Benenodin-1
In The Demon Job he's the Knot: a peptide threaded through its own ring, who keeps the Demon's books, one note per knot, and talks when the lamp gets hot.
Benenodin-1 plays The Knot in The Demon Job
A detective made of water, a client who was the first molecule there ever was, and a demon who says he can sort for nothing.
Watch from 20:18, where The Knot first appears → or from the start
Booking photographs
The suspect, from its real atomic coordinates. Drag to turn it. Height chart in nanometers, ruled every 0.1 nm. Mugshot: the form E. coli makes, five residues short. Ring dark.
Rap sheet
- Threading itself: an 8-amino-acid ring with its own tail through it, a [1]rotaxane made by bacteria.
- Sliding under heat: at 95 °C about 63% of its rings slip past a glutamine and park at a lysine.
- Keeping four addresses on one thread, without ever coming off.
- Dawdling: at 13 °C the same shift would take months (an extrapolation).
- Dodging its own enzyme: its isopeptidase cuts it open only in the first position.
- Answers to
- Benenodin-1. Lasso peptide.
- Height
- 2.3 nm, loop up, tail down.
- Weight
- 3.3 zeptograms.
- Build
- An 8-amino-acid ring (dark), its own tail threaded through.
- Topology
- [1]rotaxane: one end tied in, one loose.
- Habits
- At 95 °C its ring slips past a glutamine and parks at a lysine.
- Hours
- On a summer day back home, 13 °C, that would take months.
- Associates
- Its own enzyme cuts it open, but only in the first position.
- Last seen
- In E. coli, made from its genes, in a lab in New Jersey.
- M.O.
- Bacterial enzymes close a ring between glycine 1 and aspartate 8 with the tail threaded through it; glutamate 14 and glutamine 15 hold the ring in place. Heat lets the ring hurdle the small stoppers to the next position; bulky lysine and phenylalanine stop it.
- Associates
- Asticcacaulis benevestitus, the cold-tolerant soil bacterium whose genes encode it; BenE, its own isopeptidase; E. coli, which made every sample studied; synthetic rotaxanes, its man-made cousins
- Priors
- Found as genes and made in E. coli in 2017 (the lab couldn't find it in the bacterium itself); its four threaded positions mapped in 2022.
stops its ring can make along its own thread, without ever coming off.
You’ve never seen one.
“Heat it and it moves. Cool it and it drifts back. That's a mood, not a motor.” — Keltar, on the case
Case notes: switch or motor
The working definitions come from the synthetic molecular-machine field. A switch 'influences the system only as a function of state. Returning the components of a molecular switch to their original position undoes any work done, and so a switch cannot be used repetitively and progressively to do work.' A motor 'influences a system as a function of trajectory'.
Benenodin-1 is a switch. Heating sets up an equilibrium between threaded positions: about 63% switched at 95 °C, and the same ratio again on reheating. There is no ratchet, so there is no cumulative motion. Barriers of 23 to 27 kcal/mol freeze whatever split it had for months after cooling; at 13 °C, the summer temperature where its bacterium lives, the authors extrapolate an equilibrium of about 35%, reached only after months.
Sources
- Erbas-Cakmak S. et al. 2015, Chem. Rev. 115:10081-10206, doi:10.1021/acs.chemrev.5b00146
- Zong C. et al. 2017, J. Am. Chem. Soc. 139:10403-10409, doi:10.1021/jacs.7b04830
- Schroeder H. V. et al. 2022, Chem. Eur. J. 28:e202103615, doi:10.1002/chem.202103615
The interrogation room
Keltar is an AI character. He sticks to the file; the conversation is saved and Kent, the CEO, can read it.
The poster on the street
This is the photocopied wanted poster for Benenodin-1, No. 132 of the exotic forty. They were made for noticeboards around Boston, Cambridge and the rest of the east coast.
Found one? Scan its QR code with your phone. If you're a signed-in player, the sighting goes on your record with +1 XP.
Not a player yet? Join the Epic Quest: the real role-playing game of Molecular Reality, a nanopore lab, with the CEO as gamemaster.