Picture Source: Bordin, Nicola et al (2023). Novel machine learning approaches revolutionize protein knowledge. Trends in Biochemical Sciences, Volume 48, Issue 4, 345 - 359

Lecture

<aside> <img src="/icons/slide_green.svg" alt="/icons/slide_green.svg" width="40px" /> Lecture slides: Zhang - Protein Design - 2.25.25

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

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Recitation

<aside> <img src="/icons/slide_green.svg" alt="/icons/slide_green.svg" width="40px" /> Recitation Slides (added Feb 28):

ProteinDesign.pdf

Phage therapy.pdf

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

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Homework

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

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<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 https://docs.google.com/spreadsheets/d/19_u8Sd8TdseHP6yAVrDSjIKf0vDU9RNH3SEACx8L22Y/edit?gid=0#gid=0

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Objective:

1. Learn basic concepts: amino acid structure, 3D protein visualization, and the variety of ML-based design tools.
2. Brainstorm as a group how to apply these tools to engineer a better bacteriophage (setting the stage for the final project).

Part A. Conceptual Questions

• Answer any of the following questions by Shuguang Zhang:
  • How many molecules of amino acids do you take with a piece of 500 grams of meat? (on average an amino acid is ~100 Daltons)
  • Why humans eat beef but do not become a cow, eat fish but do not become fish?
  • Why there are only 20 natural amino acids?
  • Can you make other non-natural amino acids? Design some new amino acids.
  • Where did amino acids come from before enzymes that make them, and before life started?
  • If you make an alpha-helix using D-amino acids, what handedness (right or left) would you expect?
  • Can you discover additional helices in proteins?
  • Why most molecular helices are right-handed?
  • Why do beta-sheets tend to aggregate?
    • What is the driving force for b-sheet aggregation?
  • Why many amyloid diseases form b-sheet?
    • Can you use amyloid b-sheets as materials?
  • Design a b-sheet motif that forms a well-ordered structure.

Part B: Protein Analysis and Visualization

In this part of the homework, you will be using online resources and 3D visualization software to answer questions about proteins.

1. Pick any protein (from any organism) of your interest that has a 3D structure and answer the following questions.
   • Briefly describe the protein you selected and why you selected it.
   • Identify the amino acid sequence of your protein.
     • How long is it? What is the most frequent amino acid? You can use this notebook to count most frequent amino acid - https://colab.research.google.com/drive/1vlAU_Y84lb04e4Nnaf1axU8nQA6_QBP1?usp=sharing
     • How many protein sequence homologs are there for your protein?Hint: Use the pBLAST tool to search for homologs and ClustalOmega to align and visualize them. Tutorial Here
     • Does your protein belong to any protein family?
   • Identify the structure page of your protein in RCSB
     • When was the structure solved? Is it a good quality structure? Good quality structure is the one with good resolution. Smaller the better (Resolution: 2.70 Å)
     • Are there any other molecules in the solved structure apart from protein?
     • Does your protein belong to any structure classification family?
   • Open the structure of your protein in any 3D molecule visualization software:
     • PyMol Tutorial Here (hint: ChatGPT is good at PyMol commands)
     • Visualize the protein as "cartoon", "ribbon" and "ball and stick".
     • Color the protein by secondary structure. Does it have more helices or sheets?
     • Color the protein by residue type. What can you tell about the distribution of hydrophobic vs hydrophilic residues?
     • Visualize the surface of the protein. Does it have any "holes" (aka binding pockets)?

Part C. Using ML-Based Protein Protein Tools

<aside> <img src="/icons/snippet_lightgray.svg" alt="/icons/snippet_lightgray.svg" width="40px" /> Resources: https://colab.research.google.com/drive/1hXStRY9VCyw52n17uWdWQBj__IcR2ztK?usp=sharing#scrollTo=38gFJBazNdzJ

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• Fold your protein with AlphaFold or ESMFold or Boltz and compare it to the real structure.