The Trikafta drug combination, comprising the corrector tezacaftor (VX-661), the potentiator ivacaftor (VX-770) and the dual corrector/potentiator elexacaftor (VX-445), has been FDA-approved for treatment of cystic fibrosis caused by ~300 cystic fibrosis transmembrane conductance regulator (CFTR) mutations. Nevertheless, several CFTR variants exhibit limited response to Trikafta. To address this therapeutic gap, we investigated whether the potentiator activity of VX-445 can complement the VX-770 and preclinical “co-potentiators” activity in partially responsive CFTR mutants. Functional clustering of clinical and preclinical potentiator profiles suggests that VX-445 represents a distinct potentiator class, an inference supported by its additivity with both VX-770/VX-770-like potentiators and co-potentiators across five CFTR mutants in bronchial epithelia. This concept was further validated in gene-edited 16HBE and primary human nasal epithelia, expressing G551D-, N1303K-, and W1282X-CFTR, the 3rd, 4th, and 6th most common CF-mutations, respectively, and was confirmed at the single-channel level. Moreover, we present the development of a novel series of co-potentiator compounds that are derived from our previously described 4172 corrector scaffold, which exhibit low micromolar potency. Our findings suggest that triple potentiation can significantly enhance functional restoration of poorly responsive gating mutants, thereby uncovering novel avenues for therapeutic development.

The epithelial anion channel cystic fibrosis transmembrane conductance regulator (CFTR) is activated by cAMP-dependent protein kinase (PKA). PKA stimulates CFTR channels through two mechanisms: non-catalytically, by binding to the channel, and catalytically, by phosphorylating its regulatory (R) domain. CFTR mutations that reduce channel activity cause cystic fibrosis (CF), but clinically used modulator drugs that boost channel function can alleviate disease symptoms. The two common CF mutations, ΔF508 and G551D, have been reported to impair CFTR channel activation by PKA, but the mechanisms remain unclear. Here, we aimed to understand how the mutations impact non-catalytic vs. catalytic channel activation by PKA and how these two processes are modulated by clinically used potentiator drugs. Using current recordings from excised inside-out membrane patches superfused with the purified catalytic subunit of PKA, we confirm slowed PKA-dependent activation for both mutants but demonstrate intact binding affinity for the kinase. Furthermore, we find that non-catalytic activation dominates overall channel activity for both mutants and can be strongly enhanced by stabilization of the NBD1-NBD2-TMD interface using the ATP analogue N6-(2-phenylethyl)-ATP. For both mutants, the clinically used potentiator drug combination elexacaftor + ivacaftor boosts catalytic channel activation by PKA more efficiently than non-catalytic activation. For ΔF508 CFTR, elexacaftor + ivacaftor evokes substantial PKA-independent channel activity and entirely suppresses non-catalytic activation by PKA. These findings help us to understand the activation defects caused by two common CF mutations and suggest room for further improvement of potentiator drugs currently used in CF therapy. KEY POINTS: Protein kinase A (PKA) activates the epithelial anion channel cystic fibrosis transmembrane conductance regulator (CFTR) through two mechanisms: non-catalytically, by binding to the channel, and catalytically, by phosphorylating its regulatory (R) domain. CFTR mutations cause cystic fibrosis (CF); the two common mutations, ΔF508 and G551D, reportedly also impair channel activation by PKA. We show here, for both mutants, that PKA-dependent activation is slowed despite intact binding affinity for the kinase, and that non-catalytic activation dominates overall channel activity and might be further enhanced by stabilization of the NBD1-NBD2-TMD interface. For ΔF508 CFTR, but not for G551D CFTR, a combination of clinically used potentiator drugs evokes substantial PKA-independent channel activity but suppresses non-catalytic activation by PKA. These findings help us to understand the activation defects caused by two common CF mutations and suggest room for further improvement of potentiator drugs currently used in CF therapy.

CFTR, the anion channel mutated in cystic fibrosis patients, is a model ABC protein whose ATP-driven conformational cycle is observable at single-molecule level in patch-clamp recordings. Bursts of CFTR pore openings are coupled to tight dimerization of its two nucleotide-binding domains (NBDs) and in wild-type (WT) channels are mostly terminated by ATP hydrolysis. The slow rate of non-hydrolytic closure – which determines how tightly bursts and ATP hydrolysis are coupled – is unknown, as burst durations of catalytic site mutants span a range of ~200-fold. Here, we show that Walker A mutation K1250A, Walker B mutation D1370N, and catalytic glutamate mutations E1371S and E1371Q all completely disrupt ATP hydrolysis. True non-hydrolytic closing rate of WT CFTR approximates that of K1250A and E1371S. That rate is slowed ~15-fold in E1371Q by a non-native inter-NBD H-bond, and accelerated ~15-fold in D1370N. These findings uncover unique features of the NBD interface in human CFTR.

The CFTR anion channel is an ATP Binding Cassette protein and consists of two pore-forming transmembrane domains, two cytosolic nucleotide binding domains that bind and hydrolyze ATP to drive gating, and a cytosolic regulatory (R) domain. The catalytic subunit of protein kinase A (PKA) binds to, and phosphorylates, the R domain, causing reversible and irreversible channel activation, respectively. CFTR chloride channel mutations cause the lethal and incurable disease cystic fibrosis (CF). The most common CF mutation, ΔF508, is known to impair CFTR protein processing and channel gating, while mutation G551D disrupts ATP-dependent channel gating. In addition, ΔF508 and G551D CFTR were also shown to be defective in PKA-dependent activation. As the stimulating effect of ivacaftor, the only FDA-approved CFTR potentiator drug, depends on CFTR phosphorylation, understanding the reason for the impaired CFTR-PKA interaction in the mutants is of great significance. The reduced rate of phosphorylation of G551D or ΔF508 channels might be a consequence of impaired PKA binding to CFTR. In the presence of ATP the contributions of PKA binding vs. phosphorylation to overall channel activation are difficult to deconvolve. Therefore, we tested reversible activation by PKA of unphosphorylated and phosphorylated mutant channels gating in P-ATP, an ATP analog that supports CFTR gating but cannot be used for phosphotransfer by PKA. Using macroscopic inside-out patch clamp recordings we compared the rates and fractional amplitudes of reversible stimulation by PKA for the mutants and wild-type CFTR. Our data show that channel activation by reversible binding of PKA is preserved in the mutant CFTR channels. Additional experiments are underway to decipher the molecular mechanism for slowed activation of the mutants.

CFTR chloride channel mutations cause the lethal and incurable disease cystic fibrosis (CF). CFTR is activated by phosphorylation, and phosphorylated channels exhibit "bursting" behavior-"bursts" of openings separated by short "flickery" closures and flanked by long "interburst" closures-driven by ATP binding/hydrolysis at two nucleotide-binding domains. The human channel (hCFTR) and the distant zebrafish ortholog (zCFTR) display differences both in their gating properties and structures. In phosphorylated ATP-bound hCFTR, the hR117 side chain, conserved across evolution, forms an H-bond that stabilizes the open state. Lack of that bond in the hR117H mutant causes CF. In the phosphorylated ATP-bound zCFTR structure that H-bond is not observable. Here, we show that the zR118H mutation does not affect the function of zCFTR. Instead, we identify an H-bond between the zS109 and zS120 side chains of phosphorylated ATP-bound, but not of unphosphorylated apo-, zCFTR. We investigate the role of that interaction using thermodynamic mutant cycles built on gating parameters determined in inside-out patch clamp recordings. We find that zS109 indeed forms an H-bond with zN120 in the flickery closed state, but not in the open or interburst closed states. Although in hCFTR an isoleucine (hI119) replaces the asparagine, mutation hS108A produces a strong hR117H-like phenotype. Since the effects of the latter two mutations are not additive, we conclude that in hCFTR these two positions interact, and the hS108-hR117 and hR117-hE1124 H-bonds cooperate to stabilize the open state. These findings highlight an example of how the gating mechanism was optimized during CFTR molecular evolution.

S100 proteins are small, typically homodimeric, vertebrate-specific EF-hand proteins that establish Ca2+-dependent protein-protein interactions in the intra- and extracellular environment and are overexpressed in various pathologies. There are about 20 distinct human S100 proteins with numerous potential partner proteins. Here, we used a quantitative holdup assay to measure affinity profiles of most members of the S100 protein family against a library of chemically synthetized foldamers. The profiles allowed us to quantitatively map the binding promiscuity of each member towards the foldamer library. Since the library was designed to systematically contain most binary natural amino acid side chain combinations, the data also provide insight into the promiscuity of each S100 protein towards all potential naturally occurring S100 partners in the human proteome. Such information will be precious for future drug design to interfere with S100 related pathologies.

The phosphorylation-activated anion channel cystic fibrosis transmembrane conductance regulator (CFTR) is gated by an ATP hydrolysis cycle at its two cytosolic nucleotide-binding domains, and is essential for epithelial salt-water transport. A large number of CFTR mutations cause cystic fibrosis. Since recent breakthrough in targeted pharmacotherapy, CFTR mutants with impaired gating are candidates for stimulation by potentiator drugs. Thus, understanding the molecular pathology of individual mutations has become important. The relatively common R117H mutation affects an extracellular loop, but nevertheless causes a strong gating defect. Here, we identify a hydrogen bond between the side chain of arginine 117 and the backbone carbonyl group of glutamate 1124 in the cryo-electronmicroscopic structure of phosphorylated, ATP-bound CFTR. We address the functional relevance of that interaction for CFTR gating using macroscopic and microscopic inside-out patch-clamp recordings. Employing thermodynamic double-mutant cycles, we systematically track gating-state-dependent changes in the strength of the R117-E1124 interaction. We find that the H-bond is formed only in the open state, but neither in the short-lived 'flickery' nor in the long-lived 'interburst' closed state. Loss of this H-bond explains the strong gating phenotype of the R117H mutant, including robustly shortened burst durations and strongly reduced intraburst open probability. The findings may help targeted potentiator design.

The dynamic regulation of protein-protein interactions (PPIs) involves phosphorylation of short liner motifs in disordered protein regions modulating binding affinities. The ribosomal-S6-kinase 1 is capable of binding to scaffold proteins containing PDZ domains through a PDZ-binding motif (PBM) located at the disordered C-terminus of the kinase. Phosphorylation of the PBM dramatically changes the interactome of RSK1 with PDZ domains exerting a fine-tuning mechanism to regulate PPIs. Here we present in detail highly effective biophysical (fluorescence polarization, isothermal calorimetry) and cellular (proteinfragment complementation) methods to study the effect of phosphorylation on RSK1-PDZ interactions that can be also applied to investigate phosphoregulation of other PPIs in signaling pathways.

Abstract S100 proteins are small, typically homodimeric, vertebrate-specific EF-hand proteins that establish Ca2+-dependent protein-protein interactions in the intra- and extracellular environment and are overexpressed in various pathologies. There are about 20 distinct human S100 proteins with numerous potential partner proteins. Here, we used a quantitative holdup assay to measure affinity profiles of most members of the S100 protein family against a library of chemically synthetized foldamers. The profiles allowed us to quantitatively map the binding promiscuity of each member towards the foldamer library. Since the library was designed to systematically contain most binary natural amino acid side chain combinations, the data also provide insight into the promiscuity of each S100 protein towards all potential naturally occurring S100 partners in the human proteome. Such information will be precious for future drug design to interfere with S100 related pathologies.

The fragment-centric design promises a means to develop complex xenobiotic protein surface mimetics, but it is challenging to find locally biomimetic structures. To address this issue, foldameric local surface mimetic (LSM) libraries were constructed. Protein affinity patterns, ligand promiscuity and protein druggability were evaluated using pull-down data for targets with various interaction tendencies and levels of homology. LSM probes based on H14 helices exhibited sufficient binding affinities for the detection of both orthosteric and non-orthosteric spots, and overall binding tendencies correlated with the magnitude of the target interactome. Binding was driven by two proteinogenic side chains and LSM probes could distinguish structurally similar proteins with different functions, indicating limited promiscuity. Binding patterns displayed similar side chain enrichment values to those for native protein-protein interfaces implying locally biomimetic behavior. These analyses suggest that in a fragment-centric approach foldameric LSMs can serve as useful probes and building blocks for undruggable protein interfaces.

S100 proteins are small, typically homodimeric, vertebrate-specific EF-hand proteins that establish Ca2+-dependent protein-protein interactions in the intra- and extracellular environment and are overexpressed in various pathologies. There are about 20 distinct human S100 proteins with numerous potential partner proteins. Here, we used a quantitative holdup assay to measure affinity profiles of most members of the S100 protein family against a library of chemically synthetized foldamers. The profiles allowed us to quantitatively map the binding promiscuity of each member towards the foldamer library. Since the library was designed to systematically contain most binary natural amino acid side chain combinations, the data also provide insight into the promiscuity of each S100 protein towards all potential naturally-occurring S100 partners in the human proteome. Such information will be precious for future drug design of modulators of S100 pathological activities.

The calcium-binding, vertebrate-specific S100 protein family consists of 20 paralogs in humans (referred as the S100ome), with several clinically important members. To assess their interactome, high-throughput, systematic analysis is indispensable, which allows one to get not only qualitative but quantitative insight into their protein-protein interactions (PPIs). We have chosen an unbiased assay, fluorescence polarization (FP) that revealed a partial functional redundancy when the complete S100ome (n=20) was tested against numerous model partners (n=13). Based on their specificity, the S100ome can be grouped into two distinct classes: promiscuous and orphan. In the first group, members bound to several ligands (>4-5) with comparable high affinity, while in the second one, the paralogs bound only one partner weakly, or no ligand was identified (orphan). Our results demonstrate that in vitro FP assays are highly suitable for quantitative ligand binding studies of selected protein families. Moreover, we provide evidence that PPI-based phenotypic characterization can complement the information obtained from the sequence-based phylogenetic analysis of the S100ome, an evolutionary young protein family. Author summary Functional similarity among a protein family can be essential in order to understand proteomic data, to find biomarkers, or in inhibitor design. Proteins with similar functions can compensate the loss-of-function of the others, their expression can co-vary under pathological conditions, and simultaneous targeting can lead to better results in the clinics. To investigate this property one can use sequence-based approaches. However, this path can be difficult. In the case of the vertebrate specific, evolutionary young, S100 family, phylogenetic approaches lead to ambiguous results. To overcome this problem, we applied a high-throughput biochemical approach to experimentally measure the binding affinities of a large number of S100 interactions. We performed unbiased fluorescence polarization assay, involving the complete human S100ome (20 paralogs) and 13 known interaction partners. We used this measured 20×13 (260) protein-protein interaction array to reveal the functional relationships within the family. Our work provide a general framework for studies focusing on phenotype-based domain classification.

ABSTRACT Protein phosphorylation is a key regulator of protein-protein interactions. How does the interactome of a protein change during extracellular stimulations? While many individual examples of phosphorylation-regulated interactions were described previously, studies addressing the interactome changes induced by a particular phosphorylation event remain scarce. Here, we try to answer this question, by focusing on interactions between a phosphorylable PDZ-binding linear motif and the entire complement of human PDZ domains. Using a combination of in vitro quantitative techniques and cell-based approaches, we demonstrate that the activation of the mitotic effector kinase RSK1 causes dramatic changes in its connectivity with PDZ domain containing proteins. These changes consist of modulations of the binding affinity of numerous interactions, rather than on/off switching of a few interactions. Our results highlight the previously unappreciated role of phosphorylation in the complex and subtle rewiring of large numbers of protein-protein interactions.

S100 proteins are small, mostly dimeric, EF-hand Ca2+-binding proteins. Upon Ca2+ binding, a conformational change occurs resulting in the exposure of a shallow hydrophobic binding groove in each subunit. Interestingly, S100 proteins can interact with their partners in two ways: symmetrically, when the two partners identically bind into each groove, or asymmetrically, when only one partner binds to the S100 dimer occupying both binding pockets. Here we present a heterologous expression and purification protocol for all known human S100 proteins as well as for their partner peptides. Moreover, we provide a detailed description of three in vitro methods to determine the affinity, stoichiometry, and kinetics of S100 protein-protein interactions.