MOLECULAR STRUCTURE OF PLANT FIBERS DETERMINED BY X-RAYS

It has been shown that the wall of the plant fiber is probably built up of unit groups of atoms which have assumed the form of a space lattice. The elementary cell of the lattice is an orthorhombic structure with the dimensions 6.10 x 5.40 x 10.30 Å.u., and contains two unit groups equal in size to two C₆H₁₀O₅ groups. The crystallographic unit cell would contain 4 of these elementary cells and would be represented by Fig. 9 rather than by Fig. 3. The groups of atoms, C₆H₁₀O₅, are arranged in parallel chains running lengthwise of the fiber. In each chain the odd numbered groups have a different orientation from the even numbered. The chains, parallel to one another are spaced 6.10 Å.u. in one direction and 5.40 Å.u. at right angles to that. In these two directions the odd numbered chains also would have a different orientation from the even numbered. On account of the cylindrical shape of the fiber, the elementary cells are arranged in the form of concentric cylinders or layers. The dimensions of the fibers are such that the fiber wall is about 40,000 elementary cells in thickness, or in other words, the fiber is composed of that many concentric layers. If it could be magnified sufficiently, a cross-section of a fiber would show the end view of each cylinder as a dotted circle. The dots, representing the unit groups of atoms, would have considerable uniformity of spacing in both the tangential and the radial directions, 6.10 Å.u. in one and 5.40 Å.u. in the other. The structure could not be as rigidly exact as might be inferred, since the wall is deposited more or less rhythmically during a period of several days or weeks* in which adjustments in the arrangement of the unit groups undoubtedly occur. It is common knowledge that the fibers, under the microscope, rarely appear as true circles on cross-section; usually they appear as irregular, many-sided polygons and the wall thickness is normally uneven. For our purpose it is simpler to think of the fiber as composed of concentric cylinders with diameters so large in proportion to the size of the unit groups that in relatively large segments they closely approach the parallelism of the planes of a rectangular lattice, sufficiently close to be capable of producing diffraction patterns. Although these conclusions seem to be in agreement with the diffraction patterns obtained from various positions of a bundle of approximately parallel fibers, the fact must not be overlooked that the structure cannot be proved with as great certainty as can the structure of a well formed crystal. The very nature of the fiber, its cylindrical shape, and the many internal adjustments which must take place, militate against a clean-cut demonstration. Models, made more or less to scale, were used in working out this structure. The unit group was constructed according to Irvine''s suggestion that all the groups are glucose residues. An intensive study is now under way in which an attempt is being made to bring the models into agreement with the chemical and physical properties of the cellulose fibers and with the diffraction patterns. A report on that part of the work will soon be submitted for publication.     

Relating myocardial laminar architecture to shear strain and muscle fiber orientation

Cardiac myofibers are organized into laminar sheets about four cells thick. Recently, it has been suggested that these layers coincide with the plane of maximum shear during systole. In general, there are two such planes, which are oriented at +/-45 degrees to the main principal strain axes. These planes do not necessarily contain the fiber axis. In the present study, we explicitly added the constraint that the sheet planes should also contain the muscle fiber axis. In a mathematical analysis of previously measured three-dimensional transmural systolic strain distributions in six dogs, we computed the planes of maximum shear, adding the latter constraint by using the also-measured muscle fiber axis. Generally, for such planes two solutions were found, suggesting that two populations of sheet orientation may exist. The angles at which the predicted sheets intersected transmural tissue slices, cut along left ventricular short- or long-axis planes, were strikingly similar to experimentally measured values. In conclusion, sheets coincide with planes of maximum systolic shear subject to the constraint that the muscle fiber axis is contained in this plane. Sheet orientation is not a unique function of the transmural location but occurs in two distinct populations.     

Extracellular crystalline material in intercellular spaces of cockroach peripheral glia

Campaniform sensilla on legs of the cockroach, Blaberus discoidalis, are mechanoreceptors; each sensifum functions via a single bipolar neuron. The cell bodies of the bipolar neurons are tunicated; that is, they are spirally wrapped by one or more glial cells. An elaborate extracellular channel is defined by the plasma membranes of adjacent glial cell folds surrounding a given neuron. The electron microscope reveals that this extracellular space often contains conspicuous crystalline material whose lattice planes, oriented at right angles to the long crystal axis, are manifest as parallel electron-dense lines separated by an intercentre distance of 150 A. The chemical nature of these crystals has not been determined in the present study. Like most biological crystals, however, this precisely ordered crystalline material is probably proteinaceous.     

基于总体最小二乘法的蛋白质肽链逆运动学拟合

提出一种在给定构象下计算蛋白质多肽链中所有二面角的新方法.通过总体最小二乘法将每 个肽单位中的6个原子拟合为1个肽平面,将连续平面之间包含的角定义为二面角,并以数值实验证明了该方法的有效性.精确的二面角值对很多蛋白质分析方法意义重大,特别是将二面角作为基本结构参数的同源建模法.     

Linear dichroism properties and orientations of different ultraviolet transition moments of benzo[a]pyrene derivatives bound noncovalently and covalently to DNA

Linear dichroism and absorption methods are used to study the orientations of transition moments of absorption bands of polycyclic aromatic epoxide derivatives which overlap with those of the DNA band in the 240-300 nm region. Both the short and long axes of the pyrene residues of 1-oxiranylpyrene (1-OP) and the (+) and (-) enantiomers of trans-7,8-dihydroxy-anti-9,10-epoxy-7,8,9,10-tetrahydrobenzo[a]pyrene (BPDE) noncovalently bound to double-stranded native DNA are oriented approximately perpendicular to the axis of the DNA helix, consistent with intercalative modes of binding. The covalent binding of these three epoxide derivatives to DNA is accompanied by reorientations of both the short and long axes of the pyrene residues. Covalent adducts derived from the highly mutagenic (+)-anti-BPDE are characterized by tilts of the short axis within 35 degrees or less, and of the long axis by more than 60-80 degrees, with respect to the planes of the DNA bases. In the adducts derived from the binding of the less mutagenic (-)-anti-BPDE and 1-OP epoxide derivatives to DNA, the long axes of the pyrenyl rings are predominantly oriented within 25 degrees of the planes of the DNA bases; however, in the case of the (-) enantiomer of BPDE, there is significant heterogeneity of conformations. In the case of the 1-OP covalent DNA adducts, the short axis of the pyrene ring system is tilted away from the planes of the DNA bases, and the pyrene ring system is not intercalated between DNA base-pairs as in the noncovalent complexes. The stereochemical properties of the saturated 7,8,9,10-ring in BPDE, or the lack of the 7 and 8 carbon atoms in 1-OP, do not seem to affect noncovalent intercalative complex formation which, most likely, is influenced mainly by the flat pyrenyl residues. These structural features, however, strongly influence the conformations of the covalent adducts, which in turn may be responsible for the differences in the mutagenic activities of these molecules.     

Quantitative evaluation of cell orientation in culture.

A quantitative method to assess mutual orientation of cells in cultures on a substrate includes the following operations: (1) the cellular groups to be evaluated are chosen; (2) position of the long axis for each nucleus of the group is determined; (3) the axis OX is arbitrary chosen for every group and the angles alphai between the long axis of every nucleus i and the axis OX are measured. Every nucleus i corresponds to a vector of unit length ei with the angles 2alpha. D, the mean of the vectors ei for every cell group is calculated. This value of D is compared with a set of values of D computed according to a model of mutual orientation studies in a simulation experiment. In this model the group of n vectors consists of a fraction of Kn parallel vectors (o less than or equal to K less than or equal to I) and of (I minus K)n randomly oriented vectors. K corresponding to the computed D which is equal to the experimental value of D is considered as an index of orientation for the group. Contact orientation with respect to the relief of the substrate may be evaluated as a root mean square deviation sigma0 to the angles between the long axes of cell nuclei and the direction of relief. Examples of the measurements of K and sigma0 in cell cultures are given.     

Morphology and Function of Lateral Hypaxial Musculature in Salamanders

SYNOPSIS. The lateral hypaxial musculature (LHM) of salamandersmay serve as a useful model for understanding the functionsof LHM in tetrapods more generally. Salamanders have betweentwo and four layers of LHM, arranged segmentally in myomeres.These layers produce three primary mechanical actions: theybend the body, pressurize the body, and produce or resist torsionabout the long axis of the body. The optimum muscle fiber anglefor forceful bending is 0° to the long axis, the optimumangle for pressurization is 90°, and the optimum angle fortorsion is 45°. For generating bending and torsional moments,lateral (superficial) muscle layers have greater mechanicaladvantage than medial (deep) layers. For increasing body pressure,by contrast, medial layers have greater mechanical advantage.A comparison of muscle fiber angles in aquatic and terrestrialsalamanders reveals that some aquatic salamanders have one musclelayer with a low fiber angle which may represent a specializationfor swimming. Overall, however, the fiber angles in the LHMof terrestrial and aquatic salamanders are surprisingly similar.In contrast, the pattern of fiber angles in caecilians is different,suggesting that these amphibians use their LHM differently.The fiber angle models and morphological observations presentedhere form a framework which may be useful in future studiesof lateral hypaxial musculature.     

A motion-decomposition approach to address gimbal lock in the 3-cylinder open chain mechanism description of a joint coordinate system at the glenohumeral joint

In this study, the standard-sequence properties of a joint coordinate system were implemented for the glenohumeral joint by the use of a set of instantaneous geometrical planes. These are: a plane that is bound by the humeral long axis and an orthogonal axis that is the cross product of the scapular anterior axis and this long axis, and a plane that is bounded by the long axis of the humerus and the cross product of the scapular lateral axis and this long axis. The relevant axes are updated after every decomposition of a motion component of a humeral position. Flexion, abduction and rotation are then implemented upon three of these axes and are applied in a step-wise uncoupling of an acquired humeral motion to extract the joint coordinate system angles. This technique was numerically applied to physiological kinematics data from the literature to convert them to the joint coordinate system and to visually reconstruct the motion on a set of glenohumeral bones for validation.     

Crystalloid inclusions in the Sertoli cell of the koala,Phascolarctos cinereus (Marsupialia)

Summary Crystalloid inclusions are a common feature in the basal region of Sertoli cells in the koala, Phascolarctos cinereus. Generally located near the nucleus, they are non membrane-bounded, slender rectangular structures composed of tubules which are orientated at right angles to the long axis of the crystalloid and regularly arranged in rows parallel to this long axis. The tubules in adjacent rows are offset from one another at definite angles and extensively interconnected by filaments. Neither the composition nor function of the crystalloids has been determined, but their association with tonofilaments and the presence of ribosomes in the vicinity suggests that they are most likely proteinaceous.The authors would like to thank Mr. D. Harbrow, Mr. S. Brown and Ms. B. Canty for technical assistance; the Queensland National Parks and Wildlife Service and the Victorian Ministry of Conservation (Fisheries and Wildlife Division) for providing permits to work on this protected species; the staff of the Lone Pine Koala Sanctuary, Brisbane, for their assistance in obtaining animals. This work was supported by a grant from the Australian Research Grants Committee, Number DI-77/15525     

Polarized fluorescence from epsilon-ADP incorporated into F-actin in a myosin-free single fiber: conformation of F-actin and changes induced in it by heavy meromyosin.

Fluorescent ADP analog, ε-ADP (1:N⁶-ethenoadenosine 5′-diphosphate), was incorporated into F-actin in a myosin-free ghost single fiber and polarized fluorescence measurements were performed under a microspectrophotometer to investigate the conformation of F-actin and the changes induced in it by heavy meromyosin and subfragment-1. Four components of polarized fluorescence were obtained by exciting the fiber with light polarized parallel and perpendicular to the long axis of the fiber and measuring the intensity of emission polarized parallel and perpendicular. From these data it was shown that F-actin in the fiber was not rigid but flexible, with a value for the elastic modulus for bending of 5.3 × 10^?17 dyn cm². The angles of absorption dipole and emission dipole of bound ε-ADP with the long axis of F-actin were both about 75 °.The binding of heavy meromyosin decreased the elastic modulus of F-actin by 30% and the angles of absorption and emission dipoles by 2.5 ° and 1.5 °, respectively. The molar ratios of bound heavy meromyosin and subfragment-1 to actin in the ghost fiber at saturation were 0.3 and 0.6, respectively, being smaller than those in solution.     

Structure of rubredoxin from Desulfovibrio vulgaris at 1.5 A resolution

The X-ray model of rubredoxin from Desulfovibrio vulgaris has been refined against 1.5 A X-ray diffraction data collected on a diffractometer. The final model comprises 395 non-hydrogen protein atoms, and 180 solvent O atoms. The final R-value for the model with calculated H atom positions included as fixed contributions is 0.098 over all reflections greater than 2 sigma I from infinity to 1.5 A. The error in co-ordinates is estimated to be 0.08 A. The solvent model was twice redetermined during the later stages of refinement and was instrumental in its success. One sequence error has been detected and corrected (Thr21----Asp). The iron-sulfur site bond angles are distorted from true tetrahedral symmetry, as found in other rubredoxin structures. A significant deviation from tetrahedral angles is seen at C alpha atoms 9, 10, 42 and 43, interior angles of the loops binding the iron atom. The planes of two aromatic groups, Tyr4 and Trp37, are nearly parallel to, and lie under, an extended system of atoms that includes the peptide bonds preceding the first cysteine residue of each cysteine loop as well as the cysteine side-chain, the iron, and the cysteine side-chain of the opposite loop, forming a previously unrecognized extended system that may function in electron transfer.     

Oriented spermatozoa in the spermatophore of the palaemonid shrimp, Macrobrachium rosenbergii

Estimates of the degree of orientation of spermatozoa within spermatophores of the freshwater shrimp, Macrobrachium rosenbergii, were made using electron micrographs of ultrathin sections cut transverse and parallel to the longitudinal axis of the spermatophores. Counts of the total number of longitudinal and non-longitudinal profiles of sperm spikes in transverse sections of spermatophores indicated that 67% of the spermatozoa were oriented with their spikes approximately perpendicular to the long axis of the spermatophore. In longitudinal sections, ~30% of the sperm spike profiles were oriented parallel to the longitudinal axis of the spermatophore, leaving ~70% of the profiles oriented in planes not parallel to the longitudinal spermatophore axis. Stereologic analyses based on the number of intersections of longitudinally sectioned sperm spike profiles per unit length of test lines placed over photographic images of ultrathin sections cut in both transverse and longitudinal planes of spermatophores gave a Saltykov approximation of 0.607, favoring the view that the spermatozoa were oriented with their spikes perpendicular to the long axis of the spermatophore. This orientation brings many of the sperm bases approximately parallel to the surface of the spermatophore, an orientation which may facilitate normal sperm-egg interaction during fertilization in this species.     

Stereoradiogrammetric technique for estimating alignment of the joints in the hand and wrist

A method and apparatus for quantitative measurement of the alignment and motion of the joints of the hand in three dimensions has been developed using stereoradiogrammetric principles. Alignment in planes of flexion-extension and radial-ulnar deviation can be determined to within 2.5°; rotation about the long axis of the metacarpals or phalanges is more difficult to determine, and can be measured to within 7°. Stereo views subtending angles in the range of 40° were found to optimize the total system accuracy.     

Polarized vibrational spectroscopy of fiber polymers: hydrogen bonding in cellulose II

Vibrational spectroscopy using polarized incident radiation can be used to determine the orientation of X-H bonds with respect to coordinates such as crystallographic axes. The adaptation of this approach to polymer fibers is described here. It requires spectral intensity to be quantified around a 180 degrees range of polarization angles and not just recorded transversely and longitudinally as is normal in fiber spectroscopy. Mercerized cellulose II is used as an example. The unit cell of the cellulose II lattice contains six distinct hydroxyl groups engaged in a complex network of hydrogen bonds that hold the cellulose chains laterally together. A formalism is described to relate the variation in intensity of each O-H stretching mode to the angle between its transition moment and the chain axis as the polarization axis is rotated with respect to the fiber axis. It was necessary to include the effect of dispersion in chain orientation around the mean and the averaging of all rotational positions of the chains round their axis. The two crystallographically distinct O(2)-H groups, which are each hydrogen-bonded to only one acceptor oxygen, show a close match in orientation between the transition moments of their stretching bands and the O-H bond axis. The two O(3)-H groups each have a three-centered hydrogen bond to O-5 and O-6 of the next residue in the same chain. The transition moments of their stretching modes lay between the acceptor oxygens. Hydrogen bonding from the O(6)-H groups is still more complex but again the transition moment of each O-H bond lay within the cone of orientations described by the acceptor oxygens, provided that one additional acceptor oxygen excluded from the published crystal structure was considered. The transition moments for the O-H stretching modes were approximately aligned with the O-H bond axes, but the alignment was not necessarily exact. This approach is not restricted to hydroxyl groups, but it is particularly useful for the elucidation of hydrogen bonding in fibrous polymers for which crystallographic data on proton positions are not available.     

Conformations of A-DNA and B-DNA in agreement with fiber X-ray and infrared dichroism

Two right handed double helices are proposed as models for DNA fibers in respectively the A and the B form. The present conformations have geometrical parameters which agree very well with fiber X-ray and the orientation of their phosphate groups is in good accordance with infrared dichroïsm measurements. Dihedral angles and complete sets of atomic coordinates are given together with stereo-views and curves of the calculated diffracted intensities. Results are compared with experimental data and with preceding DNA models.     

Thickness and elasticity of gram-negative murein sacculi measured by atomic force microscopy

Atomic force microscopy was used to measure the thickness of air-dried, collapsed murein sacculi from Escherichia coli K-12 and Pseudomonas aeruginosa PAO1. Air-dried sacculi from E. coli had a thickness of 3.0 nm, whereas those from P. aeruginosa were 1.5 nm thick. When rehydrated, the sacculi of both bacteria swelled to double their anhydrous thickness. Computer simulation of a section of a model single-layer peptidoglycan network in an aqueous solution with a Debye shielding length of 0.3 nm gave a mass distribution full width at half height of 2.4 nm, in essential agreement with these results. When E. coli sacculi were suspended over a narrow groove that had been etched into a silicon surface and the tip of the atomic force microscope used to depress and stretch the peptidoglycan, an elastic modulus of 2.5 x 10(7) N/m(2) was determined for hydrated sacculi; they were perfectly elastic, springing back to their original position when the tip was removed. Dried sacculi were more rigid with a modulus of 3 x 10(8) to 4 x 10(8) N/m(2) and at times could be broken by the atomic force microscope tip. Sacculi aligned over the groove with their long axis at right angles to the channel axis were more deformable than those with their long axis parallel to the groove axis, as would be expected if the peptidoglycan strands in the sacculus were oriented at right angles to the long cell axis of this gram-negative rod. Polar caps were not found to be more rigid structures but collapsed to the same thickness as the cylindrical portions of the sacculi. The elasticity of intact E. coli sacculi is such that, if the peptidoglycan strands are aligned in unison, the interstrand spacing should increase by 12% with every 1 atm increase in (turgor) pressure. Assuming an unstressed hydrated interstrand spacing of 1.3 nm (R. E. Burge, A. G. Fowler, and D. A. Reaveley, J. Mol. Biol. 117:927-953, 1977) and an internal turgor pressure of 3 to 5 atm (or 304 to 507 kPa) (A. L. Koch, Adv. Microbial Physiol. 24:301-366, 1983), the natural interstrand spacing in cells would be 1.6 to 2.0 nm. Clearly, if large macromolecules of a diameter greater than these spacings are secreted through this layer, the local ordering of the peptidoglycan must somehow be disrupted.     

Molecular dynamics simulations of Alzheimer's beta-amyloid protofilaments

Filamentous amyloid aggregates are central to the pathology of Alzheimer's disease. We use all-atom molecular dynamics (MD) simulations with explicit solvent and multiple force fields to probe the structural stability and the conformational dynamics of several models of Alzheimer's beta-amyloid fibril structures, for both wild-type and mutated amino acid sequences. The structural models are based on recent solid state NMR data. In these models, the peptides form in-register parallel beta-sheets along the fibril axis, with dimers of two U-shaped peptides located in layers normal to the fibril axis. Four different topologies are explored for stacking the beta-strand regions against each other to form a hydrophobic core. Our MD results suggest that all four NMR-based models are structurally stable, and we find good agreement with dihedral angles estimated from solid-state NMR experiments. Asp23 and Lys28 form buried salt-bridges, resulting in an alternating arrangement of the negatively and positively charged residues along the fibril axis that is reminiscent of a one-dimensional ionic crystal. Interior water molecules are solvating the buried salt-bridges. Based on data from NMR measurements and MD simulations of short amyloid fibrils, we constructed structural models of long fibrils. Calculated X-ray fiber diffraction patterns show the characteristics of packed beta-sheets seen in experiments, and suggest new experiments that could discriminate between various fibril topologies.     

The mechanism of cellular orientation during early cartilage formation in the chick limb and regenerating amphibian limb

A characteristic feature of early cartilage formation is that as the cells at the centre differentiate into chondroblasts they become flattened at right angles to the long axis of the cell mass, whereas the cells in the region of the future perichondrium become flattened circumferentially. On the basis of EM observation a simple model is proposed which is based on matrix secretion flattening the cells.     

Microtubules and control of insect egg shape

This study evidence for tension transmission by microtubules and desmosomes in the follicular epithelium during anisometric growth of certain insect eggs. Most insect oocytes, and the follicles which surround them, grow anisometrically as they assume shapes which approximate to those of long prolate spheroids. Surface growth is most rapid in directions which parallel the polar axis of an oocyte and slowest in circumferential directions at right angles to this axis. The longitudinal axes of microtubule bundles in follicle cells of the gall midge Heteropeza and the cockroach Periplaneta are oriented circumferentially with respect to the surfaces of developing eggs and at right angles to the polar axes of eggs. At cell boundaries, the tubules appear to be attached to spot desmosomes. It is suggested that microtubules and desmosomes form a mechanical continuum throughout a follicular epithelium which transmits tensile forces around the circumference of a growing egg. Follicular resistance to circumferential expansion may be largely responsible for defining the elongate form of insect eggs.