scholarly journals X-ray studies of the structure of hair, wool, and related fibres - III—The configuration of the keratin molecule and its orientation in the biological cell

1935 ◽  
Vol 150 (871) ◽  
pp. 533-551 ◽  
Keyword(s):  
Average Distance ◽  
Three Dimensional ◽  
Side Chains ◽  
X Ray ◽  
Molecular Arrangement ◽  
Proposed Model ◽  
Basic Features ◽  
Geometrical Argument ◽  
Diffraction Effects ◽  
Physical And Chemical

One of the difficulties associated with the X-ray study of biological structures arises from the fact that such structures, while not in general unorganized “powders,” are nevertheless usually built up of numerous submicroscopic individuals of continuously varying orientation: in the typical biological “fibre,” for example, the imperfectly crystalline mole­cular aggregates all lie with one and the same crystallographic direction either approximately parallel to the fibre-axis or spirally inclined at some approximately constant angle to it; but subject to this limitation there may be present within the compass of the X-ray beam all orientations up to the maximum possible consistent with axial symmetry. This means that though we may not be condemned to work in the least profitable field of X-ray technique, that of the completely random “powder photograph,” yet we are debarred from the full geometrical advantages to be derived from operating with a single macroscopic crystal. Speaking briefly, the main trouble lies in the difficulty or impossibility of measuring sufficient inter-directional angles to define the molecular arrangement without ambiguity. Sometimes it is possible to draw very plausible conclusions, or even conclusions almost certainly correct; but in others the diffraction effects are so ill-defined as to preclude altogether the use of direct geometrical argument, and compel us to fall back on indirect reasoning based on evidence from various sources, including comparative photographs of related structures. The X-ray investigation of proteins in particular is a many-sided enquiry of this nature, for the diffraction effects are susceptible of interpretation only in relation to other physical and chemical data. The X-ray photographs then serve to give form, so to speak, to such data—to provide the three-dimensional framework necessary to build them into a coherent whole. Papers I and II in this series show how, working along these lines, it has been found possible to derive the basic features of the keratin molecule or complex, both in its unextended form (α) and in its extended form ((β), and to apply the proposed model to the interpretation of the long-range elasticity and other characteristic properties of mammalian hairs. The structure of β-keratin may be described most simply as that of a flat “polypeptide grid,” in which a succession of fully extended main-chains are bound side by side through linkages, both electrostatic and co-valent, between certain of their side-chains; while that of α-keratin (the normal equilibrium form) may be thought of as derived from (β-keratin by a regular folding of the main-chains in planes transverse to the side-chains. By this means the length of the molecule in the direction of the main-chains is reduced to approximately one-half (the average distance apart of the side-chains is decreased from rather less than 3·4 A to about 1·7 A), while the average separation of the main-chains in the plane of the side-chains (the plane of the “grid”) remains roughly constant (9·8 A). In the β-keratin crystallites the grids are piled one on top of another with the main-chains parallel and separated by a distance of 4·65 A.

Diffraction

2002 ◽  
Author(s):  
David Blow
Keyword(s):  
Red Light ◽  
Three Dimensional ◽  
Three Dimensions ◽  
X Rays ◽  
X Ray ◽  
Original Direction ◽  
Computational Procedures ◽  
Scattering Material ◽  
Opaque Object ◽  
Diffraction Effects

Diffraction refers to the effects observed when light is scattered into directions other than the original direction of the light, without change of wavelength. An X-ray photon may interact with an electron and set the electron oscillating with the X-ray frequency. The oscillating electron may radiate an X-ray photon of the same wavelength, in a random direction, when it returns to its unexcited state. Other processes may also occur, akin to fluorescence, which emit X-rays of longer wavelengths, but these processes do not give diffraction effects. Just as we see a red card because red light is scattered off the card into our eyes, objects are observed with X-rays because an illuminating X-ray beam is scattered into the X-ray detector. Our eye can analyse details of the card because its lens forms an image on the retina. Since no X-ray lens is available, the scattered X-ray beam cannot be converted directly into an image. Indirect computational procedures have to be used instead. X-rays are penetrating radiation, and can be scattered from electrons throughout the whole scattering object, while light only shows the external shape of an opaque object like a red card. This allows X-rays to provide a truly three-dimensional image. When X-rays pass near an atom, only a tiny fraction of them is scattered: most of the X-rays pass further into the object, and usually most of them come straight out the other side of the whole object. In forming an image, these ‘straight through’ X-rays tell us nothing about the structure, and they are usually captured by a beam stop and ignored. This chapter begins by explaining that the diffraction of light or X-rays can provide a precise physical realization of Fourier’s method of analysing a regularly repeating function. This method may be used to study regularly repeating distributions of scattering material. Beginning in one dimension, examples will be used to bring out some fundamental features of diffraction analysis. Graphic examples of two-dimensional diffraction provide further demonstrations. Although the analysis in three dimensions depends on exactly the same principles, diffraction by a three-dimensional crystal raises additional complications.

Collagen: the organic matrix of bone

1984 ◽  
Vol 304 (1121) ◽  
pp. 455-477 ◽  
Keyword(s):  
Self Assembly ◽  
Hexagonal Lattice ◽  
Three Dimensional ◽  
Organic Matrix ◽  
Calcium Hydroxyapatite ◽  
Collagen Molecule ◽  
Crystalline Region ◽  
X Ray ◽  
Molecular Arrangement ◽  
Diffraction Patterns

Collagen is the principal organic matrix in bone. The triple helical region of the molecule is 1014 amino acids long. In fibrils these molecules are staggered axially by integers of 234 residues or 68 nm ( D ). This axial shift occurs by self-assembly and can be understood in terms of a periodicity in the occurrence of apolar and polar residues in the amino acid sequence. Because the molecular length L = 4.47 D , there are gaps 1.5 x 36.5 nm regularly arrayed throughout the fibrils. The three-dimensional molecular arrangement is a quasi-hexagonal lattice with three distinct values for the principal interplanar spacings. Analysis of the intensity distribution in the medium-angle X -ray diffraction patterns from tendons has produced the following picture of the molecular arrangement in fibrils (Fraser et al . 1983). The molecular helices have a coherent length of 32 nm and are tilted parallel to a specific place within the lattice. A regular azimuthal interaction exists between these helices. This crystalline region could be the overlap region with a non-crystalline gap region. However, the gap is still regular axially and the molecular helices retain their structure; their lateral packing is perturbed although they retain a ‘gap’. Neutron and X -ray scattering experiments have shown that calcium hydroxyapatite crystals occur in the gap and are nucleated at a specific though unknown location within the gap. The c -axis of the apatite crystals is parallel to the fibril axis and its length c = 0.688 nm is close to the axial periodicity in a protein with an extended β-conformation. If the telopeptides at the end of a collagen molecule do have this conformation they would either have a highly heterogeneous conformation or exist in a folded manner because the overall length of the telopeptides is shorter than a regular collagen repeat of 0.029 nm would allow.

scholarly journals An X-ray study of horse methaemoglobin. II

1949 ◽  
Vol 195 (1043) ◽  
pp. 474-499 ◽  
Keyword(s):  
Short Range ◽  
Polypeptide Chain ◽  
Average Distance ◽  
Three Dimensional ◽  
Chain Structure ◽  
Closed Loops ◽  
X Ray ◽  
Vector Density ◽  
Polypeptide Chains ◽  
Haemoglobin Molecule

A complete three-dimensional Patterson synthesis of haemoglobin has been calculated, giving the distribution of vector density in thirty-one sections through the unit cell. The sections show certain concentrations of vector density which can be interpreted in terms of polypeptide chain structure. The following are the conclusions tentatively arrived at on the evidence described in this paper. The haemoglobin molecule resembles a cylinder of 57 Å diameter and 34Å height, which consists of an assembly of polypeptide chains running parallel to the base of the cylinder. The chains show a short-range fold, with a prominent vector of 5 Å parallel to the chain direction. In addition to this the chains also contain a longer fold which may extend through the whole width of the molecule. This long fold may be due either to open chains folded backwards and forwards through the molecule or to closed loops of polypeptide chains. The average distance between neighbouring chains, or neighbouring portions of the same chain folded back on itself, is 10.5 Å. The chains are arranged in four layers which are about 9 Å apart and correspond to the four layers of scattering matter described in a previous paper. The haem groups lie with their flat sides approximately normal to the chain direction.

scholarly journals Growth, Crystal Structure, Hirshfeld Surface Analysis, DFT Studies, Physicochemical Characterization And Cytotoxicity Assays of Novel Organic Triphosphate

2021 ◽  
Author(s):  
Yathreb Oueslati ◽  
Sevgi Kansız ◽  
Necmi Dege ◽  
Cristina de la Torre Paredes ◽  
Antoni Llopis Lorente ◽  
...  
Keyword(s):  
Density Functional ◽  
Three Dimensional ◽  
Physicochemical Characterization ◽  
Basis Set ◽  
Crystallographic Structure ◽  
X Ray Diffraction ◽  
Hybrid Compound ◽  
X Ray ◽  
Molecular Arrangement ◽  
Chemical Procedure

Abstract A novel interesting organic-inorganic hybrid compound, named (1-phenylpiperazinium) trihydrogen triphosphate, with the formula (C10H15N2)2H3P3O10 has been obtained by low speed of evaporation at room temperature after using the ion exchange chemical procedure. To carry out a detailed crystallographic structure analysis, single-crystal X-ray diffraction has been reported. In the molecular arrangement, the different entities are held together through N-H…O, O-H…O and C-H…O hydrogen bonds, building up a three dimensional packing. Powder X-ray diffraction analysis is acquired to confirm the purity of the product. The nature and the proportion of intermolecular interactions were investigated by Hirshfeld surfaces analysis. In order to support the experimental results, a density functional theory (DFT) calculation were performed, using the Becke-3-Parameter-Lee-Yang-Parr (B3LYP) function with LANL2DZ basis set, and the data indicate the much agreement between the experimental and the theoretical results. Thus, the physicochemical properties were studied employing a variety of techniques (FT-IR, NMR, UV-Visible and photoluminescence). To get an insight of the possible employment of the present material in biology, cell viability assays were performed.

scholarly journals The diffuse spots in X-ray photographs

1941 ◽  
Vol 179 (976) ◽  
pp. 51-60 ◽  
Keyword(s):  
Crystal Structure ◽  
Diffraction Pattern ◽  
Diffraction Grating ◽  
Calculated Result ◽  
Wave Length ◽  
Three Dimensional ◽  
Laue Pattern ◽  
X Ray ◽  
Diffraction Effects

A crystal consisting, as it does, of some molecular combination repeated as a unit at regular intervals in three directions in space can act as a three- dimensional diffraction grating. When monochromatic rays fall upon it, the scattered rays form a diffraction pattern, which can be derived by calculation from the diffraction formula. The pattern of ‘diffuse spots’ now under discussion agrees very closely, in fact within the errors of experiment so far made, with this calculated result. Either the conditions in the crystal which give rise to the diffuse spots are those which allow the diffraction pattern to be observed or they simulate them. This diffraction pattern differs from the diffraction effects so widely used in recent years in the examination of crystal structure. The Laue pattern of spots is not a true diffraction pattern because every spot in it is due to a different wave-length. In the examination of a crystal by an ionization spectrometer or in the oscillation photograph, the different spots are not observed simultaneously. In a true diffraction pattern all the spots or lines are due to monochromatic rays and are observed at one and the same time.

scholarly journals A Three-dimensional Model of the Neprilysin 2 Active Site Based on the X-ray Structure of Neprilysin

2004 ◽  
Vol 279 (44) ◽  
pp. 46172-46181 ◽  
Author(s):  
Stéphanie Voisin ◽  
Didier Rognan ◽  
Claude Gros ◽  
Tanja Ouimet
Keyword(s):  
Active Site ◽  
Three Dimensional ◽  
Physiological Role ◽  
Site Directed Mutagenesis ◽  
Three Dimensional Model ◽  
X Ray ◽  
Amide Bonds ◽  
Inhibitory Compounds ◽  
Proposed Model

Neprilysin 2 (NEP2), a recently identified member of the M13 subfamily of metalloproteases, shares the highest degree of homology with the prototypical member of the family neprilysin. Whereas the study of thein vitroenzymatic activity of NEP2 shows that it resembles that of NEP as it cleaves the same substrates often at the same amide bonds and binds the same inhibitory compounds albeit with different potencies, its physiological role remains elusive because of the lack of selective inhibitors. To aid in the design of these novel compounds and better understand the different inhibitory patterns of NEP and NEP2, the x-ray structure of NEP was used as a template to build a model of the NEP2 active site. The results of our modeling suggest that the overall structure of NEP2 closely resembles that of NEP. The model of the active site reveals a 97% sequence identity with that of NEP with differences located within the S′2subsite of NEP2 where Ser133and Leu739replace two glycine residues in NEP. To validate the proposed model, site-directed mutagenesis was performed on a series of residues of NEP2, mutants expressed in AtT20 cells, and their ability to bind various substrates and inhibitory compounds was tested. The results confirm the involvement of the conserved Arg131and Asn567in substrate binding and catalytic activity of NEP2 and further show that the modifications in its S′2pocket, particularly the presence therein of Leu739, account for a number of differences in inhibitor binding between NEP and NEP2.

Structural Evolution of Ag–Co and Ag–Ni Alloys Studied by Anomalous Small-Angle X-ray Scattering

1998 ◽  
Vol 31 (5) ◽  
pp. 783-788 ◽  
Author(s):  
C. Revenant-Brizard ◽  
J. P. Simon ◽  
J. R. Regnard ◽  
I. Manzini ◽  
B. Rodmacq
Keyword(s):  
Small Angle ◽  
Magnetic Particles ◽  
Average Distance ◽  
Three Dimensional ◽  
Structural Evolution ◽  
Anomalous Scattering ◽  
Magnetic Element ◽  
X Ray ◽  
X Ray Scattering ◽  
Ray Scattering

The structural evolution of co-sputtered Ag–20 (and 35) at.% Co and Ag–20 (and 35) at.% Ni was studied by anomalous small-angle X-ray scattering in the as-deposited state and after different anneals for 10 min at 573, 623 and 723 K. Anomalous scattering was used to separate the part of the scattering signal due to the transition metal particles from the signal of other heterogeneities. Strong segregation, involving about two-thirds of the Co (or Ni) atoms, already exists for the as-deposited state. After a 573 K anneal, the phases (Ag matrix and Co or Ni well defined particles) have almost reached equilibrium,i.e.complete immiscibility. Most of the magnetic particles are three dimensional with an average radius of 5–25 Å and the average distance between the particles varies from 17 to 110 Å, depending on the magnetic element and its concentration, and on the annealing conditions. The size distribution does not correspond to that of usual coarsening, but becomes broader after extended annealing. This is probably due to heterogeneous precipitation at grain boundaries of the Ag matrix.

The X-Ray Diagram of a Buna-S Vulcanizate

1945 ◽  
Vol 18 (1) ◽  
pp. 20-21
Author(s):  
Ross E. Morris ◽  
Charles B. Jordan
Keyword(s):  
Natural Rubber ◽  
Diffraction Pattern ◽  
Similar Pattern ◽  
Main Chain ◽  
Three Dimensional ◽  
Side Chains ◽  
X Ray Diffraction ◽  
X Ray ◽  
Synthetic Rubber

Abstract Sebrell and Dinsmore (India Rubber World 103, 37 (1944); Rubber Chem. Tech. 16, 857 (1943)) found that the x-ray diffraction pattern of Buna-S consists of a broad halo similar to that obtained with liquids. This type of pattern was obtained whether the Buna-S was unstretched or stretched. Unstretched natural rubber gives a similar pattern, but stretched natural rubber gives a characteristic fiber pattern. This fiber pattern demonstrates the existence of three-dimensional crystallites. Buna-S would not be expected to yield a fiber diagram while stretched because the molecules of this synthetic rubber are probably not constructed in a regular fashion. The styrene residues are presumably distributed at random along the length of the molecule, and there may be side-chains which branch off the main chain. However, when considerably stretched, a Buna-S vulcanizate would be expected to exhibit some indication in its x-ray diagram that alignment of the molecules has occurred.

Ribosome Structural Organization

1974 ◽  
Vol 32 ◽  
pp. 332-333
Author(s):  
James A. Lake
Keyword(s):  
Ribosomal Proteins ◽  
Structural Organization ◽  
Three Dimensional ◽  
Small Subunit ◽  
Structural Studies ◽  
X Ray Diffraction ◽  
Specific Antibodies ◽  
X Ray ◽  
E Coli ◽  
Complete Sequences

The understanding of ribosome structure has advanced considerably in the last several years. Biochemists have characterized the constituent proteins and rRNA's of ribosomes. Complete sequences have been determined for some ribosomal proteins and specific antibodies have been prepared against all E. coli small subunit proteins. In addition, a number of naturally occuring systems of three dimensional ribosome crystals which are suitable for structural studies have been observed in eukaryotes. Although the crystals are, in general, too small for X-ray diffraction, their size is ideal for electron microscopy.

3-D reconstruction of molecular shape from microcrystal thin sections

1983 ◽  
Vol 41 ◽  
pp. 748-749
Author(s):  
S. Cusack ◽  
J.-C. Jésior
Keyword(s):  
Three Dimensional ◽  
Molecular Shape ◽  
Biological Molecules ◽  
Fourier Space ◽  
Single Particles ◽  
Thin Sections ◽  
Standard Methods ◽  
X Ray ◽  
X Ray Crystallography ◽  
Dimensional Reconstruction

Three-dimensional reconstruction techniques using electron microscopy have been principally developed for application to 2-D arrays (i.e. monolayers) of biological molecules and symmetrical single particles (e.g. helical viruses). However many biological molecules that crystallise form multilayered microcrystals which are unsuitable for study by either the standard methods of 3-D reconstruction or, because of their size, by X-ray crystallography. The grid sectioning technique enables a number of different projections of such microcrystals to be obtained in well defined directions (e.g. parallel to crystal axes) and poses the problem of how best these projections can be used to reconstruct the packing and shape of the molecules forming the microcrystal.Given sufficient projections there may be enough information to do a crystallographic reconstruction in Fourier space. We however have considered the situation where only a limited number of projections are available, as for example in the case of catalase platelets where three orthogonal and two diagonal projections have been obtained (Fig. 1).

Sign in / Sign up

Export Citation Format

Share Document