Rheostats, toggles, and neutrals, Oh my! A new framework for understanding how amino acid changes modulate protein function

• Published in: The Journal of biological chemistry Vol. 300; no. 3; p. 105736
• Main Authors: Swint-Kruse, Liskin, Fenton, Aron W.
• Format: Journal Article
• Language: English
• Published: United States Elsevier Inc 01.03.2024; American Society for Biochemistry and Molecular Biology
• Subjects: Amino Acid Sequence; Amino Acid Substitution; Amino Acids - genetics; Amino Acids - metabolism; Conserved Sequence; Evolution, Molecular; Humans; Intrinsically Disordered Proteins - chemistry; Intrinsically Disordered Proteins - genetics; Intrinsically Disordered Proteins - metabolism; JBC Reviews; Membrane Proteins - chemistry; Membrane Proteins - genetics; Membrane Proteins - metabolism; personalized medicine; Protein Engineering; protein evolution; protein function; protein stability; Proteins - chemistry; Proteins - genetics; Proteins - metabolism; Structure-Activity Relationship; CIITA; Km; QFBP; ZmPYK; protein function; KFBP; OATP1b1; AUC; FBP; Kapp; NTCP; Tm; MSA; ID; WT; QAla; hLPYK; PYK; protein evolution; Vmax; ROC; KAla; SSM; protein stability; personalized medicine; ΔGu; protein engineering; Ala; GB1; Kapp-PEP; semiSM; IPTG; Kd; PEP; LacI
• ISSN: 0021-9258; 1083-351X; 1083-351X
• DOI: 10.1016/j.jbc.2024.105736

Advances in personalized medicine and protein engineering require accurately predicting outcomes of amino acid substitutions. Many algorithms correctly predict that evolutionarily-conserved positions show “toggle” substitution phenotypes, which is defined when a few substitutions at that position retain function. In contrast, predictions often fail for substitutions at the less-studied “rheostat” positions, which are defined when different amino acid substitutions at a position sample at least half of the possible functional range. This review describes efforts to understand the impact and significance of rheostat positions: (1) They have been observed in globular soluble, integral membrane, and intrinsically disordered proteins; within single proteins, their prevalence can be up to 40%. (2) Substitutions at rheostat positions can have biological consequences and ∼10% of substitutions gain function. (3) Although both rheostat and “neutral” (defined when all substitutions exhibit wild-type function) positions are nonconserved, the two classes have different evolutionary signatures. (4) Some rheostat positions have pleiotropic effects on function, simultaneously modulating multiple parameters (e.g., altering both affinity and allosteric coupling). (5) In structural studies, substitutions at rheostat positions appear to cause only local perturbations; the overall conformations appear unchanged. (6) Measured functional changes show promising correlations with predicted changes in protein dynamics; the emergent properties of predicted, dynamically coupled amino acid networks might explain some of the complex functional outcomes observed when substituting rheostat positions. Overall, rheostat positions provide unique opportunities for using single substitutions to tune protein function. Future studies of these positions will yield important insights into the protein sequence/function relationship.