Publications (19)

  • Radion Vainer · Sarit Cohen · Anat Shahar · [...] · Eyal Arbely
    [Show abstract] [Hide abstract] ABSTRACT: Normal cellular homeostasis depends on tight regulation of gene expression, which requires the modulation of transcription factors' DNA binding specificity. That said, the mechanisms that allow transcription factors to distinguish between closely related response elements following different cellular signals, are not fully understood. In the tumor suppressor protein p53, acetylation of loop L1 residue Lys120 within the DNA binding domain, has been shown to promote the transcription of pro-apoptotic proteins such as BAX. Here, we report the crystal structures of Lys120-acetylated p53 DNA binding domain in a complex with a consensus response element and with the natural BAX response element. Our structural analyses reveal that Lys120-acetylation expands the conformational space of loop L1 in the DNA-bound state. Loop L1 flexibility is known to increase p53's DNA binding specificity, and Lys120-acetylation-dependent conformational changes in loop L1 enable the formation of sequence-dependent DNA binding modes for p53. Furthermore, binding to the natural BAX response element is accompanied by global conformational changes, deformation of the DNA helical structure and formation of an asymmetric tetrameric complex. Based on these findings we suggest a model for p53's Lys120 acetylation dependent DNA binding mode.
    Article · Jun 2016 · Journal of Molecular Biology
  • Sarit Cohen · Eyal Arbely
    [Show abstract] [Hide abstract] ABSTRACT: We describe a new expression system for efficient non-canonical amino acid mutagenesis in cultured mammalian cells by using the pyrrolysine tRNA synthetase/tRNACUA (Pyl) pair. A significant improvement in the incorporation of non-canonical amino acids into proteins was obtained by combining all the required genetic components into a single and compact vector that can be efficiently delivered to different mammalian cell lines by conventional transfection reagents.
    Article · Apr 2016 · ChemBioChem
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    Charlotte A. Dodson · Eyal Arbely
    [Show abstract] [Hide abstract] ABSTRACT: The SAP domain from the Saccharomyces cerevisiae Tho1 protein is comprised of just two helices and a hydrophobic core and is one of the smallest proteins whose folding has been characterised. Φ-value analysis revealed that Tho1 SAP folds through a transition state where helix 1 is the most extensively formed element of secondary structure and flickering native-like core contacts from Leu35 are also present. The contacts that contribute most to native state stability of Tho1 SAP are not formed in the transition state. Copyright © 2015. Published by Elsevier B.V.
    Full-text Article · Jun 2015 · FEBS letters
  • Joshua Manor · Eyal Arbely · Andrè Beerlink · [...] · Isaiah T. Arkin
    [Show abstract] [Hide abstract] ABSTRACT: Solving structures of membrane proteins has always been a formidable challenge, yet even upon success, the results are normally obtained in a mimetic environment that can be substantially different from a biological membrane. Herein, we use noninvasive isotope-edited FTIR spectroscopy to derive a structural model for the SARS coronavirus E protein transmembrane domain in lipid bilayers. Molecular-dynamics-based structural refinement, incorporating the IR-derived orientational restraints points to the formation of a helical hairpin structure. Disulfide cross-linking and X-ray reflectivity depth profiling provide independent support of the results. The unusually short helical hairpin structure of the protein might explain its ability to deform bilayers and is reminiscent of other peptides with membrane disrupting fiinctionalities. Taken together, we show that isotope-edited FTIR is a powerful tool to analyze small membrane proteins in their native environment, enabling us to relate the unusual structure of the SAPS E protein to its function.
    Article · Aug 2014 · Journal of Physical Chemistry Letters
  • [Show abstract] [Hide abstract] ABSTRACT: We report the first site-specific genetic encoding of photocaged tyrosine into proteins in mammalian cells. By photocaging Tyr701 of STAT1 we demonstrate that it is possible to photocontrol tyrosine phosphorylation and signal transduction in mammalian cells.
    Article · Jul 2012 · Journal of the American Chemical Society
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    Eyal Arbely · Eviatar Natan · Tobias Brandt · [...] · Alan R Fersht
    [Show abstract] [Hide abstract] ABSTRACT: Lys120 in the DNA-binding domain (DBD) of p53 becomes acetylated in response to DNA damage. But, the role and effects of acetylation are obscure. We prepared p53 specifically acetylated at Lys120, AcK120p53, by in vivo incorporation of acetylated lysine to study biophysical and structural consequences of acetylation that may shed light on its biological role. Acetylation had no affect on the overall crystal structure of the DBD at 1.9-Å resolution, but significantly altered the effects of salt concentration on specificity of DNA binding. p53 binds DNA randomly in vitro at effective physiological salt concentration and does not bind specifically to DNA or distinguish among its different response elements until higher salt concentrations. But, on acetylation, AcK120p53 exhibited specific DNA binding and discriminated among response elements at effective physiological salt concentration. AcK120p53 and p53 had the highest affinity to the same DNA sequence, although acetylation reduced the importance of the consensus C and G at positions 4 and 7, respectively. Mass spectrometry of p53 and AcK120p53 DBDs bound to DNA showed they preferentially segregated into complexes that were either DNA(p53DBD)(4) or DNA(AcK120DBD)(4), indicating that the different DBDs prefer different quaternary structures. These results are consistent with electron microscopy observations that p53 binds to nonspecific DNA in different, relaxed, quaternary states from those bound to specific sequences. Evidence is accumulating that p53 can be sequestered by random DNA, and target search requires acetylation of Lys120 and/or interaction with other factors to impose specificity of binding via modulating changes in quaternary structure.
    Full-text Article · May 2011 · Proceedings of the National Academy of Sciences
  • Eyal Arbely · Trevor J Rutherford · Hannes Neuweiler · [...] · Alan R Fersht
    [Show abstract] [Hide abstract] ABSTRACT: The protein BBL undergoes structural transitions and acid denaturation between pH 1.2 and 8.0. Using NMR spectroscopy, we measured the pK(a) values of all the carboxylic residues in this pH range. We employed (13)C direct-detection two-dimensional IPAP (in-phase antiphase) CACO NMR spectroscopy to monitor the ionization state of different carboxylic groups and demonstrated its advantages over other NMR techniques in measuring pK(a) values of carboxylic residues. The two residues Glu161 and Asp162 had significantly lowered pK(a) values, showing that these residues are involved in a network of stabilizing electrostatic interactions, as is His166. The other carboxylates had unperturbed values. The pH dependence of the free energy of denaturation was described quantitatively by the ionizations of those three residues of perturbed pK(a), and, using thermodynamic cycles, we could calculate their pK(a)s in the native and denatured states as well as the equilibrium constants for denaturation of the different protonation states. We also measured (13)C(α) chemical shifts of individual residues as a function of pH. These shifts sense structural transitions rather than ionizations, and they titrated with pH consistent with the change in equilibrium constant for denaturation. Kinetic measurements of the folding of BBL E161Q indicated that, at pH 7, the stabilizing interactions with Glu161 are formed mainly in the transition state. We also found that local interactions still exist in the acid-denatured state of BBL, which attenuate somewhat the flexibility of the acid-denatured state.
    Article · Oct 2010 · Journal of Molecular Biology
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    Eyal Arbely · Hannes Neuweiler · Timothy D Sharpe · [...] · Alan R Fersht
    [Show abstract] [Hide abstract] ABSTRACT: Peripheral subunit binding domains (PSBDs) are integral parts of large multienzyme complexes involved in carbohydrate metabolism. PSBDs facilitate shuttling of prosthetic groups between different catalytic subunits. Their protein surface is characterized by a high density of positive charges required for binding to subunits within the complex. Here, we investigated folding thermodynamics and kinetics of the human PSBD (HSBD) using circular dichroism and tryptophan fluorescence experiments. HSBD was only marginally stable under physiological solvent conditions but folded within microseconds via a barrier-limited apparent two-state transition, analogous to its bacterial homologues. The high positive surface-charge density of HSBD leads to repulsive Coulomb forces that modulate protein stability and folding kinetics, and appear to even induce native-state movement. The electrostatic strain was alleviated at high solution-ionic-strength by Debye-Hückel screening. Differences in ionic-strength dependent characteristics among PSBD homologues could be explained by differences in their surface charge distributions. The findings highlight the trade-off between protein function and stability during protein evolution.
    Full-text Article · Sep 2010 · Protein Science
  • Eyal Arbely · Trevor J Rutherford · Timothy D Sharpe · [...] · Alan R Fersht
    [Show abstract] [Hide abstract] ABSTRACT: A dispersion of melting temperatures at pH5.3 for individual residues of the BBL protein domain has been adduced as evidence for barrier-free downhill folding. Other members of the peripheral subunit domain family fold cooperatively at pH7. To search for possible causes of anomalies in BBL's denaturation behavior, we measured the pH titration of individual residues by heteronuclear NMR. At 298 K, the pK(a) of His142 was close to that of free histidine at 6.47+/-0.04, while that of the more buried His166 was highly perturbed at 5.39+/-0.02. Protonation of His166 is thus energetically unfavorable and destabilizes the protein by approximately 1.5 kcal/mol. Changes in C(alpha) secondary shifts at pH5.3 showed a decrease in helicity of the C-terminus of helix 2, where His166 is located, which was accompanied by a measured decrease of 1.1+/-0.2 kcal/mol in stability from pH7 to 5.3. Protonation of His166 perturbs, therefore, the structure of BBL. Only approximately 1% of the structurally perturbed state will be present at the biologically relevant pH7.6. Experiments at pH5.3 report on a near-equal mixture of the two different native states. Further, at this pH, small changes of pH and pK(a) induced by changes in temperature will have near-maximal effects on pH-dependent conformational equilibria and on propagation of experimental error. Accordingly, conventional barrier-limited folding predicts some dispersion of measured thermal unfolding curves of individual residues at pH5.3.
    Article · Apr 2009 · Journal of Molecular Biology
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    [Show abstract] [Hide abstract] ABSTRACT: Na+/H+ antiporters are central to cellular salt and pH homeostasis. The structure of Escherichia coli NhaA was recently determined, but its mechanisms of transport and pH regulation remain elusive. We performed molecular dynamics simulations of NhaA that, with existing experimental data, enabled us to propose an atomically detailed model of antiporter function. Three conserved aspartates are key to our proposed mechanism: Asp164 (D164) is the Na+-binding site, D163 controls the alternating accessibility of this binding site to the cytoplasm or periplasm, and D133 is crucial for pH regulation. Consistent with experimental stoichiometry, two protons are required to transport a single Na+ ion: D163 protonates to reveal the Na+-binding site to the periplasm, and subsequent protonation of D164 releases Na+. Additional mutagenesis experiments further validated the model.
    Full-text Article · Sep 2007 · Science
  • Z Khattari · E Arbely · I T Arkin · T Salditt
    [Show abstract] [Hide abstract] ABSTRACT: We have investigated the effect of the transmembrane domain of three viral ion channel proteins on the lipid bilayer structure by X-ray reflectivity and scattering from oriented planar bilayers. The proteins show a similar effect on the lipid bilayer structural parameters: an increase in the lipid bilayer hydrophobic core, a decrease in the amplitude of the vertical density profile and a systematic change in the ordering of the acyl chains as a function of protein-to-lipid ratio. These results are discussed in a comparative view.
    Article · Jan 2007 · European Biophysics Journal
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    Eyal Arbely · Zvi Granot · Itamar Kass · [...] · Isaiah T Arkin
    [Show abstract] [Hide abstract] ABSTRACT: In an attempt to understand what distinguishes severe acute respiratory syndrome (SARS) coronavirus (SCoV) from other members of the coronaviridae, we searched for elements that are unique to its proteins and not present in any other family member. We identified an insertion of two glycine residues, forming the GxxxG motif, in the SCoV spike protein transmembrane domain (TMD), which is not found in any other coronavirus. This surprising finding raises an "oligomerization riddle": the GxxxG motif is a known dimerization signal, while the SCoV spike protein is known to be trimeric. Using an in vivo assay, we found that the SCoV spike protein TMD is oligomeric and that this oligomerization is driven by the GxxxG motif. We also found that the GxxxG motif contributes toward the trimerization of the entire spike protein; in that, mutations in the GxxxG motif decrease trimerization of the full-length protein expressed in mammalian cells. Using molecular modeling, we show that the SCoV spike protein TMD adopts a distinct and unique structure as opposed to all other coronaviruses. In this unique structure, the glycine residues of the GxxxG motif are facing each other, enhancing helix-helix interactions by allowing for the close positioning of the helices. This unique orientation of the glycine residues also stabilizes the trimeric bundle during multi-nanosecond molecular dynamics simulation in a hydrated lipid bilayer. To the best of our knowledge, this is the first demonstration that the GxxxG motif can potentiate other oligomeric forms beside a dimer. Finally, according to recent studies, the stabilization of the trimeric bundle is linked to a higher fusion activity of the spike protein, and the possible influence of the GxxxG motif on this feature is discussed.
    Full-text Article · Oct 2006 · Biochemistry
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    [Show abstract] [Hide abstract] ABSTRACT: We investigated the structure of the hydrophobic domain of the severe acute respiratory syndrome E protein in model lipid membranes by x-ray reflectivity and x-ray scattering. In particular, we used x-ray reflectivity to study the location of an iodine-labeled residue within the lipid bilayer. The label imposes spatial constraints on the protein topology. Experimental data taken as a function of protein/lipid ratio P/L and different swelling states support the hairpin conformation of severe acute respiratory syndrome E protein reported previously. Changes in the bilayer thickness and acyl-chain ordering are presented as a function of P/L, and discussed in view of different structural models.
    Full-text Article · Apr 2006 · Biophysical Journal
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    Z. Khattari · G. Brotons · E. Arbely · [...] · T. Salditt
    [Show abstract] [Hide abstract] ABSTRACT: We report on an anomalous X-ray reflectivity study to locate a labelled residue of a membrane protein with respect to the lipid bilayer. From such experiments, important constraints on the protein or peptide conformation can be derived. Specifically, our aim is to localize an iodine-labelled phenylalanine in the SARS E protein, incorporated in DMPC phospholipid bilayers, which are deposited in the form of thick multilamellar stacks on silicon surfaces. Here, we discuss the experimental aspects and the difficulties associated with the Fourier synthesis analysis that gives the electron density profile of the membranes.
    Full-text Article · Feb 2005 · Physica B Condensed Matter
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    Eyal Arbely · Ziad Khattari · Guillaume Brotons · [...] · Isaiah T Arkin
    [Show abstract] [Hide abstract] ABSTRACT: The agent responsible for the recent severe acute respiratory syndrome (SARS) outbreak is a previously unidentified coronavirus. While there is a wealth of epidemiological studies, little if any molecular characterization of SARS coronavirus (SCoV) proteins has been carried out. Here we describe the molecular characterization of SCoV E protein, a critical component of the virus responsible for virion envelope morphogenesis. We conclusively show that SCoV E protein contains an unusually short, palindromic transmembrane helical hairpin around a previously unidentified pseudo-center of symmetry, a structural feature which seems to be unique to SCoV. The hairpin deforms lipid bilayers by way of increasing their curvature, providing for the first time a molecular explanation of E protein's pivotal role in viral budding. The molecular understanding of this critical component of SCoV may represent the beginning of a concerted effort aimed at inhibiting its function, and consequently, viral infectivity.
    Full-text Article · Sep 2004 · Journal of Molecular Biology
  • Eyal Arbely · Isaiah T Arkin
    [Show abstract] [Hide abstract] ABSTRACT: Due to the apolar nature of the lipid bilayer, the weak Calpha-H...O H-bond is thought to contribute significantly toward the stability of transmembrane helical bundles such as glycophorin A (GPA). Here for the first time we measured the strength of such a bond, using vibrational frequency shifts of a dimeric and nondimeric variants of GPA containing a Gly CD2 label. Although the resulting estimated bond strength of 0.88 kcal/mol is relatively weak, several such bonds could contribute significantly toward bundle stabilization.
    Article · Jun 2004 · Journal of the American Chemical Society
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    Itamar Kass · Eyal Arbely · Isaiah T Arkin
    [Show abstract] [Hide abstract] ABSTRACT: Site-specific infrared dichroism is an emerging method capable of proposing a model for the backbone structure of a transmembrane alpha-helix within a helical bundle. Dichroism measurements of single, isotopically enhanced vibrational modes (e.g., Amide I 13C=18O or Gly CD2 stretching modes) can yield precise orientational restraints for the monomer helix protomer that can be used as refinement constraints in model building of the entire helical bundle. Essential, however, for the interpretation of the dichroism measurements, is an accurate modeling of the sample disorder. In this study we derive an enhanced and more realistic modeling of the sample disorder based on a Gaussian distribution of the chromophore around a particular angle. The enhanced utility of the Gaussian model is exemplified by the comparative data analysis based on the aforementioned model to previously employed models.
    Full-text Article · May 2004 · Biophysical Journal
  • Eyal Arbely · Itamar Kass · Isaiah T Arkin
    [Show abstract] [Hide abstract] ABSTRACT: Infrared spectroscopy has long been used to examine the average secondary structure and orientation of membrane proteins. With the recent utilization of site-specific isotope labeling (e.g., peptidic 1-(13)C = (18)O) it is now possible to examine localized properties, rather than global averages. The technique of site-specific infrared dichroism (SSID) capitalized on this fact, and derives site-specific orientational restraints for the labeled amino acids. These restraints can then be used to solve the backbone structure of simple alpha-helical bundles, emphasizing the capabilities of this approach. So far SSID has been carried out in attenuated total internal reflection optical mode, with all of the respective caveats of attenuated total internal reflection. In this report we extend SSID through the use of transmission infrared spectroscopy tilt series. We develop the corresponding theory and demonstrate that accurate site-specific orientational restraints can be derived from a simple transmission experiment.
    Article · Nov 2003 · Biophysical Journal
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    [Show abstract] [Hide abstract] ABSTRACT: Journal article
    Full-text Article ·