Oxidative refolding of rPA in l -ArgHCl and in ionic liquids: A correlation between hydrophobicity, salt effects, and refolding yield

Systematic enhancement of protein crystallization efficiency by bulk lysine-to-arginine (KR) substitution

Structural genomics consortia established that protein crystallization is the primary obstacle to structure determination using x-ray crystallography. We previously demonstrated that crystallization propensity is systematically related to primary sequence, and we subsequently performed computational analyses showing that arginine is the most overrepresented amino acid in crystal-packing interfaces in the Protein Data Bank. Given the similar physicochemical characteristics of arginine and lysine, we hypothesized that multiple lysine-to-arginine (KR) substitutions should improve crystallization. To test this hypothesis, we developed software that ranks lysine sites in a target protein based on the redundancy-corrected KR substitution frequency in homologs. This software can be run interactively on the worldwide web at https://www.pxengineering.org/. We demonstrate that three unrelated single-domain proteins can tolerate 5-11 KR substitutions with at most minor destabilization, and, for two of these three proteins, the construct with the largest number of KR substitutions exhibits significantly enhanced crystallization propensity. This approach rapidly produced a 1.9 Å crystal structure of a human protein domain refractory to crystallization with its native sequence. Structures from Bulk KR-substituted domains show the engineered arginine residues frequently make hydrogen-bonds across crystal-packing interfaces. We thus demonstrate that Bulk KR substitution represents a rational and efficient method for probabilistic engineering of protein surface properties to improve crystallization.

The temperature dependence of the Hofmeister series: thermodynamic fingerprints of cosolute-protein interactions

The Hofmeister series is a universal homologous series to rank ion-specific effects on biomolecular properties such as protein stability or aggregation propensity. Although this ranking is widely used, outliers and exceptions are discussed controversially and a molecular level understanding is still lacking. Studying the thermal unfolding equilibrium of RNase A, we here show that this ambiguity arises from the oversimplified approach to determine the ion rankings. Instead of measuring salt effects on a single point of the protein folding stability curve (e.g. the melting point T_m), we here consider the salt induced shifts of the entire protein 'stability curve' (the temperature dependence of the unfolding free energy change, ΔG_u(T)). We found multiple intersections of these curves, pinpointing a widely ignored fact: the Hofmeister cation and anion rankings are temperature dependent. We further developed a novel classification scheme of cosolute effects based on their thermodynamic fingerprints, reaching beyond salt effects to non-electrolytes.