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1950: Two-sided Interface Design

Closed since about 5 years ago

Intermediate Overall Design

Summary

Created
January 30, 2021
Expires
Max points
100
Description

Design an interface between two protein chains! In this two-sided design puzzle, you can mutate the interface residues of both chains A and B, but you may only shape the backbone of chain A. Chain A should have a substantial core to satisfy the Core Existence Objective, and it should pack tightly against chain B to satisfy the Contact Surface Objective. The goal is to create a binding interface between the two protein chains so that they will stick together in solution. However, the starting position of the two chains is important, so the locked regions are held in place by strong constraints. The only way to make the two chains bind will be to fold up a brand new interface between them.



As you build on chain A, it will be important to make a strong core so that it folds up correctly. It will also be important to have good hydrophobic packing at the interface where the two chains come together, so that they bind each other tightly. Players may add up to 40 additional residues at a cost of 55 points per residue. See the puzzle comments for Objective details.

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Comments

bkoep Staff Lv 1

Core Existence: Chain A (max +5000)
Ensures that at least 24% of residues are buried in the core of the entire solution.

Contact Surface (max +1000)
Measures how much of your binder surface is in close contact with the target protein. The goal Contact Surface is 400 or more.

Residue Count (max +2200)
Penalizes added residues at a cost of 55 pts per residue. Players may add up to 40 residues, for a total of 220.

Buried Unsats (max +500)
Penalizes polar atoms that cannot make hydrogen bonds, -50 points per atom.

Interaction Energy (max +500)
Monitors that all large PHE, TYR, and TRP residues are scoring well.

SS Design (max +500)
Penalizes all CYS residues. Penalizes GLY, ALA residues in sheets. Penalizes GLY, SER, THR in helices.

Ideal Loops (max +500)
Penalizes any loop region that does not match one of the Building Blocks in the Blueprint tool. Use "Auto Structures" to see which regions of your protein count as loops.

LociOiling Lv 1

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