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      Sticky organisms create underwater biological adhesives driven by interactions between EGF- and GlcNAc- containing polysaccharides

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          Abstract

          Marine and terrestrial organisms often utilise EGF/EGF-like domains in wet adhesives, yet their roles in adhesion remain unclear. Here, we investigate the Barbatia virescense byssal system and uncover an oxidation-independent, reversible, and robust adhesion mechanism where EGF/EGF-like domain tandem repetitions in adhesive proteins bind robustly to GlcNAc-based biopolymer. EGF/EGF-like-domain-containing proteins demonstrate over three-fold superior underwater adhesion to chitosan compared to the well-known strongest wet-adhesive proteins, mefp-5, and suckerin, when adhering to mica in an surface forces apparatus-based measurement. Additionally, as the degree of acetylation of chitosan decreases from 20.0 to 5.34%, the underwater adhesion energy between mefp-2 and chitosan decreases from |Wad | ≈ 41.80 to 12.92 ± 0.40 mJm −2. This finding highlights the importance of GlcNAc over GlcN in binding with EGF to formulate effective underwater adhesives, expanding our understanding of underwater adhesion and supporting EGF’s functional role in biomedical wet adhesive interfaces, hydrogels, and chitosan applications.

          Abstract

          This study investigates the Barbatia virescense byssal system and reveals additional function for the EGF protein, known for skin regeneration, as a biological adhesive across diverse species, highlighting its possible roles in wet-adhesion applications.

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          AutoDock Vina: improving the speed and accuracy of docking with a new scoring function, efficient optimization, and multithreading.

          AutoDock Vina, a new program for molecular docking and virtual screening, is presented. AutoDock Vina achieves an approximately two orders of magnitude speed-up compared with the molecular docking software previously developed in our lab (AutoDock 4), while also significantly improving the accuracy of the binding mode predictions, judging by our tests on the training set used in AutoDock 4 development. Further speed-up is achieved from parallelism, by using multithreading on multicore machines. AutoDock Vina automatically calculates the grid maps and clusters the results in a way transparent to the user. Copyright 2009 Wiley Periodicals, Inc.
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            MMseqs2 enables sensitive protein sequence searching for the analysis of massive data sets

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              GLYCAM06: a generalizable biomolecular force field. Carbohydrates.

              A new derivation of the GLYCAM06 force field, which removes its previous specificity for carbohydrates, and its dependency on the AMBER force field and parameters, is presented. All pertinent force field terms have been explicitly specified and so no default or generic parameters are employed. The new GLYCAM is no longer limited to any particular class of biomolecules, but is extendible to all molecular classes in the spirit of a small-molecule force field. The torsion terms in the present work were all derived from quantum mechanical data from a collection of minimal molecular fragments and related small molecules. For carbohydrates, there is now a single parameter set applicable to both alpha- and beta-anomers and to all monosaccharide ring sizes and conformations. We demonstrate that deriving dihedral parameters by fitting to QM data for internal rotational energy curves for representative small molecules generally leads to correct rotamer populations in molecular dynamics simulations, and that this approach removes the need for phase corrections in the dihedral terms. However, we note that there are cases where this approach is inadequate. Reported here are the basic components of the new force field as well as an illustration of its extension to carbohydrates. In addition to reproducing the gas-phase properties of an array of small test molecules, condensed-phase simulations employing GLYCAM06 are shown to reproduce rotamer populations for key small molecules and representative biopolymer building blocks in explicit water, as well as crystalline lattice properties, such as unit cell dimensions, and vibrational frequencies.
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                Author and article information

                Contributors
                dshwang@postech.ac.kr
                Journal
                Nat Commun
                Nat Commun
                Nature Communications
                Nature Publishing Group UK (London )
                2041-1723
                2 January 2025
                2 January 2025
                2025
                : 16
                : 233
                Affiliations
                [1 ]Division of Environmental Science and Engineering, Pohang University of Science and Technology, ( https://ror.org/04xysgw12) Pohang, South Korea
                [2 ]Institute of Chemical Process, Seoul National University, Gwanak-gu, ( https://ror.org/04h9pn542) Seoul, Republic of Korea
                Author information
                http://orcid.org/0000-0002-5313-6249
                http://orcid.org/0000-0003-1443-7118
                http://orcid.org/0000-0002-7573-5648
                http://orcid.org/0000-0002-2487-2255
                Article
                55476
                10.1038/s41467-024-55476-4
                11697411
                39747843
                dea357d6-f2bc-44ad-91da-a9bfe628fdec
                © The Author(s) 2024

                Open Access This article is licensed under a Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International License, which permits any non-commercial use, sharing, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if you modified the licensed material. You do not have permission under this licence to share adapted material derived from this article or parts of it. The images or other third party material in this article are included in the article’s Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by-nc-nd/4.0/.

                History
                : 26 February 2024
                : 13 December 2024
                Funding
                Funded by: FundRef https://doi.org/10.13039/501100003725, National Research Foundation of Korea (NRF);
                Award ID: No.2022R1A2C2007874
                Award ID: 2022R1I1A1A01064177
                Award ID: RS-2024-00340746
                Award Recipient :
                Categories
                Article
                Custom metadata
                © Springer Nature Limited 2025

                Uncategorized
                bioinspired materials,marine biology,biopolymers in vivo,computational models
                Uncategorized
                bioinspired materials, marine biology, biopolymers in vivo, computational models

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