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      Structure of a 1.5-MDa adhesin that binds its Antarctic bacterium to diatoms and ice

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          Abstract

          Structure of a bacterial adhesin reveals its role in forming a mixed-species symbiotic community with diatoms on sea ice.

          Abstract

          Bacterial adhesins are modular cell-surface proteins that mediate adherence to other cells, surfaces, and ligands. The Antarctic bacterium Marinomonas primoryensis uses a 1.5-MDa adhesin comprising over 130 domains to position it on ice at the top of the water column for better access to oxygen and nutrients. We have reconstructed this 0.6-μm-long adhesin using a “dissect and build” structural biology approach and have established complementary roles for its five distinct regions. Domains in region I (RI) tether the adhesin to the type I secretion machinery in the periplasm of the bacterium and pass it through the outer membrane. RII comprises ~120 identical immunoglobulin-like β-sandwich domains that rigidify on binding Ca 2+ to project the adhesion regions RIII and RIV into the medium. RIII contains ligand-binding domains that join diatoms and bacteria together in a mixed-species community on the underside of sea ice where incident light is maximal. RIV is the ice-binding domain, and the terminal RV domain contains several “repeats-in-toxin” motifs and a noncleavable signal sequence that target proteins for export via the type I secretion system. Similar structural architecture is present in the adhesins of many pathogenic bacteria and provides a guide to finding and blocking binding domains to weaken infectivity.

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          Most cited references 40

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          REFMAC5 dictionary: organization of prior chemical knowledge and guidelines for its use.

          One of the most important aspects of macromolecular structure refinement is the use of prior chemical knowledge. Bond lengths, bond angles and other chemical properties are used in restrained refinement as subsidiary conditions. This contribution describes the organization and some aspects of the use of the flexible and human/machine-readable dictionary of prior chemical knowledge used by the maximum-likelihood macromolecular-refinement program REFMAC5. The dictionary stores information about monomers which represent the constitutive building blocks of biological macromolecules (amino acids, nucleic acids and saccharides) and about numerous organic/inorganic compounds commonly found in macromolecular crystallography. It also describes the modifications the building blocks undergo as a result of chemical reactions and the links required for polymer formation. More than 2000 monomer entries, 100 modification entries and 200 link entries are currently available. Algorithms and tools for updating and adding new entries to the dictionary have also been developed and are presented here. In many cases, the REFMAC5 dictionary allows entirely automatic generation of restraints within REFMAC5 refinement runs.
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            Type I secretion in gram-negative bacteria.

             P Delepelaire (2004)
            In gram-negative bacteria, type I secretion is carried out by a translocator made up of three proteins that span the cell envelope. One of these proteins is a specific outer membrane protein (OMP) and the other two are cytoplasmic membrane proteins: an ATP-binding cassette (ABC) and the so-called membrane fusion or adaptor protein (MFP). Type I secretion is sec-independent and bypasses the periplasm. This widespread pathway allows the secretion of proteins of diverse sizes and functions via a C-terminal uncleaved secretion signal. This C-terminal secretion signal specifically recognizes the ABC protein, triggering the assembly of the functional trans-envelope complex. This report will mainly deal will recent data concerning the structure and assembly of the secretion complex as well as the effects and role of substrate folding on secretion by this pathway.
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              Structure and biochemistry of cadherins and catenins.

              Classical cadherins mediate specific adhesion at intercellular adherens junctions. Interactions between cadherin ectodomains from apposed cells mediate cell-cell contact, whereas the intracellular region functionally links cadherins to the underlying cytoskeleton. Structural, biophysical, and biochemical studies have provided important insights into the mechanism and specificity of cell-cell adhesion by classical cadherins and their interplay with the cytoskeleton. Adhesive binding arises through exchange of beta strands between the first extracellular cadherin domains (EC1) of partner cadherins from adjacent cells. This "strand-swap" binding mode is common to classical and desmosomal cadherins, but sequence alignments suggest that other cadherins will bind differently. The intracellular region of classical cadherins binds to p120 and beta-catenin, and beta-catenin binds to the F-actin binding protein alpha-catenin. Rather than stably bridging beta-catenin to actin, it appears that alpha-catenin actively regulates the actin cytoskeleton at cadherin-based cell-cell contacts.
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                Author and article information

                Journal
                Sci Adv
                Sci Adv
                SciAdv
                advances
                Science Advances
                American Association for the Advancement of Science
                2375-2548
                August 2017
                09 August 2017
                : 3
                : 8
                Affiliations
                [1 ]Protein Function Discovery Group and Department of Biomedical and Molecular Sciences, Queen’s University, Kingston, Ontario K7L 3N6, Canada.
                [2 ]Institute for Complex Molecular Systems, Eindhoven University of Technology, 5600 MD Eindhoven, Netherlands.
                [3 ]Laboratory of Macromolecular and Organic Chemistry of Department of Chemical Engineering and Chemistry, and Laboratory of Physical Chemistry of Department of Chemical Engineering and Chemistry, Eindhoven University of Technology, 5600 MD Eindhoven, Netherlands.
                [4 ]Faculty of Engineering and Applied Science and Department of Chemical Engineering, Queen’s University, Kingston, Ontario K7L 3N6, Canada.
                [5 ]Institute of Biochemistry, Food Science and Nutrition, Robert H. Smith Faculty of Agriculture, Food and Environment, Hebrew University of Jerusalem, Rehovot 7610001, Israel.
                Author notes
                [*]

                Present address: Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, Nova Scotia B3H 4R2, Canada.

                []Corresponding author. Email: peter.davies@ 123456queensu.ca
                Article
                1701440
                10.1126/sciadv.1701440
                5550230
                Copyright © 2017 The Authors, some rights reserved; exclusive licensee American Association for the Advancement of Science. No claim to original U.S. Government Works. Distributed under a Creative Commons Attribution NonCommercial License 4.0 (CC BY-NC).

                This is an open-access article distributed under the terms of the Creative Commons Attribution-NonCommercial license, which permits use, distribution, and reproduction in any medium, so long as the resultant use is not for commercial advantage and provided the original work is properly cited.

                Funding
                Funded by: doi http://dx.doi.org/10.13039/501100000024, Canadian Institutes of Health Research;
                Award ID: award330435
                Funded by: doi http://dx.doi.org/10.13039/501100000038, Natural Sciences and Engineering Research Council of Canada;
                Award ID: award330436
                Funded by: doi http://dx.doi.org/10.13039/501100000038, Natural Sciences and Engineering Research Council of Canada;
                Award ID: award330438
                Funded by: doi http://dx.doi.org/10.13039/501100000038, Natural Sciences and Engineering Research Council of Canada;
                Award ID: award330439
                Funded by: doi http://dx.doi.org/10.13039/501100000781, European Research Council;
                Award ID: award330440
                Funded by: doi http://dx.doi.org/10.13039/501100000781, European Research Council;
                Award ID: award330437
                Funded by: doi http://dx.doi.org/10.13039/501100000038, Natural Sciences and Engineering Research Council of Canada;
                Award ID: award330441
                Categories
                Research Article
                Research Articles
                SciAdv r-articles
                Life Sciences
                Structural Biology
                Custom metadata
                Justin Noriel

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