Single particle electron microscopy

Electron microscopy (EM) in combination with image analysis is a powerful technique to study protein structures at low, medium, and high resolution. Since electron micrographs of biological objects are very noisy, improvement of the signal-to-noise ratio by image processing is an integral part of EM, and this is performed by averaging large numbers of individual projections. Averaging procedures can be divided into crystallographic and non-crystallographic methods. The crystallographic averaging method, based on two-dimensional (2D) crystals of (membrane) proteins, yielded in solving atomic protein structures in the last century. More recently, single particle analysis could be extended to solve atomic structures as well. It is a suitable method for large proteins, viruses, and proteins that are difficult to crystallize. Because it is also a fast method to reveal the low-to-medium resolution structures, the impact of its application is growing rapidly. Technical aspects, results, and possibilities are presented

Revealing the architecture of the photosynthetic apparatus in the diatom Thalassiosira pseudonana

Diatoms are a large group of marine algae that are responsible for about one-quarter of global carbon fixation. Light-harvesting complexes of diatoms are formed by the fucoxanthin chlorophyll a/c proteins and their overall organization around core complexes of photosystems (PSs) I and II is unique in the plant kingdom. Using cryo-electron tomography, we have elucidated the structural organization of PSII and PSI supercomplexes and their spatial segregation in the thylakoid membrane of the model diatom species Thalassiosira pseudonana. 3D sub-volume averaging revealed that the PSII supercomplex of T. pseudonana incorporates a trimeric form of light-harvesting antenna, which differs from the tetrameric antenna observed previously in another diatom, Chaetoceros gracilis. Surprisingly, the organization of the PSI supercomplex is conserved in both diatom species. These results strongly suggest that different diatom classes have various architectures of PSII as an adaptation strategy, whilst a convergent evolution occurred concerning PSI and the overall plastid structure

Radical-induced hetero-nuclear mixing and low-field 13^{13}C relaxation in solid pyruvic acid

Radicals serve as a source of polarization in dynamic nuclear polarization, but may also act as polarization sink, in particular at low field. Additionally, if the couplings between the electron spins and different nuclear reservoirs are stronger than any of the reservoirs’ couplings to the lattice, radicals can mediate hetero-nuclear polarization transfer. Here, we report radical-enhanced $^{13}$C relaxation in pyruvic acid doped with trityl. Up to 40 K, we find a linear carbon $T_{1}$ field dependence between 5 mT and 2 T. We model the dependence quantitatively, and find that the presence of trityl accelerates direct hetero-nuclear polarization transfer at low fields, while at higher fields $^{13}$C relaxation is diffusion limited. Measurements of hetero-nuclear polarization transfer up to 600 mT confirm the predicted radical-mediated proton–carbon mixing

Supercomplexes of plant photosystem I with cytochrome b6f, light-harvesting complex II and NDH

Photosystem I (PSI) is a pigment-protein complex required for the light-dependent reactions of photosynthesis and participates in light-harvesting and redox-driven chloroplast metabolism. Assembly of PSI into supercomplexes with light harvesting complex (LHC) II, cytochrome b6f (Cytb6f) or NAD(P)H dehydrogenase complex (NDH) has been proposed as a means for regulating photosynthesis. However, structural details about the binding positions in plant PSI are lacking. We analyzed large data sets of electron microscopy single particle projections of supercomplexes obtained from the stroma membrane of Arabidopsis thaliana. By single particle analysis, we established the binding position of Cytb6f at the antenna side of PSI. The rectangular-shaped Cytb6f dimer binds at the side where Lhca1 is located. The complex binds with its short side rather than its long side to PSI, which may explain why these supercomplexes are difficult to purify and easily disrupted. Refined analysis of the interaction between PSI and the NDH complex indicates that in total up to 6 copies of PSI can arrange with one NDH complex. Most PSI-NDH supercomplexes appeared to have 1-3 PSI copies associated. Finally, the PSI-LHCII supercomplex was found to bind an additional LHCII trimer at two positions on the LHCI side in Arabidopsis. The organization of PSI, either in a complex with NDH or with Cytb6f, may improve regulation of electron transport by the control of binding partners and distances in small domains

Radical-Induced Low-Field 1H Relaxation in Solid Pyruvic Acid Doped with Trityl-OX063

In dynamic nuclear polarization (DNP), radicals such as trityl provide a source for high nuclear spin polarization. Conversely, during the low-field transfer of hyperpolarized solids, the radicals’ dipolar or Non-Zeeman reservoir may act as a powerful nuclear polarization sink. Here, we report the low-temperature proton spin relaxation in pyruvic acid doped with trityl, for fields from 5 mT to 2 T. We estimate the heat capacity of the radical Non-Zeeman reservoir experimentally and show that a recent formalism by Wenckebach yields a parameter-free, yet quantitative model for the entire field range

Photonic multilayer structure of Begonia chloroplasts enhances photosynthetic efficiency

Enhanced light harvesting is an area of interest for optimizing both natural photosynthesis and artificial solar energy capture1,2. Iridescence has been shown to exist widely and in diverse forms in plants and other photosynthetic organisms and symbioses3,4, but there has yet to be any direct link demonstrated between iridescence and photosynthesis. Here we show that epidermal chloroplasts, also known as iridoplasts, in shade-dwelling species of Begonia5, notable for their brilliant blue iridescence, have a photonic crystal structure formed from a periodic arrangement of the light-absorbing thylakoid tissue itself. This structure enhances photosynthesis in two ways: by increasing light capture at the predominantly green wavelengths available in shade conditions, and by directly enhancing quantum yield by 5-10% under low-light conditions. These findings together imply that the iridoplast is a highly modified chloroplast structure adapted to make best use of the extremely low-light conditions in the tropical forest understorey in which it is found5,6. A phylogenetically diverse range of shade-dwelling plant species has been found to produce similarly structured chloroplasts7-9, suggesting that the ability to produce chloroplasts whose membranes are organized as a multilayer with photonic properties may be widespread. In fact, given the well-established diversity and plasticity of chloroplasts10,11, our results imply that photonic effects may be important even in plants that do not show any obvious signs of iridescence to the naked eye but where a highly ordered chloroplast structure may present a clear blue reflectance at the microscale. Chloroplasts are generally thought of as purely photochemical; we suggest that one should also think of them as a photonic structure with a complex interplay between control of light propagation, light capture and photochemistry

Change in Magnetic Anisotropy at the Surface and in the Bulk of FINEMET Induced by Swift Heavy Ion Irradiation

57 Fe transmission and conversion electron Mössbauer spectroscopy as well as XRD were used to study the effect of swift heavy ion irradiation on stress-annealed FINEMET samples with a composition of Fe73.5 Si13.5 Nb3 B9 Cu1. The XRD of the samples indicated changes neither in the crystal structure nor in the texture of irradiated ribbons as compared to those of non-irradiated ones. However, changes in the magnetic anisotropy both in the bulk as well as at the surface of the FINEMET alloy ribbons irradiated by 160 MeV132 Xe ions with a fluence of 1013 ion cm−2 were revealed via the decrease in relative areas of the second and fifth lines of the magnetic sextets in the corresponding Mössbauer spectra. The irradiation-induced change in the magnetic anisotropy in the bulk was found to be similar or somewhat higher than that at the surface. The results are discussed in terms of the defects produced by irradiation and corresponding changes in the orientation of spins depending on the direction of the stress generated around these defects. © 2022 by the authors. Licensee MDPI, Basel, Switzerland.CZ-11/2007, MEB040806; Ministry of Education and Science of the Russian Federation, Minobrnauka: FEUZ-2020-0060; Hungarian Scientific Research Fund, OTKA: K100424, K115784, K115913, K43687, K68135; Joint Institute for Nuclear Research, JINR; Univerzita Palackého v Olomouci: CZ.02.1.01/0.0/0.0/17_049/0008408, IGA_PrF_2022_003, IGA_PrF_2022_013; Ural Federal University, UrFU: 04-5-1131-2017/2021; Nemzeti Kutatási Fejlesztési és Innovációs Hivatal, NKFIHFunding: The research was supported by grants from the Hungarian National Research, Development and Innovation Office (OTKA projects No K43687, K68135, K100424, K115913, K115784) and by the Czech-Hungarian Intergovernmental Fund, Grant No. CZ-11/2007 (MEB040806). M.I.O. was supported by the Ministry of Science and Higher Education of the Russian Federation, project No. FEUZ-2020-0060. Additionally, M.I.O. was supported in part by the Ural Federal University project within the Priority-2030 Program, funded from the Ministry of Science and Higher Education of the Russian Federation. This work was also supported by the project “Swift heavy ions in research of iron-bearing nanomaterials”, No. of theme 04-5-1131-2017/2021, solved in cooperation with the Czech Republic and the JINR (3 + 3 projects), and also by internal IGA grant of Palacký University (IGA_PrF_2022_003). The authors from Palacký University Olomouc want to thank the facilitators of project CZ.02.1.01/0.0/0.0/17_049/0008408 of the Ministry of Education, Youth & Sports of the Czech Republic for their support as well.Acknowledgments: We are grateful to Z. Klencsár (Centre for Energy Research, Budapest), M. Miglierini (Technical University, Bratislava), I. Dézsi (Wigner Research Centre for Physics, Budapest), S. Kubuki, and K. Nomura (Tokyo Metropolitan University, Tokyo) for their participation in discussions, and L. Krupa (Czech Technical University in Prague, Czech Republic and Joint Institute for Nuclear Research, Dubna) for his help with the organization of project cooperation. The support by grants from the Hungarian National Research, Development and Innovation Office and by the Czech-Hungarian Intergovernmental Fund, Grant No. CZ-11/2007 (MEB040806) are acknowledged. M.I.O. is grateful for support from the Ministry of Science and Higher Education of the Russian Federation and from the Ural Federal University project within the Priority-2030 Program. This work was also carried out within the Agreement of Cooperation between the Ural Federal University (Ekaterinburg) and the Eötvös Loránd University (Budapest) and within the Memorandum of Understanding between the Ural Federal University (Ekaterinburg) and the Palacký University (Olomouc). Authors acknowledge the support of the project “Swift heavy ions in research of iron-bearing nanomaterials”, No. of theme 04-5-1131-2017/2021, solved in cooperation with the Czech Republic and the JINR (3 + 3 projects). Authors from Palacký University Olomouc appreciate the internal IGA grant of Palacký University (IGA_PrF_2022_013) and thank the facilitators of the project CZ.02.1.01/0.0/0.0/17_049/0008408 of the Ministry of Education, Youth & Sports of the Czech Republic as well