1436: NMN Binder Design: Round 2
|Name:||1436: NMN Binder Design: Round 2|
|Expired:||10/10/2017 - 23:00|
|Description:||This is a followup to Puzzle 1422. Redesign the loops of this protein to better bind the ligand! Nicotinamide mononucleotide (NMN) is a small-molecule that makes up part of the small-molecule nicotinamide adenine dinucleotide (NAD), which is sometimes regarded as 'the molecule of youth.' Scientists know that the amount of NAD in our cells declines as we age, and so designing a protein to bind to NMN is the first step towards achieving protein-based biosensors that can detect NMN levels in cells. Such biosensors would help scientists to understand the aging process and could potentially lead to a 'cure' for aging! In this puzzle, players have a little more freedom in redesigning the NMN binding pocket. Players may load in solutions from Puzzle 1422.
The starting structure of this puzzle is a protein designed to bind NMN, but we think it can be improved. There are several loops near the NMN binding pocket that could be extended to make stronger interactions with the ligand. In the selected loops, players may insert and design up to 10 extra residues for free; additional residues may be added at a cost of 15 points per residue. Most of the protein backbone is frozen, and there are strong constraints to keep the ligand positioned in the binding pocket. There are permanent cutpoints flanking each loop, so that players may freely manipulate the loops without disturbing the rest of the structure.
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