The Blueprint of the Cell's
Cleanup Crew Is Complete

For the first time, the 3D structures of 61 proteins governing mitochondrial quality control have been mapped in a single atlas. AI-powered structure prediction made it possible.

Bluewhale AI Inc. · Entropy Lab · June 2026

When the Power Plant Fails

Every cell in your body contains thousands of mitochondria — tiny organelles that burn oxygen to generate energy. Like any machine, they wear out over time. Healthy cells continuously identify damaged mitochondria, break them down, and replace them with fresh ones. This recycling process is called mitophagy, and the surveillance network that orchestrates it is known as MitoQC (Mitochondrial Quality Control).

The challenge is that MitoQC is not a single switch — it's a team of over 60 proteins working in concert. If one member fails, the entire cleanup cascade can stall. The gene mutations most commonly found in familial Parkinson's disease — PINK1 and Parkin — are precisely the key players in this team. When they malfunction, damaged mitochondria pile up inside neurons, and those neurons begin to die.

"To design a drug, you first need to know the structure. You can't cut a key without knowing the shape of the lock."

The Map That Didn't Exist

Until now, researchers have studied each of these 61 proteins individually — a painstaking process that can take years per protein. Some had known structures; others had only partial coverage; still others had never been visualized at all. A complete "blueprint" — a single map showing the 3D architecture of every member of the MitoQC team — simply did not exist.

This study fills that gap. Using AI-powered structure prediction tools AlphaFold2 and ESMFold, we predicted the 3D structures of all 61 MitoQC proteins and organized them into eight functional modules, creating the world's first comprehensive MitoQC structural atlas.

MitoQC proteins
structurally mapped

Entirely novel folds
never seen before

Functional modules
in the atlas

What AI Changed

Determining a protein's structure experimentally has traditionally required years of work and enormous resources. In 2021, DeepMind's AlphaFold2 upended that equation — given only an amino acid sequence, it can predict a protein's 3D structure in minutes. What makes this study distinct is that we applied this technology not to a single protein, but systematically across an entire disease pathway. Think of it as switching from surveying buildings one by one to capturing an entire city from satellite in a single pass.

Particularly noteworthy are three protein-interface docking simulations: how PINK1 anchors itself to the mitochondrial membrane, how VDAC2 and BAK exchange cell-death signals at the outer membrane, and how mitochondrial targeting sequences are recognized by the import machinery. Each of these interfaces represents a potential target for future Parkinson's disease therapeutics.

Six proteins displayed folds with no structural counterpart anywhere in the global protein database. For the first time, these proteins have a three-dimensional face.

Why It Matters

Drug discovery operates on a lock-and-key principle: you need to know the shape of the lock (the protein) before you can design the key (the drug). Many MitoQC proteins have never been viable drug targets simply because their structures were unknown. This atlas delivers the blueprints for those locks — all at once.

Beyond Parkinson's disease, the framework demonstrated here — systematically covering an entire disease pathway with AI structure prediction — is immediately applicable to autophagy, the unfolded protein response, and other critical cellular pathways. This represents not just a resource for mitochondrial biology, but a new research paradigm for cell biology at large.

Contact

Richard Minryong Kim (김민용)

Senior Scientist · Bluewhale AI Inc. / Entropy Lab

richard@archora2026.com

This research is conducted at Entropy Lab, Bluewhale AI Inc. The MitoQC structural atlas dataset will be made publicly available upon publication. Target journal: Structure (Cell Press).

Entropy Lab · Bluewhale AI Inc. · 2026

The Blueprint of the Cell'sCleanup Crew Is Complete

The Blueprint of the Cell's
Cleanup Crew Is Complete