Monoclonal antibody studies of alpha-keratin low-sulfur proteins

Monoclonal antibodies to the two families of low-sulfur proteins from wool were produced. Selection was applied to identify those hybridomas secreting antibody that was effective in the Electro-blot system. The specificities of eight different monoclonal antibodies were investigated by their binding to alpha-keratin low-sulfur proteins which had been subjected to electrophoresis from wool, goat hair, porcupine quill, rat hair and echidna quill, using the Electro-blot procedure. Considerable cross-reactivity was found both within the low-sulfur protein components of individual keratins from a particular species, and also between the keratins of the different species. Some antibodies were found to bind selectively to components of one family of low-sulfur proteins in wool, while others recognized determinants in both families, indicating some homology between the two families.     

Ultrastructure of trichome of old world porcupine of Indian subcontinent

The present investigation is based on ultrastructural details of different types of quills of two species of old world porcupine (Hystrix indica and Hystrix brachyura) of Indian subcontinent using environmental scanning electron microscopy (ESEM). In H. indica, four types of quills have been detected – bristlelike spines, stilettolike spines, spikes and mane. The quills of H. brachyura are categorized into four types – broad, slender, hollow tail quill and quills of the anogenital region. The ESEM images of surface characteristic of different types of quills of both the species except the hollow tail quill showed usual scaly features without having any differences. The cross‐sectional images of quills of H. indica and H. brachyura show a narrow cortex and a broad medullary region with a network of anastomosing channels. The cortical layer is comparatively thicker in mane hairs of H. indica and in slender quills of H. brachyura. With extensive exploration of the anatomical structures of the quills by ESEM from both the species of Hystrix, we could not find ‘osmetrichia’ in any forms of quill. In contrast, we hypothesized that the channels and network of medulla are serving the purpose for transportation of pheromonal signalling molecules in old world porcupine.     

Macromolecular structure and organization of alpha keratin

The small-angle equatorial X-ray scattering of alpha keratin (African porcupine quill) was studied using a direct type of analysis, which allows the separation of the intermicro-fibrillar interference effects from those of the intramicrofibrillar scattering without the use of prior assumptions. X-ray data were obtained from 470–21 Å; their analysis by the above method resulted in a z-axis projection of the microfibrillar electron density, which extends over a diameter of 80 Å and has a core region surrounded by a peak located at a radius of 28 Å. The macromolecular organization of the 80-Å-diameter microfibrils was found to be an arc-like layer type of aggregation and not a pseudohexagonal packing. When the specimen was subjected to silver staining the aggregation of the microfibrils did not change except for a slight contraction. The z-axis projection of the stained microfibril, however, was significantly different. The silver appears to build up slightly around the outer periphery of the microfibril, stains the peripheral region very little, deposits on the inside of the peripheral region, and outlines the core area.     

Gap junction structures: Analysis of the x-ray diffraction data

Models for the spatial distribution of protein, lipid and water in gap junction structures have been constructed from the results of the analysis of X-ray diffraction data described here and the electron microscope and chemical data presented in the preceding paper (Caspar, D. L. D., D. A. Goodenough, L. Makowski, and W.C. Phillips. 1977. 74:605-628). The continuous intensity distribution on the meridian of the X-ray diffraction pattern was measured, and corrected for the effects of the partially ordered stacking and partial orientation of the junctions in the X-ray specimens. The electron density distribution in the direction perpendicular to the plane of the junction was calculated from the meridional intensity data. Determination of the interference function for the stacking of the junctions improved the accuracy of the electron density profile. The pair-correlation function, which provides information about the packing of junctions in the specimen, was calculated from the interference function. The intensities of the hexagonal lattice reflections on the equator of the X-ray pattern were used in coordination with the electron microscope data to calculate to the two-dimensional electron density projection onto the plane of the membrane. Differences in the structure of the connexons as seen in the meridional profile and equatorial projections were shown to be correlated to changes in lattice constant. The parts of the junction structure which are variable have been distinguished from the invariant parts by comparison of the X-ray data from different specimens. The combination of these results with electron microscope and chemical data provides low resolution three- dimensional representations of the structures of gap junctions.     

Demonstration of rotational symmetries in alpha-keratin microfibrils of porcupine quill tip

Selected electron micrographs of transversely, obliquely and longitudinally sectioned microfibrils of transversely sectioned porcupine quill tip are shown to possess 2-fold radial, 3-fold radial and 5-fold polygonal rotational symmetries. These symmetries are verified with a rotation technique, and are similar to edge, corner and face projections of a pentagonal dodecahedron. The a-keratin microfibril is therefore suggested to be composed of a linear arrangement of morphologically identical microfibrillar subunits which approximate the shape of a pentagonal dodecahedron. The various line patterns present in electron micrographs of microfibrils are explained by different orientations of this three-dimensional shape within the thickness of the section. Previous electron microscopic models for the structure of the microfibrils are incompatible with these results. The image averaging methods used to arrive at these earlier models are discussed, and are thought to yield results which must differ from the demonstrated rotational symmetries.     

Museums and Collections

Abstract

Certain quill techniques and buckskin shirts of the Mandan, Hidatsa, Arikara; and the Crow are discussed Described are the plaited technique, its distribution, Manufacture, variation of style, pattern, and the type of clothing upon which it appeared. Attention is drawn to specific examples in European collections. The same type of information is covered for the quill-wrapped horse hair technique and quill decorated shirts.     

Interpretation of the meridional X-ray diffraction pattern from collagen fibrils in corneal stroma

The low angle X-ray diffraction pattern from corneal stroma can be interpreted as arising from the equivalent of sharp meridional reflections due to the packing of molecules along the collagen fibrils and an equatorial pattern due to the packing of these fibrils within lamellae.Axial electron density profiles for corneal collagen fibrils have been produced by combining intensity data from the meridional pattern with two independent sets of phases. The first set was obtained using an electron microscopical technique, whereas the second set consisted of calculated tendon collagen phases given in the literature. Substantial agreement between the two electron density profiles was found.A quantitative analysis of the difference between the electron density profiles of rat tail tendon and corneal collagen showed that the step between the gap and overlap regions is smaller in cornea than in tendon. This is probably due to the binding of non-collagenous material in the gap region as occurs in bone and other tissue. Two peaks corresponding to regions where electron density is greater in the cornea are situated at the gap/overlap junctions. A third region where the corneal collagen is more electron dense is located near the centre of the gap region. The proximity of these peaks to the positions of hydroxylysine residues along the fibril axis suggests that they may be the major sites at which sugars are bound to corneal collagen.     

Small-angle neutron scattering by a strongly denatured protein: analysis using random polymer theory.

Small-angle neutron scattering profiles are presented from phosphoglycerate kinase, in the native form and strongly denatured in 4 M guanidinium chloride (GdnHCl) solution. The data are interpreted using a model in which the excess scattering density associated with the protein is represented as a finite freely jointed chain of spheres. The similarity of the model-derived scattering function to experiment increases asymptotically with the number of spheres. The improvement of the fit obtained with more than approximately 200 spheres (i.e., two residues per sphere) is insignificant. The effects of finite size of the scattering units and of scattering length variation along the polypeptide chain are examined. Improved agreement with experiment is obtained when these effects are taken into account. A method for rapid calculation of the scattering profile of a full, all-atom configuration is examined. It is found that a representation of the chain containing two scattering units per residue, placed at the backbone and side-chain scattering length centroids, reproduces the full, all-atom profile to within 2%.     

Stripes,spots, or reversed spots in two-dimensional Turing systems

Two-dimensional Turing models can generate stationary striped patterns or spotted patterns, and are used to explain the body pattern formation of animals. We studied the effects of the choice of reaction terms on pattern selection, i.e., which pattern is likely to be formed. We examined in detail a model with linear reaction terms and additional constraint terms that confine two variables within a finite range. In the one-dimensional model, a periodic stationary pattern can be formed only when the activator level is constrained both from below and from above. In the two-dimensional model, the relative distance of the equilibrium level of the activator between the upper and lower limitations determines the pattern selection. Striped patterns are produced when the equilibrium is equally distant from the upper and the lower limitations, but spotted patterns are produced when the equilibrium is clearly closer to one than to the other of two limitations. We then examined models with nonlinear reaction terms, including both activator-inhibitor and activator-depletion substrate type models; we attempted to explain the pattern selection of these nonlinear models based on the results of linear models with constraints. The distribution of the activator level is skewed positively and negatively for spotted patterns and reversed spotted patterns, respectively. In contrast, the skew of the distribution of the activator level was close to zero in the case of striped patterns. This observation provides a heuristic argument of how the location of the equilibrium between the constraints leads to pattern selection.     

Simulation Studies on Electrophoretically Detectable Genetic Variability in a Finite Population

Using a new model of isoalleles, extensive Monte Carlo experiments were performed to examine the pattern of allelic distribution in a finite population. In this model it was assumed that the set of allelic states is represented by discrete points on a one-dimensional lattice and that change of state by mutation occurs in such a way that an allele moves either one step in the positive direction or one step in the negative direction on the lattice. Such a model was considered to be appropriate for estimating theoretically the number of electrophoretically detectable alleles within a population. The evenness of allelic distribution was measured by the ratio of the effective to the actual number of alleles (n(e)/n(a)). The results of the Monte Carlo experiments have shown that this ratio is generally larger under the new model of isoalleles than under the conventional Kimura-Crow model of neutral isoalleles. In other words, the distribution of allelic frequencies within a population is expected to be more uniform in the new model. By comparing the Monte Carlo results with actual observations, it was concluded that the observed deviation from what is predicted under the new model with selective neutrality is not in the direction of conforming to the overdominance hypothesis but is, in fact, in the opposite direction.     

Periodic disorder along ramie cellulose microfibrils

Small angle neutron scattering studies have been carried out on cellulose fibers from ramie and Populus maximowicii (cotton wood). Labile hydrogen atoms were replaced by deuterium atoms, in water-accessible disordered regions of the fibers, to increase the neutron scattering contrast between the disordered and crystalline regions. A meridional Bragg reflection, corresponding to a longitudinal periodicity of 150 nm, was observed when scattering collected from hydrogenated and deuterated dry ramie fibers was subtracted. No Bragg reflection was observed with the cotton wood fibers, probably because of lower orientation of the microfibrils in the cell wall. The ramie fibers were then subjected to electron microscopy, acid hydrolysis, gel permeation chromatography, and viscosity studies. The leveling off degree of polymerization (LODP) of the hydrolyzed samples matched exactly the periodicity observed in the diffraction studies. The weight loss related to the LODP was only about 1.5%, and thus, the microfibrils can be considered to have 4-5 disordered residues every 300 residues.     

The structure of the α-keratin microfibril

Quantitative measurements of the intensity of the meridional reflections in the X-ray-diffraction pattern of alpha-keratin are shown to be consistent with a microfibril structure in which a surface lattice with an axially projected period around 200 A is subject to a periodic interruption with an axially projected period of 470 A. Taken in conjunction with recent evidence on the chemical structure of alpha-keratin and other intermediate filaments this finding enables an elaboration to be made of a model proposed earlier by RDB Fraser, TP MacRae, & E Suzuki (J. Mol. Biol. 108, 435-452, 1976) for the alpha-helical framework of the microfibril. The disposition and connectivity of the helical segments suggested here provides a straightforward explanation of a number of recent physicochemical and electron-microscopical observations on intermediate filaments and provides a starting point for the development of models for the framework of other intermediate filaments.     

Glutaraldehyde-induced changes in the axially projected fine structure of collagen fibrils

The fine structure of the collagen fibril, as seen in axial projection, is changed by treatment with glutaraldehyde. The changes are detectable in electron-optical staining patterns and in the intensities of the low-angle meridional X-ray diffraction maxima. Current knowledge of the amino acid sequence of collagen and of the axial arrangement of molecules in fibrils permits interpretation in terms of specific alterations to the axial distribution of electron density along the fibril. Analysis of fibril staining patterns from glutaraldehyde-treated calf skin collagen shows that uptake of staining ions in positive staining patterns is inhibited at residues known to interact with glutaraldehyde (lysyl, hydroxylysyl and probably histidyl side-chains) and on other charged residues in the immediate neighbourhood of the glutaraldehyde-reactive residues. This can be seen as a "stain-exclusion effect" due to the presence of bulky polymeric complexes of glutaraldehyde molecules at cross-linking sites. Such stain exclusion accounts for the drastic changes in the negative staining pattern following treatment with glutaraldehyde. The intensity changes observed in the low-angle meridional X-ray reflections from rat tail tendon, similarly treated, also can be explained by the presence of these bulky complexes. Existing data have been used to predict a model of the altered electron density profile indicating the axial distribution of glutaraldehyde along a D-period of moist tendon collagen.     

Axial electron density of human scleral collagen. Location of proteoglycans by x-ray diffraction.

The low angle meridional x-ray diffraction pattern from fresh human sclera was analyzed to ascertain if collagen-bound proteoglycans affect the axially-projected electron density distribution to the same extent as appears to occur in the cornea. The results showed that, unlike cornea, the electron density of the sclera is similar to that seen in rat tail tendon collagen. The proteoglycans were specifically stained using either Cuprolinic blue or Cupromeronic blue, both under critical electrolyte conditions. The tissue was then examined by electron microscopy and by low angle x-ray diffraction. The electron-optical observations suggested that proteoglycans associate with collagen near the d/e staining bands in the gap zone. A difference Fourier analysis from the x-ray results confirmed that these observations were not e.m. preparative artefacts and allowed a quantitative estimate to be made of the axial extent of the proteglycans in the wet tissue.     

Protein dynamics from X-ray crystallography: anisotropic, global motion in diffuse scattering patterns

Understanding X-ray crystallographic diffuse scattering is likely to improve our comprehension of equilibrium collective protein dynamics. Here, using molecular dynamics (MD) simulation, a detailed analysis is performed of the origins of diffuse scattering in crystalline Staphylococcal nuclease, for which the complete diffuse scattering pattern has been determined experimentally. The hydrogen-atom contribution and the scattering range over which the scattering can be considered to be a sum of solvent and protein scattering are determined. Two models of correlated protein motion are investigated by calculating the model-derived diffuse scattering and comparing with the scattering calculated directly from MD trajectories. In one model, previously used in diffuse scattering interpretation, the atomic displacement correlations decay isotropically with increasing separation. Model correlation lengths are obtained by refining the model scattering against the simulation-derived scattering pattern, and are found to be significantly different from those correlation lengths derived directly from the MD trajectories. Furthermore, the convergence between the model-derived and MD-derived scattering is poor. The second model, in which the displacement correlations are calculated from the principal components of the MD trajectories, is capable of fully reproducing the MD-derived diffuse scattering if the approximately 50% lowest-frequency modes are included. However, a small number ( approximately 10) of lowest-frequency and largest-amplitude modes dominates the diffuse scattering and thus the correlated protein motions. A detailed analysis of the principal components is performed. In particular, the effective free energy profile associated with each principle mode is analyzed and the eigenfrequency and damping coefficient computed using a model of Brownian dynamics. Those collective modes with effective frequencies below approximately 0.5 THz, including those that determine the diffuse scattering, are overdamped.     

Finite Element Analysis of Simulations of Cancellous Bone Resorption

A stochastic simulation of the resorption of cancellous bone has been developed and integrated with a finite element model to predict the resultant change in structural properties of bone as bone density decreases. The resorption represents the net imbalance of osteoclast and osteoblast activity that occurs in osteoporosis. A simple lattice structure of trabecular bone is considered, with an examination of the lattice geometry and discretization indicating that just five trabeculae need to be modelled. The results from the analysis show how the mechanical properties of the cancellous bone degrade with osteoporosis and demonstrate how the method can be used to predict the relationships between stiffness and density or porosity.     

Differential effects of pre-tension on shear wave propagation in elastic media with different boundary conditions as measured by magnetic resonance elastography and finite element modeling

Magnetic resonance elastography (MRE) can non-invasively determine material stiffness based on the propagating shear wavelength. Shear wave propagation in a finite homogenous isotropic material can be affected by multiple factors. In this study we examined the effects of pre-tension and frequency on MRE shear measurements of gel phantoms with different boundary conditions, frequencies, and geometries. Results from MRE measurements were compared to wave motion theory in elastic solids and qualitatively to a finite element (FE) model. Results indicated that boundary conditions, geometry and pre-tension are important factors to be considered when performing MRE tests on a finite material, and that FE modeling can help explore how the shear wave propagation is affected under various boundary conditions and axial stresses, among other potential factors.     

Low resolution structure of microtubules in solution. Synchrotron X-ray scattering and electron microscopy of taxol-induced microtubules assembled from purified tubulin in comparison with glycerol and MAP-induced microtubules.

The structure of microtubules has been characterized to 3 nm resolution employing time-resolved X-ray scattering. This has revealed detailed structural features of microtubules not observed before in solution. The polymerization of highly purified tubulin, induced by the antitumour drug taxol, has been employed as a microtubule model system. This assembly reaction requires Mg2+, is optimal at a 1:1 taxol to tubulin heterodimer molar ratio, proceeds with GTP or GDP and is intrinsically reversible. The X-ray scattering profiles are consistent with identical non-globular alpha and beta-tubulin monomers ordered within the known helical surface lattice of microtubules. Purified tubulin-taxol microtubules have a smaller mean diameter (approx. 22 nm) than those induced by microtubule associated proteins or glycerol (approx. 24 nm), but nearly identical wall substructure to the resolution of the measurements. This is because the majority of the former consist of only 12 protofilaments instead of the typical 13 protofilaments, as confirmed by electron microscopy of thin-sectioned, negatively stained and ice-embedded taxol microtubules. It may be concluded that taxol induces a slight reduction of the lateral contact curvature between tubulin monomers. The main fringe pattern observed in cryo-electron micrographs is consistent with a simple 12 protofilament 3-start skewed lattice model. Cylindrical closure of this lattice can be achieved by tilting the lattice 0.8 degrees with respect to the microtubule axis. The closure implies a discontinuity in the type of lateral contacts between the tubulin monomers (regardless of whether these are of the -alpha-beta- or the -alpha-alpha-/-beta-beta- type), which indicates that lateral contacts and the subunit specificity of taxol binding are, to a large degree, equivalent.     

Structure of type I and type III heterotypic collagen fibrils: an X-ray diffraction study

The molecular packing arrangement within collagen fibrils has a significant effect on the tensile properties of tissues. To date, most studies have focused on homotypic fibrils composed of type I collagen. This study investigates the packing of type I/III collagen molecules in heterotypic fibrils of colonic submucosa using a combination of X-ray diffraction data, molecular model building, and simulated X-ray diffraction fibre diagrams. A model comprising a 70-nm-diameter D- (approximately 65 nm) axial periodic structure containing type I and type III collagen chains was constructed from amino acid scattering factors organised in a liquid-like lateral packing arrangement simulated using a classical Lennard-Jones potential. The models that gave the most accurate correspondence with diffraction data revealed that the structure of the fibril involves liquid-like lateral packing combined with a constant helical inclination angle for molecules throughout the fibril. Combinations of type I:type III scattering factors in a ratio of 4:1 gave a reasonable correspondence with the meridional diffraction series. The attenuation of the meridional intensities may be explained by a blurring of the electron density profile of the D period caused by nonspecific or random interactions between collagen types I and III in the heterotypic fibril.     

Lateral packing of mineral crystals in bone collagen fibrils

Combined small-angle x-ray scattering and transmission electron microscopy studies of intramuscular fish bone (shad and herring) indicate that the lateral packing of nanoscale calcium-phosphate crystals in collagen fibrils can be represented by irregular stacks of platelet-shaped crystals, intercalated with organic layers of collagen molecules. The scattering intensity distribution in this system can be described by a modified Zernike-Prins model, taking preferred orientation effects into account. Using the model, the diffuse fan-shaped small-angle x-ray scattering intensity profile, dominating the equatorial region of the scattering pattern, could be quantitatively analyzed as a function of the degree of mineralization. The mineral platelets were found to be very thin (1.5 nm ∼ 2.0 nm), having a narrow thickness distribution. The thickness of the organic layers between adjacent mineral platelets within a stack is more broadly distributed with the average value varying from 6 nm to 10 nm, depending on the extent of mineralization. The two-dimensional analytical scheme also leads to quantitative information about the preferred orientation of mineral stacks and the average height of crystals along the crystallographic c axis.