المؤلفون: Suneeta Mandava, Sanghyun Park, Robert F. Fischetti, Jyotsana Lal, Lee Makowski, David Gore, Nancy T. Ho, J. Bardhan, Chien Ho, Diane J. Rodi

المصدر: Journal of Molecular Biology. 408:909-921

مصطلحات موضوعية: Models, Molecular, Chemistry, Small-angle X-ray scattering, Structural diversity, Cooperativity, Crystal structure, Crystallography, X-Ray, Article, Methemoglobin, Solutions, Crystallography, Protein structure, Allosteric Regulation, Carboxyhemoglobin, X-Ray Diffraction, Structural Biology, Scattering, Small Angle, X-ray crystallography, Animals, Humans, Cattle, Hemoglobin, Molecular Biology

الوصف: Specific ligation states of hemoglobin are, when crystallized, capable of taking on multiple quaternary structures. The relationship between these structures, captured in crystal lattices, and hemoglobin structure in solution remains uncertain. Wide-angle X-ray solution scattering (WAXS) is a sensitive probe of protein structure in solution that can distinguish among similar structures and has the potential to contribute to these issues. We used WAXS to assess the relationships among the structures of human and bovine hemoglobins in different liganded forms in solution. WAXS data readily distinguished among the various forms of hemoglobins. WAXS patterns confirm some of the relationships among hemoglobin structures that have been defined through crystallography and NMR and extend others. For instance, methemoglobin A in solution is, as expected, nearly indistinguishable from HbCO A. Interestingly, for bovine hemoglobin, the differences between deoxy-Hb, methemoglobin and HbCO are smaller than the corresponding differences in human hemoglobin. WAXS data were also used to assess the spatial extent of structural fluctuations of various hemoglobins in solution. Dynamics has been implicated in allosteric control of hemoglobin, and increased dynamics has been associated with lowered oxygen affinity. Consistent with that notion, WAXS patterns indicate that deoxy-Hb A exhibits substantially larger structural fluctuations than HbCO A. Comparisons between the observed WAXS patterns and those predicted on the basis of atomic coordinate sets suggest that the structures of Hb in different liganded forms exhibit clear differences from known crystal structures.

الوصول الحر: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::f3a6549e8b963ede1940028141bda7e3Test
https://doi.org/10.1016/j.jmb.2011.02.062Test

المؤلفون: Pawel Sikorski, Kyle L. Morris, Thomas R. Jahn, O. Sumner Makin, Pei Tian, Louise C. Serpell, Karen E. Marshall

المصدر: Journal of Molecular Biology. 395:717-727

مصطلحات موضوعية: Models, Molecular, Diffraction, Amyloid, Amyloid beta-Peptides, biology, Protein Conformation, Chemistry, macromolecular substances, In Vitro Techniques, Amyloid fibril, Fibril, Peptide Fragments, Protein Structure, Secondary, Transthyretin, Crystallography, Protein structure, X-Ray Diffraction, Structural Biology, X-ray crystallography, biology.protein, Humans, Amino Acid Sequence, Beta (finance), Molecular Biology

الوصف: Amyloid fibril deposition is central to the pathology of more than 30 unrelated diseases including Alzheimer's disease and Type 2 diabetes. It is generally accepted that amyloid fibrils share common structural features despite each disease being characterised by the deposition of an unrelated protein or peptide. The structure of amyloid fibrils has been studied using X-ray fibre diffraction and crystallography, solid-state NMR and electron paramagnetic resonance, and many different, sometimes opposing, models have been suggested. Many of these models are based on the original interpretation of the cross-beta diffraction pattern for cross-beta silk in which beta-strands run perpendicular to the fibre axis, although alternative models include beta-helices and natively structured proteins. Here, we have analysed opposing model structures and examined the necessary structural elements within the amyloid core structure, as well as producing idealised models to test the limits of the core conformation. Our work supports the view that amyloid fibrils share a number of common structural features, resulting in characteristic diffraction patterns. This pattern may be satisfied by structures in which the strands align close to perpendicular to the fibre axis and are regularly arranged to form beta-sheet ribbons. Furthermore, the fibril structure contains several beta-sheets that associate via side-chain packing to form the final protofilament structure.

الوصول الحر: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::fc57ce4420e535b243b056c17e28c40bTest
https://doi.org/10.1016/j.jmb.2009.09.039Test

المؤلفون: T Iida, Naoto Yagi, N Ohta, K Inoue

المصدر: Journal of Molecular Biology. 362:327-333

مصطلحات موضوعية: Diffraction, Amyloid, Materials science, Protein Conformation, Molecular Sequence Data, macromolecular substances, Microbeam, Fibril, Core (optical fiber), Crystallography, Reflection (mathematics), X-Ray Diffraction, Spherulite, Structural Biology, X-ray crystallography, Animals, Insulin, Cattle, Amino Acid Sequence, Particle Size, Fiber diffraction, Molecular Biology

الوصف: The peptide hormone insulin forms a spherical aggregate, called a spherulite, at low pH and high temperature. A spherulite is composed of a core and many fibrils extending from it. These fibrils are thought to be amyloid fibers with a beta-sheet structure. In the present study, spherulites with a diameter of 50-100 microm were examined by X-ray fiber diffraction using a 6 microm beam. When a spherulite was scanned with the microbeam and the observed diffraction patterns were arranged in a two-dimensional array, the direction of the scatter was centrosymmetric, demonstrating a symmetric growth of fibrils. There were diffraction peaks at Bragg spacings of 23 nm, 3.3 nm and 1.2 nm in the direction perpendicular to the fibrils and 0.48 nm along the fibrils. The 0.48 nm reflection shows that the hydrogen bonds between beta-strands are along the fibril. The 23 nm reflection corresponds to the separation between fibrils, the 3.3 nm reflection is due to the arrangement of protofilaments, and the 1.2 nm reflection arises from the arrangement of peptide chains. On the basis of these results, a model of a fibril with an extended insulin molecule is proposed.

الوصول الحر: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::cb1e2799005dba3ee7336f82156c8482Test
https://doi.org/10.1016/j.jmb.2006.07.041Test

المؤلفون: Vadim Cherezov, Martin Caffrey, Miroslav Z. Papiz, Jeffrey D. Clogston

المصدر: Journal of Molecular Biology. 357:1605-1618

مصطلحات موضوعية: Models, Molecular, Detergents, Light-Harvesting Protein Complexes, Nucleation, Receptors, Cell Surface, Crystal growth, Phase Transition, law.invention, X-Ray Diffraction, Structural Biology, law, Phase (matter), Transition Temperature, Crystallization, Bacteriochlorophylls, Molecular Biology, Integral membrane protein, Molecular Structure, Chemistry, Membrane Proteins, Mesophase, Carotenoids, Lipids, Crystallography, Membrane protein, X-ray crystallography

الوصف: The cubic phase or in meso crystallization method is responsible for almost 40 solved integral membrane protein structures. Most of these are small and compact proteins. A model for how crystals form by the in meso method has been proposed that invokes a transition between mesophases. In light of this model, we speculated that a more hydrated and open mesophase, of reduced interfacial curvature, would support facile crystallization of bigger and bulkier proteins. The proposal was explored here by performing crystallization in the presence of additives that swell the cubic phase. The additive concentration inducing swelling, as quantified by small-angle X-ray diffraction, coincided with a "crystallization window" in which two, very different transmembranal proteins produced crystals. That the swollen mesophase can grow structure-grade crystals was proven with one of these, the light-harvesting II complex. In most regards, the structural details of the corresponding complex resembled those of crystals grown by the conventional vapour diffusion method, with some important differences. In particular, packing density in the in meso-grown crystals was dramatically higher, more akin to that seen with water-soluble proteins, which accounts for their enhanced diffracting power. The layered and close in-plane packing observed has been rationalized in a model for nucleation and crystal growth by the in meso method that involves swollen mesophases. These results present a rational case for including mesophase-swelling additives in screens for in meso crystallogenesis. Their use will contribute to broadening the range of membrane proteins that yield to structure determination.

الوصول الحر: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::22758733d0ca983268c5aa407578e70eTest
https://doi.org/10.1016/j.jmb.2006.01.049Test

المؤلفون: Carlo Knupp, John M. Squire, Manfred Roessle

المصدر: Journal of Molecular Biology. 343:1345-1363

مصطلحات موضوعية: biology, Muscles, Muscle Proteins, Vertebrate, Flounder, macromolecular substances, Troponin, Nebulin, Myosin head, Crystallography, X-Ray Diffraction, Structural Biology, biology.animal, X-ray crystallography, biology.protein, Biophysics, Animals, Connectin, Titin, Hexagonal lattice, Carrier Proteins, Protein Kinases, Molecular Biology, Actin

الوصف: Previous low-angle X-ray diffraction studies of various vertebrate skeletal muscles have shown the presence of two rich layer-line patterns, one from the myosin heads and based on a 429 A axial repeat, and one from actin filaments and based on a repeat of about 360-370 A. In addition, meridional intensities have been seen from C-protein (MyBP-C; at about 440 A and its higher orders) and troponin (at about 385 A and its orders). Using preparations of intact, relaxed, bony fish fin muscles and the ID-02 low-angle X-ray camera at the ESRF with a 10 m camera length we have now seen numerous, hitherto unreported, sampled, X-ray layer-lines many of which do not fit onto the previously observed repeats and which require interpretation. The new reflections all fall on the normal ("vertical") hexagonal lattice row-lines in the highly sampled, almost "crystalline", low-angle diffraction X-ray patterns from bony fish muscle, indicating that they all arise from the muscle A-band. However, they do not fall on a single axial repeat. In direct confirmation of our previous analysis, some of these new reflections are explained by the interaction in resting muscle between the N-terminal ends of myosin-bound C-protein molecules with adjacent actin filaments, possibly through the Pro-Ala-rich region. Other newly observed reflections lie on a much longer repeat, but they are most easily interpreted in terms of the arrangement of troponin on the actin filaments. If this is so, then the implication is that the actin filaments and their troponin complexes are systematically arranged in the fish muscle A-band lattice relative to the myosin head positions, and that these newly observed X-ray reflections, when fully analysed, will report on the shape and distribution of troponin molecules in the resting muscle A-band. The less certain contributions of titin and nebulin to these new reflections have also been tested and are described. Many of the new reflections do not appear to come from these known structures. There must be structural features of the A-band that have not yet been described.

الوصول الحر: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::daca5c896e7034f773f48b5abdbb52e4Test
https://doi.org/10.1016/j.jmb.2004.08.084Test

المؤلفون: Stuart Hodson, G.F. Elliott, Justyn Wiktor Regini

المصدر: Journal of Molecular Biology. 336:179-186

مصطلحات موضوعية: Fibrillar collagen, Chemistry, Osmolar Concentration, Water, Sodium Chloride, Chloride, Ion, Collagen fibril, Cornea, Crystallography, medicine.anatomical_structure, X-Ray Diffraction, Structural Biology, Ionic strength, X-ray crystallography, medicine, Animals, Cattle, Collagen, Molecular Biology, medicine.drug

الوصف: The fixed stromal charge of bovine corneas, osmotically clamped at physiological hydration, was altered by regulating the amount of chloride ions bound to the matrix. We measured the local fibrillar collagen order using X-ray diffraction methods. As the bound anions increased up to physiological values, the local fibrillar order increased to an optimal value. The coherence distance (t) approximately doubles to a maximum value (409 nm) from 10 mM NaCl to 154 mM NaCl. This then slowly decreased as the bathing solution increased to 1000 mM. In contrast the diameter of the collagen fibrils were minimal at physiological NaCl.

الوصول الحر: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::31cbd1fdc6091738af7fd9355084e9ceTest
https://doi.org/10.1016/j.jmb.2003.12.001Test

المؤلفون: Chris Long, Melinda Balbirnie, Donald L. D. Caspar, Ruben Diaz-Avalos, David Eisenberg, Robert Grothe, Eric Fontano

المصدر: Journal of Molecular Biology. 330:1165-1175

مصطلحات موضوعية: Amyloid, Polymorphism, Genetic, Saccharomyces cerevisiae Proteins, Materials science, Prions, Protein Conformation, Beta sheet, Water, Electrons, Crystal structure, Crystallography, X-Ray, Fungal Proteins, Microscopy, Electron, Crystallography, X-Ray Diffraction, Electron diffraction, Structural Biology, X-ray crystallography, Orthorhombic crystal system, Peptides, Structure factor, Molecular Biology, Powder diffraction, Peptide Termination Factors, Monoclinic crystal system

الوصف: The seven-residue peptide GNNQQNY from the N-terminal region of the yeast prion protein Sup35, which forms amyloid fibers, colloidal aggregates and highly ordered nanocrystals, provides a model system for characterizing the elusively protean cross-beta conformation. Depending on preparative conditions, orthorhombic and monoclinic crystals with similar lath-shaped morphology have been obtained. Ultra high-resolution (

الوصول الحر: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::4dc0389121fc0066f864e8905591d95fTest
https://doi.org/10.1016/s0022-2836Test(03)00659-4

المؤلفون: R. J. Greenall, Watson Fuller, Colin Nave

المصدر: Journal of Molecular Biology. 305:669-672

مصطلحات موضوعية: Diffraction, chemistry.chemical_classification, Materials science, Water, Humidity, Zonal and meridional, DNA, Thymus Gland, Polymer, Crystallography, Biopolymers, Lattice constant, X-Ray Diffraction, Polymorphism (materials science), chemistry, Structural Biology, X-ray crystallography, Animals, Nucleic Acid Conformation, Molecule, Cattle, Desiccation, Crystallization, Molecular Biology

الوصف: When DNA fibres are stretched during drying, the polymer undergoes a conformational transition. We present quantitative results from X-ray diffraction studies on such fibres held at various ambient relative humidities. These indicate that the molecules are arranged in arrays which are crystalline in projection down the fibre axis. The packing can be explained in terms of a hexagonal cell with a lattice parameter, a , of ∼13 A which varies with humidity. The patterns contain meridional intensities at 1/3.4 A −1 and 1/6.5 A −1 , a strong off-meridional intensity at Z =1/5.6 A −1 and diffuse scatter at Z =1/28 A −1 .

الوصول الحر: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::d36cf422387bffd521a67c53209b1149Test
https://doi.org/10.1006/jmbi.2000.4325Test

المؤلفون: Gerald Stubbs, Amy Kendall, Wen Bian, Robert Tycko, Michele McDonald, Hayden Box

المصدر: Journal of molecular biology. 423(3)

مصطلحات موضوعية: Hollow core, Diffraction, Models, Molecular, Amyloid beta-Peptides, Amyloid β, Chemistry, Protein Conformation, Plaque, Amyloid, macromolecular substances, Fibril, Peptide Fragments, Article, Crystallography, Nuclear magnetic resonance, Protein structure, Solid-state nuclear magnetic resonance, X-Ray Diffraction, Structural Biology, Alzheimer Disease, X-ray crystallography, Humans, Fiber diffraction, Molecular Biology, Nuclear Magnetic Resonance, Biomolecular

الوصف: Amyloid β protein (Aβ), the principal component of the extracellular plaques found in the brains of patients with Alzheimer's disease, forms fibrils well suited to structural study by X-ray fiber diffraction. Fiber diffraction patterns from the 40-residue form Aβ(1–40) confirm a number of features of a 3-fold symmetric Aβ model from solid‐state NMR (ssNMR) but suggest that the fibrils have a hollow core not present in the original ssNMR models. Diffraction patterns calculated from a revised 3-fold hollow model with a more regular β-sheet structure are in much better agreement with the observed diffraction data than patterns calculated from the original ssNMR model. Refinement of a hollow-core model against ssNMR data led to a revised ssNMR model, similar to the fiber diffraction model.

الوصول الحر: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::c1e5a0206717448d162a71199ff750c1Test
https://pubmed.ncbi.nlm.nih.gov/22903058Test

المؤلفون: Linda Yu, Johann Deisenhofer, Chang An Yu, Di Xia

المصدر: Journal of Molecular Biology. 243:802-805

مصطلحات موضوعية: Cytochrome, Mitochondria, Heart, law.invention, Electron Transport Complex III, Tetragonal crystal system, X-Ray Diffraction, Structural Biology, law, Pressure, Animals, Mother liquor, Crystallization, Molecular Biology, biology, Chemistry, Sepharose, Resolution (electron density), Solvent, Crystallography, Electrophoresis, X-ray crystallography, Solvents, biology.protein, Cattle, Electrophoresis, Polyacrylamide Gel

الوصف: Cytochrome b-c1 complex (ubiquinol-cytochrome c reductase) of beef heart mitochondria has been crystallized. Crystals grown in capillary tubes diffracted X-rays from a laboratory source to a resolution of 7 A and synchrotron radiation to a resolution of 4.5 A in the presence of mother liquor. However, the movement of crystals in the mother liquor makes data collection very difficult. Removal of the mother liquor from the crystals causes severe loss of diffraction quality. To circumvent these difficulties we have recently developed a method for crystallization of the cytochrome b-c1 complex from a gel. The sizes, shapes and diffraction qualities of crystals grown in gel approach those of crystals obtained from liquid. Preliminary experiments on a Xuong-Hamlin area detector indicate that these crystals have the symmetry of a body centered tetragonal space group with cell constants a = b = 157 A, c = 590 A. Assuming eight cytochrome b-c1 complex dimers per unit cell, the crystals have a solvent content of 70% (v/v). Under reduced pressure the crystallization time is significantly decreased. Although crystals obtained under reduced pressure are generally smaller, the shorter crystallization time provides an opportunity to explore more crystallization conditions.

الوصول الحر: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::ca8f3611b042402188a081f846c73af4Test
https://doi.org/10.1016/0022-2836Test(94)90051-5