Homework
Weekly homework submissions:
Week 1 HW: Principles and Practices
Governance of AI-Driven Biological Design 1. Biological Engineering Application or Tool Description As the core idea of my project, I would like to develop a concept that has been under discussion in my laboratory for some time: a computational platform for the de novo design of peptide and protein ligands capable of inhibiting essential microbial processes, such as translation, with the goal of suppressing or controlling microbial growth.
Week 2 — DNA Read, Write, & Edit
Part 1: Benchling & In-silico Gel Art Simulate Restriction Enzyme Digestion with the following Enzymes: Part 3: DNA Design Challenge 3.1. Choose your protein. In recitation, we discussed that you will pick a protein for your homework that you find interesting. Which protein have you chosen and why? Using one of the tools described in recitation (NCBI, UniProt, google), obtain the protein sequence for the protein you chose.
- Article / case study: Automation at Adaptyv Bio and protein binder design competitions A prominent example of the use of automation in biology is the work carried out by Adaptyv Bio, a company specialized in laboratory automation and the integration of artificial intelligence for protein design and validation. In particular, Adaptyv Bio organized international protein design competitions, such as the Protein Binder Competition, in which thousands of computationally generated designs were experimentally tested using fully automated workflows.
Week 4 — Protein Design Part I
Part A. Conceptual Questions Why do humans eat beef but not turn into cows, and eat fish but not turn into fish? Organisms do not incorporate intact proteins. Instead, they degrade them into amino acids, which are then reassembled according to the organism’s own genome. Molecular identity is determined by genetic information, not by the origin of the raw material. Why are there only 20 natural amino acids? Only 20 were selected by early evolution because they possessed a specific chemistry that allowed for a functional balance of hydrophobicity, specific folding patterns, and various electrical charges.
Week 5 — Protein Design Part II
Part 1: Generation of Peptide Binders with PepMLM The human SOD1 sequence (P00441) was retrieved from UniProt and the A4V mutation was introduced. Using PepMLM, four peptides of length 12 amino acids were generated conditioned on the mutant SOD1 sequence. A known SOD1-binding peptide (FLYRWLPSRRGG) was added for comparison. Generated Peptides and Perplexity Scores Peptide Sequence Perplexity PepMLM-0 WRYPAAAAAHKE 8.27 PepMLM-1 WLYYVVALEWGK 23.99 PepMLM-2 WLYYAAALELKE 18.84 PepMLM-3 WRYGVAAVEWKK 15.52 Control FLYRWLPSRRGG N/A
Week 6 — Genetic Circuits Part I: Assembly Technologies
Phusion Master Mix Components This mix contains a high-fidelity polymerase with proofreading activity (3 to 5 exonuclease) to minimize sequence errors. It also includes dNTPs as DNA building blocks, an optimized buffer with salts like magnesium chloride that act as enzymatic cofactors, and stabilizers to maintain the pH and ionic strength required for the reaction. Factors Determining Annealing Temperature The annealing temperature primarily depends on the melting temperature (T_m) of the primers, which is influenced by sequence length and GC content. Other external factors include the concentration of salts (monovalent and divalent) in the PCR buffer and the concentration of the primers themselves in the mixture.
Week 7 — Genetic Circuits Part II: Neuromorphic Circuits
Assignment Part 1: Intracellular Artificial Neural Networks (IANNs) What advantages do IANNs have over traditional genetic circuits, whose input/output behaviors are Boolean functions? IANNs provide a significant advantage over Boolean genetic circuits by enabling analog computation, which allows cells to process a continuous range of signal concentrations rather than simple on/off states. This capability leads to more efficient signal integration, as a single layer can replace complex cascades of logic gates, while offering greater tunability by adjusting molecular weights like promoter strengths without re-engineering the entire system.
PART 1 Question 1: What are the main advantages of cell-free protein synthesis (CFPS) regarding flexibility and control, and name two cases where it is more beneficial? Since it is an open system, you have direct control over the chemical environment (pH, redox potential, and salts) and can add synthetic components like non-natural amino acids without being restricted by a cell membrane. Case 1: Production of cytotoxic proteins that would otherwise kill a living host cell. Case 2: Efficient incorporation of labeled isotopes or synthetic tags for precise protein engineering.