The Effect of Protonation on Structural Modification in Layers

2019 ◽  
Vol 942 ◽  
pp. 21-29
Author(s):  
Yury Borodin ◽  
Tatyana Zadorozhnaya ◽  
Sergei Ghyngazov
Keyword(s):  
Initial Phase ◽  
Structural Modification ◽  
Structural Changes ◽  
Integral Intensity ◽  
Hexagonal Lattice ◽  
Chemical Activity ◽  
Crystal Chemical ◽  
Oxygen Sublattice ◽  
Electrostatic Fields ◽  
Structural Methods

The results on protonation in solutions and melts of salts and acids, as well as structural changes associated with the formation of nanocomposition structure of materials are presented. It is shown by structural methods that proton localization is invariant to the volume in the protonated layer and is accompanied by changes between oxygen distances, enlargement of the unit cell and transition to the rhombic phase. Having the maximum crystal-chemical activity, protons create a hexagonal lattice in accordance with the features of equipotential pictures of their nonequilibrium electrostatic fields. The increase in the integral intensity of reflexes observed on neutronograms of protonated LiNbO3 (102), (111), (113) it is associated with the ordering of protons in the hexagonal oxygen sublattice of the initial phase.

STRUCTURAL CHANGES ASSOCIATED WITH THE RELEASE OF ENZYMES FROM RAT-LIVER MITOCHONDRIA BY FREEZING

1966 ◽  
Vol 44 (6) ◽  
pp. 775-781 ◽  
Author(s):  
C. V. Lusena ◽  
C. M. S. Dass
Keyword(s):  
Rat Liver ◽  
Structural Modification ◽  
Structural Changes ◽  
Sodium Deoxycholate ◽  
Liver Mitochondria ◽  
Maximum Activity ◽  
Supernatant Fraction ◽  
Rat Liver Mitochondria ◽  
Mitochondrial Disruption ◽  
Partial Release

Suspensions of rat-liver mitochondria in 0.44 M sucrose, after they were frozen and thawed under defined conditions, were partitioned into three sedimentable and one supernatant fraction by differential centrifugation. These were analyzed for optical density, protein content, and for activities of glutamate dehydrogenase (GD) and 3-hydroxybutyrate dehydrogenase (BD) with exogenous nicotinamide–adenine dinucleotide (NAD) both as maximum activity after sodium deoxycholate treatment and as activity released by freezing. Pellets of the three sedimentable fractions were also examined in the electron microscope. When dehydrogenases were not released by a freezing treatment, no structural changes were detected. Release of BD, which was accompanied by release of GD as well, was associated with mitochondrial disruption and drastic rearrangement of mitochondrial membranes. On the other hand, release of GD without BD occurred from swollen and emptied mitochondria. The partial release of enzymes in a preparation was not associated with a partial structural modification of all of the mitochondria, but rather with drastic structural changes in only some of them.

SHM System Based on Modal Filtration

2012 ◽  
Vol 518 ◽  
pp. 289-297 ◽  
Author(s):  
Krzysztof Mendrok ◽  
Tadeusz Uhl ◽  
Wojciech Maj ◽  
Paweł Paćko
Keyword(s):  
Structural Health Monitoring ◽  
Damage Detection ◽  
Health Monitoring ◽  
Structural Modification ◽  
Structural Changes ◽  
Environmental Changes ◽  
Practical Implementation ◽  
Health Monitoring System ◽  
Structural Health ◽  
Changes Detection

The modal filter has various applications, among the others for damage detection. It was shown, that a structural modification (e.g. drop of stiffness due to a crack) causes an appearance of peaks on the output of the modal filter. This peaks result from not perfect modal filtration due to system local structural changes. That makes it a great indicator for damage detection, which has fallowing advantages: low computational afford due to the data reduction, the structural health monitoring system based on it, is easy to automate. Furthermore the system is theoretically insensitive to environmental changes as temperature or humidity variation (global structural changes do not cause a drop of modal filtration accuracy). In the paper the practical implementation of the presented technique is shown. The developed structural health monitoring (SHM) system is described as well as results of its extensive simulation and laboratory testing. Finally the application of the system for the structural changes detection on the airplane parts is presented..

Scanning Probe Microscopy of Bacterial Red Light Photoreceptors

2012 ◽  
Vol 1465 ◽  
Author(s):  
Fernando G. Tobias ◽  
Anna Gawedzka ◽  
Max S. Goldmeier ◽  
Alexandra C. Sakols ◽  
Emina A. Stojković ◽  
...  
Keyword(s):  
Scanning Probe Microscopy ◽  
Structural Changes ◽  
Structural Model ◽  
Fluorescent Protein ◽  
Red Light ◽  
Hexagonal Lattice ◽  
Scanning Probe ◽  
Scanning Tunneling ◽  
Probe Microscopy ◽  
Insight Into

ABSTRACTBacteriophytochromes (Bphs) are red-light photoreceptors found in photosynthetic and non-photosynthetic bacteria that have been engineered into infrared fluorescent protein markers. Bphs are composed of a photosensory module that is covalently linked to an effector/regulatory module, usually a histidine kinase (HK) domain. Light-induced, global structural changes are proposed to originate within the covalently attached biliverdin chromophore, a linear tetrapyrrole, and propagate through the protein. Bphs undergo reversible photoconversion between two distinct red and far-red light absorbing states, denoted Pr and Pfr respectively. For most Bphs, Pr is the dark-adapted state. The energy dissipated during Pr/Pfr photoconversion is proposed to directly impact the infrared fluorescence quantum yield. At this time, only structures of three different Bphs have been published, all of truncated proteins in their respective dark-adapted states. We have utilized scanning probe microscopy (SPM) to investigate the structure of intact Bphs in the light-adapted state in order to gain new insight into the mechanism of photoconversion and fluorescence. Scanning tunneling microscopy (STM) analysis of a pair of Bphs from photosynthetic bacterium R. palustris, RpBphP2 (P2) and RpBphP3 (P3) in their light-adapted states is presented in these proceedings. The concentration of the depositing protein has a key role in the molecular arrangements observed on the highly-ordered pyrolytic graphite (HOPG) surface. For example, at a high protein concentration, a hexagonal lattice of Bphs is observed by STM on a HOPG surface. Upon dilution, the photoreceptors self-organize into fiber-like structures on the surface. In these fibers, the dimer interface and the individual domains of the Bphs can be assigned and directly compared to a structural model of the intact, full-length proteins. In summary, SPM has potential to be an effective method for gaining new insight into Bph structure and dynamics.

scholarly journals Molecular mechanisms of substrate-controlled ring dynamics and sub-stepping in a nucleic-acid dependent hexameric motor

2016 ◽  
Author(s):  
Nathan D. Thomsen ◽  
Michael R. Lawson ◽  
Lea B. Witkowsky ◽  
Song Qu ◽  
James M. Berger
Keyword(s):  
Nucleic Acid ◽  
Conformational Changes ◽  
Molecular Motors ◽  
Structural Changes ◽  
Molecular Mechanisms ◽  
Atp Hydrolysis ◽  
Ring Closure ◽  
Structural Studies ◽  
Saxs Data ◽  
Structural Methods

ABSTRACTRing-shaped hexameric helicases and translocases support essential DNA, RNA, and protein-dependent transactions in all cells and many viruses. How such systems coordinate ATPase activity between multiple subunits to power conformational changes that drive the engagement and movement of client substrates is a fundamental question. Using the E. coli Rho transcription termination factor as a model system, we have employed solution and crystallographic structural methods to delineate the range of conformational changes that accompany distinct substrate and nucleotide cofactor binding events. SAXS data show that Rho preferentially adopts an open-ring state in solution, and that RNA and ATP are both required to cooperatively promote ring closure. Multiple closed-ring structures with different RNA substrates and nucleotide occupancies capture distinct catalytic intermediates accessed during translocation. Our data reveal how RNA-induced ring closure templates a sequential ATP-hydrolysis mechanism, provide a molecular rationale for how the Rho ATPase domains distinguishes between distinct RNA sequences, and establish the first structural snapshots of substepping events in a hexameric helicase/translocase.SIGNIFICANCEHexameric, ring-shaped translocases are molecular motors that convert the chemical energy of ATP hydrolysis into the physical movement of protein and nucleic acid substrates. Structural studies of several distinct hexameric translocases have provided insights into how substrates are loaded and translocated; however, the range of structural changes required for coupling ATP turnover to a full cycle of substrate loading and translocation has not been visualized for any one system. Here, we combine low-and high-resolution structural studies of the Rho helicase, defining for the first time the ensemble of conformational transitions required both for substrate loading in solution and for substrate movement by a processive hexameric translocase.

scholarly journals Ultra-Structural Changes of the Early Childhood Caries Starting Phases of Development

2014 ◽  
Vol 18 (1) ◽  
pp. 38-40
Author(s):  
Olga Kokoceva-Ivanovska ◽  
Mile Carcev
Keyword(s):  
Early Childhood ◽  
Initial Phase ◽  
Early Childhood Caries ◽  
Structural Changes ◽  
Control Group ◽  
White Spot Lesion ◽  
Growth Trend ◽  
Initial Caries ◽  
Phases Of Development ◽  
Childhood Caries

Abstract In the recent 20 years, besides dramatic reduction of caries in many countries where complex programme of prevention is carried out, prevalence of Early Childhood Caries (ECC) has expressed continual growth trend. The aim of our research was to determine precisely ultra-structural changes in the enamel substance at the initial lesion of the ECC (white spot lesion), as initial change of great importance for its preventive aspect. Therefore, we directed our experiment to evaluate ultra-structural changes of the teeth enamel in primary teeth with circular caries in its opening stages of development: initial caries lesion and superficial form. To realize the aim of our research, in patients 6 years of age, whose teeth were already in the phase of resorption, we extracted 20 maxillary incisors (10 with initial lesion and 10 with superficial form) and 20 healthy mandibular incisors, as a control group. Investigation was done at the Institute for biomedical research of the Faculty of Medicine in Nis (Serbia), with the scanning electronic microscope. The data indicated that in the initial phase and superficial form of ECC only demineralization happened, while in the case of superficial form changes were much deeper. This speaks in favour of better understanding of ultra-structural changes of the enamel surface that happen in the initial phase of the ECC, which could help to create strategy for its successful prevention.

scholarly journals Reversible structural changes by electrostatic fields in strontium titanate at room temperature

2009 ◽  
Vol 65 (a1) ◽  
pp. s232-s232
Author(s):  
Hartmut Stöcker ◽  
Tilmann Leisegang ◽  
Matthias Zschornak ◽  
Alexandr A. Levin ◽  
Emanuel Gutmann ◽  
...  
Keyword(s):  
Strontium Titanate ◽  
Room Temperature ◽  
Structural Changes ◽  
Electrostatic Fields

The Tight-Binding Calculation Research of the Silicene Structure

2017 ◽  
Vol 727 ◽  
pp. 289-293
Author(s):  
Gen Zong Song ◽  
Lin Zhang
Keyword(s):  
Density Functional ◽  
Structural Changes ◽  
Lattice Structure ◽  
Density Functional Theory Calculation ◽  
Hexagonal Lattice ◽  
Tight Binding ◽  
Atomic Layer ◽  
Film Structure ◽  
Initial Structure ◽  
Silicon Thin Film

Silicene is a single atomic layer of silicon thin film structure, its structure is similar to the graphene, the hexagonal lattice structure with pleats. In recent years it has aroused widespread concern because of its unique physical properties. In this paper, use the tight-binding method (DFTB) of density functional theory calculation of the variation of silicene structure and structural changes in the bond lengths and bond angles. The results show that for small sized silicene its structure is unstable and relatively large changes. With the increase of the size of silicene, the structure tends to be stable and some structures appear symmetric. When the difference between the X coordinate values of the left and right borders silicene initial structure reaches 38 Å, the structure is completely symmetrical on both sides.

scholarly journals Reversible structural changes by electrostatic fields in strontium titanate at room temperature

2008 ◽  
Vol 64 (a1) ◽  
pp. C465-C465
Author(s):  
H. Stoecker ◽  
A.A. Levin ◽  
E. Gutmann ◽  
T. Weissbach ◽  
T. Leisegang ◽  
...  
Keyword(s):  
Strontium Titanate ◽  
Room Temperature ◽  
Structural Changes ◽  
Electrostatic Fields

scholarly journals Conformational dynamics of the molecular chaperone Hsp90

2011 ◽  
Vol 44 (2) ◽  
pp. 229-255 ◽  
Author(s):  
Kristin A. Krukenberg ◽  
Timothy O. Street ◽  
Laura A. Lavery ◽  
David A. Agard
Keyword(s):  
Molecular Chaperone ◽  
Structural Changes ◽  
Atp Hydrolysis ◽  
Conformational Dynamics ◽  
Resonance Energy Transfer ◽  
Resonance Energy ◽  
Post Translational Modification ◽  
Regulatory Processes ◽  
Structural Methods

AbstractThe ubiquitous molecular chaperone Hsp90 makes up 1–2% of cytosolic proteins and is required for viability in eukaryotes. Hsp90 affects the folding and activation of a wide variety of substrate proteins including many involved in signaling and regulatory processes. Some of these substrates are implicated in cancer and other diseases, making Hsp90 an attractive drug target. Structural analyses have shown that Hsp90 is a highly dynamic and flexible molecule that can adopt a wide variety of structurally distinct states. One driving force for these rearrangements is the intrinsic ATPase activity of Hsp90, as seen with other chaperones. However, unlike other chaperones, studies have shown that the ATPase cycle of Hsp90 is not conformationally deterministic. That is, rather than dictating the conformational state, ATP binding and hydrolysis only shift the equilibria between a pre-existing set of conformational states. For bacterial, yeast and human Hsp90, there is a conserved three-state (apo–ATP–ADP) conformational cycle; however; the equilibria between states are species specific. In eukaryotes, cytosolic co-chaperones regulate the in vivo dynamic behavior of Hsp90 by shifting conformational equilibria and affecting the kinetics of structural changes and ATP hydrolysis. In this review, we discuss the structural and biochemical studies leading to our current understanding of the conformational dynamics of Hsp90, as well as the roles that nucleotide, co-chaperones, post-translational modification and substrates play. This view of Hsp90's conformational dynamics was enabled by the use of multiple complementary structural methods including, crystallography, small-angle X-ray scattering (SAXS), electron microscopy, Förster resonance energy transfer (FRET) and NMR. Finally, we discuss the effects of Hsp90 inhibitors on conformation and the potential for developing small molecules that inhibit Hsp90 by disrupting the conformational dynamics.

Crystal structure and Raman spectroscopic studies of OH stretching vibrations in Zn-rich fluor-elbaite

2020 ◽  
Vol 105 (11) ◽  
pp. 1622-1630 ◽  
Author(s):  
Adam Pieczka ◽  
Andreas Ertl ◽  
Bożena Gołębiowska ◽  
Piotr Jeleń ◽  
Jakub Kotowski ◽  
...  
Keyword(s):  
Crystal Structure ◽  
Raman Spectroscopy ◽  
Electron Microprobe ◽  
Integral Intensity ◽  
Structure Refinement ◽  
Gaussian Function ◽  
Raman Shift ◽  
Crystal Chemical ◽  
Site Occupation ◽  
Stretching Vibrations

Abstract Zinc-rich fluor-elbaite from Piława Górna, Poland, was studied by electron microprobe (EPMA), single-crystal X-ray diffraction (SREF), and Raman spectroscopy (RS) to check the possibility of the application of RS to draw crystal-chemical conclusions for Al-rich and Li-bearing tourmalines on basis of the O–H stretching vibrations in the spectral range 3400–3800 cm–1. This tourmaline, forming a thin metasomatic zone around gahnite, features varying compositions with a ZnO content reaching in the studied fragment of 5.70(12) wt%. The crystal structure of this Zn-rich fluor-elbaite [a = 15.921(1), c = 7.127(1) Å] was refined with a R1 value of 1.67%. Its formula was determined on the basis of electron-microprobe and structure refinement as (Na0.84☐0.14Ca0.01)XΣ1.00(Al1.06Li0.84Zn0.69Fe0.322+Mn0.09)YΣ3.00AlZ6(BO3)3(Si6TO18)(OH)3V(F0.65OH0.26O0.09)W. The deconvolution of the O–H stretching vibration bands, performed by fitting of an input model of component bands with Gaussian function shapes for the empirical spectrum, indicates that each of the three maxima assigned for VOH bonded to YAl3+, Y2+, and YLi+ and with the total integral intensity of at least 75% of the total OH content could be resolved into 1 to 3 bands, depending on the X-site occupation (vacancies, Na+, and Ca2+). The deconvolution indicates further that several low intense bands of WO–H modes above a Raman shift of 3600 cm–1, totally reaching ≤25%, are dependent on the occupation of triplets of YYY cations bonded to the hydroxyl. These WO–H modes are also influenced by the X-site occupation. Due to ordering of all octahedral cations (except Al) at the Y site and a complete occupation of the Z site by Al and the V site by OH, it seems possible to evaluate the Li and OH contents in a Al-rich and Li-bearing tourmaline directly from the Raman spectrum. By using the ratio VOHIYAlZAlZAl/(VOHIYZZ + WOHIYYY) as evaluated from RS, corresponding to the ratio YAl/V+WOH in the crystal, the formula of the Zn-rich fluor-elbaite can be calculated as (Na0.85☐0.14Ca0.01)XΣ1.00(Al1.11Y1.112+Li0.78)YΣ3.00AlZ6(BO3)3(Si6O18)(OH)3(F0.65OH0.13O0.22), where Y 2+ = Zn + Fe + Mn. The formula, determined only on basis of EPMA and deconvolution of RS in the O–H stretching bands, corresponds very well (≤1 SD range of EPMA) to the formula determined on basis of EPMA and SREF. This result implicates that the O–H stretching vibrations, measured by Raman spectroscopy, could be applied for Al-rich and Li-bearing tourmalines as a useful tool for providing additional information for determining the crystal-chemical formula. It is also very helpful when crystal structural data are not available.

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