11 results on '"Kasim Sader"'
Search Results
2. In situ structure and organization of the influenza C virus surface glycoprotein
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Steinar Halldorsson, Kasim Sader, Jack Turner, Lesley J. Calder, and Peter B. Rosenthal
- Subjects
Science - Abstract
Influenza C virus contains a single surface glycoprotein, the haemagglutinin-esterase-fusion (HEF) protein, that mediates receptor binding, receptor destruction, and membrane fusion activities. Here, the authors apply electron cryotomography of whole virus together with subtomogram averaging to determine the HEF structure and lattice organisation on the viral membrane and they discuss mechanistic implications for virus budding and membrane fusion.
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- 2021
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3. Structural insights into blue-green light utilization by marine green algal light harvesting complex II at 2.78 Å
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Soichiro Seki, Tetsuko Nakaniwa, Pablo Castro-Hartmann, Kasim Sader, Akihiro Kawamoto, Hideaki Tanaka, Pu Qian, Genji Kurisu, and Ritsuko Fujii
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Codium fragile ,Cryo-EM ,Light-harvesting complex ,Siphonaxanthin–chlorophyll a/b-binding protein (SCP) ,Intermonomer chlorophyll b macrocluster ,Biochemistry ,QD415-436 ,Genetics ,QH426-470 - Abstract
Light-harvesting complex II (LHCII) present in plants and green algae absorbs solar energy to promote photochemical reactions. A marine green macroalga, Codium fragile, exhibits the unique characteristic of absorbing blue-green light from the sun during photochemical reactions while being underwater owing to the presence of pigment-altered LHCII called siphonaxanthin–chlorophyll a/b-binding protein (SCP). In this study, we determined the structure of SCP at a resolution of 2.78 Å using cryogenic electron microscopy. SCP has a trimeric structure, wherein each monomer containing two lutein and two chlorophyll a molecules in the plant-type LHCII are replaced by siphonaxanthin and its ester and two chlorophyll b molecules, respectively. Siphonaxanthin occupies the binding site in SCP having a polarity in the trimeric inner core, and exhibits a distorted conjugated chain comprising a carbonyl group hydrogen bonded to a cysteine residue of apoprotein. These features suggest that the siphonaxanthin molecule is responsible for the characteristic green absorption of SCP. The replaced chlorophyll b molecules extend the region of the stromal side chlorophyll b cluster, spanning two adjacent monomers.
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- 2022
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4. Structural basis for Fullerene geometry in a human endogenous retrovirus capsid
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Oliver Acton, Tim Grant, Giuseppe Nicastro, Neil J. Ball, David C. Goldstone, Laura E. Robertson, Kasim Sader, Andrea Nans, Andres Ramos, Jonathan P. Stoye, Ian A. Taylor, and Peter B. Rosenthal
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Science - Abstract
In retroviruses, the capsid protein (CA) forms a shell surrounding the viral core. Here the authors combine cryo-electron microscopy with NMR and X-ray crystallography to examine the CA structure from the human endogenous retrovirus HML2 (HERV-K) and determine the structures of four Fullerene CA closed shells that reveal the molecular basis of capsid assembly.
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- 2019
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5. Structural insights and activating mutations in diverse pathologies define mechanisms of deregulation for phospholipase C gamma enzymes
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Yang Liu, Tom D. Bunney, Sakshi Khosa, Kévin Macé, Katharina Beckenbauer, Trevor Askwith, Sarah Maslen, Christopher Stubbs, Taiana M. de Oliveira, Kasim Sader, Mark Skehel, Anne-Claude Gavin, Christopher Phillips, and Matilda Katan
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Medicine ,Medicine (General) ,R5-920 - Abstract
Background: PLCγ enzymes are key nodes in cellular signal transduction and their mutated and rare variants have been recently implicated in development of a range of diseases with unmet need including cancer, complex immune disorders, inflammation and neurodegenerative diseases. However, molecular nature of activation and the impact and dysregulation mechanisms by mutations, remain unclear; both are critically dependent on comprehensive characterization of the intact PLCγ enzymes. Methods: For structural studies we applied cryo-EM, cross-linking mass spectrometry and hydrogen-deuterium exchange mass spectrometry. In parallel, we compiled mutations linked to main pathologies, established their distribution and assessed their impact in cells and in vitro. Findings: We define structure of a complex containing an intact, autoinhibited PLCγ1 and the intracellular part of FGFR1 and show that the interaction is centred on the nSH2 domain of PLCγ1. We define the architecture of PLCγ1 where an autoinhibitory interface involves the cSH2, spPH, TIM-barrel and C2 domains; this relative orientation occludes PLCγ1 access to its substrate. Based on this framework and functional characterization, the mechanism leading to an increase in PLCγ1 activity for the largest group of mutations is consistent with the major, direct impact on the autoinhibitory interface. Interpretation: We reveal features of PLCγ enzymes that are important for determining their activation status. Targeting such features, as an alternative to targeting the PLC active site that has so far not been achieved for any PLC, could provide new routes for clinical interventions related to various pathologies driven by PLCγ deregulation. Fund: CR UK, MRC and AstaZeneca. Keywords: Disease-linked variants, Phospholipase C gamma, Structure, Mechanism
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- 2020
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6. Cryo-EM structure of the monomeric Rhodobacter sphaeroides RC-LH1 core complex at 2.5Å
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David J. K. Swainsbury, Philip J. Jackson, Jack H. Salisbury, Elizabeth C. Martin, Tristan I. Croll, C. Neil Hunter, Pu Qian, Kasim Sader, Andrew Hitchcock, Pablo Castro-Hartmann, Qian, Pu [0000-0002-5888-8546], Swainsbury, David JK [0000-0002-0754-0363], Croll, Tristan I [0000-0002-3514-8377], Salisbury, Jack H [0000-0002-9527-0593], Martin, Elizabeth C [0000-0001-9600-7298], Jackson, Philip J [0000-0001-9671-2472], Hitchcock, Andrew [0000-0001-6572-434X], Castro-Hartmann, Pablo [0000-0002-8991-9560], Sader, Kasim [0000-0002-8517-5410], Hunter, C Neil [0000-0003-2533-9783], and Apollo - University of Cambridge Repository
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quinone ,Models, Molecular ,Protein Conformation, alpha-Helical ,Light ,Cryo-electron microscopy ,Stereochemistry ,Protein subunit ,Photosynthetic Reaction Center Complex Proteins ,Light-Harvesting Protein Complexes ,Gene Expression ,Rhodobacter sphaeroides ,Bioenergetics ,Ring (chemistry) ,Biochemistry ,chemistry.chemical_compound ,Bacterial Proteins ,Structural Biology ,light harvesting ,Protein Interaction Domains and Motifs ,Photosynthesis ,Molecular Biology ,Bacteriochlorophylls ,Research Articles ,Binding Sites ,biology ,Chemistry ,bacteriochlorophyll ,Cryoelectron Microscopy ,Cell Biology ,biology.organism_classification ,Carotenoids ,Transmembrane protein ,carotenoid ,Quinone ,reaction centre ,Hydroquinones ,Protein Subunits ,Coenzyme Q – cytochrome c reductase ,Protein Conformation, beta-Strand ,Bacteriochlorophyll ,Protein Multimerization ,Peptides ,Protein Binding - Abstract
Reaction centre light-harvesting 1 (RC–LH1) complexes are the essential components of bacterial photosynthesis. The membrane-intrinsic LH1 complex absorbs light and the energy migrates to an enclosed RC where a succession of electron and proton transfers conserves the energy as a quinol, which is exported to the cytochrome bc1 complex. In some RC–LH1 variants quinols can diffuse through small pores in a fully circular, 16-subunit LH1 ring, while in others missing LH1 subunits create a gap for quinol export. We used cryogenic electron microscopy to obtain a 2.5 Å resolution structure of one such RC–LH1, a monomeric complex from Rhodobacter sphaeroides. The structure shows that the RC is partly enclosed by a 14-subunit LH1 ring in which each αβ heterodimer binds two bacteriochlorophylls and, unusually for currently reported complexes, two carotenoids rather than one. Although the extra carotenoids confer an advantage in terms of photoprotection and light harvesting, they could impede passage of quinones through small, transient pores in the LH1 ring, necessitating a mechanism to create a dedicated quinone channel. The structure shows that two transmembrane proteins play a part in stabilising an open ring structure; one of these components, the PufX polypeptide, is augmented by a hitherto undescribed protein subunit we designate as protein-Y, which lies against the transmembrane regions of the thirteenth and fourteenth LH1α polypeptides. Protein-Y prevents LH1 subunits 11–14 adjacent to the RC QB site from bending inwards towards the RC and, with PufX preventing complete encirclement of the RC, this pair of polypeptides ensures unhindered quinone diffusion.
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- 2021
7. In situ structure and organization of the influenza C virus surface glycoprotein
- Author
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Lesley J. Calder, Jack Turner, Peter B. Rosenthal, Steinar Halldorsson, and Kasim Sader
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0301 basic medicine ,Models, Molecular ,030103 biophysics ,Influenzavirus C ,Endosome ,viruses ,Science ,General Physics and Astronomy ,Hemagglutinins, Viral ,Matrix (biology) ,Membrane Fusion ,General Biochemistry, Genetics and Molecular Biology ,Virus ,Article ,Madin Darby Canine Kidney Cells ,03 medical and health sciences ,Dogs ,Animals ,chemistry.chemical_classification ,Multidisciplinary ,Membrane Glycoproteins ,Chemistry ,Virion ,Lipid bilayer fusion ,General Chemistry ,030104 developmental biology ,Membrane ,Ectodomain ,Biophysics ,Cryoelectron tomography ,Protein Multimerization ,Glycoprotein ,Influenza C Virus ,Structural biology ,Influenza virus ,Viral Fusion Proteins - Abstract
The lipid-enveloped influenza C virus contains a single surface glycoprotein, the haemagglutinin-esterase-fusion (HEF) protein, that mediates receptor binding, receptor destruction, and membrane fusion at the low pH of the endosome. Here we apply electron cryotomography and subtomogram averaging to describe the structural basis for hexagonal lattice formation by HEF on the viral surface. The conformation of the glycoprotein in situ is distinct from the structure of the isolated trimeric ectodomain, showing that a splaying of the membrane distal domains is required to mediate contacts that form the lattice. The splaying of these domains is also coupled to changes in the structure of the stem region which is involved in membrane fusion, thereby linking HEF’s membrane fusion conformation with its assembly on the virus surface. The glycoprotein lattice can form independent of other virion components but we show a major role for the matrix layer in particle formation., Influenza C virus contains a single surface glycoprotein, the haemagglutinin-esterase-fusion (HEF) protein, that mediates receptor binding, receptor destruction, and membrane fusion activities. Here, the authors apply electron cryotomography of whole virus together with subtomogram averaging to determine the HEF structure and lattice organisation on the viral membrane and they discuss mechanistic implications for virus budding and membrane fusion.
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- 2021
8. Direct imaging and chemical identification of the encapsulated metal atoms in bimetallic endofullerene peapods
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Simon R. Plant, Kasim Sader, Jamie H. Warner, Peter D. Nellist, Rebecca J. Nicholls, Kyriakos Porfyrakis, G. Andrew D. Briggs, and David J. H. Cockayne
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Condensed Matter::Quantum Gases ,Materials science ,Fullerene ,Electron energy loss spectroscopy ,General Engineering ,General Physics and Astronomy ,Direct imaging ,Characterization (materials science) ,Metal ,visual_art ,Scanning transmission electron microscopy ,Physics::Atomic and Molecular Clusters ,visual_art.visual_art_medium ,General Materials Science ,Atomic physics ,Bimetallic strip ,Beam (structure) - Abstract
In this paper, a chemically sensitive local characterization technique is used to characterize fullerene peapods containing two metal atoms within each fullerene. By combining bright-field imaging, high-angle annular dark-field imaging, and electron energy loss spectroscopy in a scanning transmission electron microscope, unambiguous identification of the metal atoms present is possible. Key to making this possible is aberration correction, which allows atomic resolution at lower beam energies. The peapods can be imaged for several consecutive scans at 80 keV beam energy, and the combination of techniques allows the position as well as the species of the encapsulated atoms to be identified. Movements of the encapsulated atoms are monitored. © 2010 American Chemical Society.
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- 2016
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9. A facile route to self-assembled Hg//MoSI nanowire networks
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Ron C. Doole, Damjan Vengust, Gareth M. Hughes, Zabeada Aslam, Peter D. Nellist, Angus I. Kirkland, A Bleloch, Nicole Grobert, Valeria Nicolosi, Dragan Mihailovic, Kasim Sader, and Neil P. Young
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Mesoscopic physics ,Nanostructure ,Chemistry ,Nanowire ,Molecular electronics ,chemistry.chemical_element ,Nanotechnology ,02 engineering and technology ,General Chemistry ,010402 general chemistry ,021001 nanoscience & nanotechnology ,01 natural sciences ,Catalysis ,0104 chemical sciences ,Self assembled ,Molybdenum ,Materials Chemistry ,Molecule ,Electronics ,0210 nano-technology - Abstract
Nanotechnology crucially depends on new molecular-scale materials with tunable properties. In molecular electronics, building blocks have been reduced to single molecules, while connectors have largely remained at the mesoscopic scale. As a result, the behaviour of such devices is largely governed by interface effects and hence, currently, attention is focused on finding suitable molecular-scale alternatives. In this paper we discuss a new generation of one-dimensional inorganic nanostructures aimed at to replacing the mesoscopic connectors currently used in the electronics industry. We demonstrate how chemical functionalisation of nanowires consisting of molybdenum, sulphur and iodine in conjunction with very low concentrations of molecular mercury leads to one-dimensional systems which can be easily connected opening up new pathways to controlled deposition and interface formation. © 2010 The Royal Society of Chemistry and the Centre National de la Recherche Scientifique.
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- 2016
10. Confined crystals of the smallest phase-change material
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S. Ravi P. Silva, Kasim Sader, Mark H. Rümmeli, Cristina E. Giusca, Bernd Büchner, Hidetsugu Shiozawa, Felix Börrnert, Jeremy Sloan, and Vlad Stolojan
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3D optical data storage ,Letter ,Materials science ,Nanowire ,Bioengineering ,Nanotechnology ,02 engineering and technology ,Carbon nanotube ,010402 general chemistry ,01 natural sciences ,law.invention ,Phase-change materials ,law ,Phase (matter) ,Limit (music) ,Miniaturization ,General Materials Science ,carbon nanotubes ,electron microscopy ,business.industry ,Mechanical Engineering ,General Chemistry ,GeTe ,021001 nanoscience & nanotechnology ,Condensed Matter Physics ,Phase-change material ,0104 chemical sciences ,scanning tunneling microscopy ,Optoelectronics ,Scanning tunneling microscope ,0210 nano-technology ,business - Abstract
The demand for high-density memory in tandem with limitations imposed by the minimum feature size of current storage devices has created a need for new materials that can store information in smaller volumes than currently possible. Successfully employed in commercial optical data storage products, phase-change materials, that can reversibly and rapidly change from an amorphous phase to a crystalline phase when subject to heating or cooling have been identified for the development of the next generation electronic memories. There are limitations to the miniaturization of these devices due to current synthesis and theoretical considerations that place a lower limit of 2 nm on the minimum bit size, below which the material does not transform in the structural phase. We show here that by using carbon nanotubes of less than 2 nm diameter as templates phase-change nanowires confined to their smallest conceivable scale are obtained. Contrary to previous experimental evidence and theoretical expectations, the nanowires are found to crystallize at this scale and display amorphous-to-crystalline phase changes, fulfilling an important prerequisite of a memory element. We show evidence for the smallest phase-change material, extending thus the size limit to explore phase-change memory devices at extreme scales.
- Published
- 2013
11. Cryo-EM structure of the dimeric Rhodobacter sphaeroides RC-LH1 core complex at 2.9 Å: the structural basis for dimerisation
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Kasim Sader, Pablo Castro-Hartmann, Philip J. Jackson, Tristan I. Croll, David J. K. Swainsbury, C. Neil Hunter, Andrew Hitchcock, Pu Qian, and Jack H. Salisbury
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Cryo-electron microscopy ,Dimer ,Biophysics ,Light-Harvesting Protein Complexes ,Rhodobacter sphaeroides ,Bioenergetics ,Ring (chemistry) ,Biochemistry ,Sulfoquinovosyl diacylglycerol ,chemistry.chemical_compound ,Bacterial Proteins ,Structural Biology ,light harvesting ,transmembrane proteins ,Photosynthesis ,Molecular Biology ,Research Articles ,biology ,Molecular Structure ,carotenoids ,Cell Biology ,biology.organism_classification ,Quinone ,reaction centre ,Crystallography ,Monomer ,chemistry ,Bacteriochlorophyll ,bacteriochlorophylls ,Dimerization - Abstract
The dimeric reaction centre light-harvesting 1 (RC-LH1) core complex of Rhodobacter sphaeroides converts absorbed light energy to a charge separation, and then it reduces a quinone electron and proton acceptor to a quinol. The angle between the two monomers imposes a bent configuration on the dimer complex, which exerts a major influence on the curvature of the membrane vesicles, known as chromatophores, where the light-driven photosynthetic reactions take place. To investigate the dimerisation interface between two RC-LH1 monomers, we determined the cryogenic electron microscopy structure of the dimeric complex at 2.9 Å resolution. The structure shows that each monomer consists of a central RC partly enclosed by a 14-subunit LH1 ring held in an open state by PufX and protein-Y polypeptides, thus enabling quinones to enter and leave the complex. Two monomers are brought together through N-terminal interactions between PufX polypeptides on the cytoplasmic side of the complex, augmented by two novel transmembrane polypeptides, designated protein-Z, that bind to the outer faces of the two central LH1 β polypeptides. The precise fit at the dimer interface, enabled by PufX and protein-Z, by C-terminal interactions between opposing LH1 αβ subunits, and by a series of interactions with a bound sulfoquinovosyl diacylglycerol lipid, bring together each monomer creating an S-shaped array of 28 bacteriochlorophylls. The seamless join between the two sets of LH1 bacteriochlorophylls provides a path for excitation energy absorbed by one half of the complex to migrate across the dimer interface to the other half.
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