Halil I. Okur
École Polytechnique Fédérale de Lausanne
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Featured researches published by Halil I. Okur.
Journal of the American Chemical Society | 2013
Halil I. Okur; Jaibir Kherb; Paul S. Cremer
We investigated salt interactions with butyramide as a simple mimic of cation interactions with protein backbones. The experiments were performed in aqueous metal chloride solutions using two spectroscopic techniques. In the first, which provided information about contact pair formation, the response of the amide I band to the nature and concentration of salt was monitored in bulk aqueous solutions via attenuated total reflection Fourier transform infrared spectroscopy. It was found that molar concentrations of well-hydrated metal cations (Ca(2+), Mg(2+), Li(+)) led to the rise of a peak assigned to metal cation-bound amides (1645 cm(-1)) and a decrease in the peak associated with purely water-bound amides (1620 cm(-1)). In a complementary set of experiments, the effect of cation identity and concentration was investigated at the air/butyramide/water interface via vibrational sum frequency spectroscopy. In these studies, metal ion-amide binding led to the ordering of the adjacent water layer. Such experiments were sensitive to the interfacial partitioning of cations in either a contact pair with the amide or as a solvent separated pair. In both experiments, the ordering of the interactions of the cations was: Ca(2+) > Mg(2+) > Li(+) > Na(+) ≈ K(+). This is a direct cationic Hofmeister series. Even for Ca(2+), however, the apparent equilibrium dissociation constant of the cation with the amide carbonyl oxygen was no tighter than ∼8.5 M. For Na(+) and K(+), no evidence was found for any binding. As such, the interactions of metal cations with amides are far weaker than the analogous binding of weakly hydrated anions.
Journal of Physical Chemistry B | 2013
Jana Paterová; Kelvin B. Rembert; Jan Heyda; Yadagiri Kurra; Halil I. Okur; Wenshe R. Liu; Christian Hilty; Paul S. Cremer; Pavel Jungwirth
Ion-specific effects on salting-in and salting-out of proteins, protein denaturation, as well as enzymatic activity are typically rationalized in terms of the Hofmeister series. Here, we demonstrate by means of NMR spectroscopy and molecular dynamics simulations that the traditional explanation of the Hofmeister ordering of ions in terms of their bulk hydration properties is inadequate. Using triglycine as a model system, we show that the Hofmeister series for anions changes from a direct to a reversed series upon uncapping the N-terminus. Weakly hydrated anions, such as iodide and thiocyanate, interact with the peptide bond, while strongly hydrated anions like sulfate are repelled from it. In contrast, reversed order in interactions of anions is observed at the positively charged, uncapped N-terminus, and by analogy, this should also be the case at side chains of positively charged amino acids. These results demonstrate that the specific chemical and physical properties of peptides and proteins play a fundamental role in ion-specific effects. The present study thus provides a molecular rationalization of Hofmeister ordering for the anions. It also provides a route for tuning these interactions by titration or mutation of basic amino acid residues on the protein surface.
Journal of Physical Chemistry B | 2017
Halil I. Okur; Jana Hladílková; Kelvin B. Rembert; Younhee Cho; Jan Heyda; Joachim Dzubiella; Paul S. Cremer; Pavel Jungwirth
Ions differ in their ability to salt out proteins from solution as expressed in the lyotropic or Hofmeister series of cations and anions. Since its first formulation in 1888, this series has been invoked in a plethora of effects, going beyond the original salting out/salting in idea to include enzyme activities and the crystallization of proteins, as well as to processes not involving proteins like ion exchange, the surface tension of electrolytes, or bubble coalescence. Although it has been clear that the Hofmeister series is intimately connected to ion hydration in homogeneous and heterogeneous environments and to ion pairing, its molecular origin has not been fully understood. This situation could have been summarized as follows: Many chemists used the Hofmeister series as a mantra to put a label on ion-specific behavior in various environments, rather than to reach a molecular level understanding and, consequently, an ability to predict a particular effect of a given salt ion on proteins in solutions. In this Feature Article we show that the cationic and anionic Hofmeister series can now be rationalized primarily in terms of specific interactions of salt ions with the backbone and charged side chain groups at the protein surface in solution. At the same time, we demonstrate the limitations of separating Hofmeister effects into independent cationic and anionic contributions due to the electroneutrality condition, as well as specific ion pairing, leading to interactions of ions of opposite polarity. Finally, we outline the route beyond Hofmeister chemistry in the direction of understanding specific roles of ions in various biological functionalities, where generic Hofmeister-type interactions can be complemented or even overruled by particular steric arrangements in various ion binding sites.
Science Advances | 2016
Yixing Chen; Halil I. Okur; Nikolaos Gomopoulos; Carlos Macias-Romero; Paul S. Cremer; Poul B. Petersen; Gabriele Tocci; David M. Wilkins; Chungwen Liang; Michele Ceriotti; Sylvie Roke
Ions induce changes in the H-bond network of water that extend by >20 nm, vary for H2O and D2O, and lead to surface tension anomalies. Electrolytes interact with water in many ways: changing dipole orientation, inducing charge transfer, and distorting the hydrogen-bond network in the bulk and at interfaces. Numerous experiments and computations have detected short-range perturbations that extend up to three hydration shells around individual ions. We report a multiscale investigation of the bulk and surface of aqueous electrolyte solutions that extends from the atomic scale (using atomistic modeling) to nanoscopic length scales (using bulk and interfacial femtosecond second harmonic measurements) to the macroscopic scale (using surface tension experiments). Electrolytes induce orientational order at concentrations starting at 10 μM that causes nonspecific changes in the surface tension of dilute electrolyte solutions. Aside from ion-dipole interactions, collective hydrogen-bond interactions are crucial and explain the observed difference of a factor of 6 between light water and heavy water.
Langmuir | 2015
Kelvin B. Rembert; Halil I. Okur; Christian Hilty; Paul S. Cremer
Herein, we use a combination of thermodynamic and spectroscopic measurements to investigate the interactions of Hofmeister anions with a thermoresponsive polymer, poly(N,N-diethylacrylamide) (PDEA). This amide-based polymer does not contain an NH moiety in its chemical structure and, thus, can serve as a model to test if anions bind to amides in the absence of an NH site. The lower critical solution temperature (LCST) of PDEA was measured as a function of the concentration for 11 sodium salts in aqueous solutions, and followed a direct Hofmeister series for the ability of anions to precipitate the polymer. More strongly hydrated anions (CO3(2-), SO4(2-), S2O3(2-), H2PO4(-), F(-), and Cl(-)) linearly decreased the LCST of the polymer with increasing the salt concentration. Weakly hydrated anions (SCN(-), ClO4(-), I(-), NO3(-), and Br(-)) increased the LCST at lower salt concentrations but salted the polymer out at higher salt concentrations. Proton nuclear magnetic resonance (NMR) was used to probe the mechanism of the salting-in effect and showed apparent binding between weakly hydrated anions (SCN(-) and I(-)) and the α protons of the polymer backbone. Additional experiments performed by attenuated total reflection Fourier transform infrared (ATR-FTIR) spectroscopy found little change in the amide I band upon the addition of salt, which is consistent with very limited, if any, interactions between the salt ions and the carbonyl moiety of the amide. These results support a molecular mechanism for ion-specific effects on proteins and model amides that does not specifically require an NH group to interact with the anions for the salting-in effect to occur.
Langmuir | 2010
Halil I. Okur; Yurdanur Türker; Ömer Dag
Cd(II) ions can be incorporated into the channels of mesostructured titania films, using the evaporation-induced self-assembly (EISA) approach, up to a record high Cd/Ti mole ratio of 25%. The film samples were obtained by spin or dip coating from a mixture of 1-butanol, [Cd(H(2)O)(4)](NO(3))(2), HNO(3), and Ti(OC(4)H(9))(4) and then aging the samples under 50% humidity at 30 degrees C (denoted as meso-xCd(II)-yTiO(2)). The nitrate ions, from nitric acid and cadmium nitrate, play important roles in the assembly process by coordinating as bidentate and bridged ligands to Cd(II) and Ti(IV) sites, respectively, in the mesostructured titania films. The film samples can be reacted under a H(2)S (or H(2)Se) gas atmosphere to produce CdS (or CdSe) on the channel surface and/or pore walls. However, the presence of such a large number of nitrate ions in the film samples also yields an extensive amount of nitric acid upon H(2)S (or H(2)Se) reaction, where the nanoparticles are not stable (they undergo decomposition back to metal ion and H(2)S or H(2)Se gas). However, this problem can be overcome by further aging the samples at 130 degrees C for a few hours before H(2)S (or H(2)Se) reaction. This step removes about 90% of the nitrate ions, eliminates the nitric acid production step, and stabilizes the CdS nanoparticles on the surface and/or walls of the pores of the coupled semiconductor films, denoted as meso-xCdS-yTiO(2). However, the H(2)Se reaction, additionally, needs to be carried at lower H(2)Se pressures in an N(2) atmosphere to produce stable CdSe nanoparticles on the surface and/or walls of the pores of the films, denoted as meso-xCdSe-yTiO(2). Otherwise, an excessive number of Se(8) particles form in the film samples.
Journal of the American Chemical Society | 2016
Nikolay Smolentsev; Cornelis Lütgebaucks; Halil I. Okur; Alex G. F. de Beer; Sylvie Roke
Variations between the inner and outer leaflets of cell membranes are crucial for cell functioning and signaling, drug-membrane interactions, and the formation of lipid domains. Transmembrane asymmetry can in principle be comprised of an asymmetric charge distribution, differences in hydration, specific headgroup/H-bonding interactions, or a difference in the number of lipids per leaflet. Here, we characterize the transmembrane asymmetry of small unilamellar liposomes consisting of zwitterionic and charged lipids in aqueous solution using vibrational sum frequency scattering and second harmonic scattering, label-free methods, specifically sensitive to lipid and water asymmetries. For single component liposomes, transmembrane asymmetry is present for the charge distribution and lipid hydration, but the leaflets are not detectably asymmetric in terms of the number of lipids per leaflet, even though geometrical packing arguments would predict so. Such a lipid transmembrane asymmetry can, however, be induced in binary lipid mixtures under conditions that enable H-bonding interactions between phosphate and amine groups. In this case, the measured asymmetry consists of a different number of lipids in the outer and inner leaflet, a difference in transmembrane headgroup hydration, and a different headgroup orientation for the interacting phosphate groups.
Nano Letters | 2015
Yixing Chen; Kailash C. Jena; Cornelis Lütgebaucks; Halil I. Okur; Sylvie Roke
A three-dimensional-phospholipid monolayer with tunable molecular structure was created on the surface of oil nanodroplets from a mixture of phospholipids, oil, and water. This simple nanoemulsion preparation technique generates an in situ prepared membrane model system with controllable molecular surface properties that resembles a lipid droplet. The molecular interfacial structure of such a nanoscopic system composed of hexadecane, 1,2-dihexadecanoyl-sn-glycero-3-phosphocholine (DPPC), and water was determined using vibrational sum frequency scattering and second harmonic scattering techniques. The droplet surface structure of DPPC can be tuned from a tightly packed liquid condensed phase like monolayer to a more dilute one that resembles the liquid condensed/liquid expanded coexistence phase by varying the DPPC/oil/water ratio. The tunability of the chemical structure, the high surface-to-volume ratio, and the small sample volume make this system an ideal model membrane for biochemical research.
Journal of the American Chemical Society | 2017
Jan Heyda; Halil I. Okur; Jana Hladílková; Kelvin B. Rembert; William Hunn; Tinglu Yang; Joachim Dzubiella; Pavel Jungwirth; Paul S. Cremer
A combination of Fourier transform infrared and phase transition measurements as well as molecular computer simulations, and thermodynamic modeling were performed to probe the mechanisms by which guanidinium (Gnd+) salts influence the stability of the collapsed versus uncollapsed state of an elastin-like polypeptide (ELP), an uncharged thermoresponsive polymer. We found that the cation’s action was highly dependent upon the counteranion with which it was paired. Specifically, Gnd+ was depleted from the ELP/water interface and was found to stabilize the collapsed state of the macromolecule when paired with well-hydrated anions such as SO42–. Stabilization in this case occurred via an excluded volume (or depletion) effect, whereby SO42– was strongly partitioned away from the ELP/water interface. Intriguingly, at low salt concentrations, Gnd+ was also found to stabilize the collapsed state of the ELP when paired with SCN–, which is a strong binder for the ELP. In this case, the anion and cation were both found to be enriched in the collapsed state of the polymer. The collapsed state was favored because the Gnd+ cross-linked the polymer chains together. Moreover, the anion helped partition Gnd+ to the polymer surface. At higher salt concentrations (>1.5 M), GndSCN switched to stabilizing the uncollapsed state because a sufficient amount of Gnd+ and SCN– partitioned to the polymer surface to prevent cross-linking from occurring. Finally, in a third case, it was found that salts which interacted in an intermediate fashion with the polymer (e.g., GndCl) favored the uncollapsed conformation at all salt concentrations. These results provide a detailed, molecular-level, mechanistic picture of how Gnd+ influences the stability of polypeptides in three distinct physical regimes by varying the anion. It also helps explain the circumstances under which guanidinium salts can act as powerful and versatile protein denaturants.
Science | 2017
Carlos Macias-Romero; Igor Nahalka; Halil I. Okur; Sylvie Roke
Imaging surfaces with water The surfaces of real materials are often highly chemically heterogeneous, and the reported values of even simple properties such as surface acidity can vary widely in many cases. Macias-Romero et al. developed a microscope that images surfaces on the basis of second-harmonic generation from the orientation of interfacial water (see the Perspective by Hunger and Parekh). They followed the deprotonation of silica along glass micropipettes by changing solution pH and found many regions where the surface acidity deviated strongly from the average for the entire micropipette. Science, this issue p. 784; see also p. 755 A wide-field second-harmonic–generation microscope images surfaces by probing the orientation order of interfacial water. We imaged the interfacial structure and dynamics of water in a microscopically confined geometry, in three dimensions and on millisecond time scales, with a structurally illuminated wide-field second harmonic microscope. The second harmonic images reported on the orientational order of interfacial water, induced by charge-dipole interactions between water molecules and surface charges. The images were converted into surface potential maps. Spatially resolved surface acid dissociation constant (pKa,s) values were determined for the silica deprotonation reaction by following pH-induced chemical changes on the curved and confined surfaces of a glass microcapillary immersed in aqueous solutions. These values ranged from 2.3 to 10.7 along the wall of a single capillary because of surface heterogeneities. Water molecules that rotate along an oscillating external electric field were also imaged.