Understanding how mutations affect protein activity and organismal fitness is a major challenge. We used saturation mutagenesis combined with deep sequencing to determine mutational sensitivity scores for 1,664 single-site mutants of the 101 residue Escherichia coli cytotoxin, CcdB at seven different expression levels. Active-site residues could be distinguished from buried ones, based on their differential tolerance to aliphatic and charged amino acid substitutions. At nonactive-site positions, the average mutational tolerance correlated better with depth from the protein surface than with accessibility. Remarkably, similar results were observed for two other small proteins, PDZ domain (PSD95pdz3) and IgG-binding domain of protein G (GB1). Mutational sensitivity data obtained with CcdB were used to derive a procedure for predicting functional effects of mutations. Results compared favorably with those of two widely used computational predictors. In vitro characterization of 80 single, nonactive-site mutants of CcdB showed that activity in vivo correlates moderately with thermal stability and solubility. The inability to refold reversibly, as well as a decreased folding rate in vitro, is associated with decreased activity in vivo. Upon probing the effect of modulating expression of various proteases and chaperones on mutant phenotypes, most deleterious mutants showed an increased in vivo activity and solubility only upon over-expression of either Trigger factor or SecB ATP-independent chaperones. Collectively, these data suggest that folding kinetics rather than protein stability is the primary determinant of activity in vivo. This study enhances our understanding of how mutations affect phenotype, as well as the ability to predict fitness effects of point mutations.

Highlights d CcdA antitoxin rejuvenates bacterial DNA gyrase by extracting bound CcdB toxin d CcdA forms transient ternary and quaternary complexes with gyrase:CcdB complex d Molecular basis for rejuvenation elucidated through computation and experiment d Similar methodology can be used to characterize other transient complexes

No abstract

To improve our understanding of the contributions of different stabilizing interactions to protein stability, including that of residual structure in the unfolded state, the small sweet protein monellin has been studied in both its two variant forms, the naturally occurring double-chain variant (dcMN) and the artificially created single-chain variant (scMN). Equilibrium guanidine hydrochloride-induced unfolding studies at pH 7 show that the standard free energy of unfolding, ΔG°(U), of dcMN to unfolded chains A and B and its dependence on guanidine hydrochloride (GdnHCl) concentration are both independent of protein concentration, while the midpoint of unfolding has an exponential dependence on protein concentration. Hence, the unfolding of dcMN like that of scMN can be described as two-state unfolding. The free energy of dissociation, ΔG°(d), of the two free chains, A and B, from dcMN, as measured by equilibrium binding studies, is significantly lower than ΔG°(U), apparently because of the presence of residual structure in free chain B. The value of ΔG°(U), at the standard concentration of 1 M, is found to be ∼5.5 kcal mol(-1) higher for dcMN than for scMN in the range from pH 4 to 9, over which unfolding appears to be two-state. Hence, dcMN appears to be more stable than scMN. It seems that unfolded scMN is stabilized by residual structure that is absent in unfolded dcMN and/or that native scMN is destabilized by strain that is relieved in native dcMN. The value of ΔG°(U) for both protein variants decreases with an increase in pH from 4 to 9, apparently because of the thermodynamic coupling of unfolding to the protonation of a buried carboxylate side chain whose pK(a) shifts from 4.5 in the unfolded state to 9 in the native state. Finally, it is shown that although the thermodynamic stabilities of dcMN and scMN are very different, their kinetic stabilities with respect to unfolding in GdnHCl are very similar.

A buried ionizable residue can have a drastic effect on the stability of a native protein, but there has been only limited investigation of how burial of an ionizable residue affects the kinetics of protein folding. In this study, the effect of burial of ionizable residues on the thermodynamics and kinetics of folding and unfolding of monellin has been investigated. The stability of wild-type (wt) monellin is known to decrease with an increase in pH from 4 to 10. The Glu24 → Ala mutation makes the stability of the resultant E24A mutant protein independent of pH in the range from 4 to 8. An additional mutation, Cys42 → Ala, results in the stability becoming independent of pH in the range from 4 to 10. Like the wt protein, E24A folds via very fast, fast, and slow folding pathways. Compared to that of the wt protein, the rate of slow folding pathway of E24A is ~7-fold faster, the rate of fast folding pathway is ~1.5-fold faster, while the rate of very fast folding pathway is similar. E24A unfolds ~7-fold slower than the wt. The extent of stabilization of the transition state (TS) observed for the slow pathway of refolding and for unfolding is the same, indicating that unfolding occurs via the TS populated on the slow pathway of refolding. The stabilization of the TS of folding (1.1 kcal mol(-1)) is less than that of the native state (2.3 kcal mol(-1)) of E24A, indicating that structure has only partially formed in the vicinity of Glu24 in the TS of folding.

The existence of parallel pathways in the folding of proteins seems intuitive, yet remains controversial. We explore the folding kinetics of the homodimeric Escherichia coli toxin CcdB (Controller of Cell Division or Death B protein) using multiple optical probes and approaches. Kinetic studies performed as a function of protein and denaturant concentrations demonstrate that the folding of CcdB is a four-state process. The two intermediates populated during folding are present on parallel pathways. Both form by rapid association of the monomers in a diffusion limited manner and appear to be largely unstructured, as they are silent to the optical probes employed in the current study. The existence of parallel pathways is supported by the insensitivity of the amplitudes of the refolding kinetic phases to the different probes used in the study. More importantly, interrupted refolding studies and ligand binding studies clearly demonstrate that the native state forms in a biexponential manner, implying the presence of at least two pathways. Our studies indicate that the CcdA antitoxin binds only to the folded CcdB dimer and not to any earlier folding intermediates. Thus, despite being part of the same operon, the antitoxin does not appear to modulate the folding pathway of the toxin encoded by the downstream cistron. This study highlights the utility of ligand binding in distinguishing between sequential and parallel pathways in protein folding studies, while also providing insights into molecular interactions during folding in Type II toxin-antitoxin systems.

Direct evidence of the presence of competing pathways for the folding or unfolding reactions of proteins is difficult to obtain. A direct signature for multiple pathways, seen so far only rarely in folding or unfolding studies, is an upward curvature in the dependence of the logarithm of the observed rate constant (λU) of folding on denaturant concentration. In this study, the unfolding mechanism of the wild-type (wt) and E24A variants of monellin has been investigated, and both variants are shown to display upward curvatures in plots of log λU versus denaturant concentration. Curvature is distinctly more pronounced for E24A than for the wt protein. Kinetic unfolding studies of E24A were conducted over a range of denaturant concentrations and across a range of temperatures, and the kinetic data were globally analyzed assuming two parallel pathways L and H, which proceed through transition states TS(L) and TS(H), respectively. The observation of the upward curvature in the unfolding kinetics permitted a thermodynamic analysis of how unfolding switches from one pathway to the other upon a change in unfolding conditions. The m −N and ΔCp values indicate that TSL is more compact than TS(H). The major contribution to the free energy of activation on either pathway is seen to be enthalpic and not entropic in origin.

No abstract