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Alternative Computational Protocols for Supercharging Protein Surfaces for Reversible Unfolding and Retention of Stability

Figure 4

Rosetta and AvNAPSA supercharge protocols mutate different residues.

A) AvNAPSA-mutated residue positions (white) are highly exposed and are often in loop regions, while Rosetta-mutated residue positions (blue) are less exposed and two mutations are in stable secondary structures. Native side chains of the mutated positions are shown in spheres to convey that Rosetta can mutate hydrophobic and small-polar residues. We emphasize that no mutations are shared between the two approaches in this low-charge design. B) Moderate supercharging was performed on 600 monomeric proteins, and the mutated residues were compared – each monomer was designed with the same net charge in both approaches. Rosetta requires more mutations to achieve the same net charge (solid v. empty). For negative-charge designs, 9% of mutated residue positions are shared (black, left). For positive-charge designs, 6% of mutated residue positions are shared (black, right). Shared mutations decrease an additional ∼2-fold considering that the chosen residue type differs ∼50% of the time for the shared residue positions – AvNAPSA never uses arginine, and AvNAPSA only uses aspartate if the native residue is asparagine.

Figure 4