MotorSmiths
I rebuilt nature's strongest molecular motor — the phi29 gp16 DNA-packaging ATPase — as a single programmable protein, entirely in silico.
Core trick
Fuses five identical ring subunits into one covalent chain via circular permutation, making each seat individually addressable, then validates it with structure prediction and molecular dynamics.
Tags
Description
I rebuilt nature's strongest molecular motor — the phi29 gp16 DNA-packaging ATPase — as a single programmable protein, entirely in silico.
The motor is a ring of five identical subunits. That sameness is a wall: you cannot tune one subunit, read the firing order, or even model the oligomer. I fused the five subunits into one covalent chain (cp233, 1,750 aa) using circular permutation, so every seat becomes individually addressable and the ring becomes computable.
I then evaluated it. Structurally it is indistinguishable from native: three independent predictors agree 5/5, subunit RMSD 1.80 A / TM 0.94, and it threads dsDNA at the native contacts — designs that merely close the ring cannot. Driven molecular dynamics plus a mechanochemical-ratchet model predict a hand-over-hand mechanism with a falsifiable 3D-MINFLUX signature. The design method generalizes across 13 ring motors and passes a blind retrospective test on ClpX (6/6 working, 0/6 dead mutants).
Why it matters: this turns the strongest packaging machine in biology into one that is both readable — mechanism resolvable one seat at a time — and tunable, a concrete step toward programmable viral DNA packaging (phage engineering, viral-vector production, DNA nanotechnology). Everything is computational, cross-checked, and honestly bounded; it hands the wet lab a concrete, testable to-do list.
README excerpt
# Rebuilding Molecular Motors towards Programmable Viral DNA Packaging **A single-chain, genetically-addressable φ29 gp16 DNA-packaging ring — designed *and* evaluated end-to-end, entirely in silico.** *Longfu Xu, Ph.D · Bustamante Lab, UC Berkeley / HHMI · Built with Claude Science + Claude Code* *"Built with Claude: Life Sciences" (Anthropic × Gladstone) — Research track.* This README is the guide to the whole submission: where the idea came from, what we did, what we found, and where every material lives. Watch the 3-minute video for the story; browse this repo for the storyline; read the report if you want the rigorous detail. --- ## ▶ Start here | | | | |---|---|---| | **Demo video** (3 min, narrated) | the whole story, start to finish | [**▶ Watch on YouTube**](https://youtu.be/ZxMc6qudB5Q) · [download mp4](https://github.com/longfuxu/Rebuilding-motor-hackathon/raw/master/gp16_demo.mp4) | | **Deck** (10 slides, animated) | the same story as slides | [**⬇ gp16_deck.pptx**](https://github.com/longfuxu/Rebuilding-motor-hackathon/raw/master/gp16_deck.pptx) | | **Full report** (13 pp, rigorous) | every claim, with figures and honest bounds | [`report.pdf`](report.pdf) | --- ## Where this came from I am a wet-lab single-molecule biophysicist. I have spent my career at the bench measuring molecular motors one molecule at a time, and I had never done computational protein design — I had never written simulation code. This project is my first entirely in-silico work, and