Статті в журналах: "Filament packings"

1

Hall, Douglas M., and Gregory M. Grason. "How geometric frustration shapes twisted fibres, inside and out: competing morphologies of chiral filament assembly." Interface Focus 7, no. 4 (June 16, 2017): 20160140. http://dx.doi.org/10.1098/rsfs.2016.0140.

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Chirality frustrates and shapes the assembly of flexible filaments in rope-like, twisted bundles and fibres by introducing gradients of both filament shape (i.e. curvature) and packing throughout the structure. Previous models of chiral filament bundle formation have shown that this frustration gives rise to several distinct morphological responses, including self-limiting bundle widths, anisotropic domain (tape-like) formation and topological defects in the lateral inter-filament order. In this paper, we employ a combination of continuum elasticity theory and discrete filament bundle simulations to explore how these distinct morphological responses compete in the broader phase diagram of chiral filament assembly. We show that the most generic model of bundle formation exhibits at least four classes of equilibrium structure—finite-width, twisted bundles with isotropic and anisotropic shapes, with and without topological defects, as well as bulk phases of untwisted, columnar assembly (i.e. ‘frustration escape’). These competing equilibrium morphologies are selected by only a relatively small number of parameters describing filament assembly: bundle surface energy, preferred chiral twist and stiffness of chiral filament interactions, and mechanical stiffness of filaments and their lateral interactions. Discrete filament bundle simulations test and verify continuum theory predictions for dependence of bundle structure (shape, size and packing defects of two-dimensional cross section) on these key parameters.

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2

Madden, T. L., and J. Herzfeld. "Crowding-induced organization of cytoskeletal elements: II. Dissolution of spontaneously formed filament bundles by capping proteins." Journal of Cell Biology 126, no. 1 (July 1, 1994): 169–74. http://dx.doi.org/10.1083/jcb.126.1.169.

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Through calculations of molecular packing constraints in crowded solutions, we have previously shown that dispersions of filament forming proteins and soluble proteins can be unstable at physiological concentrations, such that tight bundles of filaments are formed spontaneously, in the absence of any accessory binding proteins. Here we consider the modulation of this phenomenon by capping proteins. The theory predicts that, by shortening the average filament length, capping alleviates the packing problem. As a result, the dispersed isotropic solution is stable over an expanded range of compositions.

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3

Riley, Danny A., James L. W. Bain, Joyce L. Thompson, Robert H. Fitts, Jeffrey J. Widrick, Scott W. Trappe, Todd A. Trappe, and David L. Costill. "Thin filament diversity and physiological properties of fast and slow fiber types in astronaut leg muscles." Journal of Applied Physiology 92, no. 2 (February 1, 2002): 817–25. http://dx.doi.org/10.1152/japplphysiol.00717.2001.

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Slow type I fibers in soleus and fast white (IIa/IIx, IIx), fast red (IIa), and slow red (I) fibers in gastrocnemius were examined electron microscopically and physiologically from pre- and postflight biopsies of four astronauts from the 17-day, Life and Microgravity Sciences Spacelab Shuttle Transport System-78 mission. At 2.5-μm sarcomere length, thick filament density is ∼1,012 filaments/μm2 in all fiber types and unchanged by spaceflight. In preflight aldehyde-fixed biopsies, gastrocnemius fibers possess higher percentages (∼23%) of short thin filaments than soleus (9%). In type I fibers, spaceflight increases short, thin filament content from 9 to 24% in soleus and from 26 to 31% in gastrocnemius. Thick and thin filament spacing is wider at short sarcomere lengths. The Z-band lattice is also expanded, except for soleus type I fibers with presumably stiffer Z bands. Thin filament packing density correlates directly with specific tension for gastrocnemius fibers but not soleus. Thin filament density is inversely related to shortening velocity in all fibers. Thin filament structural variation contributes to the functional diversity of normal and spaceflight-unloaded muscles.

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4

Drenckhahn, D., K. Engel, D. Höfer, C. Merte, L. Tilney, and M. Tilney. "Three different actin filament assemblies occur in every hair cell: each contains a specific actin crosslinking protein." Journal of Cell Biology 112, no. 4 (February 15, 1991): 641–51. http://dx.doi.org/10.1083/jcb.112.4.641.

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The apex of hair cells of the chicken auditory organ contains three different kinds of assemblies of actin filaments in close spatial proximity. These are (a) paracrystals of actin filaments with identical polarity in stereocilia, (b) a dense gellike meshwork of actin filaments forming the cuticular plate, and (c) a bundle of parallel actin filaments with mixed polarities that constitute the circumferential filament belt attached to the cytoplasmic aspect of the zonula adhaerens (ZA). Each different supramolecular assembly of actin filaments contains a specific actin filament cross-linking protein which is unique to that particular assembly. Thus fimbrin appears to be responsible for paracrystallin packing of actin filaments in stereocillia; an isoform of spectrin resides in the cuticular plate where it forms the whisker-like crossbridges, and alpha actinin is the actin crosslinking protein of the circumferential ZA bundle. Tropomyosin, which stabilizes actin filaments, is present in all the actin filament assemblies except for the stereocilia. Another striking finding was that myosin appears to be absent from the ZA ring and cuticular plate of hair cells although present in the ZA ring of supporting cells. The abundance of myosin in the ZA ring of the surrounding supporting cells means that it may be important in forming a supporting tensile cellular framework in which the hair cells are inserted.

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5

Skubiszak, Ludmila, and Leszek Kowalczyk. "Myosin molecule packing within the vertebrate skeletal muscle thick filaments. A complete bipolar model." Acta Biochimica Polonica 49, no. 4 (December 31, 2002): 829–40. http://dx.doi.org/10.18388/abp.2002_3743.

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Computer modelling related to the real dimensions of both the whole filament and the myosin molecule subfragments has revealed two alternative modes for myosin molecule packing which lead to the head disposition similar to that observed by EM on the surface of the cross-bridge zone of the relaxed vertebrate skeletal muscle thick filaments. One of the modes has been known for three decades and is usually incorporated into the so-called three-stranded model. The new mode differs from the former one in two aspects: (1) myosin heads are grouped into asymmetrical cross-bridge crowns instead of symmetrical ones; (2) not the whole myosin tail, but only a 43-nm C-terminus of each of them is straightened and near-parallel to the filament axis, the rest of the tail is twisted. Concurrent exploration of these alternative modes has revealed their influence on the filament features. The parameter values for the filament models as well as for the building units depicting the myosin molecule subfragments are verified by experimental data found in the literature. On the basis of the new mode for myosin molecule packing a complete bipolar structure of the thick filament is created.

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6

Gotow, T., T. Tanaka, Y. Nakamura, and M. Takeda. "Dephosphorylation of the largest neurofilament subunit protein influences the structure of crossbridges in reassembled neurofilaments." Journal of Cell Science 107, no. 7 (July 1, 1994): 1949–57. http://dx.doi.org/10.1242/jcs.107.7.1949.

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Phosphorylation-dependent change in electrophoretic mobility is the most unique characteristic of NF-H, the largest molecular mass subunit of the neurofilament. We dephosphorylated NF-H using Escherichia coli alkaline phosphatase, then reassembled it into neurofilaments with NF-M and NF-L, and into NF-H filaments with NF-H alone. We compared these dephosphorylated filaments with control: projections by low-angle rotary-shadow, crossbridges by quick-freeze deep-etch, and core filament packing density by thin-section electron microscopy. Projections in the dephosphorylated filaments were basically similar in structure to those in control, although there was a tendency for them to be wider and less dense, especially in NF-H filaments. Dephosphorylated filaments were still able to form crossbridges between core filaments, but their crossbridges were significantly wider, less dense, more branched and more irregular than crossbridges in control, and core filaments were more densely packed. These structural differences may be brought about by the removal of phosphate groups from NF-H tail and consequent reduction of electrostatic repulsion between adjacent crossbridges extending from the same core filament. The results indicate that phosphorylation of NF-H is necessary for forming well developed crossbridges, straight and at constant intervals, like those of in vivo axonal neurofilaments.

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7

Trybus, K. M., and S. Lowey. "Assembly of smooth muscle myosin minifilaments: effects of phosphorylation and nucleotide binding." Journal of Cell Biology 105, no. 6 (December 1, 1987): 3007–19. http://dx.doi.org/10.1083/jcb.105.6.3007.

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Small bipolar filaments, or "minifilaments," are formed when smooth muscle myosin is dialyzed against low ionic strength pyrophosphate or citrate/Tris buffers. Unlike synthetic filaments formed at approximately physiological ionic conditions, minifilaments are homogeneous as indicated by their hypersharp boundary during sedimentation velocity. Electron microscopy and hydrodynamic techniques were used to show that 20-22S smooth muscle myosin minifilaments are 380 nm long and composed of 12-14 molecules. By varying solvents, a continuum of different size polymers in the range of 15-30S could be obtained. Skeletal muscle myosin, in contrast, preferentially forms a stable 32S minifilament (Reisler, E., P. Cheung, and N. Borochov. 1986. Biophys. J. 49:335-342), suggesting underlying differences in the assembly properties of the two myosins. Addition of salt to the smooth muscle myosin minifilaments caused unidirectional growth into a longer "side-polar" type of filament, whereas bipolar filaments were consistently formed by skeletal muscle myosin. As with synthetic filaments, addition of 1 mM MgATP caused dephosphorylated minifilaments to dissociate to a mixture of folded monomers and dimers. Phosphorylation of the regulatory light chain prevented disassembly by nucleotide, even though it had no detectable effect on the structure of the minifilament. These results suggest that differences in filament stability as a result of phosphorylation are due largely to conformational changes occurring in the myosin head, and are not due to differences in filament packing.

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8

Rovner, Arthur S., Patricia M. Fagnant, Susan Lowey, and Kathleen M. Trybus. "The carboxyl-terminal isoforms of smooth muscle myosin heavy chain determine thick filament assembly properties." Journal of Cell Biology 156, no. 1 (January 7, 2002): 113–24. http://dx.doi.org/10.1083/jcb.200107131.

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The alternatively spliced SM1 and SM2 smooth muscle myosin heavy chains differ at their respective carboxyl termini by 43 versus 9 unique amino acids. To determine whether these tailpieces affect filament assembly, SM1 and SM2 myosins, the rod region of these myosin isoforms, and a rod with no tailpiece (tailless), were expressed in Sf 9 cells. Paracrystals formed from SM1 and SM2 rod fragments showed different modes of molecular packing, indicating that the tailpieces can influence filament structure. The SM2 rod was less able to assemble into stable filaments than either SM1 or the tailless rods. Expressed full-length SM1 and SM2 myosins showed solubility differences comparable to the rods, establishing the validity of the latter as a model for filament assembly. Formation of homodimers of SM1 and SM2 rods was favored over the heterodimer in cells coinfected with both viruses, compared with mixtures of the two heavy chains renatured in vitro. These results demonstrate for the first time that the smooth muscle myosin tailpieces differentially affect filament assembly, and suggest that homogeneous thick filaments containing SM1 or SM2 myosin could serve distinct functions within smooth muscle cells.

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9

Sazzed, Salim, Peter Scheible, Jing He, and Willy Wriggers. "Spaghetti Tracer: A Framework for Tracing Semiregular Filamentous Densities in 3D Tomograms." Biomolecules 12, no. 8 (July 23, 2022): 1022. http://dx.doi.org/10.3390/biom12081022.

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Within cells, cytoskeletal filaments are often arranged into loosely aligned bundles. These fibrous bundles are dense enough to exhibit a certain regularity and mean direction, however, their packing is not sufficient to impose a symmetry between—or specific shape on—individual filaments. This intermediate regularity is computationally difficult to handle because individual filaments have a certain directional freedom, however, the filament densities are not well segmented from each other (especially in the presence of noise, such as in cryo-electron tomography). In this paper, we develop a dynamic programming-based framework, Spaghetti Tracer, to characterizing the structural arrangement of filaments in the challenging 3D maps of subcellular components. Assuming that the tomogram can be rotated such that the filaments are oriented in a mean direction, the proposed framework first identifies local seed points for candidate filament segments, which are then grown from the seeds using a dynamic programming algorithm. We validate various algorithmic variations of our framework on simulated tomograms that closely mimic the noise and appearance of experimental maps. As we know the ground truth in the simulated tomograms, the statistical analysis consisting of precision, recall, and F1 scores allows us to optimize the performance of this new approach. We find that a bipyramidal accumulation scheme for path density is superior to straight-line accumulation. In addition, the multiplication of forward and backward path densities provides for an efficient filter that lifts the filament density above the noise level. Resulting from our tests is a robust method that can be expected to perform well (F1 scores 0.86–0.95) under experimental noise conditions.

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10

Hasegawa, Kazuya, Ichiro Yamashita, Yuko Mimori-Kiyosue, Ferenc Vonderviszt, and Keiichi Namba. "Molecular Mechanisms of Self-Assembly and Polymorphic Switching of the Bacterial Flagellum." Microscopy and Microanalysis 5, S2 (August 1999): 1034–35. http://dx.doi.org/10.1017/s1431927600018493.

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Bacterial flagellum is a helical filament by means of which bacteria swim. Each filament rotated by the motor at its base works as a screw that propels the cell, but it is not simply a rigid propeller. The filament is normally in a left-handed supercoiled form and several of them form a bundle when bacteria swim. Upon quick reversal of the motor rotation, which occurs every few seconds, the filament switches into a right-handed supercoil, making the filament bundle fall apart and enabling the cell to tumble for its tactic behavior. The filament is a tubular structure formed by helical assembly of single protein, flagellin, whose molecular mass is 51.5 kDa in the case of Salmonella typhimurium, which we study. The supercoiling of the filament is thought to involve two distinct subunit conformations and/or packing, whose mechanism is interesting in terms of conformational distinctness and adaptability of flagellin.To understand the mechanisms of self-assembly and polymorphism of the filament, electron cryomicroscopy (EM) and X-ray fiber diffraction have been used to analyze the structures of two straight filaments with distinct helical symmetries.

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11

Shimizu, T., J. E. Dennis, T. Masaki, and D. A. Fischman. "Axial arrangement of the myosin rod in vertebrate thick filaments: immunoelectron microscopy with a monoclonal antibody to light meromyosin." Journal of Cell Biology 101, no. 3 (September 1, 1985): 1115–23. http://dx.doi.org/10.1083/jcb.101.3.1115.

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A monoclonal antibody, MF20, which has been shown previously to bind the myosin heavy chain of vertebrate striated muscle, has been proven to bind the light meromyosin (LMM) fragment by solid phase radioimmune assay with alpha-chymotryptic digests of purified myosin. Epitope mapping by electron microscopy of rotary-shadowed, myosin-antibody complexes has localized the antibody binding site to LMM at a point approximately 92 nm from the C-terminus of the myosin heavy chain. Since this epitope in native thick filaments is accessible to monoclonal antibodies, we used this antibody as a high affinity ligand to analyze the packing of LMM along the backbone of the thick filament. By immunofluorescence microscopy, MF20 was shown to bind along the entire A-band of chicken pectoralis myofibrils, although the epitope accessibility was greater near the ends than at the center of the A-bands. Thin-section, transmission electron microscopy of myofibrils decorated with MF20 revealed 50 regularly spaced, cross-striations in each half A-band, with a repeat distance of approximately 13 nm. These were numbered consecutively, 1-50, from the A-band to the last stripe, approximately 68 nm from the filament tips. These same striations could be visualized by negative staining of native thick filaments labeled with MF20. All 50 striations were of a consecutive, uninterrupted repeat which approximated the 14-15-nm axial translation of cross-bridges. Each half M-region contained five MF20 striations (approximately 13 nm apart) with a distance between stripes 1 and 1', on each half of the bare zone, of approximately 18 nm. This is compatible with a packing model with full, antiparallel overlap of the myosin rods in the bare zone region. Differences in the spacings measured with negatively stained myofilaments and thin-sectioned myofibrils have been shown to arise from specimen shrinkage in the fixed and embedded preparations. These observations provide strong support for Huxley's original proposal for myosin packing in thick filaments of vertebrate muscle (Huxley, H. E., 1963, J. Mol. Biol., 7:281-308) and, for the first time, directly demonstrate that the 14-15-nm axial translation of LMM in the thick filament backbone corresponds to the cross-bridge repeat detected with x-ray diffraction of living muscle.

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12

Xiong, Qinsi, Ziye Liu, and Wei Han. "Sequence-Dependent Nanofiber Structures of Phenylalanine and Isoleucine Tripeptides." International Journal of Molecular Sciences 21, no. 22 (November 10, 2020): 8431. http://dx.doi.org/10.3390/ijms21228431.

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The molecular design of short peptides to achieve a tailor-made functional architecture has attracted attention during the past decade but remains challenging as a result of insufficient understanding of the relationship between peptide sequence and assembled supramolecular structures. We report a hybrid-resolution model to computationally explore the sequence–structure relationship of self-assembly for tripeptides containing only phenylalanine and isoleucine. We found that all these tripeptides have a tendency to assemble into nanofibers composed of laterally associated filaments. Molecular arrangements within the assemblies are diverse and vary depending on the sequences. This structural diversity originates from (1) distinct conformations of peptide building blocks that lead to different surface geometries of the filaments and (2) unique sidechain arrangements at the filament interfaces for each sequence. Many conformations are available for tripeptides in solution, but only an extended β-strand and another resembling a right-handed turn are observed in assemblies. It was found that the sequence dependence of these conformations and the packing of resulting filaments are determined by multiple competing noncovalent forces, with hydrophobic interactions involving Phe being particularly important. The sequence pattern for each type of assembly conformation and packing has been identified. These results highlight the importance of the interplay between conformation, molecular packing, and sequences for determining detailed nanostructures of peptides and provide a detailed insight to support a more precise design of peptide-based nanomaterials.

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13

Kouklis, P. D., T. Papamarcaki, A. Merdes, and S. D. Georgatos. "A potential role for the COOH-terminal domain in the lateral packing of type III intermediate filaments." Journal of Cell Biology 114, no. 4 (August 15, 1991): 773–86. http://dx.doi.org/10.1083/jcb.114.4.773.

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To identify sites of self-association in type III intermediate filament (IF) proteins, we have taken an "anti-idiotypic antibody" approach. A mAb (anti-Ct), recognizing a similar feature near the end of the rod domain of vimentin, desmin, and peripherin (epsilon site or epsilon epitope), was characterized. Anti-idiotypic antibodies, generated by immunizing rabbits with purified anti-Ct, recognize a site (presumably "complementary" to the epsilon epitope) common among vimentin, desmin, and peripherin (beta site or beta epitope). The beta epitope is represented in a synthetic peptide (PII) modeled after the 30 COOH-terminal residues of peripherin, as seen by comparative immunoblotting assays. Consistent with the idea of an association between the epsilon and the beta site, PII binds in vitro to intact IF proteins and fragments containing the epsilon epitope, but not to IF proteins that do not react with anti-Ct. Microinjection experiments conducted in vivo and filament reconstitution assays carried out in vitro further demonstrate that "uncoupling" of this site-specific association (by competition with PII or anti-Ct) interferes with normal IF architecture, resulting in the formation of filaments and filament bundles with diameters much greater than that of the normal IFs. These thick fibers are very similar to the ones observed previously when a derivative of desmin missing 27 COOH-terminal residues was assembled in vitro (Kaufmann, E., K. Weber, and N. Geisler. 1985. J. Mol. Biol. 185:733-742). As a molecular explanation, we propose here that the epsilon and the beta sites of type III IF proteins are "complementary" and associate during filament assembly. As a result of this association, we further postulate the formation of a surface-exposed "loop" or "hairpin" structure that may sterically prevent inappropriate filament-filament aggregation and regulate filament thickness.

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14

Skubiszak, Ludmila, and Leszek Kowalczyk. "The vertebrate skeletal muscle thick filaments are not three-stranded. Reinterpretation of some experimental data." Acta Biochimica Polonica 49, no. 4 (December 31, 2002): 841–53. http://dx.doi.org/10.18388/abp.2002_3744.

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Computer simulation of mass distribution within the model and Fourier transforms of images depicting mass distribution are explored for verification of two alternative modes of the myosin molecule arrangement within the vertebrate skeletal muscle thick filaments. The model well depicting the complete bipolar structure of the thick filament and revealing a true threefold-rotational symmetry is a tube covered by two helices with a pitch of 2 x 43 nm due to arrangement of the myosin tails along a helical path and grouping of all myosin heads in the crowns rotated by 240 degrees and each containing three cross-bridges separated by 0 degrees, 120 degrees, and 180 degrees. The cross-bridge crown parameters are verified by EM images as well as by optical and low-angle X-ray diffraction patterns found in the literature. The myosin tail arrangement, at which the C-terminus of about 43-nm length is near-parallel to the filament axis and the rest of the tail is quite strongly twisted around, is verified by the high-angle X-ray diffraction patterns. A consequence of the new packing is a new way of movement of the myosin cross-bridges, namely, not by bending in the hinge domains, but by unwrapping from the thick filament surface towards the thin filaments along a helical path.

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15

Hervas, Ruben, Michael J. Rau, Younshim Park, Wenjuan Zhang, Alexey G. Murzin, James A. J. Fitzpatrick, Sjors H. W. Scheres, and Kausik Si. "Cryo-EM structure of a neuronal functional amyloid implicated in memory persistence in Drosophila." Science 367, no. 6483 (March 12, 2020): 1230–34. http://dx.doi.org/10.1126/science.aba3526.

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How long-lived memories withstand molecular turnover is a fundamental question. Aggregates of a prion-like RNA-binding protein, cytoplasmic polyadenylation element–binding (CPEB) protein, is a putative substrate of long-lasting memories. We isolated aggregated Drosophila CPEB, Orb2, from adult heads and determined its activity and atomic structure, at 2.6-angstrom resolution, using cryo–electron microscopy. Orb2 formed ~75-nanometer-long threefold-symmetric amyloid filaments. Filament formation transformed Orb2 from a translation repressor to an activator and “seed” for further translationally active aggregation. The 31–amino acid protofilament core adopted a cross-β unit with a single hydrophilic hairpin stabilized through interdigitated glutamine packing. Unlike the hydrophobic core of pathogenic amyloids, the hydrophilic core of Orb2 filaments suggests how some neuronal amyloids could be a stable yet regulatable substrate of memory.

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16

Prasath, S. Ganga, Joel Marthelot, Rama Govindarajan, and Narayanan Menon. "Shapes of a filament on the surface of a bubble." Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 477, no. 2253 (September 2021): 20210353. http://dx.doi.org/10.1098/rspa.2021.0353.

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The shape assumed by a slender elastic structure is a function both of the geometry of the space in which it exists and the forces it experiences. We explore, by experiments and theoretical analysis, the morphological phase space of a filament confined to the surface of a spherical bubble. The morphology is controlled by varying bending stiffness and weight of the filament, and its length relative to the bubble radius. When the dominant considerations are the geometry of confinement and elastic energy, the filament lies along a geodesic and when gravitational energy becomes significant, a bifurcation occurs, with a part of the filament occupying a longitude and the rest along a curve approximated by a latitude. Far beyond the transition, when the filament is much longer than the diameter, it coils around the selected latitudinal region. A simple model with filament shape as a composite of two arcs captures the transition well. For better quantitative agreement with the subcritical nature of bifurcation, we study the morphology by numerical energy minimization. Our analysis of the filament’s morphological space spanned by one geometric parameter, and one parameter that compares elastic energy with body forces, may provide guidance for packing slender structures on complex surfaces.

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17

Tilney, LG, Y. Fukui, and DJ DeRosier. "Movement of the actin filament bundle in Mytilus sperm: a new mechanism is proposed." Journal of Cell Biology 104, no. 4 (April 1, 1987): 981–93. http://dx.doi.org/10.1083/jcb.104.4.981.

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An actin filament bundle approximately 2-5 microns in length is present in the sperm of the blue mussel, Mytilus. In unfired sperm this bundle extends from the midpiece through a canal in the center of the nucleus to terminate on the membrane limiting the inside of the cone-shaped acrosomal vacuole. The bundle is composed of 45-65 actin filaments which are hexagonally packed and regularly cross-bridged together to form an actin paracrystal so well ordered that it has six nearly equal faces. Upon induction of the acrosomal reaction, a needle-like process is formed in a few seconds. Within this process is the actin filament bundle which appears unchanged in filament number and packing as determined by optical diffraction methods. Using fluorescein-conjugated phalloidin we were able to establish that the bundle does not change length but instead is projected anteriorly out of the midpiece and nuclear canal like an arrow. Existing mechanisms to explain this extension cannot apply. Specifically, the bundle does not increase in length (no polymerization), does not change its organization (no change in actin twist), does not change filament number (no filament sliding), and cannot move by myosin (wrong polarity). Thus we are forced to look elsewhere for a mechanism and have postulated that at least a component of this movement, or cell elongation, is the interaction of the actin filament bundle with the plasma membrane.

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18

Meyer, R. K., and U. Aebi. "Bundling of actin filaments by alpha-actinin depends on its molecular length." Journal of Cell Biology 110, no. 6 (June 1, 1990): 2013–24. http://dx.doi.org/10.1083/jcb.110.6.2013.

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Cross-linking of actin filaments (F-actin) into bundles and networks was investigated with three different isoforms of the dumbbell-shaped alpha-actinin homodimer under identical reaction conditions. These were isolated from chicken gizzard smooth muscle, Acanthamoeba, and Dictyostelium, respectively. Examination in the electron microscope revealed that each isoform was able to cross-link F-actin into networks. In addition, F-actin bundles were obtained with chicken gizzard and Acanthamoeba alpha-actinin, but not Dictyostelium alpha-actinin under conditions where actin by itself polymerized into disperse filaments. This F-actin bundle formation critically depended on the proper molar ratio of alpha-actinin to actin, and hence F-actin bundles immediately disappeared when free alpha-actinin was withdrawn from the surrounding medium. The apparent dissociation constants (Kds) at half-saturation of the actin binding sites were 0.4 microM at 22 degrees C and 1.2 microM at 37 degrees C for chicken gizzard, and 2.7 microM at 22 degrees C for both Acanthamoeba and Dictyostelium alpha-actinin. Chicken gizzard and Dictyostelium alpha-actinin predominantly cross-linked actin filaments in an antiparallel fashion, whereas Acanthamoeba alpha-actinin cross-linked actin filaments preferentially in a parallel fashion. The average molecular length of free alpha-actinin was 37 nm for glycerol-sprayed/rotary metal-shadowed and 35 nm for negatively stained chicken gizzard; 46 and 44 nm, respectively, for Acanthamoeba; and 34 and 31 nm, respectively, for Dictyostelium alpha-actinin. In negatively stained preparations we also evaluated the average molecular length of alpha-actinin when bound to actin filaments: 36 nm for chicken gizzard and 35 nm for Acanthamoeba alpha-actinin, a molecular length roughly coinciding with the crossover repeat of the two-stranded F-actin helix (i.e., 36 nm), but only 28 nm for Dictyostelium alpha-actinin. Furthermore, the minimal spacing between cross-linking alpha-actinin molecules along actin filaments was close to 36 nm for both smooth muscle and Acanthamoeba alpha-actinin, but only 31 nm for Dictyostelium alpha-actinin. This observation suggests that the molecular length of the alpha-actinin homodimer may determine its spacing along the actin filament, and hence F-actin bundle formation may require "tight" (i.e., one molecule after the other) and "untwisted" (i.e., the long axis of the molecule being parallel to the actin filament axis) packing of alpha-actinin molecules along the actin filaments.

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19

Coulombe, P. A., and E. Fuchs. "Elucidating the early stages of keratin filament assembly." Journal of Cell Biology 111, no. 1 (July 1, 1990): 153–69. http://dx.doi.org/10.1083/jcb.111.1.153.

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Because of extraordinarily tight coiled-coil associations of type I and type II keratins, the composition and structure of keratin subunits has been difficult to determine. We report here the use of novel genetic and biochemical methods to explore the early stages of keratin filament assembly. Using bacterially expressed humans K5 and K14, we show that remarkably, these keratins behave as 1:1 complexes even in 9 M urea and in the presence of a reducing agent. Gel filtration chromatography and chemical cross-linking were used to identify heterodimers and heterotetramers as the most stable building blocks of keratin filament assembly. EM suggested that the dimer consists of a coiled-coil of K5 and K14 aligned in register and in parallel fashion, and the tetramer consists of two dimers in antiparallel fashion, without polarity. In 4 M urea, both end-to-end and lateral packing of tetramers occurred, leading to a variety of larger heteromeric complexes. The coexistence of multiple, higher-ordered associations under strongly denaturing conditions suggests that there may not be a serial sequence of events leading to the assembly of keratin intermediate filaments, but rather a number of associations may take place in parallel.

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20

Fraser, R. D. Bruce, and David A. D. Parry. "Molecular packing in the feather keratin filament." Journal of Structural Biology 162, no. 1 (April 2008): 1–13. http://dx.doi.org/10.1016/j.jsb.2008.01.011.

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21

Pasternak, C., P. F. Flicker, S. Ravid, and J. A. Spudich. "Intermolecular versus intramolecular interactions of Dictyostelium myosin: possible regulation by heavy chain phosphorylation." Journal of Cell Biology 109, no. 1 (July 1, 1989): 203–10. http://dx.doi.org/10.1083/jcb.109.1.203.

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Dictyostelium myosin has been examined under conditions that reveal intramolecular and intermolecular interactions that may be important in the process of assembly and its regulation. Rotary shadowed myosin molecules exhibit primarily two configurations under these conditions: straight parallel dimers and folded monomers. All of the monomers bend in a specific region of the 1860-A-long tail that is 1200 A from the head-tail junction. Molecules in parallel dimers are staggered by 140 A, which is a periodicity in the packing of myosin molecules originally observed in native thick filaments of muscle. The most common region for interaction in the dimers is a segment of the tail about 200-A-long, extending from 900 to 1100 A from the head-tail junction. Parallel dimers form tetramers by way of antiparallel interactions in their tail regions with overlaps in multiples of 140 A. The folded configuration of the myosin molecules is promoted by phosphorylation of the heavy chain by Dictyostelium myosin heavy chain kinase. It appears that the bent monomers are excluded from filaments formed upon addition of salt while the dimeric molecules assemble. These results may provide the structural basis for primary steps in myosin filament assembly and its regulation by heavy chain phosphorylation.

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22

Bruss, I. R., and G. M. Grason. "Non-Euclidean geometry of twisted filament bundle packing." Proceedings of the National Academy of Sciences 109, no. 27 (June 18, 2012): 10781–86. http://dx.doi.org/10.1073/pnas.1205606109.

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23

Ortega Varela de Seijas, Manuel, Andreas Bardenhagen, Thomas Rohr, and Enrico Stoll. "Indirect Induction Sintering of Metal Parts Produced through Material Extrusion Additive Manufacturing." Materials 16, no. 2 (January 16, 2023): 885. http://dx.doi.org/10.3390/ma16020885.

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Avoiding loose powders and resins, material extrusion additive manufacturing is a powerful technique to produce near-net shape parts, being a cheap and safe alternative for developing complex industrial-grade products. Filaments embedded with a high packing density of metallic or ceramic granules are being increasingly used, resulting in almost fully dense parts, whereby geometries are shaped, debinded and sintered sequentially until the completion of the part. Traditionally, “brown” debinded geometries are transported to conventional furnaces to densify the powder compacts, requiring careful tailoring of the heating profiles and sintering environment. This approach is decoupled and often involves time-consuming post-processing, whereby after the completion of the shaping and debinding steps, the parts need to be transported to a sintering furnace. Here, it is shown that sintering via indirect induction heating of a highly filled commercially available filament embedded with stainless steel 316L powder can be an effective route to densify Fused Filament Fabricated (FFF) parts. The results show that densities of 99.8% can be reached with very short soaking times, representing a significant improvement compared to prior methods. A hybrid machine is proposed, whereby a custom-built machine is integrated with an induction heater to combine FFF with local indirect induction sintering. Sintering in situ, without the need for part transportation, simplifies the processing of metal parts produced through material extrusion additive manufacturing.

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24

James, Veronica J., та Yoshiyuki Amemiya. "Intermediate Filament Packing in α-Keratin of Echidna Quill". Textile Research Journal 68, № 3 (березень 1998): 167–70. http://dx.doi.org/10.1177/004051759806800303.

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25

Fischman, D. A., J. E. Dennis, T. Obinata, and H. Takano-Ohmuro. "Distribution of c-protein isoforms in sarcomeres of developing chick skeletal muscle." Proceedings, annual meeting, Electron Microscopy Society of America 46 (1988): 226–27. http://dx.doi.org/10.1017/s042482010010319x.

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C-protein is a 150 kDa protein found within the A bands of all vertebrate cross-striated muscles. By immunoelectron microscopy, it has been demonstrated that C-protein is distributed along a series of 7-9 transverse stripes in the medial, cross-bridge bearing zone of each A band. This zone is now termed the C-zone of the sarcomere. Interest in this protein has been sparked by its striking distribution in the sarcomere: the transverse repeat between C-protein stripes is 43 nm, almost exactly 3 times the 14.3 nm axial repeat of myosin cross-bridges along the thick filaments. The precise packing of C-protein in the thick filament is still unknown. It is the only sarcomeric protein which binds to both myosin and actin, and the actin-binding is Ca-sensitive. In cardiac and slow, but not fast, skeletal muscles C-protein is phosphorylated. Amino acid composition suggests a protein of little or no αhelical content. Variant forms (isoforms) of C-protein have been identified in cardiac, slow and embryonic muscles.

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26

Krey, Jocelyn F., Evan S. Krystofiak, Rachel A. Dumont, Sarath Vijayakumar, Dongseok Choi, Francisco Rivero, Bechara Kachar, Sherri M. Jones, and Peter G. Barr-Gillespie. "Plastin 1 widens stereocilia by transforming actin filament packing from hexagonal to liquid." Journal of Cell Biology 215, no. 4 (November 3, 2016): 467–82. http://dx.doi.org/10.1083/jcb.201606036.

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With their essential role in inner ear function, stereocilia of sensory hair cells demonstrate the importance of cellular actin protrusions. Actin packing in stereocilia is mediated by cross-linkers of the plastin, fascin, and espin families. Although mice lacking espin (ESPN) have no vestibular or auditory function, we found that mice that either lacked plastin 1 (PLS1) or had nonfunctional fascin 2 (FSCN2) had reduced inner ear function, with double-mutant mice most strongly affected. Targeted mass spectrometry indicated that PLS1 was the most abundant cross-linker in vestibular stereocilia and the second most abundant protein overall; ESPN only accounted for ∼15% of the total cross-linkers in bundles. Mouse utricle stereocilia lacking PLS1 were shorter and thinner than wild-type stereocilia. Surprisingly, although wild-type stereocilia had random liquid packing of their actin filaments, stereocilia lacking PLS1 had orderly hexagonal packing. Although all three cross-linkers are required for stereocilia structure and function, PLS1 biases actin toward liquid packing, which allows stereocilia to grow to a greater diameter.

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27

Maggioni, Francesca, and Renzo L. Ricca. "Writhing and coiling of closed filaments." Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 462, no. 2074 (May 16, 2006): 3151–66. http://dx.doi.org/10.1098/rspa.2006.1719.

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The kinematics of writhing and coiling of circular filaments is here analysed by new equations that govern the evolution of curves generated by epicycloids and hypocycloids. We show how efficiency of coil formation and compaction depend on writhing rates, relative bending, torsion and mean twist energy. We demonstrate that for coiling formation hypocycloid evolution achieves higher writhing rates, but in terms of deformation energy, the epicycloid evolution is much more effective. We also show how the occurrence and multiple appearance of inflexional configurations determine coil formation. Compaction and packing rate are also briefly examined. These results are fundamental and provide useful information for physical applications and for modelling natural phenomena, including relaxation of magnetic fields in the solar corona, magnetic dynamos in astrophysical flows, tertiary folding of macromolecules in chemical-physics, and DNA packing in cell biology.

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28

Gravel, E. M., and T. D. Papathanasiou. "Development of Permeability Models for Saturated Fluid Flow across Arrays of Fibre Clusters." Advanced Composites Letters 11, no. 3 (May 2002): 096369350201100. http://dx.doi.org/10.1177/096369350201100303.

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Dual porosity fibrous media are important in a number of applications, ranging from bioreactor design and transport in living systems to composites manufacturing. In the present study we are concerned with the development of predictive models for the hydraulic permeability ( Kp) of various arrays of fibre bundles. For this we carry out extensive computations for viscous flow through arrays of fibre bundles using the Boundary Element Method (BEM) implemented on a multi-processor computer. Up to 350 individual filaments, arranged in square or hexagonal packing within bundles, which are also arranged in square of hexagonal packing, are included in each simulation. These are simple but not trivial models for fibrous preforms used in composites manufacturing – dual porosity systems characterised by different inter- and intra-tow porosities. The way these porosities affect the hydraulic permeability of such media is currently unknown and is elucidated through our simulations. Following numerical solution of the governing equations, ( Kp) is calculated from the computed flowrate through Darcy's law and is expressed as function of the inter- and intra-tow porosities (φ, φt) and of the filament radius ( Rf). Numerical results are also compared to analytical models. The latter form the starting point in the development of a dimensionless correlation for the permeability of such dual porosity media. It is found that the numerically computed permeabilities follow that correlation for a wide range of φ i, φt and Rf.

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29

Wright, D. M., V. C. Duance, T. J. Wess, C. M. Kielty, and P. P. Purslow. "The supramolecular organisation of fibrillin-rich microfibrils determines the mechanical properties of bovine zonular filaments." Journal of Experimental Biology 202, no. 21 (November 1, 1999): 3011–20. http://dx.doi.org/10.1242/jeb.202.21.3011.

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The zonular filaments from the eyes of cows are rich in microfibrils containing fibrillin. Tensile tests, stress-relaxation tests and X-ray diffraction studies were used to study the relationship between the mechanical behaviour of zonular filaments and the molecular packing and structure of the fibrillin-rich microfibrils. Zonular filaments show a non-linear (J-shaped) stress-strain curve and appreciable stress-relaxation. It is proposed that the non-linear properties are due to local variations in waviness in the microfibrils or assemblies of microfibrils, which straighten out and become more regularly aligned with strain. Previous and current X-ray diffraction results consistently show a partial ordering of microfibrils in zonular filaments into staggered aggregates which become more ordered and laterally aligned on stretching. Although the removal and re-addition of Ca(2+) is known to change the molecular structure of fibrillin, no effect was observed on the tensile properties of the zonular filaments. It is hypothesised that strain-induced deformation in the supramolecular aggregate packing may not be Ca(2+)-sensitive but could dominate the mechanical behaviour of microfibrillar arrays in zonular filaments.

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30

Miroshnichenko, N. "PACKING OF MYOSIN MOLECULES IN MUSCLE THICK FILAMENTS." Cell Biology International 24, no. 6 (June 2000): 327–33. http://dx.doi.org/10.1006/cbir.1999.0514.

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31

Squire, John, Marie Cantino, Michael Chew, Richard Denny, Jeff Harford, Liam Hudson, and Pradeep Luther. "Myosin Rod-Packing Schemes in Vertebrate Muscle Thick Filaments." Journal of Structural Biology 122, no. 1-2 (1998): 128–38. http://dx.doi.org/10.1006/jsbi.1998.3995.

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32

Miao, L., O. Vanderlinde, J. Liu, R. P. Grant, A. Wouterse, K. Shimabukuro, A. Philipse, M. Stewart, and T. M. Roberts. "The role of filament-packing dynamics in powering amoeboid cell motility." Proceedings of the National Academy of Sciences 105, no. 14 (April 2, 2008): 5390–95. http://dx.doi.org/10.1073/pnas.0708416105.

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33

Grason, Gregory M. "Colloquium: Geometry and optimal packing of twisted columns and filaments." Reviews of Modern Physics 87, no. 2 (May 14, 2015): 401–19. http://dx.doi.org/10.1103/revmodphys.87.401.

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34

Feughelman, M., та Veronica James. "Hexagonal Packing of Intermediate Filaments (Microfibrils) in α-Keratin Fibers". Textile Research Journal 68, № 2 (лютий 1998): 110–14. http://dx.doi.org/10.1177/004051759806800205.

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35

Grason, Gregory M. "Frustration and packing in curved-filament assemblies: from isometric to isomorphic bundles." Soft Matter 9, no. 29 (2013): 6761. http://dx.doi.org/10.1039/c3sm50229e.

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36

Takatera, Masayuki, Tamotsu Arichi, Julie Peiffer, Chunhong Zhu, and KyoungOk Kim. "Continuous measurement of apparent Poisson’s ratio for yarn based on omni-directional diameters." Textile Research Journal 87, no. 6 (July 20, 2016): 739–46. http://dx.doi.org/10.1177/0040517516639817.

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We proposed a new method for measuring apparent Poisson’s ratio for yarn and developed a new tensile tester equipped with a digital micrometer that can measure the omni-directional diameter of the yarn annularly while the yarn is elongated. Values of apparent Poisson’s ratio were obtained from the longitudinal and transverse strains continuously. The mean diameter measured omni-directionally was used to calculate the transverse strain for each longitudinal strain. We tested five spun yarns, one monofilament yarn and two filament yarns and obtained values of apparent Poisson’s ratio against longitudinal strain for all samples. Apparent Poisson’s ratio was not constant for spun and filament yarns, while it was constant for monofilament yarn. When the longitudinal strain was low, apparent Poisson’s ratios of ring spun yarns and filament yarns were large, owing to the fiber packing density. As the longitudinal strain increased, apparent Poisson’s ratio gradually decreased. Furthermore, we approximated the relationship between apparent Poisson’s ratio and the longitudinal strain using a power function. The apparent Poisson values can be used in the simulation of fabrics.

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37

Evans, Myfanwy E., and Stephen T. Hyde. "From three-dimensional weavings to swollen corneocytes." Journal of The Royal Society Interface 8, no. 62 (March 11, 2011): 1274–80. http://dx.doi.org/10.1098/rsif.2010.0722.

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A novel technique to generate three-dimensional Euclidean weavings, composed of close-packed, periodic arrays of one-dimensional fibres, is described. Some of these weavings are shown to dilate by simple shape changes of the constituent fibres (such as fibre straightening). The free volume within a chiral cubic example of a dilatant weaving, the ideal conformation of the G 129 weaving related to the Σ + rod packing, expands more than fivefold on filament straightening. This remarkable three-dimensional weaving, therefore, allows an unprecedented variation of packing density without loss of structural rigidity and is an attractive design target for materials. We propose that the G 129 weaving (ideal Σ + weaving) is formed by keratin fibres in the outermost layer of mammalian skin, probably templated by a folded membrane.

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38

Stewart, M., R. A. Quinlan, and R. D. Moir. "Molecular interactions in paracrystals of a fragment corresponding to the alpha-helical coiled-coil rod portion of glial fibrillary acidic protein: evidence for an antiparallel packing of molecules and polymorphism related to intermediate filament structure." Journal of Cell Biology 109, no. 1 (July 1, 1989): 225–34. http://dx.doi.org/10.1083/jcb.109.1.225.

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We have expressed in Escherichia coli a fragment of c-DNA that broadly corresponds to the alpha-helical coiled-coil rod section of glial fibrillary acidic protein (GFAP) and have used the resultant protein to prepare paracrystals in which molecular interactions can be investigated. An engineered fragment of mouse GFAP c-DNA was inserted into a modified version of the E. coli expression vector pLcII, from which large quantities of a lambda cII-GFAP rod fusion protein were prepared. A protein fragment corresponding to the GFAP rod was then obtained by proteolysis with thrombin. Paracrystals of this material were produced using divalent cations (Mg, Ca, Ba) in the presence of a chaotrophic agent such as thiocyanate. These paracrystals showed a number of polymorphic patterns that were based on a fundamental pattern that had dyad symmetry and an axial repeat of 57 nm. Analysis of both positive and negative staining patterns showed that this fundamental pattern was consistent with a unit cell containing two 48-nm-long molecules in an antiparallel arrangement with their NH2 termini overlapping by approximately 34 nm. More complicated patterns were produced by stacking the fundamental pattern with staggers of approximately 1/5, 2/5, and 1/2 the axial repeat. The molecular packing the unit cell was consistent with a range of solution studies on intermediate filaments that have indicated that a molecular dimer (i.e., a tetramer containing four chains or two coiled-coil molecules) is an intermediate in filament assembly. Moreover, these paracrystals allow the molecular interactions involved in the tetramer to be investigated in some detail.

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39

Nowak, Roberta B., Robert S. Fischer, Rebecca K. Zoltoski, Jerome R. Kuszak, and Velia M. Fowler. "Tropomodulin1 is required for membrane skeleton organization and hexagonal geometry of fiber cells in the mouse lens." Journal of Cell Biology 186, no. 6 (September 14, 2009): 915–28. http://dx.doi.org/10.1083/jcb.200905065.

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Hexagonal packing geometry is a hallmark of close-packed epithelial cells in metazoans. Here, we used fiber cells of the vertebrate eye lens as a model system to determine how the membrane skeleton controls hexagonal packing of post-mitotic cells. The membrane skeleton consists of spectrin tetramers linked to actin filaments (F-actin), which are capped by tropomodulin1 (Tmod1) and stabilized by tropomyosin (TM). In mouse lenses lacking Tmod1, initial fiber cell morphogenesis is normal, but fiber cell hexagonal shapes and packing geometry are not maintained as fiber cells mature. Absence of Tmod1 leads to decreased γTM levels, loss of F-actin from membranes, and disrupted distribution of β2-spectrin along fiber cell membranes. Regular interlocking membrane protrusions on fiber cells are replaced by irregularly spaced and misshapen protrusions. We conclude that Tmod1 and γTM regulation of F-actin stability on fiber cell membranes is critical for the long-range connectivity of the spectrin–actin network, which functions to maintain regular fiber cell hexagonal morphology and packing geometry.

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40

Patient, Romuald, Christophe Hourioux, Pierre-Yves Sizaret, Sylvie Trassard, Camille Sureau, and Philippe Roingeard. "Hepatitis B Virus Subviral Envelope Particle Morphogenesis and Intracellular Trafficking." Journal of Virology 81, no. 8 (January 31, 2007): 3842–51. http://dx.doi.org/10.1128/jvi.02741-06.

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ABSTRACT Hepatitis B virus (HBV) is unusual in that its surface proteins (small [S], medium, and large [L]) are not only incorporated into the virion envelope but they also bud into empty subviral particles in great excess over virions. The morphogenesis of these subviral envelope particles remains unclear, but the S protein is essential and sufficient for budding. We show here that, in contrast to the presumed model, the HBV subviral particle formed by the S protein self-assembles into branched filaments in the lumen of the endoplasmic reticulum (ER). These long filaments are then folded and bridged for packing into crystal-like structures, which are then transported by ER-derived vesicles to the ER-Golgi intermediate compartment (ERGIC). Within the ERGIC, they are unpacked and relaxed, and their size and shape probably limits further progression through the secretory pathway. Such progression requires their conversion into spherical particles, which occurred spontaneously during the purification of these filaments by affinity chromatography. Small branched filaments are also formed by the L protein in the ER lumen, but these filaments are not packed into transport vesicles. They are transported less efficiently to the ERGIC, potentially accounting for the retention of the L protein within cells. These findings shed light on an important step in the HBV infectious cycle, as the intracellular accumulation of HBV subviral filaments may be directly linked to viral pathogenesis.

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41

Yi, Hong, Norman E. Williams, Virginia M. Dress, and Kenneth C. Moore. "Immunolocalization of individual filament-forming proteins in the cytoskeleton of Tetrahymena." Proceedings, annual meeting, Electron Microscopy Society of America 48, no. 3 (August 12, 1990): 476–77. http://dx.doi.org/10.1017/s0424820100159928.

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Four polypeptides (tetrins I-IV) have been isolated from the ciliated protozoan Tetrahvmena pyriformis. These polypeptides assemble in vitro into 3-4 nm filaments identical with those present in abundance in a cytoskeletal framework associated with the feeding organelle system (oral apparatus) of this cell type. The polypeptides ranging in molecular weights from 79-89 kDa are not similar to each other in either biochemical or immunological properties. In vivo, the filaments are organized into higher order structures described as cages, cables, and networks. The specific hypothesis arises that the alternate packing arrangements may correlate with different distributions of the individual tetrin polypeptides. We report the production of monoclonal antibodies for each tetrin polypeptide, and the determination of the location of each within the cell using confocal microscopy and immunogold-silver enhancement procedures in conjunction with transmission electron microscopy (TEM).Cell samples for confocal microscopy were labelled according to conventional immunofluorescent procedures and examined with a Bio-Rad MRC-600 laser scanning confocal microscope.

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42

Hasegawa, K., K. Imada, S. Maki-Yonekura, K. Yonekura, F. Samatey, I. Yamashita та K. Namba. "Possible packing of terminal α-helices in the inner-core of the bacterial flagellar filament". Acta Crystallographica Section A Foundations of Crystallography 58, s1 (6 серпня 2002): c164. http://dx.doi.org/10.1107/s0108767302091584.

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43

Reichwein, Lars, Johannes Thomas, and Alexander Pukhov. "The filamented electron bunch of the bubble regime." Laser and Particle Beams 38, no. 2 (April 16, 2020): 121–27. http://dx.doi.org/10.1017/s0263034620000130.

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AbstractWe present a theory for describing the inner structure of the electron bunch in the bubble regime starting from a random distribution of electrons inside the bubble and subsequently minimizing the system's energy. Consequently, we find a filament-like structure in the direction of propagation that is surrounded by various shells consisting of further electrons. If we specify a two-dimensional (2D) initial structure, we observe a hexagonal structure for a high number of particles, corresponding to the close packing of spheres in two dimensions. The 2D structures are in agreement with the equilibrium slice model.

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44

Chew, M. W. K., та J. M. Squire. "Packing of α-Helical Coiled-Coil Myosin Rods in Vertebrate Muscle Thick Filaments". Journal of Structural Biology 115, № 3 (листопад 1995): 233–49. http://dx.doi.org/10.1006/jsbi.1995.1048.

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45

Clapin, D. F., and V. J. A. Montpetit. "Liquid crystalline ordering of paired helical filaments in neurofibrillary tangles of Alzheimer's disease." Proceedings, annual meeting, Electron Microscopy Society of America 44 (August 1986): 348–49. http://dx.doi.org/10.1017/s0424820100143365.

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Анотація:

Alzheimer's disease is characterized by the accumulation of abnormal filamentous proteins. The most important of these are amyloid fibrils and paired helical filaments (PHF). PHF are located intraneuronally forming bundles called neurofibrillary tangles. The designation of these structures as "tangles" is appropriate at the light microscopic level. However, localized domains within individual tangles appear to demonstrate a regular spacing which may indicate a liquid crystalline phase. The purpose of this paper is to present a statistical geometric analysis of PHF packing.

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46

Wang, Fengbin, Ying Liu, Zhangli Su, Tomasz Osinski, Guilherme A. P. de Oliveira, James F. Conway, Stefan Schouten, Mart Krupovic, David Prangishvili, and Edward H. Egelman. "A packing for A-form DNA in an icosahedral virus." Proceedings of the National Academy of Sciences 116, no. 45 (October 21, 2019): 22591–97. http://dx.doi.org/10.1073/pnas.1908242116.

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Studies on viruses infecting archaea living in the most extreme environments continue to show a remarkable diversity of structures, suggesting that the sampling continues to be very sparse. We have used electron cryo-microscopy to study at 3.7-Å resolution the structure of the Sulfolobus polyhedral virus 1 (SPV1), which was originally isolated from a hot, acidic spring in Beppu, Japan. The 2 capsid proteins with variant single jelly-roll folds form pentamers and hexamers which assemble into a T = 43 icosahedral shell. In contrast to tailed icosahedral double-stranded DNA (dsDNA) viruses infecting bacteria and archaea, and herpesviruses infecting animals and humans, where naked DNA is packed under very high pressure due to the repulsion between adjacent layers of DNA, the circular dsDNA in SPV1 is fully covered with a viral protein forming a nucleoprotein filament with attractive interactions between layers. Most strikingly, we have been able to show that the DNA is in an A-form, as it is in the filamentous viruses infecting hyperthermophilic acidophiles. Previous studies have suggested that DNA is in the B-form in bacteriophages, and our study is a direct visualization of the structure of DNA in an icosahedral virus.

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47

Zhang, Yuchen, Richard J. Alsop, Asfia Soomro, Fei-Chi Yang, and Maikel C. Rheinstädter. "Effect of shampoo, conditioner and permanent waving on the molecular structure of human hair." PeerJ 3 (October 1, 2015): e1296. http://dx.doi.org/10.7717/peerj.1296.

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Анотація:

The hair is a filamentous biomaterial consisting of thecuticle, thecortexand themedulla, all held together by the cell membrane complex. Thecortexmostly consists of helical keratin proteins that spiral together to form coiled-coil dimers, intermediate filaments, micro-fibrils and macro-fibrils. We used X-ray diffraction to study hair structure on the molecular level, at length scales between ∼3–90 Å, in hopes of developing a diagnostic method for diseases affecting hair structure allowing for fast and noninvasive screening. However, such an approach can only be successful if common hair treatments do not affect molecular hair structure. We found that a single use of shampoo and conditioner has no effect on packing of keratin molecules, structure of the intermediate filaments or internal lipid composition of the membrane complex. Permanent waving treatments are known to break and reform disulfide linkages in the hair. Single application of a perming product was found to deeply penetrate the hair and reduce the number of keratin coiled-coils and change the structure of the intermediate filaments. Signals related to the coiled-coil structure of theα-keratin molecules at 5 and 9.5 Å were found to be decreased while a signal associated with the organization of the intermediate filaments at 47 Å was significantly elevated in permed hair. Both these observations are related to breaking of the bonds between two coiled-coil keratin dimers.

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48

Hughes, Spencer A., Fengbin Wang, Shengyuan Wang, Mark A. B. Kreutzberger, Tomasz Osinski, Albina Orlova, Joseph S. Wall, Xiaobing Zuo, Edward H. Egelman, and Vincent P. Conticello. "Ambidextrous helical nanotubes from self-assembly of designed helical hairpin motifs." Proceedings of the National Academy of Sciences 116, no. 29 (July 1, 2019): 14456–64. http://dx.doi.org/10.1073/pnas.1903910116.

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Tandem repeat proteins exhibit native designability and represent potentially useful scaffolds for the construction of synthetic biomimetic assemblies. We have designed 2 synthetic peptides, HEAT_R1 and LRV_M3Δ1, based on the consensus sequences of single repeats of thermophilic HEAT (PBS_HEAT) and Leucine-Rich Variant (LRV) structural motifs, respectively. Self-assembly of the peptides afforded high-aspect ratio helical nanotubes. Cryo-electron microscopy with direct electron detection was employed to analyze the structures of the solvated filaments. The 3D reconstructions from the cryo-EM maps led to atomic models for the HEAT_R1 and LRV_M3Δ1 filaments at resolutions of 6.0 and 4.4 Å, respectively. Surprisingly, despite sequence similarity at the lateral packing interface, HEAT_R1 and LRV_M3Δ1 filaments adopt the opposite helical hand and differ significantly in helical geometry, while retaining a local conformation similar to previously characterized repeat proteins of the same class. The differences in the 2 filaments could be rationalized on the basis of differences in cohesive interactions at the lateral and axial interfaces. These structural data reinforce previous observations regarding the structural plasticity of helical protein assemblies and the need for high-resolution structural analysis. Despite these observations, the native designability of tandem repeat proteins offers the opportunity to engineer novel helical nanotubes. Moreover, the resultant nanotubes have independently addressable and chemically distinguishable interior and exterior surfaces that would facilitate applications in selective recognition, transport, and release.

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HARADA, Shunsuke, Yoshio ARAI, Wakako ARAKI, Takafumi IIJIMA, Akimoto KUROSAWA, Tomoyuki OHBUCHI, and Noriyuki SASAKI. "Effect of fiber packing inhomogeneity on burst pressure of type III filament wound CFRP composite vessels." Proceedings of the Materials and Mechanics Conference 2017 (2017): OS1807. http://dx.doi.org/10.1299/jsmemm.2017.os1807.

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50

White, Glenn E., and Harold P. Erickson. "Sequence divergence of coiled coils—structural rods, myosin filament packing, and the extraordinary conservation of cohesins." Journal of Structural Biology 154, no. 2 (May 2006): 111–21. http://dx.doi.org/10.1016/j.jsb.2006.01.001.

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