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75 items found (0 items not approved), displaying 1 to 10.[First/Prev] 1, 2, 3, 4, 5, 6, 7, 8 [Next/Last]

Instruments / Technical Area	Publication Details	Published
I03-Macromolecular Crystallography	Resurrection of plant disease resistance proteins via helper NLR bioengineering Mauricio P. Contreras , Hsuan Pai , Muniyandi Selvaraj , Amirali Toghani , David M. Lawson , Yasin Tumtas , Cian Duggan , Enoch Lok Him Yuen , Clare E. M. Stevenson , Adeline Harant , Abbas Maqbool , Chih-Hang Wu , Tolga O. Bozkurt , Sophien Kamoun , Lida Derevnina Science Advances 9 DOI: 10.1126/sciadv.adg3861 Diamond Proposal Number(s): [18565] Open Access Show Abstract ▼ Abstract: Parasites counteract host immunity by suppressing helper nucleotide binding and leucine-rich repeat (NLR) proteins that function as central nodes in immune receptor networks. Understanding the mechanisms of immunosuppression can lead to strategies for bioengineering disease resistance. Here, we show that a cyst nematode virulence effector binds and inhibits oligomerization of the helper NLR protein NRC2 by physically preventing intramolecular rearrangements required for activation. An amino acid polymorphism at the binding interface between NRC2 and the inhibitor is sufficient for this helper NLR to evade immune suppression, thereby restoring the activity of multiple disease resistance genes. This points to a potential strategy for resurrecting disease resistance in crop genomes.	May 2023
Krios II-Titan Krios II at Diamond	Diverse cytomotive actins and tubulins share a polymerization switch mechanism conferring robust dynamics James Wagstaff , Vicente J. Planelles-Herrero , Grigory Sharov , Aisha Alnami , Frank Kozielski , Emmanuel Derivery , Jan Lowe Science Advances 9 DOI: 10.1126/sciadv.adf3021 Diamond Proposal Number(s): [23268] Open Access Show Abstract ▼ Abstract: Protein filaments are used in myriads of ways to organize other molecules within cells. Some filament-forming proteins couple the hydrolysis of nucleotides to their polymerization cycle, thus powering the movement of other molecules. These filaments are termed cytomotive. Only members of the actin and tubulin protein superfamilies are known to form cytomotive filaments. We examined the basis of cytomotivity via structural studies of the polymerization cycles of actin and tubulin homologs from across the tree of life. We analyzed published data and performed structural experiments designed to disentangle functional components of these complex filament systems. Our analysis demonstrates the existence of shared subunit polymerization switches among both cytomotive actins and tubulins, i.e., the conformation of subunits switches upon assembly into filaments. These cytomotive switches can explain filament robustness, by enabling the coupling of kinetic and structural polarities required for cytomotive behaviors and by ensuring that single cytomotive filaments do not fall apart.	Mar 2023
I18-Microfocus Spectroscopy	Observational constraints on the process and products of Martian serpentinization Benjamin M. Tutolo , Nicholas J. Tosca Science Advances 9 DOI: 10.1126/sciadv.add8472 Diamond Proposal Number(s): [15947] Open Access Show Abstract ▼ Abstract: The alteration of olivine-rich rocks to serpentine minerals, (hydr)oxides, and aqueous hydrogen through serpentinization is long thought to have influenced the distribution of habitable environments on early Mars and the evolution of the early Martian hydrosphere and atmosphere. Nevertheless, the planetary importance of Martian serpentinization has remained a matter of debate. To constrain the process and products of Martian serpentinization, we studied serpentinized iron-rich olivines from the 1.1-billion-year Duluth Complex. These data indicate that serpentinized iron-rich olivine would have been accompanied by a fivefold increase in hydrogen production relative to serpentinized terrestrial mantle peridotites. In contrast to previous expectations, this style of serpentinization yields hisingerite as the dominant iron serpentine mineral at comparatively low temperature and pH, consistent with meteorite mineralogy and in situ rover data. The widespread occurrence of oxidized iron-bearing phyllosilicates in highly magnetized regions of the Martian crust supports the hypothesis that serpentinization was more pervasive on early Mars than currently estimated.	Feb 2023
I05-ARPES	Electronic structure and correlations in planar trilayer nickelate Pr4Ni3O8 Haoxiang Li , Peipei Hao , Junjie Zhang , Kyle Gordon , A. Garrison Linn , Xinglong Chen , Hong Zheng , Xiaoqing Zhou , J. F. Mitchell , D. S. Dessau Science Advances 9 DOI: 10.1126/sciadv.ade4418 Diamond Proposal Number(s): [17595] Open Access Show Abstract ▼ Abstract: The discovery of superconductivity in planar nickelates raises the question of how the electronic structure and correlations of Ni1+ compounds compare to those of the Cu2+ cuprate superconductors. Here, we present an angle-resolved photoemission spectroscopy (ARPES) study of the trilayer nickelate Pr4Ni3O8, revealing a Fermi surface resembling that of the hole-doped cuprates but with critical differences. Specifically, the main portions of the Fermi surface are extremely similar to that of the bilayer cuprates, with an additional piece that can accommodate additional hole doping. We find that the electronic correlations are about twice as strong in the nickelates and are almost k-independent, indicating that they originate from a local effect, likely the Mott interaction, whereas cuprate interactions are somewhat less local. Nevertheless, the nickelates still demonstrate the strange-metal behavior in the electron scattering rates. Understanding the similarities and differences between these two families of strongly correlated superconductors is an important challenge.	Jan 2023
Krios I-Titan Krios I at Diamond	Mechanisms of DNA opening revealed in AAA+ transcription complex structures Fuzhou Ye , Forson Gao , Xiaojiao Liu , Martin Burt , Xiaodong Zhang Science Advances 8 DOI: 10.1126/sciadv.add3479 Open Access Show Abstract ▼ Abstract: Gene transcription is carried out by RNA polymerase (RNAP) and requires the conversion of the initial closed promoter complex, where DNA is double stranded, to a transcription-competent open promoter complex, where DNA is opened up. In bacteria, RNAP relies on σ factors for its promoter specificities. Using a special form of sigma factor (σ54), which forms a stable closed complex and requires its activator that belongs to the AAA+ ATPases (ATPases associated with diverse cellular activities), we obtained cryo–electron microscopy structures of transcription initiation complexes that reveal a previously unidentified process of DNA melting opening. The σ54 amino terminus threads through the locally opened up DNA and then becomes enclosed by the AAA+ hexameric ring in the activator-bound intermediate complex. Our structures suggest how ATP hydrolysis by the AAA+ activator could remove the σ54 inhibition while helping to open up DNA, using σ54 amino-terminal peptide as a pry bar.	Dec 2022
I04-Macromolecular Crystallography	Fragment-based computational design of antibodies targeting structured epitopes Mauricio Aguilar Rangel , Alice Bedwell , Elisa Costanzi , Ross J. Taylor , Rosaria Russo , Gonçalo J. L. Bernardes , Stefano Ricagno , Judith Frydman , Michele Vendruscolo , Pietro Sormanni Science Advances 8 DOI: 10.1126/sciadv.abp9540 Diamond Proposal Number(s): [20221] Open Access Show Abstract ▼ Abstract: De novo design methods hold the promise of reducing the time and cost of antibody discovery while enabling the facile and precise targeting of predetermined epitopes. Here, we describe a fragment-based method for the combinatorial design of antibody binding loops and their grafting onto antibody scaffolds. We designed and tested six single-domain antibodies targeting different epitopes on three antigens, including the receptor-binding domain of the SARS-CoV-2 spike protein. Biophysical characterization showed that all designs are stable and bind their intended targets with affinities in the nanomolar range without in vitro affinity maturation. We further discuss how a high-resolution input antigen structure is not required, as similar predictions are obtained when the input is a crystal structure or a computer-generated model. This computational procedure, which readily runs on a laptop, provides a starting point for the rapid generation of lead antibodies binding to preselected epitopes.	Nov 2022
I18-Microfocus Spectroscopy	Single-crystal organometallic perovskite optical fibers Yongfeng Zhou , Michael A. Parkes , Jinshuai Zhang , Yufei Wang , Michael Ruddlesden , Helen H. Fielding , Lei Su Science Advances 8 DOI: 10.1126/sciadv.abq8629 Diamond Proposal Number(s): [31047, 26697] Open Access Show Abstract ▼ Abstract: Semiconductors in their optical-fiber forms are desirable. Single-crystal organometallic halide perovskites have attractive optoelectronic properties and therefore are suitable fiber-optic platforms. However, single-crystal organometallic perovskite optical fibers have not been reported before due to the challenge of one-directional single-crystal growth in solution. Here, we report a solution-processed approach to continuously grow single-crystal organometallic perovskite optical fibers with controllable diameters and lengths. For single-crystal MAPbBr3 (MA = CH3NH3+) perovskite optical fiber made using our method, it demonstrates low transmission losses (<0.7 dB/cm), mechanical flexibilities (a bending radius down to 3.5 mm), and mechanical deformation–tunable photoluminescence in organometallic perovskites. Moreover, the light confinement provided by our organometallic perovskite optical fibers leads to three-photon absorption (3PA), in contrast with 2PA in bulk single crystals under the same experimental conditions. The single-crystal organometallic perovskite optical fibers have the potential in future optoelectronic applications.	Sep 2022
I24-Microfocus Macromolecular Crystallography	Patched 1 regulates Smoothened by controlling sterol binding to its extracellular cysteine-rich domain Maia Kinnebrew , Rachel E. Woolley , T. Bertie Ansell , Eamon F. X. Byrne , Sara Frigui , Giovanni Luchetti , Ria Sircar , Sigrid Nachtergaele , Laurel Mydock-Mcgrane , Kathiresan Krishnan , Simon Newstead , Mark S. P. Sansom , Douglas F. Covey , Christian Siebold , Rajat Rohatgi Science Advances 8 DOI: 10.1126/sciadv.abm5563 Diamond Proposal Number(s): [14744, 19946] Open Access Show Abstract ▼ Abstract: Smoothened (SMO) transduces the Hedgehog (Hh) signal across the plasma membrane in response to accessible cholesterol. Cholesterol binds SMO at two sites: one in the extracellular cysteine-rich domain (CRD) and a second in the transmembrane domain (TMD). How these two sterol-binding sites mediate SMO activation in response to the ligand Sonic Hedgehog (SHH) remains unknown. We find that mutations in the CRD (but not the TMD) reduce the fold increase in SMO activity triggered by SHH. SHH also promotes the photocrosslinking of a sterol analog to the CRD in intact cells. In contrast, sterol binding to the TMD site boosts SMO activity regardless of SHH exposure. Mutational and computational analyses show that these sites are in allosteric communication despite being 45 angstroms apart. Hence, sterols function as both SHH-regulated orthosteric ligands at the CRD and allosteric ligands at the TMD to regulate SMO activity and Hh signaling.	Jun 2022
I03-Macromolecular Crystallography	Structural basis for long-chain isoprenoid synthesis by cis-prenyltransferases Moshe Giladi , Michal Lisnyansky Bar-El , Pavla Vaňková , Alisa Ferofontov , Emelia Melvin , Suha Alkaderi , Daniel Kavan , Boris Redko , Elvira Haimov , Reuven Wiener , Petr Man , Yoni Haitin Science Advances 8 DOI: 10.1126/sciadv.abn1171 Diamond Proposal Number(s): [19884] Open Access Show Abstract ▼ Abstract: Isoprenoids are synthesized by the prenyltransferase superfamily, which is subdivided according to the product stereoisomerism and length. In short- and medium-chain isoprenoids, product length correlates with active site volume. However, enzymes synthesizing long-chain products and rubber synthases fail to conform to this paradigm, because of an unexpectedly small active site. Here, we focused on the human cis-prenyltransferase complex (hcis-PT), residing at the endoplasmic reticulum membrane and playing a crucial role in protein glycosylation. Crystallographic investigation of hcis-PT along the reaction cycle revealed an outlet for the elongating product. Hydrogen-deuterium exchange mass spectrometry analysis showed that the hydrophobic active site core is flanked by dynamic regions consistent with separate inlet and outlet orifices. Last, using a fluorescence substrate analog, we show that product elongation and membrane association are closely correlated. Together, our results support direct membrane insertion of the elongating isoprenoid during catalysis, uncoupling active site volume from product length.	May 2022
Krios I-Titan Krios I at Diamond	A bioactive phlebovirus-like envelope protein in a hookworm endogenous virus Monique Merchant , Carlos P. Mata , Yangci Liu , Haoming Zhai , Anna V. Protasio , Yorgo Modis Science Advances 8 DOI: 10.1126/sciadv.abj6894 Diamond Proposal Number(s): [17434, 20121] Open Access Show Abstract ▼ Abstract: Endogenous viral elements (EVEs), accounting for 15% of our genome, serve as a genetic reservoir from which new genes can emerge. Nematode EVEs are particularly diverse and informative of virus evolution. We identify Atlas virus—an intact retrovirus-like EVE in the human hookworm Ancylostoma ceylanicum, with an envelope protein genetically related to GN-GC glycoproteins from the family Phenuiviridae. A cryo-EM structure of Atlas GC reveals a class II viral membrane fusion protein fold not previously seen in retroviruses. Atlas GC has the structural hallmarks of an active fusogen. Atlas GC trimers insert into membranes with endosomal lipid compositions and low pH. When expressed on the plasma membrane, Atlas GC has cell-cell fusion activity. With its preserved biological activities, Atlas GC has the potential to acquire a cellular function. Our work reveals structural plasticity in reverse-transcribing RNA viruses.	May 2022

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