Rotamer libraries of spin labelled cysteines for protein studies

Studies of structure and dynamics of proteins using site-directed spin labelling rely on explicit modelling of spin label conformations. The large computational effort associated with such modelling with molecular dynamics (MD) simulations can be avoided by a rotamer library approach based on a coarse-grained representation of the conformational space of the spin label. We show here that libraries of about 200 rotamers, obtained by iterative projection of a long MD trajectory of the free spin label onto a set of canonical dihedral angles, provide a representation of the underlying trajectory adequate for EPR distance measurements. Rotamer analysis was performed on selected X-ray structures of spin labelled T4 lysozyme mutants to characterize the spin label rotamer ensemble on a single protein site. Furthermore, predictions based on the rotamer library approach are shown to be in nearly quantitative agreement with electron paramagnetic resonance (EPR) distance data on the Na(+)/H(+) antiporter NhaA and on the light-harvesting complex LHCII whose structures are known from independent cryo electron microscopy and X-ray studies, respectively. Suggestions for the selection of labelling sites in proteins are given, limitations of the approach discussed, and requirements for further development are outlined.     

Interaction of tetraphenyl-porphyrin derivatives with DPPC-liposomes: an EPR study

The effect of the symmetry and polarity of the porphyrin molecules on their membrane localization and interaction with membrane lipids were investigated by electron paramagnetic resonance (EPR). For this purpose, two glycoconjugated tetraphenyl porphyrin derivatives were selected, respectively, symmetrically and asymmetrically substituted. Small unilamellar liposomes composed of dipalmitoylphosphatidylcholine (DPPC) and spin labeled stearic acids were prepared. The spin probe was located at the 5th or 7th or 12th or 16th position of the hydrocarbon chain in order to monitor various regions of the lipid bilayer. EPR spectra of porphyrin-free and porphyrin-bound liposomes were recorded at various temperatures below and above the phase transition temperature of DPPC. The effect on membrane fluidity proved to be stronger with the asymmetrical porphyrin derivative than with the symmetrical one. The rigidity increased when the spin label was near lipid head groups. The difference observed between control and porphyrin-treated samples when measured below the main lipid transition temperature disappeared at higher temperature. When the spin label was near the end of the hydrophobic tails, the symmetrical porphyrin derivative caused increase in fluidity, while the asymmetrical one slightly decreased it. To explain this phenomenon we propose that the asymmetrical derivative exerts a stronger ordering effect caused by its fluorophenyl group located at the level of the lipid heads, which is attenuated to the hydrophobic tails. The perturbing effect of the symmetric derivative could not lead to similar extent of ordering at the head groups and looses the hydrocarbon chains deeper in the membrane.     

Effects of the inclusion of the spin label 10-doxyl-stearic acid on the structure and dynamics of model bilayers in water: stearic acid and stearic acid/cholesterol (50:20)

The effects of the insertion of a spin-labeled molecule (10-doxyl-stearic acid) on the structure and dynamics of model lipid bilayers in gel-like as well as in liquid-ordered-like phases are studied using molecular dynamic simulations. The perturbing effects of the labeled molecule on the structure of the bilayers are analyzed. We have also studied the relationship between the structural and dynamic properties of the bilayer phase and those of the labeled molecule. We found that the insertion of the labeled molecule in the bilayer at the concentration considered here (1:70) produces local and global perturbations in the gel-like phase. There is an increase of the area associated with the lipid molecules that produces a larger tilting angle of this condensed phase. In this gel-like phase, we also found that the z component of the order parameter of the labeled molecule associated with the electron paramagnetic resonance (EPR) spectra has the same temperature dependence as the axial correlation times of the lipid molecules. The mechanism by which the doxyl reorientation senses the dynamics of the layers is determined by the correlation between the gauche defect transitions of the labeled alkyl chain and its environment. For the liquid-ordered-like phase, we found that cholesterol molecules play the role of wedges that open free spaces in the lipid structure below the ring position and order the alkyl chains at the depths of the rings, leading to small inclination angles. The doxyl ring of the labeled molecule is located just below the cholesterol ring moiety, having fewer gauche defects than in the case of the gel-like phase. The change in depth of the doxyl ring causes a reorientation of this group that leads to an increase of the order parameter as the temperature rises.     

SimLabel: a graphical user interface to simulate continuous wave EPR spectra from site‐directed spin labeling experiments

Site‐directed spin labeling (SDSL) combined with continuous wave electron paramagnetic resonance (cw EPR) spectroscopy is a powerful technique to reveal, at the residue level, structural transitions in proteins. SDSL‐EPR is based on the selective grafting of a paramagnetic label on the protein under study, followed by cw EPR analysis. To extract valuable quantitative information from SDSL‐EPR spectra and thus give reliable interpretation on biological system dynamics, numerical simulations of the spectra are required. Such spectral simulations can be carried out by coding in MATLAB using functions from the EasySpin toolbox. For non‐expert users of MATLAB, this could be a complex task or even impede the use of such simulation tool. We developed a graphical user interface called SimLabel dedicated to run cw EPR spectra simulations particularly coming from SDSL‐EPR experiments. Simlabel provides an intuitive way to visualize, simulate, and fit such cw EPR spectra. An example of SDSL‐EPR spectra simulation concerning the study of an intrinsically disordered region undergoing a local induced folding is described and discussed. We believe that this new tool will help the users to rapidly obtain reliable simulated spectra and hence facilitate the interpretation of their results. Copyright © 2017 John Wiley & Sons, Ltd.     

Phase behavior of bile acid/lipid/water systems containing model dietary lipids

Dietary lipids are solubilized in bile acid micelles in the small intestine. In the present study, we investigate the phase behavior of bile acid/model rapeseed oil (or model beef tallow)/water systems to predict interfacial phenomena during consumption of a variety of foods. The structures of molecular assemblies are identified based on polarizing microscope images, wide-angle X-ray diffraction (WAXD) and small-angle X-ray scattering (SAXS). The results of in vitro tests suggest that an increase in the intake of model rapeseed oil causes the formation of multi-lamellar vesicles and lamellar liquid crystals. The molecules in the lamellar liquid crystal are formed highly ordered layer structure with the spacing of 8.8 nm along the c-axis, while monoclinic packed structure is constructed as two-dimensional structure in ab-plane due to bulky molecular structures of bile acid and unsaturated fatty acid. When the model beef tallow composition in the model system is more than several wt.%, stearic acid crystals are extracted. Moreover, bicarbonate ions are important ingredients to solubilize >10 wt.% of the model lipids. These phase transitions might be induced by the addition of dietary lipids in vivo during the consumption of oil or meat. Our findings are significant for understanding the lipid absorption process in the small intestine, and for developing medical and healthcare products.     

Electron beam radiation effects on UHMWPE: an EPR study

Electron paramagnetic resonance (EPR) technique has been employed to detect and characterise a series of different radical species generated in ultra‐high molecular weight polyethylene (UHMWPE) via electron beam irradiation. Three different radical species have been found and assigned on the basis of their EPR spectra and of the related computer simulations. A secondary alkyl species, the prevalent one, is present immediately after irradiation, an allyl species appears only 24 h after irradiation when the alkyl species disappears.The third species, clearly visible at high microwave power only, has been observed for the first time and assigned to a tertiary alkyl carbon radical, whose formation is strictly connected with a Y‐shape crosslink and a migration of the unpaired electron on a carbon atom localised in an adjacent position. Copyright © 2011 John Wiley & Sons, Ltd.     

Role of hydration in determining the structure and vibrational spectra of L-alanine and N-acetyl L-alanine N′-methylamide in aqueous solution: a combined theoretical and experimental approach

In this work we have utilized recent density functional theory Born-Oppenheimer molecular dynamics simulations to determine the first principles locations of the water molecules in the first solvation shell which are responsible for stabilizing the zwitterionic structure of L-alanine. Previous works have used chemical intuition or classical molecular dynamics simulations to position the water molecules. In addition, a complete shell of water molecules was not previously used, only the water molecules which were thought to be strongly interacting (H-bonded) with the zwitterionic species. In a previous work by Tajkhorshid et al. (J Phys Chem B 102:5899) the L-alanine zwitterion was stabilized by 4 water molecules, and a subsequent work by Frimand et al. (Chem Phys 255:165) the number was increased to 9 water molecules. Here we found that 20 water molecules are necessary to fully encapsulate the zwitterionic species when the molecule is embedded within a droplet of water, while 11 water molecules are necessary to encapsulate the polar region with the methyl group exposed to the surface, where it migrates during the MD simulation. Here we present our vibrational absorption, vibrational circular dichroism and Raman and Raman optical activity simulations, which we compare to the previous simulations and experimental results. In addition, we report new VA, VCD, Raman and ROA measurements for L-alanine in aqueous solution with the latest commercially available FTIR VA/VCD instrument (Biotools, Jupiter, FL, USA) and Raman/ROA instrument (Biotools). The signal to noise of the spectra of L-alanine measured with these new instruments is significantly better than the previously reported spectra. Finally we reinvestigate the causes for the stability of the P_π structure of the alanine dipeptide, also called N-acetyl-L-alanine N′-methylamide, in aqueous solution. Previously we utilized the B3LYP/6-31G* + Onsager continuum level of theory to investigate the stability of the NALANMA4WC Han et al. (J Phys Chem B 102:2587) Here we use the B3PW91 and B3LYP hybrid exchange correlation functionals, the aug-cc-pVDZ basis set and the PCM and CPCM (COSMO) continuum solvent models, in addition to the Onsager and no continuum solvent model. Here by the comparison of the VA, VCD, Raman and ROA spectra we can confirm the stability of the NALANMA4WC due to the strong hydrogen bonding between the four water molecules and the peptide polar groups. Hence we advocate the use of explicit water molecules and continuum solvent treatment for all future spectral simulations of amino acids, peptides and proteins in aqueous solution, as even the structure (conformer) present cannot always be found without this level of theory. Festschift in Honor of Philip J. Stephens’ 65th Birthday. During the proof stage of this article a very relevant article has been published by M. Losada and Y. Xu titled “Chirality transfer through hydrogen-bonding: Experimental and ab initio analyses of vibrational circular dichroism spectra of methyl lactate in water” in Phys Chem Chem Phys 2007, 9: 3127–3135. In that work they confirm that the effects of water are seen in the VCD spectra and hence it is fundamental to include explicit water molecules in modeling studies of the vibrational spectra of biomolecules in aqueous solution.     

Molecular Dynamic Studies on Langmuir Monolayers of Stearic Acid

Compression isotherm for stearic acid was obtained by means of molecular dynamic simulation and compared to experimentally measured values for the Langmuir monolayers. Compared to the previous simulation, the present simulation has provided a method to reproduce the compression of the monolayer. The result is consistent with other experimental results. By analyzing the alkyl tails, the configuration of stearic acid molecules during the compression process was studied and a uniform monolayer was obtained after compression. Stearic acid molecules were observed to form fine organized monolayer from completely random structure. Hexatic order of the arrangement has been identified for the distribution of stearic acid molecules in the monolayer. At the end of the compression, the stearic acid molecules were tightly packed in the gap of two other molecules. At last, the hydrogen bonds in the system were analyzed. The main hydrogen bonds were from stearic acid-water interaction and their intensities constantly decreased with the decreased of surface area per molecule. The weak hydrogen bond interaction between stearic acid molecules may be the reason of easy collapse.     

Hydrophobic mechanochemical treatment of metallic surfaces wettability measurements as a means of assessing homogeneity

Hydrophobicity, lubrication and anticorrosion properties of steel substrates have been obtained by a deposition of thin film (i.e. by mechanochemical treatment) at room conditions. Stearic acid and paraffin were chosen as reactive molecules. Different abrasive powders were selected to generate active sites on the treated surfaces for adsorption of the reactive molecules and then, the results were compared. The surfaces were analyzed by reflection-absorption infrared spectroscopy (RAIRS). The results emphasize that, a thick layer of mixed stearic acid/paraffin was deposited onto the metallic surface after the treatment. After hexane rinsing we could only detect a very thin layer of oriented stearic acid molecules chemically adsorbed onto the metallic surface and which engages strong interactions with it. Whereas, RAIRS only provides molecular analysis, the XPS technique was complementary for discriminating the different surfaces. It was possible to show differences in thickness as well as in coverage according to the size and shape of abrasive particles. Furthermore, we could conclude that deposit layer is not uniform. Defects were always present and were dependent on abrasive powders used. Then wettability was assessed as a way to test the homogeneity of thin films generated by the mechanochemical treatment. In agreement with theoretical data, receding contact angle was very dependent on the defects in the deposited film. If holes or aggregates were increased in the deposit layer, the receding contact angle was decreased while advancing contact angles and equilibrium contact angles remained constant. A very important point for technological applications was that the homogeneity of the deposited film was governed by abrasive powder involved in mechanochemical treatment and contact angle values were a direct measurement of the homogeneity of surfaces generated by mechanochemical treatment.     

Autoxidation products of normal and genetically modified canola oil varieties determined using liquid chromatography with mass spectrometric detection

Normal, high stearic acid and high lauric acid canola oil varieties were heated in the presence of air to allow autoxidation to occur. After the reaction, the oils were analyzed using a non-aqueous reversed-phase high-performance liquid chromatographic separation followed by detection using atmospheric pressure chemical ionization mass spectrometry. Oxidized products were separated and identified. The major autoxidation products which remained intact were epoxides and hydroperoxides. Two classes of epoxy triacylglycerols (TAGs) were formed. One class with the epoxy group replacing a site of unsaturation and one class adjacent to a site of unsaturation, as was previously reported for model TAGs. Intact oxidation products resulted mostly from oxidation of oleic acid, while oxidation products of linoleic and linolenic acid chains decomposed to yield chain-shortened species. Both neutral and polar chain-shortened products were observed. Polar chain-shortened decomposition products eluted at very short retention times and required a different chromatographic gradient to separate the molecules. This class of molecules was tentatively identified as core aldehydes. The high stearic acid canola oil yielded more intact oxidation products containing stearic acid, as expected. The high lauric acid oil produced intact oxidation products which contained lauric acid.     

Small-angle X-ray scattering and electron paramagnetic resonance study of the interaction of bovine serum albumin with ionic surfactants

Small-angle X-ray scattering (SAXS) and electron paramagnetic resonance (EPR) techniques have been used to monitor the interaction of bovine serum albumin (BSA) with ionic surfactants such as anionic sodium dodecyl sulfate (SDS), zwitterionic N-hexadecyl-N,N-dimethyl-3-ammonium-1-propane sulfonate (HPS), and cationic cethyltrimethylammonium chloride (CTAC) at pH 7.0. The SAXS results have shown that in the presence of 5 mM SDS and HPS the radius of gyration (Rg) almost does not change as compared to the BSA free-surfactant solution; its value is ca. 30 Angstroms. In the presence of 5 mM CTAC the SAXS data indicate the presence of a particle with a Rg of at least 63 Angstroms, suggesting that in this case, a kind of protein aggregation takes place. In the presence of SDS and HPS surfactants at concentrations above 10 mM, a characteristic broad peak in the region of 0.12-0.18 Angstroms(-1) indicates the presence of micelle-like aggregates in solution. The SAXS curves are consistent with the "pearl necklace" model, where micelle-like aggregates are randomly distributed around the polypeptide chain. EPR results using 5-DSA and 16-DSA spin labels show that in the presence of BSA the EPR spectra are composed of two label populations, one contacting the protein and a second one due to label localization in the micelles. Evidence is also obtained for a competition of the surfactants with the spin labels for the high-affinity binding sites of the stearic acid spin labels as monitored by changes in the fractions of the two label populations as the surfactant concentration is increased. The effect of SDS seems to be stronger in the sense that increased SDS concentration leads to a complete transfer of spin labels from close protein contact sites to micelles, while for HPS, a significant immobilization of probe apparently remains even at higher surfactant concentrations. These two techniques are quite useful since SAXS monitors the overall properties of the scattering particle, while EPR gives information on the dynamics inside this particle and associated with label localization and motion.     

Spin labeling of Natronomonas pharaonis halorhodopsin: probing the cysteine residues environment

Halorhodopsin from Natronomonas pharaonis (pHR) is a light-driven chloride pump that transports a chloride anion across the plasma membrane following light absorption by a retinal chromophore which initiates a photocycle. Analysis of the amino acid sequence of pHR reveals three cysteine residues (Cys160, Cys184, and Cys186) in helices D and E. Here we have labeled the cysteine residues with nitroxide spin labels and studied using electron paramagnetic resonance (EPR) spectroscopy their mobility, accessibility to various reagents, and the distance between the labels. It was revealed by following the d(1)/d parameter that the distance between the spin labels is ca. 13-15 Angstrom. The EPR spectrum suggests that one label has a restricted mobility while the other two are more mobile. Only one label is accessible to hydrophilic paramagnetic broadening reagents leading to the conclusion that this label is exposed to the water phase. All three labels are reduced by ascorbic acid and reoxidized by molecular oxygen. The rate of the oxidation is accelerated following retinal irradiation indicating that the protein experiences conformation alterations in the vicinity of the labels during the pigment photocycle. It is suggested that Cys186 is exposed to the bulk medium while Cys184, located close to the retinal ionone ring, exhibits an immobilized EPR signal and is characterized by a hydrophobic environment.     

A new glucosamine-containing amphiphilic spin probe

A new, nonionic amphiphilic spin probe for investigating the extracellular matrix close to the cell membrane by EPR spectroscopy has been synthesized and characterized. A pyrrolidine type nitroxide spin-label has been introduced to the third position of a nonionic sugar polar head (glucosamine) bonded to a lipophilic stearic acid acyl chain anchor. The compound is soluble in polar organic solvents such as ethanol and chloroform, but is sparingly soluble in water.     

Nanostructuring of CyPLOS (Cyclic Phosphate-Linked OligoSaccharides), novel saccharide-based synthetic ion transporters

Ionophores are an important class of synthetic molecules which mimic natural ion channels or carriers. Here we report the aggregation behavior in pseudo-physiological environment of three Cyclic Phosphate-Linked Oligosaccharides (CyPLOS) derivatives, synthetic ion transporters based on cyclic, phosphate-linked disaccharide skeleton differing for the nature of the tails (tetraethylene-TEG glycol and/or n-undecyl chains) attached to the C-2 and C-3 of the constitutive monosaccharides. Their aggregation behavior has been studied by a combined use of dynamic light scattering (DLS), electron paramagnetic resonance spectroscopy (EPR) and Small Angle Neutron Scattering (SANS). DLS measurements were performed to reveal the formation and size distribution of the CyPLOS aggregates. EPR measurements, by using 5-doxyl stearic acid (5-DSA) as spin-probe, showed that the aggregates are mainly due to the formation of double layers and allowed to analyze the local fluidity. Finally, SANS measurements allowed estimating the layer thickness of the double layers. Our results indicate that the three CyPLOS analogs show self-aggregation properties that depend on the different nature of the inserted tails.     

Ab initio molecular dynamics simulations and g-tensor calculations of aqueous benzosemiquinone radical anion: effects of regular and "T-stacked" hydrogen bonds

Car-Parrinello molecular dynamics (CP-MD) simulations of the benzosemiquinone radical anion in aqueous solution have been performed at ambient conditions. Analysis of the trajectory shows not only extensive hydrogen bonding to the carbonyl oxygen atoms (ca. 4-5.6 water molecules depending on distance criteria), but also relatively long-lived "T-stacked" hydrogen bonds to the semiquinone pi-system. These results are discussed in the context of recent findings on semiquinone-protein interactions in photosynthetic reaction centers, and of EPR and vibration spectroscopical data for the aqueous system. Snapshots from the CP-MD trajectory are used for the first quantum chemical analyses of dynamical effects on electronic g-tensors, using cluster models and a recently developed density functional method. In particular, the effects of intermolecular hydrogen-bond dynamics on the g-tensor components are examined, in comparison with recent EPR and ENDOR studies.     

A Nitroxide‐Tagged Platinum(II) Complex Enables the Identification of a DNA G‐Quadruplex Binding Mode

We reported a novel strategy for investigating small molecule binding to G‐quadruplexes (GQs). A newly synthesized dinuclear platinum(II) complex (Pt₂L) containing a nitroxide radical was shown to selectively bind a GQ‐forming sequence derived from human telomere (hTel). Using the nitroxide moiety as a spin label, electron paramagnetic resonance (EPR) spectroscopy was carried out to investigate binding between Pt₂L and hTel GQ. Measurements indicated that two molecules of Pt₂L bind with one molecule of hTel GQ. The inter‐spin distance measured between the two bound Pt₂L, together with molecular docking analyses, revealed that Pt₂L predominately binds to the neighboring narrow and wide grooves of the G‐tetrads as hTel adopts the antiparallel conformation. The design and synthesis of nitroxide tagged GQ binders, and the use of spin‐labeling/EPR to investigate their interactions with GQs, will aid the development of small molecules for manipulating GQs involved in crucial biological processes.     

Molecular organization of DHP membrane fragments

The phase transition of dihexadecyl phosphate (DHP) bilayered disks has been studied using EPR spectroscopy. In the acid form of DHP, a phase transition temperature exists, that we have monitored through the spin-spin interaction between the nitroxide molecules at high concentration (8%) in DHP bilayers. This spin-spin interaction is due to the gathering of solutes in a fluid defect of the membrane: the border. The fluorescence quenching of two probes by the nitroxide stearic acids in DHP bilayers has been studied by stationary and time-resolved fluorescence measurements. The quenching process is mainly static. Both magnetic and fluorescent probes are localized in the periphery of the bilayered disks. An erratum to this article is available at .     

A Monte Carlo study of the mesophases formed by polar bent-shaped molecules

Liquid crystal phases formed by bent-shaped (or "banana") molecules are currently of great interest. Here we investigate by Monte Carlo computer simulations the phases formed by rigid banana molecules modeled combining three Gay-Berne sites and containing either one central or two lateral and transversal dipoles. We show that changing the dipole position and orientation has a profound effect on the mesophase stability and molecular organization. In particular, we find a uniaxial nematic phase only for off-center dipolar models and tilted phases only for the one with terminal dipoles.     

四硫富瓦烯衍生物/硬脂酸LB膜的表征

研究了四（苄硫基）四硫富瓦烯／硬脂酸（TBT－TTF／SA）（1：1）LB膜、二（亚乙二硫基）四硫富瓦烯／硬脂酸（BEDT－TTF／SA）（1：1）LB膜和四（十六烷硫基）四硫富瓦烯／硬脂酸（THT－TTF／SA）（1：1）LB膜的结构．从X射线衍射结果得到了LB膜的层间距离．X射线衍射图显示了TBT－TTF／SALB膜和BEDT－TTF／SALB膜的层间结构由硬脂酸控制．从偏振红外结果计算出硬脂酸和四硫富瓦烯衍生物在LB膜中的取向角．根据分子取向角确定了LB膜的层间结构．用分子长度和分子取向角得到的层间距离与从X射线衍射得到的层间距离相吻合．     

Dynamics of p-terphenyl crystals at the phase transition temperature: a zero-field EPR study of the photoexcited triplet state of pentacene in p-terphenyl crystals

Pulsed zero-field electron paramagnetic resonance free induction decay (ZF EPR FID) techniques are employed to study the phase transition of p-terphenyl crystals (Tc = 193 K) by measuring selectively populated photoexcited triplet ZF transitions of dilute pentacene molecules in p-terphenyl single crystals. The sensitivity of ZF spectroscopy to small shifts in local magnetic fields enables the studies of guest-host configuration changes over a wide temperature range. Here we report the observation of guest pentacene (-h(14) and -d(14)) triplet ZF EPR FID spectra that disappear abruptly at Tc and of spectral broadening and shift below Tc. We interpret these spectral changes as evidence for guest couplings to host phenyl rings. Further, these data allow assignments of spectroscopic sites to crystallographic sites that occur in the phase transition.