Arginine to Lysine Mutations Increase the Aggregation Stability of a Single-Chain Variable Fragment through Unfolded-State Interactions

• Published in: Biochemistry (Easton) 2019-08, Vol.58 (32), p.3413-3421
• Main Authors: Austerberry, James I, Thistlethwaite, Angela, Fisher, Karl, Golovanov, Alexander P, Pluen, Alain, Esfandiary, Reza, van der Walle, Christopher F, Warwicker, Jim, Derrick, Jeremy P, Curtis, Robin
• Format: Article
• Language: English
• ISSN: 0006-2960; 1520-4995
• DOI: 10.1021/acs.biochem.9b00367

Increased protein solubility is known to correlate with an increase in the proportion of lysine over arginine residues. Previous work has shown that the aggregation propensity of a single-chain variable fragment (scFv) does not correlate with its conformational stability or native-state protein–protein interactions. Here, we test the hypothesis that aggregation is driven by the colloidal stability of partially unfolded states, studying the behavior of scFv mutants harboring single or multiple site-specific arginine to lysine mutations in denaturing buffers. In 6 M guanidine hydrochloride (GdmCl) or 8 M urea, repulsive protein–protein interactions were measured for the wild-type and lysine-enriched (4RK) scFvs reflecting weakened short-range attractions and increased excluded volume. In contrast to the arginine-enriched mutant (7KR) scFv exhibited strong reversible association. In 3 M GdmCl, the minimum concentration at which the scFvs were unfolded, the hydrodynamic radius of 4RK remained constant but increased for the wild type and especially for 7KR. Studies of single-point arginine to lysine scFv mutants indicated that the observed aggregation propensity of arginine under denaturing conditions was nonspecific. Interestingly, one such swap generated a scFv with especially low aggregation rates under low/high ionic strengths and denaturing buffers; molecular modeling identified hydrogen bonding between the arginine side chain and main chain peptide groups, stabilizing the structure. The arginine/lysine ratio is not routinely considered in biopharmaceutical scaffold design or current amyloid prediction methods. This work therefore suggests a simple method for increasing the stability of a biopharmaceutical protein against aggregation.