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1935: Two-Sided Interface Design

Closed since about 5 years ago

Intermediate Overall Design

Summary

Created
December 25, 2020
Expires
Max points
100
Description

Design an interface between two protein chains! This puzzle is much like Puzzle 1929, with a suite of Core Existence Objectives to ensure that both chains have a substantial core. The starting structure includes two helical hairpins that are frozen in place and separated from one another. We want to build on these hairpins to create a binding interface between the two protein chains. However, the starting position of the hairpins is important, so the locked hairpins 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 the two hairpins, it will be important to make a strong core with each chain, so that the chains fold up correctly. It will also be important to have a strong core at the interface where the two chains come together, so that they bind each other tightly. Keep an eye on the Core Existence Objective, which tracks all of these core residues together. Players may add up to 40 additional residues at a cost of 50 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.

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

Core Existence: Total (max +5000)
Ensures that at least 30% of residues are buried in the core of the entire solution.

Residue Count (max +2000 +2200)
Penalizes added residues at a cost of 50 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, -150 -50 points per atom (not including symmetric copies).

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.

grogar7 Lv 1

I checked and the maximum on the residue count filter is 2200 points. Each additional residue costs 55 points, with a maximum added count of 40 bringing the filter bonus down to 0 points.