LIVIVO - The Search Portal for Life Sciences

zur deutschen Oberfläche wechseln
Advanced search

Search results

Result 1 - 10 of total 95

Search options

  1. Article: Neutron macromolecular crystallography.

    Blakeley, Matthew P / Podjarny, Alberto D

    Emerging topics in life sciences

    2021  Volume 2, Issue 1, Page(s) 39–55

    Abstract: Neutron diffraction techniques permit direct determination of the hydrogen (H) and deuterium (D) positions in crystal structures of biological macromolecules at resolutions of ∼1.5 and 2.5 Å, respectively. In addition, neutron diffraction data can be ... ...

    Abstract Neutron diffraction techniques permit direct determination of the hydrogen (H) and deuterium (D) positions in crystal structures of biological macromolecules at resolutions of ∼1.5 and 2.5 Å, respectively. In addition, neutron diffraction data can be collected from a single crystal at room temperature without radiation damage issues. By locating the positions of H/D-atoms, protonation states and water molecule orientations can be determined, leading to a more complete understanding of many biological processes and drug-binding. In the last ca. 5 years, new beamlines have come online at reactor neutron sources, such as BIODIFF at Heinz Maier-Leibnitz Zentrum and IMAGINE at Oak Ridge National Laboratory (ORNL), and at spallation neutron sources, such as MaNDi at ORNL and iBIX at the Japan Proton Accelerator Research Complex. In addition, significant improvements have been made to existing beamlines, such as LADI-III at the Institut Laue-Langevin. The new and improved instrumentations are allowing sub-mm3 crystals to be regularly used for data collection and permitting the study of larger systems (unit-cell edges >100 Å). Owing to this increase in capacity and capability, many more studies have been performed and for a wider range of macromolecules, including enzymes, signalling proteins, transport proteins, sugar-binding proteins, fluorescent proteins, hormones and oligonucleotides; of the 126 structures deposited in the Protein Data Bank, more than half have been released since 2013 (65/126, 52%). Although the overall number is still relatively small, there are a growing number of examples for which neutron macromolecular crystallography has provided the answers to questions that otherwise remained elusive.
    Language English
    Publishing date 2021-01-28
    Publishing country England
    Document type Journal Article
    ZDB-ID 2882721-1
    ISSN 2397-8554 ; 2397-8554 ; 2397-8562
    ISSN (online) 2397-8554
    ISSN 2397-8554 ; 2397-8562
    DOI 10.1042/ETLS20170083
    Database MEDical Literature Analysis and Retrieval System OnLINE

    More links

    Kategorien

  2. Article ; Online: Neutron diffraction from a microgravity-grown crystal reveals the active site hydrogens of the internal aldimine form of tryptophan synthase.

    Drago, Victoria N / Devos, Juliette M / Blakeley, Matthew P / Forsyth, V Trevor / Parks, Jerry M / Kovalevsky, Andrey / Mueser, Timothy C

    Cell reports. Physical science

    2024  Volume 5, Issue 2

    Abstract: Pyridoxal 5'-phosphate (PLP), the biologically active form of vitamin ... ...

    Abstract Pyridoxal 5'-phosphate (PLP), the biologically active form of vitamin B
    Language English
    Publishing date 2024-02-12
    Publishing country United States
    Document type Journal Article
    ISSN 2666-3864
    ISSN (online) 2666-3864
    DOI 10.1016/j.xcrp.2024.101827
    Database MEDical Literature Analysis and Retrieval System OnLINE

    More links

    Kategorien

  3. Article ; Online: Revealing protonation states and tracking substrate in serine hydroxymethyltransferase with room-temperature X-ray and neutron crystallography.

    Drago, Victoria N / Campos, Claudia / Hooper, Mattea / Collins, Aliyah / Gerlits, Oksana / Weiss, Kevin L / Blakeley, Matthew P / Phillips, Robert S / Kovalevsky, Andrey

    Communications chemistry

    2023  Volume 6, Issue 1, Page(s) 162

    Abstract: Pyridoxal 5'-phosphate (PLP)-dependent enzymes utilize a vitamin ... ...

    Abstract Pyridoxal 5'-phosphate (PLP)-dependent enzymes utilize a vitamin B
    Language English
    Publishing date 2023-08-03
    Publishing country England
    Document type Journal Article
    ZDB-ID 2929562-2
    ISSN 2399-3669 ; 2399-3669
    ISSN (online) 2399-3669
    ISSN 2399-3669
    DOI 10.1038/s42004-023-00964-9
    Database MEDical Literature Analysis and Retrieval System OnLINE

    More links

    Kategorien

  4. Article ; Online: Neutron crystallography reveals mechanisms used by Pseudomonas aeruginosa for host-cell binding.

    Gajdos, Lukas / Blakeley, Matthew P / Haertlein, Michael / Forsyth, V Trevor / Devos, Juliette M / Imberty, Anne

    Nature communications

    2022  Volume 13, Issue 1, Page(s) 194

    Abstract: The opportunistic pathogen Pseudomonas aeruginosa, a major cause of nosocomial infections, uses carbohydrate-binding proteins (lectins) as part of its binding to host cells. The fucose-binding lectin, LecB, displays a unique carbohydrate-binding site ... ...

    Abstract The opportunistic pathogen Pseudomonas aeruginosa, a major cause of nosocomial infections, uses carbohydrate-binding proteins (lectins) as part of its binding to host cells. The fucose-binding lectin, LecB, displays a unique carbohydrate-binding site that incorporates two closely located calcium ions bridging between the ligand and protein, providing specificity and unusually high affinity. Here, we investigate the mechanisms involved in binding based on neutron crystallography studies of a fully deuterated LecB/fucose/calcium complex. The neutron structure, which includes the positions of all the hydrogen atoms, reveals that the high affinity of binding may be related to the occurrence of a low-barrier hydrogen bond induced by the proximity of the two calcium ions, the presence of coordination rings between the sugar, calcium and LecB, and the dynamic behaviour of bridging water molecules at room temperature. These key structural details may assist in the design of anti-adhesive compounds to combat multi-resistance bacterial infections.
    MeSH term(s) Bacterial Adhesion/genetics ; Binding Sites ; Calcium/metabolism ; Cloning, Molecular ; Cross Infection/microbiology ; Crystallography, X-Ray ; Deuterium/chemistry ; Escherichia coli/genetics ; Escherichia coli/metabolism ; Fucose/chemistry ; Fucose/metabolism ; Gene Expression ; Genetic Vectors/chemistry ; Genetic Vectors/metabolism ; Humans ; Hydrogen Bonding ; Lectins/chemistry ; Lectins/genetics ; Lectins/metabolism ; Ligands ; Neutrons ; Protein Binding ; Pseudomonas Infections/microbiology ; Pseudomonas aeruginosa/chemistry ; Pseudomonas aeruginosa/genetics ; Pseudomonas aeruginosa/metabolism ; Recombinant Proteins/chemistry ; Recombinant Proteins/genetics ; Recombinant Proteins/metabolism ; Water/metabolism
    Chemical Substances LecB protein, Pseudomonas aeruginosa ; Lectins ; Ligands ; Recombinant Proteins ; Water (059QF0KO0R) ; Fucose (28RYY2IV3F) ; Deuterium (AR09D82C7G) ; Calcium (SY7Q814VUP)
    Language English
    Publishing date 2022-01-11
    Publishing country England
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 2553671-0
    ISSN 2041-1723 ; 2041-1723
    ISSN (online) 2041-1723
    ISSN 2041-1723
    DOI 10.1038/s41467-021-27871-8
    Database MEDical Literature Analysis and Retrieval System OnLINE

    More links

    Kategorien

  5. Article: Microgravity crystallization of perdeuterated tryptophan synthase for neutron diffraction.

    Drago, Victoria N / Devos, Juliette M / Blakeley, Matthew P / Forsyth, V Trevor / Kovalevsky, Andrey Y / Schall, Constance A / Mueser, Timothy C

    NPJ microgravity

    2022  Volume 8, Issue 1, Page(s) 13

    Abstract: Biologically active vitamin ... ...

    Abstract Biologically active vitamin B
    Language English
    Publishing date 2022-05-04
    Publishing country United States
    Document type Journal Article
    ZDB-ID 2823626-9
    ISSN 2373-8065
    ISSN 2373-8065
    DOI 10.1038/s41526-022-00199-3
    Database MEDical Literature Analysis and Retrieval System OnLINE

    More links

    Kategorien

  6. Article ; Online: Room temperature crystallography of human acetylcholinesterase bound to a substrate analogue 4K-TMA: Towards a neutron structure.

    Gerlits, Oksana / Blakeley, Matthew P / Keen, David A / Radić, Zoran / Kovalevsky, Andrey

    Current research in structural biology

    2021  Volume 3, Page(s) 206–215

    Abstract: Acetylcholinesterase (AChE) catalyzes hydrolysis of acetylcholine thereby terminating cholinergic nerve impulses for efficient neurotransmission. Human AChE (hAChE) is a target of nerve agent and pesticide organophosphorus compounds that covalently ... ...

    Abstract Acetylcholinesterase (AChE) catalyzes hydrolysis of acetylcholine thereby terminating cholinergic nerve impulses for efficient neurotransmission. Human AChE (hAChE) is a target of nerve agent and pesticide organophosphorus compounds that covalently attach to the catalytic Ser203 residue. Reactivation of inhibited hAChE can be achieved with nucleophilic antidotes, such as oximes. Understanding structural and electrostatic (i.e. protonation states) determinants of the catalytic and reactivation processes is crucial to improve design of oxime reactivators. Here we report X-ray structures of hAChE conjugated with a reversible covalent inhibitor 4K-TMA (4K-TMA:hAChE) at 2.8 ​Å resolution and of 4K-TMA:hAChE conjugate with oxime reactivator methoxime, MMB4 (4K-TMA:hAChE:MMB4) at 2.6 ​Å resolution, both at physiologically relevant room temperature, as well as cryo-crystallographic structure of 4K-TMA:hAChE at 2.4 ​Å resolution. 4K-TMA acts as a substrate analogue reacting with the hydroxyl of Ser203 and generating a reversible tetrahedral hemiketal intermediate that closely resembles the first tetrahedral intermediate state during hAChE-catalyzed acetylcholine hydrolysis. Structural comparisons of room temperature with cryo-crystallographic structures of 4K-TMA:hAChE and published mAChE complexes with 4K-TMA, as well as the effect of MMB4 binding to the peripheral anionic site (PAS) of the 4K-TMA:hAChE complex, revealed only discrete, minor differences. The active center geometry of AChE, already highly evolved for the efficient catalysis, was thus indicative of only minor conformational adjustments to accommodate the tetrahedral intermediate in the hydrolysis of the neurotransmitter acetylcholine (ACh). To map protonation states in the hAChE active site gorge we collected 3.5 ​Å neutron diffraction data paving the way for obtaining higher resolution datasets that will be needed to determine locations of individual hydrogen atoms.
    Language English
    Publishing date 2021-09-06
    Publishing country Netherlands
    Document type Journal Article
    ISSN 2665-928X
    ISSN (online) 2665-928X
    DOI 10.1016/j.crstbi.2021.08.003
    Database MEDical Literature Analysis and Retrieval System OnLINE

    More links

    Kategorien

  7. Article ; Online: Perdeuterated GbpA Enables Neutron Scattering Experiments of a Lytic Polysaccharide Monooxygenase.

    Sørensen, H V / Montserrat-Canals, Mateu / Loose, Jennifer S M / Fisher, S Zoë / Moulin, Martine / Blakeley, Matthew P / Cordara, Gabriele / Bjerregaard-Andersen, Kaare / Krengel, Ute

    ACS omega

    2023  Volume 8, Issue 32, Page(s) 29101–29112

    Abstract: Lytic polysaccharide monooxygenases (LPMOs) are surface-active redox enzymes that catalyze the degradation of recalcitrant polysaccharides, making them important tools for energy production from renewable sources. In addition, LPMOs are important ... ...

    Abstract Lytic polysaccharide monooxygenases (LPMOs) are surface-active redox enzymes that catalyze the degradation of recalcitrant polysaccharides, making them important tools for energy production from renewable sources. In addition, LPMOs are important virulence factors for fungi, bacteria, and viruses. However, many knowledge gaps still exist regarding their catalytic mechanism and interaction with their insoluble, crystalline substrates. Moreover, conventional structural biology techniques, such as X-ray crystallography, usually do not reveal the protonation state of catalytically important residues. In contrast, neutron crystallography is highly suited to obtain this information, albeit with significant sample volume requirements and challenges associated with hydrogen's large incoherent scattering signal. We set out to demonstrate the feasibility of neutron-based techniques for LPMOs using
    Language English
    Publishing date 2023-07-31
    Publishing country United States
    Document type Journal Article
    ISSN 2470-1343
    ISSN (online) 2470-1343
    DOI 10.1021/acsomega.3c02168
    Database MEDical Literature Analysis and Retrieval System OnLINE

    More links

    Kategorien

  8. Article: Joint neutron/X-ray crystal structure of a mechanistically relevant complex of perdeuterated urate oxidase and simulations provide insight into the hydration step of catalysis.

    McGregor, Lindsay / Földes, Tamás / Bui, Soi / Moulin, Martine / Coquelle, Nicolas / Blakeley, Matthew P / Rosta, Edina / Steiner, Roberto A

    IUCrJ

    2021  Volume 8, Issue Pt 1, Page(s) 46–59

    Abstract: Cofactor-independent urate oxidase (UOX) is an ∼137 kDa tetrameric enzyme essential for uric acid (UA) catabolism in many organisms. UA is first oxidized by ... ...

    Abstract Cofactor-independent urate oxidase (UOX) is an ∼137 kDa tetrameric enzyme essential for uric acid (UA) catabolism in many organisms. UA is first oxidized by O
    Language English
    Publishing date 2021-01-01
    Publishing country England
    Document type Journal Article
    ZDB-ID 2754953-7
    ISSN 2052-2525
    ISSN 2052-2525
    DOI 10.1107/S2052252520013615
    Database MEDical Literature Analysis and Retrieval System OnLINE

    More links

    Kategorien

  9. Article ; Online: Protein kinase A in the neutron beam: Insights for catalysis from directly observing protons.

    Gerlits, Oksana / Weiss, Kevin L / Blakeley, Matthew P / Veglia, Gianluigi / Taylor, Susan S / Kovalevsky, Andrey

    Methods in enzymology

    2020  Volume 634, Page(s) 311–331

    Abstract: Protein kinases transmit chemical signals by phosphorylating substrate proteins, thus regulating a multitude of cellular processes. cAMP-dependent protein kinase (PKA), a prototypical enzyme for the whole kinase family, has been the focus of research for ...

    Abstract Protein kinases transmit chemical signals by phosphorylating substrate proteins, thus regulating a multitude of cellular processes. cAMP-dependent protein kinase (PKA), a prototypical enzyme for the whole kinase family, has been the focus of research for several decades, however, the details of the chemical mechanism of phosphoryl group transfer have remained unknown. We used neutron crystallography to map key proton sites and hydrogen bonding interactions in the PKA catalytic subunit (PKAc) in a product complex containing adenosine diphosphate (ADP) and the phosphorylated high affinity protein kinase substrate (pPKS) peptide. To improve neutron diffraction, we deuterated PKAc allowing us to use very small crystals. In the product complex, the phosphoryl group of pPKS is protonated whereas the catalytic Asp166 is not. H/D exchange analysis of the main-chain amides and comparison with the NMR analysis of PKAc with inhibitor peptide complex revealed exchangeable amides that may distinguish the catalytic and inhibited states.
    MeSH term(s) Catalysis ; Cyclic AMP-Dependent Protein Kinases ; Models, Molecular ; Neutrons ; Protons
    Chemical Substances Protons ; Cyclic AMP-Dependent Protein Kinases (EC 2.7.11.11)
    Language English
    Publishing date 2020-01-17
    Publishing country United States
    Document type Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't ; Research Support, U.S. Gov't, Non-P.H.S.
    ISSN 1557-7988
    ISSN (online) 1557-7988
    DOI 10.1016/bs.mie.2019.12.003
    Database MEDical Literature Analysis and Retrieval System OnLINE

    More links

    Kategorien

  10. Article: Neutron structures of

    Kelpšas, Vinardas / Caldararu, Octav / Blakeley, Matthew P / Coquelle, Nicolas / Wierenga, Rikkert K / Ryde, Ulf / von Wachenfeldt, Claes / Oksanen, Esko

    IUCrJ

    2021  Volume 8, Issue Pt 4, Page(s) 633–643

    Abstract: Triosephosphate isomerase (TIM) is a key enzyme in glycolysis that catalyses the interconversion of glyceraldehyde 3-phosphate and dihydroxy-acetone phosphate. This simple reaction involves the shuttling of protons mediated by protolysable side chains. ... ...

    Abstract Triosephosphate isomerase (TIM) is a key enzyme in glycolysis that catalyses the interconversion of glyceraldehyde 3-phosphate and dihydroxy-acetone phosphate. This simple reaction involves the shuttling of protons mediated by protolysable side chains. The catalytic power of TIM is thought to stem from its ability to facilitate the deprotonation of a carbon next to a carbonyl group to generate an enediolate intermediate. The enediolate intermediate is believed to be mimicked by the inhibitor 2-phosphoglycolate (PGA) and the subsequent enediol intermediate by phosphoglycolohydroxamate (PGH). Here, neutron structures of
    Language English
    Publishing date 2021-06-03
    Publishing country England
    Document type Journal Article
    ZDB-ID 2754953-7
    ISSN 2052-2525
    ISSN 2052-2525
    DOI 10.1107/S2052252521004619
    Database MEDical Literature Analysis and Retrieval System OnLINE

    More links

    Kategorien

To top