Nowe metody przetwarzania losowo próbkowanych wielowymiarowych eksperymentów NMR

The topic of this dissertation is a new algorithm for processing of sparsely sampled data sets from multidimensional nuclear magnetic resonance (NMR) experiments. NMR remains one of the major experimental technique for studying biological macromolecules. However, increasing size of investigated objects poses a challenge for NMR due to rapidly decreasing sensitivity and increasing signal crowding. The first chapter focuses on recent advances in sensitivity enhancements and summarises a few solutions for resolution of spectral overlap. Subsequently, one describes the crucial and limiting problem of signal sampling in multidimensional NMR, which, up to recently, has impeded the widespread use of high-dimensional NMR methods. Major fast acquisition and non-uniform sampling (NUS) approaches are presented. The particular emphasis was put on detailed discussion of competetive approaches to processing of data from NUS experiments. In chapter 3 the new iterative algorithm is proposed for artefact suppression in high-resolution NMR spectra. The detailed description of its design and implementation is given, and followed by comparison with selected processing methods. The efficacy of the algorithm is demonstrated on model synthetic and experimental data. The last chapter of the thesis shows various applications of the proposed method to existing and new four- and five-dimensional NMR experiments. The algorithm is proven most beneficial in challenging applications including spectra for assignment of sidechain resonances in protein and nucleic acids, NOESY spectra for structural analysis, and cross-correlated relaxation measurements for proteins. // Niniejsza praca jest poświecona nowej metodzie przetwarzania danych pochodzących z oszczędnie próbkowanych wielowymiarowych eksperymentów jądrowego rezonansu magnetycznego (ang. Nuclear Magnetic Resonance, NMR). Technika ta jest, obok krystalografii rentgenowskiej, główną eksperymentalną metodą badawczą pozwalającą na określenie struktury i dynamiki makromolekuł o znaczeniu biologicznym. Jednakże NMR napotyka dwie istotne przeszkody w odniesieniu do dużych biomolekuł, a mianowicie gwałtownie pogarszającą się czułość oraz krytyczne zatłoczenie sygnałów w widmach. W rozdziale pierwszym przedstawiono ostatnie osiagnięcia w poprawie czułości technik NMR oraz rozwiązania służące podniesieniu rozdzielczości widm. Następnie opisano kluczowy problem próbkowania wielowymiarowych sygnałów NMR, który do niedawna uniemożliwiał wykorzystanie pełnego potencjału tych technik do rozdzielenia sygnałów. Omówiono pokrótce współczesne podejścia do szybkiej akwizycji i oszczędnego próbkowania sygnałów NMR (ang. non-uniform sampling, NUS). Szczególny nacisk położono na porównanie i dyskusje wad i zalet stosowanych obecnie metod przetwarzania sygnałów niejednorodnie próbkowanych. W rozdziale 3-cim opisano nowy iteracyjny algorytm oparty o transformacje Fouriera, usuwający artefakty oszczędnego próbkowania w wysokorozdzielczych widmach NMR. Szczegółowo omówiono schemat algorytmu oraz jego programową implementację. Rozdział uzupełnia porównanie wyników algorytmu oraz wybranych metod przetwarzania na wysymulowanych oraz modelowych danych eksperymentalnych. W ostatnim rozdziale pracy zademonstrowano użyteczność nowej metody do literaturowych oraz nowych cztero- i pieciowymiarowych eksperymentów NMR. Wśród proponowanych zastosowań wymienić można widma do przypisania sygnałów w łańcuchach bocznych aminokwasów (w białkach) i pierścieniach rybozy (w kwasach rybonukleinowych), widma NOESY służące określeniu struktury trójwymiarowej biomolekuł, oraz pomiary szybkości relaksacji skorelowanej w łańcuchach głównych białek

Phase composition of metallurgical slag studied by Mössbauer spectroscopy

The iron bearing phase composition of metallurgical slag currently produced in a tub, converter and electrical furnaces were determined from the Mössbauer spectra and compared with the composition of the slag stored for decades on the dump

Sedimentation of Fe_{2}O_{3} and metallic iron nanoparticles exhibiting Brownian movement

Sedimentation of nanoparticles in water solutions was studied in situ by transmission Mossbauer spectroscopy in horizontal and vertical geometry. The studied specimens were Fe_{2}O_{3} of a commercial pigment and metallic iron nanoparticles in slurry used in a water purification technology. The sedimentation is selective and leads to the gradual removing of the bigger particles from a solution. The iron nanoparticles in the solution are relatively chemically stable until, due to the drying, the sediment becomes exposed to the air

Local electronic and charge state of iron in FeTe_{2}

From 57Fe Mössbauer spectrum of FeTe2 taken in high external magnetic field (B = 4.6 T), the sign of electric field gradient was determined as negative, with an asymmetry parameter of 0.2. A comparison of these data with results of calculation of the electric field gradient within point charge model suggests the lattice character of electric field gradient with some contribution from covalency effects. The effective magnetic field acting on 57Fe is less than the applied, which points out the diamagnetic Fe+2 state of iron. This "electronic state" is in a contradiction to Fe+3 "charge state" concluded from 125Te experiments on 3d transition metal ditellurides as well as from 57Fe quadrupole splitting and isomer shift

Application of Mössbauer spectroscopy in study of selected biochemical processes

The $\text{}^{57}$Fe, $\text{}^{119}$Sn, $\text{}^{129}$I, and $\text{}^{151}$Eu Mössbauer spectroscopy, scanning force microscopy, and optical fluorescence method were applied to study biological systems starting from porphyrins, through cytochromes and cell membranes until such a complex system as photosystem II. In Fe-porphyrin aggregates iron atoms are able to trap an electron exhibiting the mixed valence Fe$\text{}^{3+}$-Fe$\text{}^{2+}$ relaxation process. In ironcytochrome c the presence of two different Fe$\text{}^{3+}$ states are indicated, while in tincytochrome Sn appears in Sn$\text{}^{4+}$ and Sn$\text{}^{2+}$ states. From the temperature dependence of the mean square displacement of the resonance nuclei and from the diffusional broadening of the Mössbauer line it was possible to separate the vibrational, fast collective and slow collective motions in tinporphyrin and in iron- and tin-cytochrome c. The electronic state of iodine in oleic acid, the main constituent of cellular membranes, was determined. The molecular mechanism of triphenyltin interaction with membrane of red blood cells has been suggested and the model of haemolysis has been proposed. In photosystem II, Eu ions replacing calcium showed Eu$\text{}^{3+}$ to Eu$\text{}^{2+}$ transition after illumination with light, which points out the possible role of Ca$\text{}^{2+}$ ions in electron transfer in the process of photosynthetic water splitting process

Brownian movement of inorganic nanoparticles in sediments

The 100 nm particles of $Fe_{2}O_{3}$ and metallic Fe sedimented jointly with $Al_{2}O_{3}$ powder from their suspension in oleic acid exhibit distinguished mobility which depends on the concentration of aluminum oxide. This observation is interpreted as the result of the interparticle Fe-Fe magnetic interactions which lead to the formation of the rigid network of magnetic metallic iron nanoparticles

Simultaneous transmission and scattering Mössbauer measurements of powder samples

A vertical experimental set-up for simultaneous recording transmission and scattering Mössbauer spectra is described. Application of the apparatus for the study of model powder mixture of two components with different grain sizes shows differences in the relative intensity ratio of these fractions in absorption and conversion electron Mössbauer spectroscopy (CEMS) spectra. This effect, explained as a result of the size selectivity of CEMS technique, is parameterized by the grain radius ratio of components. The possible application for investigation of isolated surface nano- and microobjects is discussed

Mobility of interacting inorganic nanoparticles

The mobility of the 110 nm-Fe_{2}O_{3} particles in a viscous sucrose solution depends on the concentration of the nanoparticles. When the average particle particle nearest neighbor distance is less than 250 rim, the particle interaction slows down their mobility. When is more than 170 rim, the small mobility of nanoparticles does not depend on their concentration. The critical distance is approximately equal to 2R_{h} = 260 nm, where R_{h} is the hydrodynamic radius, determined by the dynamic light scattering (DLS) method

Magnetic interactions in frozen solutions of ironporphyrins

The powder samples of meso-tetraphenyloporphyrin iron(III) chloride and ferriprotoporphyrin IX chloride and their frozen in solutions N,N-dimethylformamide were studied by Mossbauer spectroscopy. The variation of the outer ligands of the porphyrin rings modifies their magnetic properties but the major influence on the magnetic relaxation process exerts the intermolecular magnetic interactions, which are eliminated in dilute solutions