Tools to Assist Determination and Validation of Carbohydrate 3D Structure Data

Author(s):  
Paul Emsley ◽  
Axel T. Brunger ◽  
Thomas Lütteke
Keyword(s):  
1997 ◽  
Vol 274 (3) ◽  
pp. 421-435 ◽  
Author(s):  
Masashi Suzuki ◽  
Naoki Amano ◽  
Jun Kakinuma ◽  
Masaru Tateno

2012 ◽  
Vol 195-196 ◽  
pp. 391-396
Author(s):  
Xi Chen ◽  
Hao Jiang ◽  
Wai Ki Ching ◽  
Li Min Li

Protein 3D structure is one of the main factors in reecting gene functions. The availability of protein structure data in Protein Data Bank (PDB) allows us to conduct gene function analysis based on protein structure data. However, the molecules in PDB, whose structures having been determined, are always not corresponding to a unique gene. That is to say, the mapping from a gene to the PDB is not one-to-one. This feature complicates the situation and increases the difculty of gene function analysis. In this paper, we attempt to tackle this problem and also study the problem of predicting gene function from protein structures based on the gene-PDB mapping. We rst obtain the gene-PDB mapping, which is used to represent a gene by the structure set of all its corresponding PDB molecules. We then dene a new gene-gene similarity measurement based on the structure similarity between PDB molecules, and we further show that this new measurement matches with the gene functional similarity. This means that the measurement we dened here can be used effectively for gene function prediction.


Author(s):  
W. Hua ◽  
Y. Qiao ◽  
M. Hou

Abstract. Laser scanning or photogrammetry are useful individual techniques for digital documentation of cultural heritage sites. However, these techniques are of limited usage if cultural heritage such as the Great Wall is in harsh geographical conditions. The Great Wall is usually built on the ridge with cliffs on both sides, so it is very difficult to construct scaffolding. Therefore, the three-dimensional (3D) data obtained from the traditional 3D laser scanning is not complete. As UAV cannot enter the enemy tower, the 3D structure data inside the enemy tower with unmanned aerial vehicle (UAV) photogrammetry is missing. In order to explore effective methods to completely collect the 3D data of cultural heritage under harsh geographical environment, this study focuses on establishing a 3D model and the associated digital documentation for the No.15 enemy tower of the New Guangwu Great Wall using a combination of terrestrial laser scanning and UAV photogrammetry. This paper proposes an integrated data collection method and reduces the layout of image control points using RTK-UAV technology, which improved work efficiency and reduced work risks as well. In this paper, the internal structure data of the Great Wall enemy tower was collected by laser scanning, the external structure data was collected by UAV photogrammetry, and data fusion was based on ICP algorithm. Finally, we obtained the complete and high quality 3D digital documentation of the Great Wall enemy tower, the data can be displayed digitally and help heritage experts complete the Great Wall's restoration. This study demonstrates the potential of integrating terrestrial laser scanning and UAV photogrammetry in 3D digital documentation of cultural heritage sites.


2000 ◽  
Vol 28 (1) ◽  
pp. 243-245 ◽  
Author(s):  
Y. Wang
Keyword(s):  

Author(s):  
A. Engel ◽  
D.L. Dorset ◽  
A. Massalski ◽  
J.P. Rosenbusch

Porins represent a group of channel forming proteins that facilitate diffusion of small solutes across the outer membrane of Gram-negative bacteria, while excluding large molecules (>650 Da). Planar membranes reconstituted from purified matrix porin (OmpF protein) trimers and phospholipids have allowed quantitative functional studies of the voltage-dependent channels and revealed concerted activation of triplets. Under the same reconstitution conditions but using high protein concentrations porin aggregated to 2D lattices suitable for electron microscopy and image processing. Depending on the lipid-to- protein ratio three different crystal packing arrangements were observed: a large (a = 93 Å) and a small (a = 79 Å) hexagonal and a rectangular (a = 79 Å b = 139 Å) form with p3 symmetry for the hexagonal arrays. In all crystal forms distinct stain filled triplet indentations could be seen and were found to be morphologically identical within a resolution of (22 Å). It is tempting to correlate stain triplets with triple channels, but the proof of this hypothesis requires an analysis of the structure in 3 dimensions.


Author(s):  
Vijay Krishnamurthi ◽  
Brent Bailey ◽  
Frederick Lanni

Excitation field synthesis (EFS) refers to the use of an interference optical system in a direct-imaging microscope to improve 3D resolution by axially-selective excitation of fluorescence within a specimen. The excitation field can be thought of as a weighting factor for the point-spread function (PSF) of the microscope, so that the optical transfer function (OTF) gets expanded by convolution with the Fourier transform of the field intensity. The simplest EFS system is the standing-wave fluorescence microscope, in which an axially-periodic excitation field is set up through the specimen by interference of a pair of collimated, coherent, s-polarized beams that enter the specimen from opposite sides at matching angles. In this case, spatial information about the object is recovered in the central OTF passband, plus two symmetric, axially-shifted sidebands. Gaps between these bands represent "lost" information about the 3D structure of the object. Because the sideband shift is equal to the spatial frequency of the standing-wave (SW) field, more complete recovery of information is possible by superposition of fields having different periods. When all of the fields have an antinode at a common plane (set to be coincident with the in-focus plane), the "synthesized" field is peaked in a narrow infocus zone.


Author(s):  
J. Frank ◽  
B. F. McEwen ◽  
M. Radermacher ◽  
C. L. Rieder

The tomographic reconstruction from multiple projections of cellular components, within a thick section, offers a way of visualizing and quantifying their three-dimensional (3D) structure. However, asymmetric objects require as many views from the widest tilt range as possible; otherwise the reconstruction may be uninterpretable. Even if not for geometric obstructions, the increasing pathway of electrons, as the tilt angle is increased, poses the ultimate upper limitation to the projection range. With the maximum tilt angle being fixed, the only way to improve the faithfulness of the reconstruction is by changing the mode of the tilting from single-axis to conical; a point within the object projected with a tilt angle of 60° and a full 360° azimuthal range is then reconstructed as a slightly elliptic (axis ratio 1.2 : 1) sphere.


Author(s):  
Z. Hong Zhou ◽  
Jing He ◽  
Joanita Jakana ◽  
J. D. Tatman ◽  
Frazer J. Rixon ◽  
...  

Herpes simplex virus-1 (HSV-1) is a ubiquitous virus which is implicated in diseases ranging from self-curing cold sores to life-threatening infections. The 2500 Å diameter herpes virion is composed of a glycoprotein spike containing, lipid envelope, enclosing a protein layer (the tegument) in which is embedded the capsid (which contains the dsDNA genome). The B-, and A- and C-capsids, representing different morphogenetic stages in HSV-1 infected cells, are composed of 7, and 5 structural proteins respectively. The three capsid types are organized in similar T=16 icosahedral shells with 12 pentons, 150 hexons, and 320 connecting triplexes. Our previous 3D structure study at 26 Å revealed domain features of all these structural components and suggested probable locations for the outer shell proteins, VP5, VP26, VP19c and VP23. VP5 makes up most of both pentons and hexons. VP26 appeared to bind to the VP5 subunit in hexon but not to that in penton.


Author(s):  
Jaap Brink ◽  
Wah Chiu

The crotoxin complex is a potent neurotoxin composed of a basic subunit (Mr = 12,000) and an acidic subunit (M = 10,000). The basic subunit possesses phospholipase activity whereas the acidic subunit shows no enzymatic activity at all. The complex's toxocity is expressed both pre- and post-synaptically. The crotoxin complex forms thin crystals suitable for electron crystallography. The crystals diffract up to 0.16 nm in the microscope, whereas images show reflections out to 0.39 nm2. Ultimate goal in this study is to obtain a three-dimensional (3D-) structure map of the protein around 0.3 nm resolution. Use of 100 keV electrons in this is limited; the unit cell's height c of 25.6 nm causes problems associated with multiple scattering, radiation damage, limited depth of field and a more pronounced Ewald sphere curvature. In general, they lead to projections of the unit cell, which at the desired resolution, cannot be interpreted following the weak-phase approximation. Circumventing this problem is possible through the use of 400 keV electrons. Although the overall contrast is lowered due to a smaller scattering cross-section, the signal-to-noise ratio of especially higher order reflections will improve due to a smaller contribution of inelastic scattering. We report here our preliminary results demonstrating the feasability of the data collection procedure at 400 kV.Crystals of crotoxin complex were prepared on carbon-covered holey-carbon films, quench frozen in liquid ethane, inserted into a Gatan 626 holder, transferred into a JEOL 4000EX electron microscope equipped with a pair of anticontaminators operating at −184°C and examined under low-dose conditions. Selected area electron diffraction patterns (EDP's) and images of the crystals were recorded at 400 kV and −167°C with dose levels of 5 and 9.5 electrons/Å, respectively.


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