIKGLTEGLHGFHVHEFGDNTAGCTSAGPHFNPLSRKHGGPKDEERHVGDLGNVTADKDGVADVSIEDSVISLSGDHCIIGRTLVVHEKADDLGKGGNEESTKTGNAGSRLACGVIGIAQ

  1. Enter your mutated SOD1 sequence into the PepMLM inference API and generate 4 peptides of length 12 amino acids (Step 5 takes a while so you can also just pick 1 or 2 peptides)

MATKVVCVLKGDGPVQGIINFEQKESNGPVKVWGSIKGLTEGLHGFHVHEFGDNTAGCTSAGPHFNPLSRKHGGPKDEERHVGDLGNVTADKDGVADVSIEDSVISLSGDHCIIGRTLVVHEKADDLGKGGNEESTKTGNAGSRLACGVIGIAQ

What is top K value?

  1. To your list, add this known SOD1-binding peptide to your list: FLYRWLPSRRGG [from -https://genesdev.cshlp.org/content/22/11/1451]

WWWDPVAGAKKWAKK SWWGVYAGVVAAKAK SWWDVYVAVVELKKK

  1. Go to AlphaFold-Multimer (https://colab.research.google.com/github/sokrypton/ColabFold/blob/main/AlphaFold2.ipynb). This is similar to what you did for homework last week but instead for a protein-peptide complex

    1. Set model_type: alphafold2_multimer_v3 (this model has been shown to recapitulate peptide-protein binding accurately: https://www.frontiersin.org/articles/10.3389/fbinf.2022.959160/full). * Add your query sequence - Its the SOD1Sequence:PeptideSequence.

    *MATKVVCVLKGDGPVQGIINFEQKESNGPVKVWGSIKGLTEGLHGFHVHEFGDNTAGCTSAGPHFNPLSRKHGGPKDEERHVGDLGNVTADKDGVADVSIEDSVISLSGDHCIIGRTLVVHEKADDLGKGGNEESTKTGNAGSRLACGVIGIAQ:*WWWDPVAGAKKWAKK:SWWGVYAGVVAAKAK:SWWDVYVAVVELKKK

  2. After running AlphaFold-Multimer with your 5 peptides alongside your mutated SOD1 sequence, plot the ipTM scores, which measures the relative confidence of the binding region.

image.png

  1. Provide a 1 paragraph write-up of your results I really don’t know how to open .json files that contain iptm scores. But learning…

Part B (Final Project: L-Protein Mutants)

<aside> ⚠️ Mandatory for MIT/Harvard Students and Committed Listeners. Due at the start of class March 12

</aside>

<aside> <img src="/icons/exclamation-mark_red.svg" alt="/icons/exclamation-mark_red.svg" width="40px" /> This homework requires computation that might take you a while to run. So please get started early.

</aside>