Yasar Akdogan

Effect of ionic liquids on the solution structure of human serum albumin.

The effect of several ionic liquids (ILs) on the solution structure of human serum albumin (HSA) is revealed by continuous wave electron paramagnetic resonance (EPR) spectroscopy and nanoscale distance measurements with double electron-electron resonance (DEER) spectroscopy. HSA, the most abundant protein in human blood, is able to bind and transport multiple fatty acids (FAs). Using spin-labeled FA, the uptake of the FA by the protein and their spatial distribution in the protein can be monitored. The FA distribution provides an indirect yet effective way to characterize the structure of the protein in solution. Addition of imidazolium-based ILs to an aqueous solution of HSA/FA conjugates is accompanied by significant destabilization and unfolding of the proteins tertiary structure. In contrast, HSA maintains its tertiary structure when choline dihydrogenphosphate (dhp) is added. The comparison of FA distance distributions in HSA with and without choline dhp surprisingly revealed that with this IL, the FA anchoring units are in better agreement with the crystallographic data. Furthermore, the FA entry point distribution appears widened and more asymmetric than in pure buffer. These results indicate that choline dhp as a cosolvent may selectively stabilize HSA conformations closer to the crystal structure out of the overall conformational ensemble.

Evidence for Water-Tuned Structural Differences in Proteins: An Approach Emphasizing Variations in Local Hydrophilicity

We present experimental evidence for the significant effect that water can have on the functional structure of proteins in solution. Human (HSA) and Bovine Serum Albumin (BSA) have an amino acid sequence identity of 75.52% and are chosen as model proteins. We employ EPR-based nanoscale distance measurements using double electron-electron resonance (DEER) spectroscopy and both albumins loaded with long chain fatty acids (FAs) in solution to globally (yet indirectly) characterize the tertiary protein structures from the bound ligands’ points of view. The complete primary structures and crystal structures of HSA and as of recently also BSA are available. We complement the picture as we have recently determined the DEER-derived solution structure of HSA and here present the corresponding BSA solution structure. The characteristic asymmetric FA distribution in the crystal structure of HSA can surprisingly be observed by DEER in BSA in solution. This indicates that the BSA conformational ensemble in solution seems to be narrow and close to the crystal structure of HSA. In contrast, for HSA in solution a much more symmetric FA distribution was found. Thus, conformational adaptability and flexibility dominate in the HSA solution structure while BSA seems to lack these properties. We further show that differences in amino acid hydropathies of specific structural regions in both proteins can be used to correlate the observed difference in the global (tertiary) solution structures with the differences on the primary structure level.

The solvation of nitroxide radicals in ionic liquids studied by high-field EPR spectroscopy

Ionic liquids (ILs) feature a variety of properties that make them a unique class of solvents. To gain a better understanding of how ILs solvate compounds of different chemical structure, we used pulsed high-field electron paramagnetic resonance (EPR) spectroscopy at W-band (approximately 94 GHz) and continuous wave EPR at X-band (approximately 9.4 GHz) on three TEMPO-based spin probes with different substitutions at the 4-position: 4-R-2,2,6,6-tetramethylpiperidine-1-oxyl, with R = N(CH(3))(3)(+), Cat-1, R = COO(-), TEMPO-4-carboxylate, and R = OH, TEMPOL. The spin probes are dissolved in imidazolium based ILs with different alkyl chain lengths (-C(2)H(5), -C(4)H(9), -C(6)H(13)) and anions (BF(4)(-), PF(6)(-)) and also in molecular solvents (methanol, water-glycerol). X-Band EPR at RT shows that the reorientational motion of the charged spin probes in ILs is about fivefold slower than that of the TEMPOL. Moreover, anion variation from BF(4)(-) to PF(6)(-) in ILs most strongly slows down the rotational motion (as measured by the rotational correlation time tau(r)) of Cat-1, followed by TEMPOL, while tau(r) of TEMPO-4-carboxylate is least affected. The EPR parameters g(xx) and A(zz) (tensor elements of the g- and hyperfine tensor) are sensitive to environmental effects and are only fully resolved at the high field used in this study. Changes of g(xx) and A(zz) values of the Cat-1 in ILs and methanol are very small especially compared to that of TEMPO-4-carboxylate, indicating that Cat-1 is located in a polar region of the ILs resembling the situation in methanol. On the other hand, the g(xx) value of TEMPO-4-carboxylate is sensitive to the length of alkyl group which shows that TEMPO-4-carboxylate is close to the nonpolar region of ILs. The small differences in the chemical substitution of the spin probes used here are sufficient for the molecules to reside in different domains of different dielectric properties in ILs. Our combined results are in good agreement with a picture of a nanophase separation, in which the charged cations and anions form polar regions and the hydrophobic alkyl chains of the IL cations form non-polar regions.

Solvent-Induced Protein Refolding at Low Temperatures

Protein refolding at low temperatures is shown for a self-assembled system of human serum albumin (HSA) and spin-labeled fatty acids (FAs), in ternary solvent mixtures with usually denaturing cosolvents ethanol or ionic liquids (ILs). When HSA is natively folded, it offers FA binding sites, and the uptake and the distribution of these FA binding pockets have characteristic continuous wave electron paramagnetic resonance (CW EPR) and double electron-electron resonance (DEER) signatures. At room temperature, CW EPR shows that the addition of 35% (v/v) of ethanol or IL leads to HSA being unfolded. A temperature decrease yields bimodal CW EPR spectra with bound FA and free FA signals, indicating at least partial refolding of HSA, which is also confirmed by corresponding DEER data. This finding is based on increased protein stability at lower temperatures and a change in the preferential solvation of the protein by glycerol in the ternary solvent mixtures.

Synthesis of solid solutions of Cd1−xZnxS nanocrystals in the channels of mesostructured silica films

In this contribution, we introduce the use of metal ion (Cd(II) and Zn(II)) modified mesostructured silica as a reaction medium, to produce a solid solution of Cd1−xZnxS nanocrystals as a thin film. With this approach, a true liquid crystalline templating (TLCT) and liquid crystalline mesophase of transition metal salt ∶ oligo(ethylene oxide) non-ionic surfactant (((1 − x)[Cd(H2O)4](NO3)2 + x[Zn(H2O)6](NO3)2) ∶ CH3(CH2)11(OCH2CH2)10OH, (MLC)), systems were collectively used to synthesise mesostructured silica films. The film samples were reacted at room temperature (RT) in an H2S atmosphere to produce zinc blend Cd1−xZnxS nanocrystals in the channels of mesostructured silica. The initial Zn(II) and Cd(II) ion concentrations in the reaction media determine the final composition and band gap of the Cd1−xZnxS nanocrystals. The growth process of the Cd1−xZnxS nanocrystals in the pores is influenced by the silica walls. If the walls are rigid (well polymerized, obtained by aging the samples before H2S treatment), then the Cd1−xZnxS nanoparticles are smaller in size and more uniform in size distribution.

Host–guest interactions in polycationic human serum albumin bioconjugates

Polycationic human serum albumin, cHSA, as well as cHSA conjugates with multiple polyethylene(oxide) chains of two different lengths were synthesized, and the uptake and release of spin-labeled fatty acid (FA) ligands were quantitatively analyzed by continuous wave (CW) electron paramagnetic resonance (EPR) spectroscopy and nanoscale distance measurements with double electron–electron resonance (DEER) spectroscopy. It is found that the seven FA binding pockets of native HSA are less well accessible by FAs in cHSA and its PEO-conjugates. A large number (at least 25) of FAs can diffusely and electrostatically be bound to the surface of all highly cationic serum albumin variants. These bound FAs show a remarkable resilience against release from both cHSA and PEO conjugates. Conjugation of PEO chains to cHSA had only minute effects on all EPR data, indicating that PEO grafts can be used without reduction of effectiveness in the ligand binding.

Signature of an aggregation-prone conformation of tau

The self-assembly of the microtubule associated tau protein into fibrillar cell inclusions is linked to a number of devastating neurodegenerative disorders collectively known as tauopathies. The mechanism by which tau self-assembles into pathological entities is a matter of much debate, largely due to the lack of direct experimental insights into the earliest stages of aggregation. We present pulsed double electron-electron resonance measurements of two key fibril-forming regions of tau, PHF6 and PHF6*, in transient as aggregation happens. By monitoring the end-to-end distance distribution of these segments as a function of aggregation time, we show that the PHF6(*) regions dramatically extend to distances commensurate with extended β-strand structures within the earliest stages of aggregation, well before fibril formation. Combined with simulations, our experiments show that the extended β-strand conformational state of PHF6(*) is readily populated under aggregating conditions, constituting a defining signature of aggregation-prone tau, and as such, a possible target for therapeutic interventions.

Conformational changes of the chaperone SecB upon binding to a model substrate - bovine pancreatic trypsin inhibitor (BPTI)

Abstract SecB is a homotetrameric cytosolic chaperone that forms part of the protein translocation machinery in E. coli. Due to SecB, nascent polypeptides are maintained in an unfolded translocation-competent state devoid of tertiary structure and thus are guided to the translocon. In vitro SecB rapidly binds to a variety of ligands in a non-native state. We have previously investigated the bound state conformation of the model substrate bovine pancreatic trypsin inhibitor (BPTI) as well as the conformation of SecB itself by using proximity relationships based on site-directed spin labeling and pyrene fluorescence methods. It was shown that SecB undergoes a conformational change during the process of substrate binding. Here, we generated SecB mutants containing but a single cysteine per subunit or an exposed highly reactive new cysteine after removal of the nearby intrinsic cysteines. Quantitative spin labeling was achieved with the methanethiosulfonate spin label (MTS) at positions C97 or E90C, respectively. Highfield (W-band) electron paramagnetic resonance (EPR) measurements revealed that with BPTI present the spin labels are exposed to a more polar/hydrophilic environment. Nanoscale distance measurements with double electron-electron resonance (DEER) were in excellent agreement with distances obtained by molecular modeling. Binding of BPTI also led to a slight change in distances between labels at C97 but not at E90C. While the shorter distance in the tetramer increased, the larger diagonal distance decreased. These findings can be explained by a widening of the tetrameric structure upon substrate binding much like the opening of two pairs of scissors.

Spin probing of supramolecular structures in 1-butyl-3-methyl-imidazolium tetrafluoroborate/water mixtures

We have systematically studied micro-heterogeneous mixtures of the room temperature ionic liquid 1-butyl-3-methyl-imidazolium tetrafluoroborate ([bmim+][BF4−]) and water using continuous wave electron paramagnetic resonance (CW EPR) and the spin-probing methodology. Using cryo TEM, a mesoscopic picture of the micro-heterogeneous mixtures could be revealed. Six spin-probes differing in polarity, charge and Lewis basicity have been used to map the dependence of the micro-polarity and rotation motion of the probe on the ionic liquid (IL) concentration. The electron paramagnetic resonance (EPR) spectra of all probe molecules have been found to be unimodal. The critical aggregation concentration has been determined and the local water concentration sensed by the probes extracted from the Mukerjee hydrophilicity index. Surprisingly, four probes of the piperidinoxyl type were found to sense very similar local water concentrations irrespective of the substituent, monovalent ionic or H-bonding, at the 4-position. Using a simple geometrical model of the primary IL aggregates observed in the micro-heterogeneous concentration range, we show that these probes cannot be statically located within the aggregates on the EPR timescale. Instead, diffusive trajectories of the probe molecules extend into the aqueous phase, i.e. aqueous and [bmim+][BF4−]-rich phases are sampled by the probes in swift succession. No details of the internal structure of the [bmim+][BF4−] aggregates can in general be elucidated by the spin-probing methodology under these conditions. On the other hand, the dianionic Fremys salt binds to the surface of the IL aggregates thereby sampling predominantly the aqueous phase. At large IL concentrations, a micro-viscosity drastically smaller than the macroscopic viscosity is typically observed. Supplementary Materials (Figures S1–S5) for this paper are available online on the journal website.

Spontaneous Adhesion of DOPA and Tryptophan Functionalized PEG to Polystyrene Nanobeads: An EPR Study

Wet adhesion is achieved by mussels so naturally. Their adhesion mechanism has inspired scientists to obtain wet adhesives for a long time. The amino acid 3,4-dihydroxyphenylalanine (DOPA) produced by mussels adheres to different types of surfaces and also contributes to cohesive interactions. Here, we showed the spontaneous adhesion of DOPA functionalized four armed poly (ethylene glycol) (PEG) polymer to spin labeled polystyrene (SL-PS) nanosurfaces by electron paramagnetic resonance (EPR) spectroscopy. In addition to DOPA, adhesion property of another amino acid of tryptophan (Trp) was studied. Trp attached four armed PEG polymers did not adhere to the surface of SL-PS in the force free condition. However, two armed DOPA and two armed Trp functionalized PEG adhere to the PS.