Surveying protein structure and function using bis-arsenical small molecules

Biarsenical fluorescent probes for multifunctional site-specific modification of proteins applicable in life sciences: an overview and future outlook

Fluorescent modification of proteins of interest (POI) in living cells is desired to study their behaviour and functions in their natural environment. In a perfect setting it should be easy to perform, inexpensive, efficient and site-selective. Although multiple chemical and biological methods have been developed, only a few of them are applicable for cellular studies thanks to their appropriate physical, chemical and biological characteristics. One such successful system is a tetracysteine tag/motif and its selective biarsenical binders (e.g. FlAsH and ReAsH). Since its discovery in 1998 by Tsien and co-workers, this method has been enhanced and revolutionized in terms of its efficiency, formed complex stability and breadth of application. Here, we overview the whole field of knowledge, while placing most emphasis on recent reports. We showcase the improvements of classical biarsenical probes with various optical properties as well as multifunctional molecules that add new characteristics to proteins. We also present the evolution of affinity tags and motifs of biarsenical probes demonstrating much more possibilities in cellular applications. We summarize protocols and reported observations so both beginners and advanced users of biarsenical probes can troubleshoot their experiments. We address the concerns regarding the safety of biarsenical probe application. We showcase examples in virology, studies on receptors or amyloid aggregation, where application of biarsenical probes allowed observations that previously were not possible. We provide a summary of current applications ranging from bioanalytical sciences to allosteric control of selected proteins. Finally, we present an outlook to encourage more researchers to use these magnificent probes.

Allosteric Inhibition of the Epidermal Growth Factor Receptor

We previously reported a family of hydrocarbon-stapled peptides designed to interact with the epidermal growth factor receptor (EGFR) juxtamembrane (JM) segment, blocking its ability to form a coiled coil dimer that is essential for receptor activation. These hydrocarbon-stapled peptides, most notably E1^S, decreased the proliferation of cell lines that express wild-type EGFR (H2030 and A431) as well as those expressing the oncogenic mutants EGFR L858R (H3255) and L858R/T790M (H1975). Although our previous investigations provided evidence that E1^S interacted with EGFR directly, the location and details of these interactions were not established. Here we apply biochemical and cross-linking mass spectrometry tools to better define the interactions between E1^S and EGFR. Taken with previously reported structure-activity relationships, our results support a model in which E1^S interacts simultaneously with both the JM and the C-lobe of the activator kinase, effectively displacing the JM of the receiver kinase. Our results also reveal potential interactions between E1^S and the N-terminal region of the C-terminal tail. We propose a model in which E1^S inhibits EGFR by both mimicking and inhibiting JM coiled coil formation. This model could be used to design novel, allosteric (and perhaps nonpeptidic) EGFR inhibitors.

Discrete Coiled Coil Rotamers Form within the EGFRvIII Juxtamembrane Domain

Mutations in the epidermal growth factor receptor (EGFR) extracellular domain (ECD) are implicated in the development of glioblastoma multiforme (GBM), which is a highly aggressive form of brain cancer. Of particular interest to GBM is the EGFR variant known as EGFRvIII, which is distinguished by an in-frame deletion of exons 2-7, which encode ECD residues 6-273. Included within the deleted region is an autoinhibitory tether, whose absence, alongside unique disulfide interactions within the truncated ECD, supports assembly of a constitutively active asymmetric kinase dimer. Previous studies have shown that the binding of growth factors to the ECD of wild-type EGFR leads to the formation of two distinct coiled coil dimers in the cytoplasmic juxtamembrane (JM) segment, whose identities correlate with the downstream phenotype. One coiled coil contains leucine residues at the interhelix interface (EGF-type), whereas the other contains charged and polar side chains (TGF-α-type). It has been proposed that growth-factor-dependent structural changes in the ECD and adjacent transmembrane helix are transduced into distinct JM coiled coils. Here, we show that, in the absence of this growth-factor-induced signal, the JM of EGFRvIII adopts both EGF-type and TGF-α-type structures, providing direct evidence for this hypothesis. These studies confirm that the signals that define JM coiled coil identity begin within the ECD, and support a model in which growth-factor-induced conformational changes are transmitted from the ECD through the transmembrane helix to favor different coiled coil isomers within the JM.

Rational design of small molecule fluorescent probes for biological applications

Fluorescent small molecules are powerful tools for visualizing biological events, embodying an essential facet of chemical biology. Since the discovery of the first organic fluorophore, quinine, in 1845, both synthetic and theoretical efforts have endeavored to "modulate" fluorescent compounds. An advantage of synthetic dyes is the ability to employ modern organic chemistry strategies to tailor chemical structures and thereby rationally tune photophysical properties and functionality of the fluorophore. This review explores general factors affecting fluorophore excitation and emission spectra, molar absorption, Stokes shift, and quantum efficiency; and provides guidelines for chemist to create novel probes. Structure-property relationships concerning the substituents are discussed in detail with examples for several dye families. We also present a survey of functional probes based on PeT, FRET, and environmental or photo-sensitivity, focusing on representative recent work in each category. We believe that a full understanding of dyes with diverse chemical moieties enables the rational design of probes for the precise interrogation of biochemical and biological phenomena.

Engineering of a Red Fluorogenic Protein/Merocyanine Complex for Live-Cell Imaging

A reengineered human cellular retinol binding protein II (hCRBPII), a 15-kDa protein belonging to the intracellular lipid binding protein (iLBP) family, generates a highly fluorescent red pigment through the covalent linkage of a merocyanine aldehyde to an active site lysine residue. The complex exhibits "turn-on" fluorescence, due to a weakly fluorescent aldehyde that "lights up" with subsequent formation of a strongly fluorescent merocyanine dye within the binding pocket of the protein. Cellular penetration of merocyanine is rapid, and fluorophore maturation is nearly instantaneous. The hCRBPII/merocyanine complex displays high quantum yield, low cytotoxicity, specificity in labeling organelles, and compatibility in both cancer cell lines and yeast cells. The hCRBPII/merocyanine tag is brighter than most common red fluorescent proteins.

Organic Arsenicals as Functional Motifs in Polymer and Biomaterials Science

Arsenic (As) exhibits diverse (bio)chemical reactivity and biological activity depending upon its oxidation state. However, this distinctive reactivity has been largely overlooked across many fields owing to concerns regarding the toxicity of arsenic. Recently, a clinical renaissance in the use of arsenicals, including organic arsenicals that are known to be less toxic than inorganic arsenicals, alludes to the possibility of broader acceptance and application in the field of polymer and biomaterials science. Here, current examples of polymeric/macromolecular arsenicals are reported to stimulate interest and highlight their potential as a novel platform for functional, responsive, and bioactive materials.

Mechanism of Allosteric Coupling into and through the Plasma Membrane by EGFR

Epidermal growth factor receptor (EGFR) interacts through its extracellular domain with seven different growth factors. These factors induce different structures within the cytoplasmic juxtamembrane (JM) segment of the dimeric receptor and propagate different growth factor-dependent signals to the cell interior. How this process occurs is unknown. Here we apply diverse experimental and computational tools to show that growth factor identity is encoded by the EGFR transmembrane (TM) helix into discrete helix dimer populations that differ in both cross-location and cross-angle. Helix dimers with smaller cross-angles at multiple cross locations are decoded to induce an EGF-type coiled coil in the adjacent JM, whereas helix dimers with larger cross-angles at fewer cross locations induce the TGF-α-type coiled coil. We propose an updated model for how conformational coupling across multiple EGFR domains results in growth factor-specific information transfer, and demonstrate that this model applies to both EGFR and the related receptor ErbB2.

Conformational studies of Ant–Pro motif-incorporated cyclic peptides: gramicidin S and avellanin

Conformational studies suggest that an Ant^DPro motif-incorporated synthetic gramicidin S analog retains β-sheet conformation, while its truncated analog avellanin disturbs the β-sheet conformation.

Transpeptidation-directed intramolecular bipartite tetracysteine display for sortase activity assay

We developed a simple, label-free and homogenous assay to quantitively evaluate SrtA-catalyzed transpeptidation reaction.

Detection of oligonucleotides by PNA-peptide conjugates recognizing the biarsenical fluorescein complex FlAsH-EDT2

We report the application of the arsenical complex FlAsH-EDT₂ for the identification of oligonucleotide sequences. We designed PNA sequences conjugated to either a tetracysteine motif and to split tetracysteine sequences, that are recognized by FlAsH. The effect of conjugation of the PNA to the tetracysteine peptide and RNA hybridization on the fluorescence of the arsenical complex has been investigated. The reconstitution of the tetracysteine motif, starting from 15-mer PNAs conjugated to split tetracysteine sequences and hybridized to a complementary oligonucleotide was also explored.

On the Origins of Nonradiative Excited State Relaxation in Aryl Sulfoxides Relevant to Fluorescent Chemosensing

We provide herein a mechanistic analysis of aryl sulfoxide excited state processes, inspired by our recent report of aryl sulfoxide based fluorescent chemosensors. The use of aryl sulfoxides as reporting elements in chemosensor development is a significant deviation from previous approaches, and thus warrants closer examination. We demonstrate that metal ion binding suppresses nonradiative excited state decay by blocking formation of a previously unrecognized charge transfer excited state, leading to fluorescence enhancement. This charge transfer state derives from the initially formed locally excited state followed by intramolecular charge transfer to form a sulfoxide radical cation/aryl radical anion pair. With the aid of computational studies, we map out ground and excited state potential energy surface details for aryl sulfoxides, and conclude that fluorescence enhancement is almost entirely the result of excited state effects. This work expands previous proposals that excited state pyramidal inversion is the major nonradiative decay pathway for aryl sulfoxides. We show that pyramidal inversion is indeed relevant, but that an additional and dominant nonradiative pathway must also exist. These conclusions have implications for the design of next generation sulfoxide based fluorescent chemosensors.

Site-Specific Bioorthogonal Labeling for Fluorescence Imaging of Intracellular Proteins in Living Cells

Over the past years, fluorescent proteins (e.g., green fluorescent proteins) have been widely utilized to visualize recombinant protein expression and localization in live cells. Although powerful, fluorescent protein tags are limited by their relatively large sizes and potential perturbation to protein function. Alternatively, site-specific labeling of proteins with small-molecule organic fluorophores using bioorthogonal chemistry may provide a more precise and less perturbing method. This approach involves site-specific incorporation of unnatural amino acids (UAAs) into proteins via genetic code expansion, followed by bioorthogonal chemical labeling with small organic fluorophores in living cells. While this approach has been used to label extracellular proteins for live cell imaging studies, site-specific bioorthogonal labeling and fluorescence imaging of intracellular proteins in live cells is still challenging. Herein, we systematically evaluate site-specific incorporation of diastereomerically pure bioorthogonal UAAs bearing stained alkynes or alkenes into intracellular proteins for inverse-electron-demand Diels-Alder cycloaddition reactions with tetrazine-functionalized fluorophores for live cell labeling and imaging in mammalian cells. Our studies show that site-specific incorporation of axial diastereomer of trans-cyclooct-2-ene-lysine robustly affords highly efficient and specific bioorthogonal labeling with monosubstituted tetrazine fluorophores in live mammalian cells, which enabled us to image the intracellular localization and real-time dynamic trafficking of IFITM3, a small membrane-associated protein with only 137 amino acids, for the first time. Our optimized UAA incorporation and bioorthogonal labeling conditions also enabled efficient site-specific fluorescence labeling of other intracellular proteins for live cell imaging studies in mammalian cells.

High Affinity Immobilization of Proteins Using the CrAsH/TC Tag

Protein microarrays represent important tools for biomedical analysis. We have recently described the use of the biarsenical-tetracysteine (TC) tag for the preparation of protein microarrays. The unique feature of this tag enables the site-specific immobilization of TC-containing proteins on biarsenical-modified surfaces, resulting in a fluorescence enhancement that allows the direct quantification of the immobilized proteins. Moreover, the reversibility of the binding upon incubation with large quantities of thiols permits the detachment of the proteins from the surface, thereby enabling recovery of the substrate to extend the life time of the slide. Herein, we describe our recent results that further extend the applicability of the CrAsH/TC tag to the fabrication of biochips. With this aim, the immobilization of proteins on surfaces has been investigated using two different spacers and two TC tags, the minimal TC sequence (CCPGCC) and an optimized motif (FLNCCPGCCMEP). While the minimal peptide motif enables a rapid recycling of the slide, the optimized TC sequence reveals an increased affinity due to its greater resistance to displacement by thiols. Moreover, the developed methodology was applied to the immobilization of proteins via on-chip ligation of recombinant protein thioesters.

Rotamer-Restricted Fluorogenicity of the Bis-Arsenical ReAsH

Fluorogenic dyes such as FlAsH and ReAsH are used widely to localize, monitor, and characterize proteins and their assemblies in live cells. These bis-arsenical dyes can become fluorescent when bound to a protein containing four proximal Cys thiols-a tetracysteine (Cys4) motif. Yet the mechanism by which bis-arsenicals become fluorescent upon binding a Cys4 motif is unknown, and this nescience limits more widespread application of this tool. Here we probe the origins of ReAsH fluorogenicity using both computation and experiment. Our results support a model in which ReAsH fluorescence depends on the relative orientation of the aryl chromophore and the appended arsenic chelate: the fluorescence is rotamer-restricted. Our results do not support a model in which fluorogenicity arises from the relief of ring strain. The calculations identify those As-aryl rotamers that support fluorescence and those that do not and correlate well with prior experiments. The rotamer-restricted model we propose is supported further by biophysical studies: the excited-state fluorescence lifetime of a complex between ReAsH and a protein bearing a high-affinity Cys4 motif is longer than that of ReAsH-EDT2, and the fluorescence intensity of ReAsH-EDT2 increases in solvents of increasing viscosity. By providing a higher resolution view of the structural basis for fluorogenicity, these results provide a clear strategy for the design of more selective bis-arsenicals and better-optimized protein targets, with a concomitant improvement in the ability to characterize previously invisible protein conformational changes and assemblies in live cells.

Growth Factor Identity Is Encoded by Discrete Coiled-Coil Rotamers in the EGFR Juxtamembrane Region

Binding of transforming growth factor α (TGF-α) to the epidermal growth factor receptor (EGFR) extracellular domain is encoded through the formation of a unique antiparallel coiled coil within the juxtamembrane segment. This new coiled coil is an "inside-out" version of the coiled coil formed in the presence of epidermal growth factor (EGF). A third, intermediary coiled-coil interface is formed in the juxtamembrane region when EGFR is stimulated with betacellulin. The seven growth factors that activate EGFR in mammalian systems (EGF, TGF-α, epigen, epiregulin, betacellulin, heparin-binding EGF, and amphiregulin) fall into distinct categories in which the structure of the coiled coil induced within the juxtamembrane region correlates with cell state. The observation that coiled-coil state tracks with the downstream signaling profiles for each ligand provides evidence for growth factor functional selectivity by EGFR. Encoding growth factor identity in alternative coiled-coil rotamers provides a simple and elegant method for communicating chemical information across the plasma membrane.

The molecular mechanism of heme loss from oxidized soluble guanylate cyclase induced by conformational change

Heme oxidation and loss of soluble guanylate cyclase (sGC) is thought to be an important contributor to the development of cardiovascular diseases. Nevertheless, it remains unknown why the heme loses readily in oxidized sGC. In the current study, the conformational change of sGC upon heme oxidation by ODQ was studied based on the fluorescence resonance energy transfer (FRET) between the heme and a fluorophore fluorescein arsenical helix binder (FlAsH-EDT2) labeled at different domains of sGC β1. This study provides an opportunity to monitor the domain movement of sGC relative to the heme. The results indicated that heme oxidation by ODQ in truncated sCC induced the heme-associated αF helix moving away from the heme, the Per/Arnt/Sim domain (PAS) domain moving closer to the heme, but led the helical domain going further from the heme. We proposed that the synergistic effect of these conformational changes of the discrete region upon heme oxidation forces the heme pocket open, and subsequent heme loss readily. Furthermore, the kinetic studies suggested that the heme oxidation was a fast process and the conformational change was a relatively slow process. The kinetics of heme loss from oxidized sGC was monitored by a new method based on the heme group de-quenching the fluorescence of FlAsH-EDT2.

Development of a red fluorescent light-up probe for highly selective and sensitive detection of vicinal dithiol-containing proteins in living cells

Vicinal dithiol-containing proteins (VDPs) play a key role in cellular redox homeostasis and are responsible for many diseases. Here, we develop a red fluorescent light-up probe FAsH for the highly selective and sensitive detection of VDPs using the environment-sensitive 2-(4-dimethylaminophenyl)-4-(2-carboxyphenyl)-7-diethylamino-1-benzopyrylium (F1) as the fluorescent reporter and cyclic dithiaarsane as the targeting unit. FAsH is almost nonfluorescent in aqueous solution. However, it exhibits intense fluorescence emission upon binding to reduced bovine serum albumin (rBSA, selected as the model protein). The fluorescence intensity of FAsH is directly proportional to the concentration of rBSA over the range of 0.06-0.9 μM, with a detection limit (3δ) of 0.015 μM. Importantly, the fast kinetics of binding between FAsH and VDPs (∼2.5 min) enables the dynamic tracing of VDPs in biological systems. Preliminary experiments show that FAsH can be used for the no-wash imaging of endogenous VDPs in living cells. In addition, our study shows that F1 presents both high environment-sensitivity and good fluorescence properties, and is promising for the development of no-wash fluorescent light-up probes for target-specific proteins in living cells.

Using modified aptamers for site specific protein-aptamer conjugations

We have developed a new method for the selective conjugation of target proteins at lysine residues through a protein–aptamer template-directed reaction.

Conjugation of DNA to defined locations on a protein surface will be a powerful tool for positioning functional groups and molecules in biological and biomedical studies. However, tagging protein with DNA is challenging in physiological environments, and requires a bioorthogonal approach. Here, we report a chemical solution to selectively conjugate DNA aptamers with a protein by protein–aptamer template (PAT)-directed reactions. Since protein–aptamer interactions are bioorthogonal, we exploit the PAT as a unique platform for specific DNA–protein cross-linking. We develop a series of modified oligonucleotides for PAT-directed reactions and find an F-carboxyl group as a suitable functionality for selective and site-specific conjugation. The functionality is incorporated into aptamers in our F-carboxyl phosphoramidite with an easy synthesis. We also demonstrate the necessity of a linker between the reactive functionality and the aptamer sequences.

Multiply labeling proteins for studies of folding and stability

Fluorescence spectroscopy is a powerful method for monitoring protein folding in real-time with high resolution and sensitivity, but requires the site-specific introduction of labels into the protein. The ability to genetically incorporate unnatural amino acids (Uaas) allows for the efficient synthesis of fluorescently labeled proteins with minimally perturbing fluorophores. Here, we describe recent uses of labeled proteins in dynamic structure determination experiments and advances in unnatural amino acid incorporation for dual site-specific fluorescent labeling. The advent of increasingly sophisticated bioorthogonal chemistry reactions and the diversity of Uaas available for incorporation will greatly enable protein folding and stability studies.

Direct Chemical Activation of a Rationally Engineered Signaling Enzyme

Few chemical strategies for activating enzymes have been developed. Here we show that a biarsenical compound (FlAsH) can directly activate a rationally engineered protein tyrosine phosphatase (Shp2 PTP) by disrupting autoinhibitory interactions between Shp2's N-terminal SH2 domain and its PTP domain. We found that introducing a tricysteine motif at a loop of Shp2's N-SH2 domain confers affinity for FlAsH; binding of FlAsH to the cysteine-enriched loop relieves Shp2's inhibitory interdomain interaction and substantially increases the enzyme's PTP activity. Activation of engineered Shp2 is substrate independent and is observed in the contexts of both purified enzyme and complex proteomes. A chemical means for activating Shp2 could be useful for investigating its roles in signaling and oncogenesis, and the loop-targeting strategy described herein could provide a blueprint for the development of target-specific activators of other autoinhibited enzymes.

Structural Differences between Wild-Type and Double Mutant EGFR Modulated by Third-Generation Kinase Inhibitors

Mutations in the EGFR kinase domain are implicated in non-small-cell lung cancer. Of particular interest is the drug-resistant double mutant (L858R/T790M, DM EGFR), which is not inhibited selectively by any approved kinase inhibitor. Here we apply bipartite tetracysteine display to demonstrate that DM and WT EGFR differ in structure outside the kinase domain. The structural difference is located within the cytoplasmic juxtamembrane segment (JM) that links the kinase domain with the extracellular and transmembrane regions and is essential for EGFR activation. We show further that third-generation DM EGFR-selective TKIs alter JM structure via allostery to restore the conformation found when WT EGFR is activated by the growth factors EGF and HB-EGF. This work suggests that the oncogenic activity of DM EGFR may extend beyond kinase activity per se to include kinase-independent activities. As JM structure may provide a biomarker for these kinase-independent functions, these insights could guide the development of allosteric, DM-selective inhibitors.

Metallomic and metalloproteomic strategies in elucidating the molecular mechanisms of metallodrugs

Advances in the mechanistic studies of metallodrugs by metallomic and metalloproteomic approaches will improve our understanding of the mechanism of action and allow more metallodrugs to be developed.

Therapeutic and analytical applications of arsenic binding to proteins

Knowledge of arsenic binding to proteins advances the development of bioanalytical techniques and therapeutic drugs.

Multivalency in the inhibition of oxidative protein folding by arsenic(III) species

The renewed use of arsenicals as chemotherapeutics has rekindled interest in the biochemistry of As(III) species. In this work, simple bis- and tris-arsenical derivatives were synthesized with the aim of exploiting the chelate effect in the inhibition of thiol-disulfide oxidoreductases (here, Quiescin sulfhydryl oxidase, QSOX, and protein disulfide isomerase, PDI) that utilize two or more CxxC motifs in the catalysis of oxidative protein folding. Coupling 4-aminophenylarsenoxide (APAO) to acid chloride or anhydride derivatives yielded two bis-arsenical prototypes, BA-1 and BA-2, and a tris-arsenical, TA-1. Unlike the monoarsenical, APAO, these new reagents proved to be strong inhibitors of oxidative protein folding in the presence of a realistic intracellular concentration of competing monothiol (here, 5 mM reduced glutathione, GSH). However, this inhibition does not reflect direct inactivation of QSOX or PDI, but avid binding of MVAs to the reduced unfolded protein substrates themselves. Titrations of reduced riboflavin-binding protein with MVAs show that all 18 protein −SH groups can be captured by these arsenicals. With reduced RNase, addition of substoichiometric levels of MVAs is accompanied by the formation of Congo Red- and Thioflavin T-positive fibrillar aggregates. Even with K_d values of ∼50 nM, MVAs are ineffective inhibitors of PDI in the presence of millimolar levels of competing GSH. These results underscore the difficulties of designing effective and specific arsenical inhibitors for folded enzymes and proteins. Some of the cellular effects of arsenicals likely reflect their propensity to associate very tightly and nonspecifically to conformationally mobile cysteine-rich regions of proteins, thereby interfering with folding and/or function.

Influence of macrocyclization on allosteric, juxtamembrane-derived, stapled peptide inhibitors of the epidermal growth factor receptor (EGFR)

The hydrocarbon-stapled peptide E1(S) allosterically inhibits the kinase activity of the epidermal growth factor receptor (EGFR) by blocking a distant but essential protein-protein interaction: a coiled coil formed from the juxtamembrane segment (JM) of each member of the dimeric partnership.1 Macrocyclization is not required for activity: the analogous unstapled (but alkene-bearing) peptide is equipotent in cell viability, immunoblot, and bipartite display experiments to detect coiled coil formation on the cell surface.

Inhibiting epidermal growth factor receptor at a distance

The epidermal growth factor receptor (EGFR) tyrosine kinase is implicated in a large number of human cancers. Most EGFR inhibitors target the extracellular, growth factor-binding domain or the intracellular, ATP-binding domain. Here we describe molecules that inhibit the kinase activity of EGFR in a new way, by competing with formation of an essential intradimer coiled coil containing the juxtamembrane segment from each member of the receptor partnership. The most potent molecules we describe bind EGFR directly, decrease the proliferation of wild-type and mutant EGFR-dependent cells lines, inhibit phosphorylation of EGFR and downstream targets, and block coiled coil formation as judged by bipartite tetracysteine display. Potency is directly correlated with the ability to block coiled coil formation within full-length EGFR in cells.

Synthetic turn mimetics and hairpin nucleators: Quo Vadimus?

Structural mimicry of peptides has witnessed perceptible progress in the last three decades. Reverse turn and β-hairpin units are the smallest secondary structural motifs that are some of the most scrutinized functional cores of peptides and proteins. The practice of mimicking, without altering the function of the bioactive core, ranges from conformational locking of the basic skeleton to total replacement of structural architecture using synthetic analogues. Development of heterogeneous backbones--using unnatural residues in place of natural ones--has broadened further opportunities for efficient structural rigidification. This feature article endeavours to trail the path of progress achieved hitherto and envisage the possibilities that lie ahead in the development of synthetic turn mimetics and hairpin nucleators.

Interactions of AsCy3 with cysteine-rich peptides

There is great interest in fluorogenic compounds that tag biomolecules within cells. Biarsenicals are fluorogenic compounds that become fluorescent upon binding four proximal Cys thiols, a tetracysteine (Cys₄) motif. This work details interactions between the biarsenical AsCy3 and Cys₄ peptides. Maximal affinity was observed when two Cys-Cys pairs were separated by at least 8 amino acids; the highest affinity ligand bound in the nanomolar concentration range (K_app = 43 nM) and with a significant (3.2-fold) fluorescence enhancement.

Finding the right (bioorthogonal) chemistry

Bioorthogonal chemistries can be used to tag diverse classes of biomolecules in cells and other complex environments. With over 20 unique transformations now available, though, selecting an appropriate reaction for a given experiment is challenging. In this article, we compare and contrast the most common classes of bioorthogonal chemistries and provide a framework for matching the reactions with downstream applications. We also discuss ongoing efforts to identify novel biocompatible reactions and methods to control their reactivity. The continued expansion of the bioorthogonal toolkit will provide new insights into biomolecule networks and functions and thus refine our understanding of living systems.

Small molecule probes to quantify the functional fraction of a specific protein in a cell with minimal folding equilibrium shifts

Although much is known about protein folding in buffers, it remains unclear how the cellular protein homeostasis network functions as a system to partition client proteins between folded and functional, soluble and misfolded, and aggregated conformations. Herein, we develop small molecule folding probes that specifically react with the folded and functional fraction of the protein of interest, enabling fluorescence-based quantification of this fraction in cell lysate at a time point of interest. Importantly, these probes minimally perturb a protein's folding equilibria within cells during and after cell lysis, because sufficient cellular chaperone/chaperonin holdase activity is created by rapid ATP depletion during cell lysis. The folding probe strategy and the faithful quantification of a particular protein's functional fraction are exemplified with retroaldolase, a de novo designed enzyme, and transthyretin, a nonenzyme protein. Our findings challenge the often invoked assumption that the soluble fraction of a client protein is fully folded in the cell. Moreover, our results reveal that the partitioning of destabilized retroaldolase and transthyretin mutants between the aforementioned conformational states is strongly influenced by cytosolic proteostasis network perturbations. Overall, our results suggest that applying a chemical folding probe strategy to other client proteins offers opportunities to reveal how the proteostasis network functions as a system to regulate the folding and function of individual client proteins in vivo.

Visualizing and quantifying protein polySUMOylation at the single-molecule level

Protein polySUMOylation, the attachment of small ubiquitin-like modifier (SUMO) chains to the target protein, is associated with a variety of physiological processes. However, the analysis of protein polySUMOylation is often complicated by the heterogeneity of SUMO-target conjugates. Here, we develop a new strategy to visualize and quantify polySUMOylation at the single-molecule level by integrating the tetracysteine (TC) tag labeling technology and total internal reflection fluorescence (TIRF)-based single-molecule imaging. As a proof-of-concept, we employ the human SUMO-2 as the model. The addition of TC tag to SUMO-2 can specifically translate the SUMO-mediated modification into visible fluorescence signal without disturbing the function of SUMO-2. The SUMO monomers display homogeneous fluorescence spots at the single-molecule level, whereas the mixed SUMO chains exhibit nonuniform fluorescence spots with a wide range of intensities. Analysis of the number and the brightness of fluorescence spots enable quantitative measurement of the polySUMOylation degree inside the cells under different physiological conditions. Due to the frequent occurrence of posttranslational modification by polymeric chains in cells, this single-molecule strategy has the potential to be broadly applied for studying protein posttranslational modification in normal cellular physiology and disease etiology.

Optimized design and synthesis of a cell-permeable biarsenical cyanine probe for imaging tagged cytosolic bacterial proteins

To optimize cellular delivery and specific labeling of tagged cytosolic proteins by biarsenical fluorescent probes built around a cyanine dye (Cy3) scaffold, we have systematically varied the polarity of the N-alkyl chain (i.e., 4-5 methylene groups appended by a sulfonate or methoxy ester moiety) and arsenic capping reagent (ethanedithiol versus benzenedithiol). Optimal live-cell labeling and visualization of tagged cytosolic proteins is reported using an ethanedithiol capping reagent with the uncharged methoxy ester functionalized N-alkyl chains. These measurements demonstrate the general utility of this new class of photostable and highly fluorescent biarsenical probes based on the cyanine dye scaffold for in vivo labeling of tagged cellular proteins for live cell imaging measurements of protein dynamics.