Publications

2019

Protein phosphorylation barcodes, clusters of several phosphorylation sites within a short unfolded region, control many cellular processes. Existing biochemical methods used to study the roles of these barcodes suffer from low selectivity and provide only qualitative data. Chemically synthesized multiphosphopeptides libraries are selective and specific, but their synthesis is extremely difficult using the current peptide synthesis methods. Here we decribe a new microwave assisted approach for synthesizing a library of multiphosphopeptides, using the C-terminus of rhodopsin as a proof of concept. Our approch utilizes multiple protocols for synthesizing libraries of multiphosphopeptides instead of the inefficent single protocol methods curretnly used. Using our approach we demonstrated the synthesis of with up to seven phosphorylated amino acids, sometimes next to each other, an accomplishment that was impractical before. Synthesizing the Rhodopsin derived multiphosphopeptide library enabled dissecting the precise phosphorylation barcode required for the recruitment, activation and modulation of the conformation of Arrestin. Since phosphorylation barcodes modulate the activity of hundreds of GPCRs, synthesizing libraries of multiphosphopeptides is the method of choice for studying their molecular mechanisms of action. Our approach provides an invaluable tool for evaluating how protein phosphorylation barcodes regulate their activity.

    D. Mayer, F. F. Damberger, S. Mamidi, M. Feldmueller, Z. Vuckovic, T. Flock, B. Bauer, E. Mutt, F. Zosel, F. H. T. Allain, J. Standfuss, G. F. X. Schertler, X. Deupi, M. E. Sommer, M. Hurevich, A. Friedler, and D. B. Veprintsev. 3/19/2019. “Distinct G protein-coupled receptor phosphorylation motifs modulate arrestin affinity and activation and global conformation.” Nat. Commun. Link Abstract

    Cellular functions of arrestins are determined in part by the pattern of phosphorylation on the G protein-coupled receptors (GPCRs) to which arrestins bind. Despite high-resolution structural data of arrestins bound to phosphorylated receptor C-termini, the functional role of each phosphorylation site remains obscure. Here, we employ a library of synthetic phosphopeptide analogues of the GPCR rhodopsin C-terminus and determine the ability of these peptides to bind and activate arrestins using a variety of biochemical and biophysical methods. We further characterize how these peptides modulate the conformation of arrestin-1 by nuclear magnetic resonance (NMR). Our results indicate different functional classes of phosphorylation sites: ‘key sites’ required for arrestin binding and activation, an ‘inhibitory site’ that abrogates arrestin binding, and ‘modulator sites’ that influence the global conformation of arrestin. These functional motifs allow a better understanding of how different GPCR phosphorylation patterns might control how arrestin functions in the cell.

    Iosub-Amir A., Bai F., Sohn Y. S., Song L., Tamir S., Marjault H. B., Mayer G., Karmi O., Jennings P. A., Mittler R., Onuchic J. N., Friedler A., and Nechushtai R. 2019. “The anti-apoptotic proteins NAF-1 and iASPP interact to drive apoptosis in cancer cells.” Chem Sci. Link Abstract

    Suppression of apoptosis is a key Hallmark of cancer cells, and reactivation of apoptosis is a major avenue for cancer therapy. We reveal an interaction between the two anti-apoptotic proteins iASPP and NAF-1, which are overexpressed in many types of cancer cells and tumors. iASPP is an inhibitory member of the ASPP protein family, whereas NAF-1 belongs to the NEET 2Fe–2S protein family. We show that the two proteins are stimulated to interact in cells during apoptosis. Using peptide array screening and computational methods we mapped the interaction interfaces of both proteins to residues 764–778 of iASPP that bind to a surface groove of NAF-1. A peptide corresponding to the iASPP 764–780 sequence stabilized the NAF-1 cluster, inhibited NAF-1 interaction with iASPP, and inhibited staurosporine-induced apoptosis activation in human breast cancer, as well as in PC-3 prostate cancer cells in which p53 is inactive. The iASPP 764–780 IC50 value for inhibition of cell death in breast cancer cells was 13 ± 1 μM. The level of cell death inhibition by iASPP 764–780 was altered in breast cancer cells expressing different levels and/or variants of NAF-1, indicating that the peptide activity is associated with NAF-1 function. We propose that the interaction between iASPP and NAF-1 is required for apoptosis activation in cancer cells. This interaction uncovers a new layer in the highly complex regulation of cell death in cancer cells and opens new avenues of exploration into the development of novel anticancer drugs that reactivate apoptosis in malignant tumors.

    2018
    Amartely H., Avraham O., Friedler A., Livnah O., and Lebendiker M. 2018. “Coupling Multi Angle Light Scattering to Ion Exchange chromatography (IEX-MALS) for protein characterization.” Sci. Rep. Link Abstract

    Multi-angle light scattering coupled with size exclusion chromatography (SEC-MALS) is a standard and common approach for characterizing protein mass, overall shape, aggregation, oligomerization, interactions and purity. The limited resolution of analytical SEC restricts in some instances the accurate analysis that can be accomplished by MALS. These include mixtures of protein populations with identical or very similar molecular masses, oligomers with poor separation and short peptides. Here we show that combining MALS with the higher resolution separation technique ion exchange (IEX-MALS) can allow precise analyses of samples that cannot be resolved by SEC-MALS. We conclude that IEX-MALS is a valuable and complementary method for protein characterization, especially for protein systems that could not be fully analyzed by SEC-MALS.

    Katz C, Low-Calle A. M., Choe J. .H, Laptenko O., Tong D., Joseph-Chowdhury J. N., Garofalo F., Zhu Y., Friedler A., and Prives C. 2018. “Wild-type and cancer-related p53 proteins are preferentially degraded by MDM2 as dimers rather than tetramers.” Genes Dev. Abstract

    The p53 tumor suppressor protein is the most well studied as a regulator of transcription in the nucleus, where it exists primarily as a tetramer. However, there are other oligomeric states of p53 that are relevant to its regulation and activities. In unstressed cells, p53 is normally held in check by MDM2 that targets p53 for transcriptional repression, proteasomal degradation, and cytoplasmic localization. Here we discovered a hydrophobic region within the MDM2 N-terminal domain that binds exclusively to the dimeric form of the p53 C-terminal domain in vitro. In cell-based assays, MDM2 exhibits superior binding to, hyperdegradation of, and increased nuclear exclusion of dimeric p53 when compared with tetrameric wild-type p53. Correspondingly, impairing the hydrophobicity of the newly identified N-terminal MDM2 region leads to p53 stabilization. Interestingly, we found that dimeric mutant p53 is partially unfolded and is a target for ubiquitin-independent degradation by the 20S proteasome. Finally, forcing certain tumor-derived mutant forms of p53 into dimer configuration results in hyperdegradation of mutant p53 and inhibition of p53-mediated cancer cell migration. Gaining insight into different oligomeric forms of p53 may provide novel approaches to cancer therapy.

    Rimon A., Dwivedi M., Friedler A., and Padan E. 2018. “Asp133 Residue in NhaA Na+/H+ Antiporter Is Required for Stability Cation Binding and Transport.” J. Mol. Biol. Link Abstract

    Na+/H+ antiporters have a crucial role in pH and Na+ homeostasis in cells. The crystal structure of NhaA, the main antiporter of Escherichia coli, has provided general insights into antiporter mechanisms and revealed a previously unknown structural fold, which has since been identified in several secondary active transporters. This unique structural fold is very delicately electrostatically balanced. Asp133 and Lys 300 have been ascribed essential roles in this balance and, more generally, in the structure and function of the antiporter. In this work, we show the multiple roles of Asp133 in NhaA: (i) The residue's negative charge is critical for the stability of the NhaA structure. (ii) Its main chain is part of the active site. (iii) Its side chain functions as an alkaline-pH-dependent gate, changing the protein's conformation from an inward-facing conformation at acidic pH to an outward-open conformation at alkaline pH, opening the periplasm funnel. On the basis of the experimental data, we propose a tentative mechanism integrating the structural and functional roles of Asp133.

    Faust O., Grunhaus D., Shimshon O., Yavin E., and Friedler A. 2018. “Protein Regulation by Intrinsically Disordered Regions: A Role for Subdomains in the IDR of the HIV-1 Rev Protein.” Chembiochem. Link Abstract

    Intrinsically disordered regions (IDRs) in proteins are highly abundant, but they are still commonly viewed as long stretches of polar, solvent accessible residues. Here we show that the disordered C-terminal domain of HIV-1 Rev has two sub-regions that carry out two distinct complementary roles of regulating oligomerization and contributing to stability. We propose this is carried out by a delicate balance between charged and hydrophobic residues within the IDR. We suggest that intrinsically disordered regions in proteins should be divided to sub domains similarly to structured regions, rather than being viewed as a long flexible stretches. This implicates that mutations in IDRs can affect protein function in disease just like known mutations in structured regions.

    2017
    Petersen J., Wright S.C., Rodríguez D., Matricon P., Lahav N., Vromen A., Friedler A., Strömqvist J., Wennmalm S., Carlsson J., and Schulte G. 2017. “Agonist-induced dimer dissociation as a macromolecular step in G protein-coupled receptor signaling.” Nat. Commun. Link Abstract

    G protein-coupled receptors (GPCRs) constitute the largest family of cell surface receptors. They can exist and act as dimers, but the requirement of dimers for agonist-induced signal initiation and structural dynamics remains largely unknown. Frizzled 6 (FZD6) is a member of Class F GPCRs, which bind WNT proteins to initiate signaling. Here, we show that FZD6dimerizes and that the dimer interface of FZD6 is formed by the transmembrane α-helices four and five. Most importantly, we present the agonist-induced dissociation/re-association of a GPCR dimer through the use of live cell imaging techniques. Further analysis of a dimerization-impaired FZD6 mutant indicates that dimer dissociation is an integral part of FZD6 signaling to extracellular signal-regulated kinases1/2. The discovery of agonist-dependent dynamics of dimers as an intrinsic process of receptor activation extends our understanding of Class F and other dimerizing GPCRs, offering novel targets for dimer-interfering small molecules.Frizzled 6 (FZD6) is a G protein-coupled receptor (GPCR) involved in several cellular processes. Here, the authors use live cell imaging and spectroscopy to show that FZD6 forms dimers, whose association is regulated by WNT proteins and that dimer dissociation is crucial for FZD6 signaling.

    Chandra K., Das P., Metanis N., Friedler A., and Reches M. 2017. “Peptide fibrils as monomer storage of the covalent HIV-1 integrase inhibitor.” J. Pept. Sci. Link Abstract

    We have recently reported the covalent inhibition of HIV-1 integrase by an N-terminal succinimide-modified lens epithelium-derived growth factor (361-370) peptide. We also showed that this peptide is proteolytically stable. Here, we show that this inhibitor is stored as fibrils that serve as a stock for the inhibitory monomers. The fibrils increase the local concentration of the peptide at the target protein. When the monomers bind integrase, the equilibrium between the fibrils and their monomers shifts towards the formation of peptide monomers. The combination of fibril formation and subsequent proteolytic stability of the peptide may bring to new strategy for developing therapeutic agents.

    Oren T., Nimri L., Yehuda-Shnaidman E., Staikin K., Hadar Y., Friedler A., Amartely H., Slutzki M., Pizio A. D., Niv M.Y., Peri I., Graeve L., and Schwartz B. 2017. “Recombinant ostreolysin induces brown fat-like phenotype in HIB-1B cells.” Mol. Nutr. Food Res. Publisher's Version Abstract
    SCOPE:
    Brown adipose tissue (BAT) is the main regulator of thermogenesis by increasing energy expenditure through the uncoupling of oxidative metabolism from ATP synthesis. There is a growing body of evidence for BAT being the key responsible organ in combating obesity and its related disorders. Herein we propose the fungal protein ostreolysin (Oly), which has been previously shown to bind to cholesterol-enriched raft-like membrane domains (lipid rafts) of mammalian cells, as a suitable candidate for interaction with brown preadipocytes. The aim of the present study was therefore to characterize the mechanism by which a recombinant version of ostreolysin (rOly) induces brown adipocyte differentiation.
    METHODS AND RESULTS:
    Primary isolated brown preadipocytes or HIB-1B brown preadipocyte cells were treated with rOly and the effects on morphology, lipid accumulation, respiration rate, and associated gene and protein expression were measured. rOly upregulated mRNA and protein levels of factors related to brown adipocyte differentiation, induced lipid droplet formation, and increased cellular respiration rate due to expression of uncoupling protein 1. rOly also upregulated β-tubulin expression, and therefore microtubules might be involved in its mechanism of action.
    CONCLUSION:
    rOly promotes brown adipocyte differentiation, suggesting a new mechanism for rOly's contribution to the battle against obesity.
    Rimon O., Suss O., Goldenberg M., Fassler R., Yogev O., Amartely H., Propper G., Friedler A., and Reichmann D. 2017. “A Role of Metastable Regions and Their Connectivity in the Inactivation of a Redox-Regulated Chaperone and Its Inter-Chaperone Crosstalk.” Antioxid Redox Signal. Link Abstract
    AIMS:
    A recently discovered group of conditionally disordered chaperones share a very unique feature; they need to lose structure to become active as chaperones. This activation mechanism makes these chaperones particularly suited to respond to protein-unfolding stress conditions, such as oxidative unfolding. However, the role of this disorder in stress-related activation, chaperone function, and the crosstalk with other chaperone systems is not yet clear. Here, we focus on one of the members of the conditionally disordered chaperones, a thiol-redox switch of the bacterial proteostasis system, Hsp33.
    RESULTS:
    By modifying the Hsp33's sequence, we reveal that the metastable region has evolved to abolish redox-dependent chaperone activity, rather than enhance binding affinity for client proteins. The intrinsically disordered region of Hsp33 serves as an anchor for the reduced, inactive state of Hsp33, and it dramatically affects the crosstalk with the synergetic chaperone system, DnaK/J. Using mass spectrometry, we describe the role that the metastable region plays in determining client specificity during normal and oxidative stress conditions in the cell. Innovation and Conclusion: We uncover a new role of protein plasticity in Hsp33's inactivation, client specificity, crosstalk with the synergistic chaperone system DnaK/J, and oxidative stress-specific interactions in bacteria. Our results also suggest that Hsp33 might serve as a member of the house-keeping proteostasis machinery, tasked with maintaining a "healthy" proteome during normal conditions, and that this function does not depend on the metastable linker region.
    2016
    Chandra K., Das P., Mamidi S., Hurevich M., Iosub-Amir A., Metanis N., Reches M., and Friedler A. 2016. “Covalent Inhibition of HIV-1 Integrase by N-Succinimidyl Peptides.” ChemMedChem. Link Abstract

    We present a new approach for the covalent inhibition of HIV‐1 integrase (IN) by an LEDGF/p75‐derived peptide modified with an N‐terminal succinimide group. The covalent inhibition is mediated by direct binding of the succinimide to the amine group of a lysine residue in IN. The peptide serves as a specific recognition sequence for the target protein, while the succinimide serves as the binding moiety. The combination of a readily synthesizable peptide precursor with easy and efficient binding to the target protein makes this approach a promising new strategy for designing lead compounds.

    Amartely H., David A., Shamir M., Lebendiker M., Izraeli S., and Friedler A. 2016. “Differential effects of Zinc binding on structured and disordered regions in the multidomain STIL protein.” Chem. Sci. Link Abstract

    Binding of metal ions is an important regulatory mechanism in proteins. Specifically, Zn2+ binding to disordered regions commonly induces a disorder to order transition and gain of structure or oligomerization. Here we show that simultaneous binding of Zn2+ ions has different effects on structured and disordered domains in the same multidomain protein. The centrosomal STIL protein bound Zn2+ions via both its structured N-terminal domain (NTD) and disordered central region (IDR). Zn2+ binding induced structural rearrangement of the structured NTD but promoted oligomerization of the IDR. We suggest that by binding Zn2+ STIL acquires a different conformation, which allows its oligomerization and induces its activity. Sequence alignment of the oligomerization region revealed a new suggested motif, SxKxS/SxHxS/SxLxS, which may participate in STIL oligomerization. Binding of the same metal ion through a disordered and a structured domain in the same protein is a property that may have implications in regulating the protein activity. By doing so, the protein achieves two parallel outcomes: structural changes and oligomerization that can take place together. Our results describe a new important role of the delicate interplay between structure and intrinsic disorder in proteins.

    Koler M., Frank V., Amartely H., Friedler A., and Vaknin A. 2016. “Dynamic Clustering of the Bacterial Sensory Kinase BaeS.” PLoS One. Link Abstract

    Several bacterial sensory-kinase receptors form clusters on the cell membrane. However, the dynamics of sensory-kinase clustering are largely unclear. Using measurements of fluorescence anisotropy and time-lapse imaging of Escherichia coli cells, we demonstrate that copper ions trigger self-association of BaeS receptors and lead to rapid formation of clusters, which can be reversibly dispersed by a metal chelator. Copper ions did not trigger self-association of other fluorescently tagged sensory kinases, and other divalent metal ions could not elicit self-association of BaeS. The histidine residues in the BaeS periplasmic domain are essential for copper binding in vitro and are important for the copper-induced BaeS responses in vivo. BaeS clustering was triggered also under conditions that directly triggered BaeS-dependent transcriptional responses. Thus, clustering of sensory kinase receptors can be dynamic and context dependent and can be triggered by specific environmental cues.

    David A., Amartely H., Rabinowicz N., Shamir M., Friedler A., and Izraeli S. 2016. “Molecular basis of the STIL coiled coil oligomerization explains its requirement for de-novo formation of centrosomes in mammalian cells.” Sci Rep. Link Abstract

    The STIL protein is essential for centriole replication and for the non-templated, de novo centriole biogenesis that is required for mammalian embryogenesis. Here we performed quantitative biophysical and structural analysis of the central short coiled coil domain (CCD) of STIL that is critical for its function. Using biophysical, biochemical and cell biology approaches, we identified the specific residues in the CCD that mediate the oligomerization, centrosomal localization and protein interactions of STIL. We characterized the structural properties of the coiled coil peptide using circular dichroism spectroscopy and size exclusion chromatography. We identified two regions in this domain, containing eight hydrophobic residues, which mediate the coiled coil oligomerization. Mutations in these residues destabilized the coiled coil thermodynamically but in most cases did not affect its secondary structure. Reconstituting mouse embryonic fibroblasts lacking endogenous Stil, we show that STIL oligomerization mediated by these residues is not only important for the centrosomal functions of STIL during the canonical duplication process but also for de-novo formation of centrosomes.

    Zhuravel R., Amit E., Elbaz S., Rotem D., Chen Y.-J., Friedler A., Yitzchaik S., and Porath D. 2016. “Atomic force microscopy characterization of kinase-mediated phosphorylation of a peptide monolayer.” Sci. Rep. Link Abstract

    We describe the detailed microscopic changes in a peptide monolayer following kinase-mediated phosphorylation. A reversible electrochemical transformation was observed using square wave voltammetry (SWV) in the reversible cycle of peptide phosphorylation by ERK2 followed by dephosphorylation by alkaline phosphatase. A newly developed method for analyzing local roughness, measured by atomic force microscope (AFM), showed a bimodal distribution. This may indicate either a hole-formation mechanism and/or regions on the surface in which the peptide changed its conformation upon phosphorylation, resulting in increased roughness and current. Our results provide the mechanistic basis for developing biosensors for detecting kinase-mediated phosphorylation in disease.

    Postel S., Deredge D., Bonsor D. A., Yu X., Diederichs K., Helmsing S., Vromen A., Friedler A., Hust M., Egelman E. H., Beckett D., Wintrode P. L., and Sundberg E. J. 2016. “Bacterial flagellar capping proteins adopt diverse oligomeric states.” eLife . Link Abstract

    Flagella are crucial for bacterial motility and pathogenesis. The flagellar capping protein (FliD) regulates filament assembly by chaperoning and sorting flagellin (FliC) proteins after they traverse the hollow filament and exit the growing flagellum tip. In the absence of FliD, flagella are not formed, resulting in impaired motility and infectivity. Here, we report the 2.2 Å resolution X-ray crystal structure of FliD from Pseudomonas aeruginosa, the first high-resolution structure of any FliD protein from any bacterium. Using this evidence in combination with a multitude of biophysical and functional analyses, we find that Pseudomonas FliD exhibits unexpected structural similarity to other flagellar proteins at the domain level, adopts a unique hexameric oligomeric state, and depends on flexible determinants for oligomerization. Considering that the flagellin filaments on which FliD oligomers are affixed vary in protofilament number between bacteria, our results suggest that FliD oligomer stoichiometries vary across bacteria to complement their filament assemblies.

    The Na+, Li+/H+ antiporter of Escherichia coli (Ec-NhaA) maintains pH, Na+ homeostasis in enterobacteria. We used isothermal titration calorimetry to perform a detailed thermodynamic analysis of Li+ binding to Ec-NhaA and several of its mutants. We found that, in line with the canonical alternative access mechanistic model of secondary transporters, Li+/H+ binding to the antiporter is antagonistically coupled. Binding of Li+ displaces 2 H+from the binding site. The process is enthalpically driven, the enthalpic gain just compensating for an entropic loss and the buffer-associated enthalpic changes dominate the overall free-energy change. Li+binding, H+ release and antiporter activity were all affected to the same extent by mutations in the Li+binding site (D163E, D163N, D164N, D164E), while D133C changed the H+/Li+ stoichiometry to 4. Most striking, however, was the mutation, A167P, which converted the Ec-NhaA antagonistic binding into synergistic binding which is only known to occur in Cl/H+ antiporter.

    2015
    Iosub-Amir A., Rosmalen M., Mayer G., Lebendiker M., Danieli T., and Friedler A. 2015. “Highly homologous proteins exert opposite biological activities by using different interaction interfaces.” Sci. Rep. Link Abstract

    We present a possible molecular basis for the opposite activity of two homologues proteins that bind similar ligands and show that this is achieved by fine-tuning of the interaction interface. The highly homologous ASPP proteins have opposite roles in regulating apoptosis: ASPP2 induces apoptosis while iASPP inhibits it. The ASPP proteins are regulated by an autoinhibitory interaction between their Ank-SH3 and Pro domains. We performed a detailed biophysical and molecular study of the Pro – Ank-SH3 interaction in iASPP and compared it to the interaction in ASPP2. We found that iASPP Pro is disordered and that the interaction sites are entirely different: iASPP Ank-SH3 binds iASPP Pro via its fourth Ank repeat and RT loop while ASPP2 Ank-SH3 binds ASPP2 Pro via its first Ank repeat and the n-src loop. It is possible that by using different moieties in the same interface, the proteins can have distinct and specific interactions resulting in differential regulation and ultimately different biological activities.

    Snir E., Amit E., Friedler A., and Yitzchaik S. 2015. “A Highly Sensitive Square Wave Voltammetry Based Biosensor for Kinase Activity Measurements.” Biopolymers. Link Abstract
    An electrochemical biosensor has been developed for ultrasensitive, label‐free determination of protein kinase activity. The sensor is composed of a unique peptide monolayer on a gold electrode. It identifies the order change in the monolayer upon phosphorylation, via square wave voltametry (SWV) measurements. Disorder caused by the introduction of the phosphate groups onto the middle of the peptide sequence results in pinhole formation and therefore an increase in the electrochemical signal. The measured sensitivity was 100 nM of kinase and the dynamic range was 100 nM up to 11 μM. Sensitivity was an order of magnitude higher, and the dynamic range wider by two orders of magnitude, as compared to our previously reported impedimetric method, in which the sensitivity was 1 μM, and the dynamic range was 1–20 μM.