scholarly journals Interactions of Pleiotrophin with a Structurally Defined Heparin Hexasaccharide

Biomolecules ◽  
2021 ◽  
Vol 12 (1) ◽  
pp. 50
Author(s):  
Eathen O. Ryan ◽  
Zhoumai Jiang ◽  
Hoa Nguyen ◽  
Xu Wang
Keyword(s):  
High Resolution ◽  
Structural Information ◽  
Biological Activities ◽  
Solution Nmr ◽  
Strong Interactions ◽  
Nmr Data ◽  
Intermolecular Contacts

Pleiotrophin (PTN) is a potent cytokine that plays an important role in neural generation, angiogenesis, inflammation, and cancers. Its interactions with the polysaccharide glycosaminoglycan (GAG) are crucial to PTN’s biological activities. In this study, we investigated the interaction of selectively protonated PTN with the heparin hexasaccharide ΔUA2S-(GlcNS6S-IdoA2S)2-GlcNS6S using solution NMR. The use of a structurally defined oligosaccharide and selectively protonated PTN enabled us to obtain intermolecular contacts using unfiltered NOESY experiments, significantly increasing the amount of high-resolution structural information obtainable. Our data showed that PTN’s arginines, lysines, and tryptophans in the two structured domains have strong interactions with the 2-O-sulfated uronate protons in the heparin hexasaccharide. Consistent with the NMR data is the observation that 2-O-desulfation and N-desulfation/N-acetylation significantly decreased heparin hexasaccharides’ affinity for PTN, while 6-O-desulfation only modestly affected the interactions with PTN. These results allowed us to hypothesize that PTN has a preference for sulfate clusters centered on the GlcNS6S-IdoA2S disaccharide. Using these data and the fact that PTN domains mostly bind heparin hexasaccharides independently, models of the PTN-heparin complex were constructed.

High-Resolution Scanning Electron Microscopy of Biological Specimens

1988 ◽  
Vol 46 ◽  
pp. 186-187
Author(s):  
M. Müller ◽  
R. Hermann
Keyword(s):  
High Resolution ◽  
Freeze Drying ◽  
Room Temperature ◽  
Structural Information ◽  
Freeze Substitution ◽  
Critical Point Drying ◽  
Sem Study ◽  
Major Factors ◽  
Structural Preservation ◽  
Preparation Techniques

Three major factors must be concomitantly assessed in order to extract relevant structural information from the surface of biological material at high resolution (2-3nm).Procedures based on chemical fixation and dehydration in graded solvent series seem inappropriate when aiming for TEM-like resolution. Cells inevitably shrink up to 30-70% of their initial volume during gehydration; important surface components e.g. glycoproteins may be lost. These problems may be circumvented by preparation techniques based on cryofixation. Freezedrying and freeze-substitution followed by critical point drying yields improved structural preservation in TEM. An appropriate preservation of dimensional integrity may be achieved by freeze-drying at - 85° C. The sample shrinks and may partially collapse as it is warmed to room temperature for subsequent SEM study. Observations at low temperatures are therefore a necessary prerequisite for high fidelity SEM. Compromises however have been unavoidable up until now. Aldehyde prefixation is frequently needed prior to freeze drying, rendering the sample resistant to treatment with distilled water.

Progress in high-resolution CRYO-SEM imaging of viral particles

1996 ◽  
Vol 54 ◽  
pp. 818-819
Author(s):  
Ya Chen ◽  
Geoffrey Letchworth ◽  
John White
Keyword(s):  
Electron Microscopy ◽  
Scanning Electron Microscopy ◽  
High Resolution ◽  
Structural Information ◽  
Signal To Noise Ratio ◽  
Flexible Structures ◽  
Simian Virus ◽  
Topographic Features ◽  
Viral Particles ◽  
Scanning Electron

Low-temperature high-resolution scanning electron microscopy (cryo-HRSEM) has been successfully utilized to image biological macromolecular complexes at nanometer resolution. Recently, imaging of individual viral particles such as reovirus using cryo-HRSEM or simian virus (SIV) using HRSEM, HV-STEM and AFM have been reported. Although conventional electron microscopy (e.g., negative staining, replica, embedding and section), or cryo-TEM technique are widely used in studying of the architectures of viral particles, scanning electron microscopy presents two major advantages. First, secondary electron signal of SEM represents mostly surface topographic features. The topographic details of a biological assembly can be viewed directly and will not be obscured by signals from the opposite surface or from internal structures. Second, SEM may produce high contrast and signal-to-noise ratio images. As a result of this important feature, it is capable of visualizing not only individual virus particles, but also asymmetric or flexible structures. The 2-3 nm resolution obtained using high resolution cryo-SEM made it possible to provide useful surface structural information of macromolecule complexes within cells and tissues. In this study, cryo-HRSEM is utilized to visualize the distribution of glycoproteins of a herpesvirus.

Atomic chemistry by HREM and image simulations?

1986 ◽  
Vol 44 ◽  
pp. 828-829
Author(s):  
J.M. Howe ◽  
R. Gronsky
Keyword(s):  
Electron Microscopy ◽  
High Resolution ◽  
Structural Information ◽  
High Resolution Electron Microscopy ◽  
Resolution Electron ◽  
Image Simulations

The technique of high-resolution electron microscopy (HREM) is invaluable to the materials scientist because it allows examination of microstructural features at levels of resolution that are unobtainable by most other methods. Although the structural information which can be determined by HREM and accompanying image simulations has been well documented in the literature, there have only been a few cases where this technique has been used to reveal the chemistry of individual columns or planes of atoms, as occur in segregated and ordered materials.

New form of Transmission Cross Coefficient for High-Resolution Imaging

1990 ◽  
Vol 48 (1) ◽  
pp. 60-61
Author(s):  
Kazuo Ishizuka
Keyword(s):  
Electron Microscope ◽  
High Resolution ◽  
Transmission Function ◽  
Incident Beam ◽  
Optical Microscope ◽  
Strong Interactions ◽  
Small Range ◽  
Specimen Thickness ◽  
Beam Direction ◽  
Diffracted Waves

It is well known that taking into account spacial and temporal coherency of illumination as well as the wave aberration is important to interpret an image of a high-resolution electron microscope (HREM). This occues, because coherency of incident electrons restricts transmission of image information. Due to its large spherical and chromatic aberrations, the electron microscope requires higher coherency than the optical microscope. On an application of HREM for a strong scattering object, we have to estimate the contribution of the interference between the diffracted waves on an image formation. The contribution of each pair of diffracted waves may be properly represented by the transmission cross coefficients (TCC) between these waves. In this report, we will show an improved form of the TCC including second order derivatives, and compare it with the first order TCC.In the electron microscope the specimen is illuminated by quasi monochromatic electrons having a small range of illumination directions. Thus, the image intensity for each energy and each incident direction should be summed to give an intensity to be observed. However, this is a time consuming process, if the ranges of incident energy and/or illumination direction are large. To avoid this difficulty, we can use the TCC by assuming that a transmission function of the specimen does not depend on the incident beam direction. This is not always true, because dynamical scattering is important owing to strong interactions of electrons with the specimen. However, in the case of HREM, both the specimen thickness and the illumination angle should be small. Therefore we may neglect the dependency of the transmission function on the incident beam direction.

Pushing the Envelope

2018 ◽  
Author(s):  
Eaton E. Lattman ◽  
Thomas D. Grant ◽  
Edward H. Snell
Keyword(s):  
High Resolution ◽  
Electron Density ◽  
Structural Information ◽  
Hydration Shell ◽  
Three Dimensional ◽  
Scattering Data ◽  
Saxs Data ◽  
Electron Density Function ◽  
Angle Scattering ◽  
Iterative Structure

Direct electron density determination from SAXS data opens up new opportunities. The ability to model density at high resolution and the implicit direct estimation of solvent terms such as the hydration shell may enable high-resolution wide angle scattering data to be used to calculate density when combined with additional structural information. Other diffraction methods that do not measure three-dimensional intensities, such as fiber diffraction, may also be able to take advantage of iterative structure factor retrieval. While the ability to reconstruct electron density ab initio is a major breakthrough in the field of solution scattering, the potential of the technique has yet to be fully uncovered. Additional structural information from techniques such as crystallography, NMR, and electron microscopy and density modification procedures can now be integrated to perform advanced modeling of the electron density function at high resolution, pushing the boundaries of solution scattering further than ever before.

Investigation by NMR spectroscopy of the structural characteristics of modified oligo-nucleotides with pendant porphyrins

2019 ◽  
Vol 23 (07n08) ◽  
pp. 797-812 ◽  
Author(s):  
Sonja Merkaš ◽  
Mladen Žinić ◽  
Régis Rein ◽  
Nathalie Solladié
Keyword(s):  
Nmr Spectroscopy ◽  
Structural Characteristics ◽  
Strong Interactions ◽  
Light Harvesting Complexes ◽  
The Past ◽  
Naturally Occurring ◽  
Nmr Data ◽  
Intermolecular Distances ◽  
Uracil Base ◽  
Biopolymer Scaffolds

During the past years, we focused on exerting control over the position and distance of porphyrins along our specifically designed oligonucleotidic scaffold. Indeed, in naturally occurring light-harvesting complexes, biopolymer scaffolds hold pigments at intermolecular distances that optimize photon capture, electronic coupling, and energy transfer. To this end, four uridine-porphyrin conjugates (a monomer, a dimer, a tetramer and an octamer) were subjected to a comprehensive conformational analysis by using NMR spectroscopy. The collected NOE NMR data highlighted characteristic and strong interactions indicating that the glycosidic angle between the ribose and uracil base is anti. In order to further investigate the conformation of this family of molecules, NMR experiments were carried out at variable temperatures. At low temperature, the signals of the porphyrinic protons decoalesce, showing two sets of [Formula: see text]-pyrrolic protons. Similar observations are made for signals corresponding to sugar moieties and especially the H1′ protons, indicating molecular motions within our porphyrin-uridin arrays. These results testify in favor of the existence of a dynamic process between C3′-endo and C2′-endo conformations.

Characterization of Tilt Boundaries by Ultra High Resolution Electron Microscopy

1984 ◽  
Vol 41 ◽  
Author(s):  
W. Krakow ◽  
J. T. Wetzel ◽  
D. A. Smith ◽  
G. Trafas
Keyword(s):  
High Resolution ◽  
Grain Boundary ◽  
Structural Information ◽  
Theoretical Work ◽  
High Resolution Electron Microscopy ◽  
Point Of View ◽  
Experimental Point ◽  
Structure Information ◽  
Resolution Electron ◽  
Tilt Boundaries

AbstractA high resolution electron microscope study of grain boundary structures in Au thin films has been undertaken from both a theoretical and experimental point of view. The criteria necessary to interpret images of tilt boundaries at the atomic level, which include electron optical and specimen effects, have been considered for both 200kV and the newer 400kV medium voltage microscopes. So far, the theoretical work has concentrated on two different [001] tilt bounda-ries where a resolution of 2.03Å is required to visualize bulk lattice structures on either side of the interface. Both a high angle boundary, (210) σ=5, and a low angle boundary, (910) σ=41, have been considered. Computational results using multislice dynamical diffraction and image simulations of relaxed bounda-ries viewed edge-on and with small amounts of beam and/or specimen inclina-tion have been obtained. It will be shown that some structural information concerning grain boundary dislocations can be observed at 200kV. However, many difficulties occur in the exact identification of the interface structure viewed experimentally for both [001] and [011] boundaries since the resolution required is near the performance limit of a 200kV microscope. The simulated results at 400kV indicate a considerable improvement will be realized in obtain-ing atomic structure information at the interface.

scholarly journals Measurement of synchrotron-radiation-excited Kossel patterns

2016 ◽  
Vol 23 (1) ◽  
pp. 214-218 ◽  
Author(s):  
G. Bortel ◽  
G. Faigel ◽  
M. Tegze ◽  
A. Chumakov
Keyword(s):  
High Resolution ◽  
Dynamic Range ◽  
Structural Information ◽  
Photon Counting ◽  
Spot Size ◽  
Low Noise ◽  
X Rays ◽  
Technical Problems ◽  
Pixel Detectors ◽  
Exciting Beam

Kossel line patterns contain information on the crystalline structure, such as the magnitude and the phase of Bragg reflections. For technical reasons, most of these patterns are obtained using electron beam excitation, which leads to surface sensitivity that limits the spatial extent of the structural information. To obtain the atomic structure in bulk volumes, X-rays should be used as the excitation radiation. However, there are technical problems, such as the need for high resolution, low noise, large dynamic range, photon counting, two-dimensional pixel detectors and the small spot size of the exciting beam, which have prevented the widespread use of Kossel pattern analysis. Here, an experimental setup is described, which can be used for the measurement of Kossel patterns in a reasonable time and with high resolution to recover structural information.

Three-Dimensional High Resolution Scaffold Fiber Architecture and Morphology in Tissue Engineered Heart Valve Tissue

2010 ◽  
Author(s):  
Chad E. Eckert ◽  
Brandon T. Mikulis ◽  
Dane Gerneke ◽  
Danielle Gottlieb ◽  
Bruce Smaill ◽  
...  
Keyword(s):  
Mechanical Properties ◽  
High Resolution ◽  
Heart Valve ◽  
Structural Information ◽  
Three Dimensional ◽  
Tissue Scaffold ◽  
Valve Tissue ◽  
Sampling Protocols ◽  
Heart Valve Tissue

Engineered heart valve tissue (EHVT) has received much attention as a potential pediatric valve replacement therapy, offering prospective long-term functional improvements over current options. A significant gap in the literature exists, however, regarding estimating tissue mechanical properties from tissue-scaffold composites. Detailed three-dimensional structural information prior to implantation (in vitro) and after implantation in (in vivo) is needed for improved modeling of tissue properties. As such, a novel high-resolution imaging technique will be employed to obtain three-dimensional microstructural information. Analysis techniques will be used to fully quantify constituents of interest including scaffold, collagen, and cellular information and to develop appropriate two-dimensional sectioning sampling protocols. It is the intent of this work to guide modeling efforts to better elucidate EHVT tissue-specific mechanical properties.

Towards a structural understanding of drug and peptide transport within the proton-dependent oligopeptide transporter (POT) family

2011 ◽  
Vol 39 (5) ◽  
pp. 1353-1358 ◽  
Author(s):  
Simon Newstead
Keyword(s):  
High Resolution ◽  
Anticancer Agents ◽  
Targeted Delivery ◽  
Drug Transport ◽  
Structural Information ◽  
Sequence Similarity ◽  
The Body ◽  
Peptide Transport ◽  
Peptide Transporter ◽  
Starting Point

One of the principal aims of modern drug design is the targeted delivery of drugs within the body, such as to the central nervous system, combined with their exclusion from the liver and kidneys, which break down foreign molecules and subsequently eliminate them. Many of the commonly prescribed drugs are transported into cells and across the plasma membrane via endogenous membrane transporters, whose principal roles are the uptake of essential nutrients for metabolism. In many cases, such drug transport is serendipitous as they are simply mistaken as ‘natural’ compounds. Many of these transporters could, however, be targeted more efficiently, improving drug absorption, distribution and retention. The molecular details of these drug–transporter interactions, however, are at best poorly understood, in large part through the absence of any high-resolution structural information. To address this issue, we recently determined the structure of a prokaryotic peptide transporter, PepTSo from Shewanella oneidensis, which shares a high degree of sequence similarity and functional characteristics with the human PepT1 and PepT2 proteins. PepT1 and PepT2 contribute significantly to the oral bioavailability and pharmacokinetic properties of a number of important drug families, including antibiotics, antivirals and anticancer agents. The crystal structure of PepTSo provides the first high-resolution model of a drug importer and provides the starting point for understanding drug and peptide transport within the human body.

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