SDSL-ESR-based protein structure characterization

As proteins are key molecules in living cells, knowledge about their structure can provide important insights and applications in science, biotechnology, and medicine. However, many protein structures are still a big challenge for existing high-resolution structure-determination methods, as can be seen in the number of protein structures published in the Protein Data Bank. This is especially the case for less-ordered, more hydrophobic and more flexible protein systems. The lack of efficient methods for structure determination calls for urgent development of a new class of biophysical techniques. This work attempts to address this problem with a novel combination of site-directed spin labelling electron spin resonance spectroscopy (SDSL-ESR) and protein structure modelling, which is coupled by restriction of the conformational spaces of the amino acid side chains. Comparison of the application to four different protein systems enables us to generalize the new method and to establish a general procedure for determination of protein structur

The nature of chlorine-inhibition of photocatalytic degradation of dichloroacetic acid in a TiO2-based microreactor

Photocatalytic degradation of dichloroacetic acid (DCA) was studied in a continuous-flow set-up using a titanium microreactor with an immobilized double-layered TiO2 nanoparticle/nanotube film. Chloride ions, formed during the degradation process, negatively affect the photocatalytic efficiency and at a certain concentration (approximately 0.5 mM) completely stop the reaction in the microreactor. Two proposed mechanisms of inhibition with chloride ions, competitive adsorption and photogenerated-hole scavenging, have been proposed and investigated by adsorption isotherms and electron paramagnetic resonance (EPR) measurements. The results show that chloride ions block the DCA adsorption sites on the titania surface and reduce the amount of adsorbed DCA molecules. The scavenging effect of chloride ions during photocatalysis through the formation of chlorine radicals was not detected.Slovenian Research Agency/P2-0084Slovenian Research Agency/J2-4309Slovene Human Resources Development and Scholarship Fund/Ad Futur

Isolation of Bacterial Ribosomes with Monolith Chromatography

We report the development of a rapid chromatographic method for the isolation of bacterial ribosomes from crude cell lysates in less than ten minutes. Our separation is based on the use of strong anion exchange monolithic columns. Using a simple stepwise elution program we were able to purify ribosomes whose composition is comparable to those isolated by sucrose gradient ultracentrifugation, as confirmed by quantitative proteomic analysis (iTRAQ). The speed and simplicity of this approach could accelerate the study of many different aspects of ribosomal biology

Speeding up a genetic algorithm for EPR-based spin label characterization of biosystem complexity

Complexity of biological systems is one of the toughest problems for any experimental technique. Complex biochemical composition and a variety of biophysical interactions governing the evolution of a state of a biological system imply that the experimental response of the system would be superimposed of many different responses. To obtain a reliable characterization of such a system based on spin-label Electron Paramagnetic Resonance (EPR) spectroscopy, multiple Hybrid Evolutionary Optimization (HEO) combined with spectral simulation can be applied. Implemented as the GHOST algorithm this approach is capable of handling the huge solution space and provides an insight into the "quasicontinuous© distribution of parameters that describe the biophysical properties of an experimental system. However, the analysis procedure requires several hundreds of runs of the evolutionary optimization routine making this algorithm extremely computationally demanding. As only the best parameter sets from each run are assumed to contribute into the final solution, this algorithm appears far from being optimized. The goal of this study is to modify the optimization routine in a way that 20-40 runs would be enough to obtain qualitatively the same characterization. However, to keep the solution diversity throughout the HEO run, fitness sharing and newly developed shaking mechanisms are applied and tested on various test EPR spectra. In addition, other evolutionary optimization parameters such as population size and probability of genetic operators were also varied to tune the algorithm. According to the testing examples a speed-up factor of 5-7 was achieved

Exploring the local conformational space of a membrane protein by site-directed spin labeling

Molecular modeling based on a hybrid evolutionary optimization and an information condensation algorithm, called GHOST, of spin label ESR spectra was applied to study the structure and dynamics of membrane proteins. The new method is capable of providing detailed molecular information about the conformational space of the spin-labeled segment of the protein in a membrane system. The method is applied to spin-labeled bacteriophage M13 major coat protein, which is used as a model membrane protein. Single cysteine mutants of the coat protein were labeled with nitroxide spin labels and incorporated in 1,2-dioleoyl-sn- glycero-3-phosphocholine (DOPC) bilayers. The new computational method allows us to monitor distributions of local spatial constraints and molecular mobility, in addition to information about the location of the protein in a membrane. Furthermore, the results suggest that different local conformations may coexist in the membrane protein. The knowledge of different local conformations may help us to better understand the function - structure relationship of membrane proteins

Analysis of side chain rotational restrictions of membrane-embedded proteins by spin-label ESR spectroscopy

Site-directed spin-labeling electron spin resonance (SDSL-ESR) is a promising tool for membrane protein structure determination. Here we propose a novel way to translate the local structural constraints gained by SDSL-ESR data into a low-resolution structure of a protein by simulating the restrictions of the local conformational spaces of the spin label attached at different protein sites along the primary structure of the membrane-embedded protein. We test the sensitivity of this approach for membrane-embedded M13 major coat protein decorated with a limited number of strategically placed spin labels employing high-throughput site-directed mutagenesis. We find a reasonably good agreement of the simulated and the experimental data taking a protein conformation close to the one determined by fluorescence resonance energy transfer analysis [P.V. Nazarov, R.B.M. Koehorst, W.L. Vos, V.V. Apanasovich, M.A. Hemminga, FRET study of membrane proteins: determination of the tilt and orientation of the N-terminal domain of M13 major coat protein, Biophys. J. 92 (2007) 1296–1305]

Spin label EPR-based characterization of biosystem complexity

Following the widely spread EPR spin-label applications for biosystem characterization, a novel approach is proposed for EPR-based characterization of biosystem complexity. Hereto a computational method based on a hybrid evolutionary optimization (HEO) is introduced. The enormous volume of information obtained from multiple HEO runs is reduced with a novel so-called GHOST condensation method for automatic detection of the degree of system complexity through the construction of two-dimensional solution distributions. The GHOST method shows the ability of automatic quantitative characterization of groups of solutions, e.g. the determination of average spectral parameters and group contributions. The application of the GHOST condensation algorithm is demonstrated on four synthetic examples of different complexity and applied to two physiologically relevant examples- the determination of domains in biomembranes (lateral heterogeneity) and the study of the low-resolution structure of membrane proteins

How perifosine affects liposome-encapsulated drug delivery across a cell barrier

BACKGROUND: The development of efficient drug delivery systems to transport therapeutics across barrier-forming cells remains a challenge. Recently it was shown that liposomes containing perifosine, a synthetic analog of lysophosphatidylcholine, efficiently deliver liposome encapsulated content across barrier-forming cells. METHODS: To elucidate the mechanism of the delivery, fluorescent and spin labeled analog of perifosine were synthesized and their transport from liposomes to the barrier-forming MDKC cells was measured. RESULTS & CONCLUSION: Perifosine analogs are rapidly transported from liposomes into cell membranes. The total amount of perifosine accumulated in plasma membranes seems to be the most important factor in efficient transepithelial transport of liposome-encapsulated substances. Lysolipid-containing liposomal formulations seem to be promising candidates as drug delivery systems in general

Single cell temperature probed by Eu 3 doped TiO2 nanoparticles luminescence

Abstract Temperature is a critical parameter in biology, affecting the speed of reactions that occur in living systems. Nevertheless, measuring temperature with subcellular resolution (micrometric scale) and reliability remains a challenge to overcome. In this perspective, luminescence nanothermometry is a non‐contact technique which aims to measure temperature with a sub‐micrometric spatial resolution through the use of nanomaterials whose luminescence is affected solely by changes in temperature. Here, TiO2 nanoparticles doped with Eu+3 ions (Eu+3‐TiO2) are used for sensing temperature differences within single living cells. XRD, XPS, SEM, TEM and NEXAFS analysis allow the determination of the physicochemical characteristics of the Eu+3‐TiO2 nanoparticles and, the variation of the luminescence intensity of the Eu+3‐TiO2 nanoparticles with their temperature is investigated. The successful internalization of Eu+3‐TiO2 nanoparticles in different types of cells is observed. The luminescence of nanoparticles internalized in L929 fibroblast cells is measured when the system is heated in a biological relevant temperature range. Making use of an appropriate calibration curve the temperature variation inside the cells is determined with sensitivity of 0.5 K per 1% of luminosity change when heated