Studies of structure and specificity of some antigen-antibody complexes

1989 ◽  
Vol 323 (1217) ◽  
pp. 487-494
Keyword(s):  
Monoclonal Antibodies ◽  
Three Dimensional ◽  
High Specificity ◽  
Single Amino Acid ◽  
Dimensional Structure ◽  
X Ray ◽  
Homologous Antigen ◽  
Significant Difference ◽  
Antigen Antibody ◽  
Antibody Interactions

By using X -ray diffraction and immunochemical techniques, we have exploited the use of monoclonal antibodies raised against hen egg lysozyme (HEL) to study systematically those factors responsible for the high specificity of antigen -antibody interactions. HEL was chosen for our investigations because its three-dimensional structure and immunochemistry have been well characterized and because naturally occurring sequence variants from different avian species are readily available to test the fine specificity of the antibodies. The X-ray crystal structure of a complex formed between HEL and the Fab D1.3 shows a large complementary surface with close interatomic contacts between antigen and antibody. Thus single amino acid sequence changes in heterologous antigens give antigen-antibody association constants that are several orders of magnitude smaller than that of the homologous antigen. For example, a substitution of His for Glu at position 121 in the antigen is sufficient to diminish significantly the binding between D1.3 and the variant lysozyme. The conformation of HEL when complexed to D1.3 shows no significant difference from that seen in the free molecule, and immunobinding studies with other anti-HEL antibodies suggest that this observation may be generally true for the system of monoclonal antibodies that we have studied.

Revealing gross three-dimensional structure in the SEM

1987 ◽  
Vol 45 ◽  
pp. 656-657
Author(s):  
Sterling P. Newberry
Keyword(s):  
Freeze Drying ◽  
Three Dimensional ◽  
Dimensional Structure ◽  
Small Object ◽  
Final Solution ◽  
Dimensional Representation ◽  
X Ray ◽  
Three Dimensional Representation ◽  
Freeze Dried ◽  
Critical Point Drying

The beautiful three dimensional representation of small object surfaces by the SEM leads one to search for ways to open up the sample and look inside. Could this be the answer to a better microscopy for gross biological 3-D structure? We know from X-Ray microscope images that Freeze Drying and Critical Point Drying give promise of adequately preserving gross structure. Can we slice such preparations open for SEM inspection? In general these preparations crush more readily than they slice. Russell and Dagihlian got around the problem by “deembedding” a section before imaging. This some what defeats the advantages of direct dry preparation, thus we are reluctant to accept it as the final solution to our problem. Alternatively, consider fig 1 wherein a freeze dried onion root has a window cut in its surface by a micromanipulator during observation in the SEM.

Characterization of Monoclonal Anti-human Factor VII Antibody (B101/B1) that Recognized Three-dimensional Structures near Arg at Position 79 in the First EGF-like Domain

1998 ◽  
Vol 79 (01) ◽  
pp. 104-109 ◽  
Author(s):  
Osamu Takamiya
Keyword(s):  
Monoclonal Antibodies ◽  
Tissue Factor ◽  
Human Factor ◽  
Solid Phase ◽  
Three Dimensional ◽  
Coagulation Factors ◽  
Factor Vii ◽  
Dimensional Structure ◽  
Epidermal Growth

SummaryMurine monoclonal antibodies (designated hVII-B101/B1, hVIIDC2/D4 and hVII-DC6/3D8) directed against human factor VII (FVII) were prepared and characterized, with more extensive characterization of hVII-B101/B1 that did not bind reduced FVIIa. The immunoglobulin of the three monoclonal antibodies consisted of IgG1. These antibodies did not inhibit procoagulant activities of other vitamin K-dependent coagulation factors except FVII and did not cross-react with proteins in the immunoblotting test. hVII-DC2/D4 recognized the light chain after reduction of FVIIa with 2-mercaptoethanol, and hVIIDC6/3D8 the heavy chain. hVII-B101/B1 bound FVII without Ca2+, and possessed stronger affinity for FVII in the presence of Ca2+. The Kd for hVII-B101/B1 to FVII was 1.75 x 10–10 M in the presence of 5 mM CaCl2. The antibody inhibited the binding of FVII to tissue factor in the presence of Ca2+. hVII-B101/B1 also inhibited the activation of FX by the complex of FVIIa and tissue factor in the presence of Ca2+. Furthermore, immunoblotting revealed that hVII-B101/B1 reacted with non-reduced γ-carboxyglutaminic acid (Gla)-domainless-FVII and/or FVIIa. hVII-B101/B1 showed a similar pattern to that of non-reduced proteolytic fragments of FVII by trypsin with hVII-DC2/D4 on immunoblotting test. hVII-B101/B1 reacted differently with the FVII from the dysfunctional FVII variant, FVII Shinjo, which has a substitution of Gln for Arg at residue 79 in the first epidermal growth factor (1st EGF)-like domain (Takamiya O, et al. Haemosta 25, 89-97,1995) compared with normal FVII, when used as a solid phase-antibody for ELISA by the sandwich method. hVII-B101/B1 did not react with a series of short peptide sequences near position 79 in the first EGF-like domain on the solid-phase support for epitope scanning. These results suggested that the specific epitope of the antibody, hVII-B101/B1, was located in the three-dimensional structure near position 79 in the first EGF-like domain of human FVII.

The three-dimensional structure of interleukin-1β

1988 ◽  
Vol 16 (6) ◽  
pp. 949-953 ◽  
Author(s):  
JOHN P. PRIESTLE ◽  
HANS-PETER SCHÄR ◽  
MARKUS G. GRÜTTER
Keyword(s):  
Polypeptide Chain ◽  
Three Dimensional ◽  
Interleukin 1Β ◽  
Dimensional Structure ◽  
X Ray ◽  
Three Dimensional Structure ◽  
R Factor ◽  
The Core ◽  
Internal Sequence ◽  
Network Of Hydrogen Bonds

Summary The three-dimensional structure of human recombinant interleukin-1β has been determined at 0.24 nm resolution by X-ray crystallographic techniques. The partially refined model has a crystallographic R-factor of just under 19%. The structure is composed of 12 β-strands forming a complex network of hydrogen bonds. The core of the structure can best be described as a tetrahedron whose edges are each formed by two antiparallel β-strands. The interior of this structure is filled with hydrophobic side-chains. There is a 3-fold repeat in the folding of the polypeptide chain. Although this folding pattern suggests gene triplication, no significant internal sequence homology between topologically corresponding residues exists. The folding topology of interleukin-1β is very similar to that described by A. D. McLachlan [(1979) J. Mol. Biol. 133, 557–563] for soybean trypsin inhibitor.

scholarly journals Crystallization and preliminary X-ray analysis of the major peanut allergen Ara h 1 core region

2010 ◽  
Vol 66 (9) ◽  
pp. 1071-1073 ◽  
Author(s):  
Cerrone Cabanos ◽  
Hiroyuki Urabe ◽  
Taro Masuda ◽  
Mary Rose Tandang-Silvas ◽  
Shigeru Utsumi ◽  
...  
Keyword(s):  
Sodium Citrate ◽  
Three Dimensional ◽  
Core Region ◽  
Dimensional Structure ◽  
Monoclinic Space Group ◽  
X Ray ◽  
Cell Parameters ◽  
Peg 400 ◽  
Ara H 1 ◽  
Peanut Allergens

Peanuts contain some of the most potent food allergens known to date. Ara h 1 is one of the three major peanut allergens. As a first step towards three-dimensional structure elucidation, recombinant Ara h 1 core region was cloned, expressed inEscherichia coliand purified to homogeneity. Crystals were obtained using 0.1 Msodium citrate pH 5.6, 0.1 MNaCl, 15% PEG 400 as precipitant. The crystals diffracted to 2.25 Å resolution using synchrotron radiation and belonged to the monoclinic space groupC2, with unit-cell parametersa= 156.521,b= 88.991,c= 158.971 Å, β = 107.144°. Data were collected at the BL-38B1 station of SPring-8 (Hyogo, Japan).

scholarly journals Determination of the Three-dimensional Structure of Dislocations by Synchrotron White X-ray Topography Combined with a Topo-tomographic Technique

Materia Japan ◽  
2007 ◽  
Vol 46 (12) ◽  
pp. 823-823
Author(s):  
Seiji Kawado ◽  
Toshinori Taishi ◽  
Satoshi Iida ◽  
Yoshifumi Suzuki ◽  
Yoshinori Chikaura ◽  
...  
Keyword(s):  
Three Dimensional ◽  
Dimensional Structure ◽  
X Ray ◽  
Three Dimensional Structure ◽  
Tomographic Technique

A three-dimensional structure of vanadium malonate: synthesis, characterization and X-ray structure of [Na2VO(C3H2O4)2(H2O)2]n

2004 ◽  
Vol 693 (1-3) ◽  
pp. 199-203 ◽  
Author(s):  
Quan-Zheng Zhang ◽  
Can-Zhong Lu ◽  
Wen-Bin Yang ◽  
Shu-Mei Chen ◽  
Ya-Qin Yu
Keyword(s):  
Three Dimensional ◽  
Dimensional Structure ◽  
X Ray ◽  
Three Dimensional Structure

Three-dimensional structure of the calcite–water interface by surface X-ray scattering

2004 ◽  
Vol 573 (2) ◽  
pp. 191-203 ◽  
Author(s):  
P. Geissbühler ◽  
P. Fenter ◽  
E. DiMasi ◽  
G. Srajer ◽  
L.B. Sorensen ◽  
...  
Keyword(s):  
Three Dimensional ◽  
Dimensional Structure ◽  
Water Interface ◽  
X Ray ◽  
Three Dimensional Structure ◽  
X Ray Scattering ◽  
Ray Scattering

Three-dimensional X-ray diffraction imaging of process-induced dislocation loops in silicon

2011 ◽  
Vol 44 (3) ◽  
pp. 526-531 ◽  
Author(s):  
David Allen ◽  
Jochen Wittge ◽  
Jennifer Stopford ◽  
Andreas Danilewsky ◽  
Patrick McNally
Keyword(s):  
Semiconductor Industry ◽  
Three Dimensional ◽  
Crystal Defects ◽  
Three Dimensions ◽  
Dimensional Structure ◽  
Dislocation Loops ◽  
X Ray Diffraction ◽  
X Ray ◽  
Diffraction Imaging ◽  
Relationship Of

In the semiconductor industry, wafer handling introduces micro-cracks at the wafer edge and the causal relationship of these cracks to wafer breakage is a difficult task. By way of understanding the wafer breakage process, a series of nano-indents were introduced both into 20 × 20 mm (100) wafer pieces and into whole wafers as a means of introducing controlled strain. Visualization of the three-dimensional structure of crystal defects has been demonstrated. The silicon samples were then treated by various thermal anneal processes to initiate the formation of dislocation loops around the indents. This article reports the three-dimensional X-ray diffraction imaging and visualization of the structure of these dislocations. A series of X-ray section topographs of both the indents and the dislocation loops were taken at the ANKA Synchrotron, Karlsruhe, Germany. The topographs were recorded on a CCD system combined with a high-resolution scintillator crystal and were measured by repeated cycles of exposure and sample translation along a direction perpendicular to the beam. The resulting images were then rendered into three dimensions utilizing open-source three-dimensional medical tomography algorithms that show the dislocation loops formed. Furthermore this technique allows for the production of a video (avi) file showing the rotation of the rendered topographs around any defined axis. The software also has the capability of splitting the image along a segmentation line and viewing the internal structure of the strain fields.

scholarly journals Quantitative Characterization of Bamboo Cortex’structure Based on X-ray Microtomography

2021 ◽  
Author(s):  
Xianke Wang ◽  
Lin Chen ◽  
Bin Huang ◽  
Jin Yuan ◽  
Lili Shang ◽  
...  
Keyword(s):  
Natural Fiber ◽  
Fiber Composite ◽  
Three Dimensional ◽  
Middle Layer ◽  
Dimensional Structure ◽  
Vascular Bundles ◽  
Layer Transition ◽  
Average Pore ◽  
X Ray ◽  
Three Dimensional Structure

Abstract Bamboo is a natural fiber composite with layered structure. Millions of years of evolution have endowed bamboo with the most effective structure in nature. The ingenious microstructure provides bamboo with excellent mechanical properties. Bamboo culm is composed of the cortex, a middle layer, and a pith ring. The cortex refers to the area starting from the periphery of the culm wall to the vascular bundles. The present study obtained the two-dimensional microstructure of bamboo cortex cells by optical microscopy and characterized the three-dimensional structure through high-resolution X-ray microtomography (µCT). Based on the analysis, the bamboo cortex cells were classified into four layers: epidermis layer, hypodermis layer, transitional layer, and parenchyma layer. The average pore volume of the bamboo cortex was about 1.54×10-6 mm3, the porosity was 36.1%, and the relative density was 0.639. The epidermis layer, hypodermis layer, transition layer, and parenchyma layer cells had a cell cavity volume of 917.81 µm3, 714.22 µm3, 1258.19 µm3, and 3117.65 µm3, respectively, an average length3d (L) of 19.38 µm, 25.84 µm, 26.46 µm, and 34.88 µm, respectively, an average breadth3d (W) of 14.11 µm, 9.44 µm, 15.22 µm, and 16.6 µm, respectively, and sphericity of 0.85, 0.76, 0.75, and 0.78, respectively. Studies on bamboo anatomical structure, especially three-dimensional digital characterization, will enrich the bamboo microstructure database. Besides, the three-dimensional structure of the bamboo cortex revealed in this study can provide a reference for optimizing composite material hierarchy and biomimetic design.

Diffraction by crystals

2002 ◽  
Author(s):  
David Blow
Keyword(s):  
Fourier Transform ◽  
Three Dimensional ◽  
Incident Beam ◽  
Two Dimensions ◽  
Three Dimensions ◽  
Dimensional Structure ◽  
Angle Of Incidence ◽  
X Ray ◽  
Max Von Laue ◽  
The Fourier Transform

In Chapter 4 many two-dimensional examples were shown, in which a diffraction pattern represents the Fourier transform of the scattering object. When a diffracting object is three-dimensional, a new effect arises. In diffraction by a repetitive object, rays are scattered in many directions. Each unit of the lattice scatters, but a diffracted beam arises only if the scattered rays from each unit are all in phase. Otherwise the scattering from one unit is cancelled out by another. In two dimensions, there is always a direction where the scattered rays are in phase for any order of diffraction (just as shown for a one-dimensional scatterer in Fig. 4.1). In three dimensions, it is only possible for all the points of a lattice to scatter in phase if the crystal is correctly oriented in the incident beam. The amplitudes and phases of all the scattered beams from a three-dimensional crystal still provide the Fourier transform of the three-dimensional structure. But when a crystal is at a particular angular orientation to the X-ray beam, the scattering of a monochromatic beam provides only a tiny sample of the total Fourier transform of its structure. In the next section, we are going to find what is needed to allow a diffracted beam to be generated. We shall follow a treatment invented by Lawrence Bragg in 1913. Max von Laue, who discovered X-ray diffraction in 1912, used a different scheme of analysis; and Paul Ewald introduced a new way of looking at it in 1921. These three methods are referred to as the Laue equations, Bragg’s law and the Ewald construction, and they give identical results. All three are described in many crystallographic text books. Bragg’s method is straightforward, understandable, and suffices for present needs. I had heard J.J. Thomson lecture about…X-rays as very short pulses of radiation. I worked out that such pulses…should be reflected at any angle of incidence by the sheets of atoms in the crystal as if these sheets were mirrors.…It remained to explain why certain of the atomic mirrors in the zinc blende [ZnS] crystal reflected more powerfully than others.

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