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

Figure 5

Low-charge variant residue energy changes per structure (600 total) broken down by each weighted score term.

Red: negative-charge variants. Blue: positive-charge variants. Solid bars: Rosetta designs. Empty bars: AvNAPSA designs. AvNAPSA mutations have little effect on computed energy, on average (right, empty bars). Rosetta improves total energy primarily through Lennard-Jones attraction (fa_atr), charge complementarity (fa_pair), and reference energy, and a minor improvement results from addition of hydrogen bonds (left, solid bars). Rosetta mutations lead to increases in solvation energy (fa_sol) for negative supercharging. Not all score terms are included because their values cannot change in fixed backbone design (backbone-backbone hydrogen bonds, disulfides, proline closure, omega angle planarity). total: total residue energy, fa_atr: Lennard-Jones attraction, fa_rep: Lennard-Jones repulsion, fa_sol: Lazaridus-Karplus implicit solvation (penalizes buried polar atoms, slightly rewards buried carbon atoms), fa_pair: knowledge-based statistical term favoring oppositely-charged residues in close proximity, hbond_bb_sc: geometric score for backbone-sidechain hydrogen bonds, hbond_sc: geometric score for sidechain-sidechain hydrogen bonds.

Figure 5

doi: https://doi.org/10.1371/journal.pone.0064363.g005