scholarly journals Decline of protein structure rigidity with interatomic distance

2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Oliviero Carugo
Keyword(s):  
Protein Structure ◽  
High Resolution ◽  
Interatomic Distance ◽  
Euclidean Distance ◽  
Protein Crystal ◽  
Covalent Bonds ◽  
Structural Rigidity ◽  
Upper Limit ◽  
Wide Range ◽  
The Difference

Abstract Background Protein structural rigidity was analyzed in a non-redundant ensemble of high-resolution protein crystal structures by means of the Hirshfeld test, according to which the components (uX and uY) of the B-factors of two atoms (X and Y) along the interatomic direction is related to their degree of rigidity: the atoms may move as a rigid body if uX = uY and they cannot if uX ≠ uY. Results It was observed that the rigidity degree diminishes if the number of covalent bonds intercalated between the two atoms (d_seq) increases, while it is rather independent on the Euclidean distance between the two atoms (d): for a given value of d_seq, the difference between uX and uY does not depend on d. No additional rigidity decline is observed when d_seq ≥  ~ 30 and this upper limit is very modest, close to 0.015 Å. Conclusions This suggests that protein flexibility is not fully described by B-factors that capture only partially the wide range of distortions that proteins can afford.

High-Resolution Hydroxyl Radical Protein Footprinting: Biophysics Tool for Drug Discovery

2018 ◽  
Vol 47 (1) ◽  
pp. 315-333 ◽  
Author(s):  
Janna Kiselar ◽  
Mark R. Chance
Keyword(s):  
Protein Structure ◽  
High Resolution ◽  
Hydroxyl Radical ◽  
Solvent Accessibility ◽  
Side Chains ◽  
Protein Footprinting ◽  
Hydroxyl Radical Protein Footprinting ◽  
Wide Range ◽  
Hydroxyl Radical Footprinting

Hydroxyl radical footprinting (HRF) of proteins with mass spectrometry (MS) is a widespread approach for assessing protein structure. Hydroxyl radicals react with a wide variety of protein side chains, and the ease with which radicals can be generated (by radiolysis or photolysis) has made the approach popular with many laboratories. As some side chains are less reactive and thus cannot be probed, additional specific and nonspecific labeling reagents have been introduced to extend the approach. At the same time, advances in liquid chromatography and MS approaches permit an examination of the labeling of individual residues, transforming the approach to high resolution. Lastly, advances in understanding of the chemistry of the approach have led to the determination of absolute protein topologies from HRF data. Overall, the technology can provide precise and accurate measures of side-chain solvent accessibility in a wide range of interesting and useful contexts for the study of protein structure and dynamics in both academia and industry.

Development of a conical anode Fe-gun for low voltage SEM

1988 ◽  
Vol 46 ◽  
pp. 978-979
Author(s):  
T. Miyokawa ◽  
S. Norioka ◽  
S. Goto
Keyword(s):  
High Resolution ◽  
Field Emission ◽  
Low Voltage ◽  
Irradiation Damage ◽  
Cold Cathode ◽  
Virtual Source ◽  
Source Position ◽  
Electrostatic Lens ◽  
Electrostatic Lenses ◽  
Wide Range

Field emission SEMs (FE-SEMs) are becoming popular due to their high resolution needs. In the field of semiconductor product, it is demanded to use the low accelerating voltage FE-SEM to avoid the electron irradiation damage and the electron charging up on samples. However the accelerating voltage of usual SEM with FE-gun is limited until 1 kV, which is not enough small for the present demands, because the virtual source goes far from the tip in lower accelerating voltages. This virtual source position depends on the shape of the electrostatic lens. So, we investigated several types of electrostatic lenses to be applicable to the lower accelerating voltage. In the result, it is found a field emission gun with a conical anode is effectively applied for a wide range of low accelerating voltages.A field emission gun usually consists of a field emission tip (cold cathode) and the Butler type electrostatic lens.

Three-fold astigmatism: An important TEM aberration

1993 ◽  
Vol 51 ◽  
pp. 972-973 ◽  
Author(s):  
O.L. Krivanek ◽  
M.L. Leber
Keyword(s):  
High Resolution ◽  
Spatial Frequency ◽  
Field Emission ◽  
Azimuthal Angle ◽  
Hollow Cone ◽  
Small Probe ◽  
Wide Range ◽  
High Resolution Images ◽  
Image Position

Three-fold astigmatism resembles regular astigmatism, but it has 3-fold rather than 2-fold symmetry. Its contribution to the aberration function χ(q) can be written as:where A3 is the coefficient of 3-fold astigmatism, λ is the electron wavelength, q is the spatial frequency, ϕ the azimuthal angle (ϕ = tan-1 (qy/qx)), and ϕ3 the direction of the astigmatism.Three-fold astigmatism is responsible for the “star of Mercedes” aberration figure that one obtains from intermediate lenses once their two-fold astigmatism has been corrected. Its effects have been observed when the beam is tilted in a hollow cone over a wide range of angles, and there is evidence for it in high resolution images of a small probe obtained in a field emission gun TEM/STEM instrument. It was also expected to be a major aberration in sextupole-based Cs correctors, and ways were being developed for dealing with it on Cs-corrected STEMs.

Origin of the alternate bright/dark contrast in HREM images of hexagonal crystals, particularly 6H-SiC

1993 ◽  
Vol 51 ◽  
pp. 914-915
Author(s):  
J.S. Bow ◽  
R.W. Carpenter ◽  
M.J. Kim
Keyword(s):  
High Resolution ◽  
Incident Beam ◽  
Hexagonal Crystal ◽  
Detailed Explanation ◽  
Similar Character ◽  
High Resolution Images ◽  
The Difference ◽  
Zigzag Shape ◽  
Hexagonal Crystals ◽  
Dark Contrast

A prominent characteristic of high-resolution images of 6H-SiC viewed from [110] is a zigzag shape with a period of 6 layers as shown in Fig.1. Sometimes the contrast is same through the 6 layers of (0006) planes (Fig.1a), but in most cases it appears as in Fig.1b -- alternate bright/dark contrast among every three (0006) planes. Alternate bright/dark contrast is most common for the thicker specimens. The SAD patterns of these two types of image are almost same, and there is no indication that the difference results from compositional ordering. O’Keefe et al. concluded this type of alternate contrast was due to crystal tilt in thick parts of the specimen. However, no detailed explanation was given. Images of similar character from Ti3Al, which is also a hexagonal crystal, were reported by Howe et al. Howe attributed the bright/dark contrast among alternate (0002) Ti3Al planes to phase shifts produced by incident beam tilt.

Scanning tunneling microscopy of polymers: A status report

1989 ◽  
Vol 47 ◽  
pp. 330-331
Author(s):  
P.E. Russell ◽  
I.H. Musselman
Keyword(s):  
High Resolution ◽  
Scanning Tunneling Microscopy ◽  
Sample Surface ◽  
Atomic Scale ◽  
Constant Current ◽  
Scanning Tunneling ◽  
Status Report ◽  
Tunneling Microscopy ◽  
Research Issues ◽  
Wide Range

Scanning tunneling microscopy (STM) has evolved rapidly in the past few years. Major developments have occurred in instrumentation, theory, and in a wide range of applications. In this paper, an overview of the application of STM and related techniques to polymers will be given, followed by a discussion of current research issues and prospects for future developments. The application of STM to polymers can be conveniently divided into the following subject areas: atomic scale imaging of uncoated polymer structures; topographic imaging and metrology of man-made polymer structures; and modification of polymer structures. Since many polymers are poor electrical conductors and hence unsuitable for use as a tunneling electrode, the related atomic force microscopy (AFM) technique which is capable of imaging both conductors and insulators has also been applied to polymers.The STM is well known for its high resolution capabilities in the x, y and z axes (Å in x andy and sub-Å in z). In addition to high resolution capabilities, the STM technique provides true three dimensional information in the constant current mode. In this mode, the STM tip is held at a fixed tunneling current (and a fixed bias voltage) and hence a fixed height above the sample surface while scanning across the sample surface.

Structural Transformation of a Germanium Σ=13 (510) [001] Tilt Grain Boundary under the Electron Beam

1990 ◽  
Vol 48 (1) ◽  
pp. 52-53 ◽  
Author(s):  
Jean-Luc Rouvière ◽  
Alain Bourret
Keyword(s):  
Electron Microscopy ◽  
High Resolution ◽  
Grain Boundary ◽  
Structural Transformation ◽  
Mirror Symmetry ◽  
High Resolution Electron Microscopy ◽  
Structural Transformations ◽  
Covalent Bonds ◽  
Resolution Electron ◽  
Tilt Grain Boundary

The possible structural transformations during the sample preparations and the sample observations are important issues in electron microscopy. Several publications of High Resolution Electron Microscopy (HREM) have reported that structural transformations and evaporation of the thin parts of a specimen could happen in the microscope. Diffusion and preferential etchings could also occur during the sample preparation.Here we report a structural transformation of a germanium Σ=13 (510) [001] tilt grain boundary that occurred in a medium-voltage electron microscopy (JEOL 400KV).Among the different (001) tilt grain boundaries whose atomic structures were entirely determined by High Resolution Electron Microscopy (Σ = 5(310), Σ = 13 (320), Σ = 13 (510), Σ = 65 (1130), Σ = 25 (710) and Σ = 41 (910), the Σ = 13 (510) interface is the most interesting. It exhibits two kinds of structures. One of them, the M-structure, has tetracoordinated covalent bonds and is periodic (fig. 1). The other, the U-structure, is also tetracoordinated but is not strictly periodic (fig. 2). It is composed of a periodically repeated constant part that separates variable cores where some atoms can have several stable positions. The M-structure has a mirror glide symmetry. At Scherzer defocus, its HREM images have characteristic groups of three big white dots that are distributed on alternatively facing right and left arcs (fig. 1). The (001) projection of the U-structure has an apparent mirror symmetry, the portions of good coincidence zones (“perfect crystal structure”) regularly separate the variable cores regions (fig. 2).

Comparative Effects of High-Tech Visual Scene Displays and Low-Tech Isolated Picture Symbols on Engagement From Students With Multiple Disabilities

2019 ◽  
Vol 50 (4) ◽  
pp. 693-702 ◽  
Author(s):  
Christine Holyfield ◽  
Sydney Brooks ◽  
Allison Schluterman
Keyword(s):  
Language Learning ◽  
Augmentative And Alternative Communication ◽  
Visual Analysis ◽  
Multiple Disabilities ◽  
Visual Scene ◽  
Future Research ◽  
High Tech ◽  
Single Subject ◽  
Wide Range ◽  
The Difference

Purpose Augmentative and alternative communication (AAC) is an intervention approach that can promote communication and language in children with multiple disabilities who are beginning communicators. While a wide range of AAC technologies are available, little is known about the comparative effects of specific technology options. Given that engagement can be low for beginning communicators with multiple disabilities, the current study provides initial information about the comparative effects of 2 AAC technology options—high-tech visual scene displays (VSDs) and low-tech isolated picture symbols—on engagement. Method Three elementary-age beginning communicators with multiple disabilities participated. The study used a single-subject, alternating treatment design with each technology serving as a condition. Participants interacted with their school speech-language pathologists using each of the 2 technologies across 5 sessions in a block randomized order. Results According to visual analysis and nonoverlap of all pairs calculations, all 3 participants demonstrated more engagement with the high-tech VSDs than the low-tech isolated picture symbols as measured by their seconds of gaze toward each technology option. Despite the difference in engagement observed, there was no clear difference across the 2 conditions in engagement toward the communication partner or use of the AAC. Conclusions Clinicians can consider measuring engagement when evaluating AAC technology options for children with multiple disabilities and should consider evaluating high-tech VSDs as 1 technology option for them. Future research must explore the extent to which differences in engagement to particular AAC technologies result in differences in communication and language learning over time as might be expected.

COMBINATORIAL POLYNOMIALLY COMPUTABLE CHARACTERISTICS OF SUBSTITUTIONS AND THEIR PROPERTIES

2020 ◽  
Vol 7 (2) ◽  
pp. 34-41
Author(s):  
VLADIMIR NIKONOV ◽  
◽  
ANTON ZOBOV ◽  
Keyword(s):  
Mathematical Expectation ◽  
Point Of View ◽  
Small Range ◽  
Computational Point ◽  
Wide Range ◽  
Bijective Function ◽  
The Difference ◽  
Element Base ◽  
Selection Of

The construction and selection of a suitable bijective function, that is, substitution, is now becoming an important applied task, particularly for building block encryption systems. Many articles have suggested using different approaches to determining the quality of substitution, but most of them are highly computationally complex. The solution of this problem will significantly expand the range of methods for constructing and analyzing scheme in information protection systems. The purpose of research is to find easily measurable characteristics of substitutions, allowing to evaluate their quality, and also measures of the proximity of a particular substitutions to a random one, or its distance from it. For this purpose, several characteristics were proposed in this work: difference and polynomial, and their mathematical expectation was found, as well as variance for the difference characteristic. This allows us to make a conclusion about its quality by comparing the result of calculating the characteristic for a particular substitution with the calculated mathematical expectation. From a computational point of view, the thesises of the article are of exceptional interest due to the simplicity of the algorithm for quantifying the quality of bijective function substitutions. By its nature, the operation of calculating the difference characteristic carries out a simple summation of integer terms in a fixed and small range. Such an operation, both in the modern and in the prospective element base, is embedded in the logic of a wide range of functional elements, especially when implementing computational actions in the optical range, or on other carriers related to the field of nanotechnology.

Generalized Heterodyne Configurations for Photo-induced Force Microscopy

2019 ◽  
Author(s):  
Le Wang ◽  
Devon Jakob ◽  
Haomin Wang ◽  
Alexis Apostolos ◽  
Marcos M. Pires ◽  
...  
Keyword(s):  
Spatial Resolution ◽  
Repetition Rate ◽  
Modulation Frequency ◽  
High Harmonic ◽  
Chemical Imaging ◽  
Heterodyne Detection ◽  
Force Microscopy ◽  
Wide Range ◽  
The Difference ◽  
Afm Cantilever

<div>Infrared chemical microscopy through mechanical probing of light-matter interactions by atomic force microscopy (AFM) bypasses the diffraction limit. One increasingly popular technique is photo-induced force microscopy (PiFM), which utilizes the mechanical heterodyne signal detection between cantilever mechanical resonant oscillations and the photo induced force from light-matter interaction. So far, photo induced force microscopy has been operated in only one heterodyne configuration. In this article, we generalize heterodyne configurations of photoinduced force microscopy by introducing two new schemes: harmonic heterodyne detection and sequential heterodyne detection. In harmonic heterodyne detection, the laser repetition rate matches integer fractions of the difference between the two mechanical resonant modes of the AFM cantilever. The high harmonic of the beating from the photothermal expansion mixes with the AFM cantilever oscillation to provide PiFM signal. In sequential heterodyne detection, the combination of the repetition rate of laser pulses and polarization modulation frequency matches the difference between two AFM mechanical modes, leading to detectable PiFM signals. These two generalized heterodyne configurations for photo induced force microscopy deliver new avenues for chemical imaging and broadband spectroscopy at ~10 nm spatial resolution. They are suitable for a wide range of heterogeneous materials across various disciplines: from structured polymer film, polaritonic boron nitride materials, to isolated bacterial peptidoglycan cell walls. The generalized heterodyne configurations introduce flexibility for the implementation of PiFM and related tapping mode AFM-IR, and provide possibilities for additional modulation channel in PiFM for targeted signal extraction with nanoscale spatial resolution.</div>

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