151
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Yui T, Uto T, Noda K. Extended Ensemble Molecular Dynamics Study of Ammonia-Cellulose I Complex Crystal Models: Free-Energy Landscape and Atomistic Pictures of Ammonia Diffusion in the Crystalline Phase. J Chem Inf Model 2023. [PMID: 37366678 DOI: 10.1021/acs.jcim.3c00106] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/28/2023]
Abstract
Here, we report extended ensemble molecular dynamics simulations of ammonia-cellulose I complex crystal models to evaluate the diffusion behavior of the guest ammonia molecules and the potential of mean force (PMF), namely, the free energy change along the chosen reaction coordinate, for migration of an ammonia molecule in the crystal models. Accelerated molecular dynamics simulations confirmed that ammonia molecules almost exclusively diffused through the hydrophilic channel even when the crystal framework was retained. Adaptive steered molecular dynamics simulations detected distinct PMF peaks with heights of approximately 7 kcal/mol as the ammonia molecule passed through the cellulose-chain layers. Introducing hybrid quantum mechanical and molecular mechanics theory to the adaptive steered molecular dynamics simulation effectively lowered the heights of the PMF peaks to approximately 5 kcal/mol, accompanied by a slight decrease in the baseline. Removal of the ammonia molecules in the neighboring channels resulted in a continuous increase in the baseline for the migration of an ammonia molecule in the hydrophilic channel. When the halves of the crystal model were separated to widen the hydrophilic channel to 0.2 nm, the PMF profiles exhibited an unexpected increase. This resulted from water structuring in the expanded hydrophilic channel, which disappeared with further expansion of the hydrophilic channel to 0.3 nm.
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Affiliation(s)
- Toshifumi Yui
- Department of Applied Chemistry, Faculty of Engineering, University of Miyazaki, Nishi 1-1, Gakuen Kibanadai, Miyazaki 889-2192, Japan
| | - Takuya Uto
- Department of Applied Chemistry, Faculty of Engineering, University of Miyazaki, Nishi 1-1, Gakuen Kibanadai, Miyazaki 889-2192, Japan
- Department of Engineering, Graduate School of Engineering, University of Miyazaki, Nishi 1-1, Gakuen Kibanadai, Miyazaki 889-2192, Japan
| | - Kotaro Noda
- Design Engineering Section, Ceramic Packages Division 1, KYOCERA Corporation, Kokubu Yamashita-cho 1-1, Kirishima, Kagoshima 899-4396, Japan
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152
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Lenza MP, Egia-Mendikute L, Antoñana-Vildosola A, Soares CO, Coelho H, Corzana F, Bosch A, Manisha P, Quintana JI, Oyenarte I, Unione L, Moure MJ, Azkargorta M, Atxabal U, Sobczak K, Elortza F, Sutherland JD, Barrio R, Marcelo F, Jiménez-Barbero J, Palazon A, Ereño-Orbea J. Structural insights into Siglec-15 reveal glycosylation dependency for its interaction with T cells through integrin CD11b. Nat Commun 2023; 14:3496. [PMID: 37311743 DOI: 10.1038/s41467-023-39119-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2022] [Accepted: 05/26/2023] [Indexed: 06/15/2023] Open
Abstract
Sialic acid-binding Ig-like lectin 15 (Siglec-15) is an immune modulator and emerging cancer immunotherapy target. However, limited understanding of its structure and mechanism of action restrains the development of drug candidates that unleash its full therapeutic potential. In this study, we elucidate the crystal structure of Siglec-15 and its binding epitope via co-crystallization with an anti-Siglec-15 blocking antibody. Using saturation transfer-difference nuclear magnetic resonance (STD-NMR) spectroscopy and molecular dynamics simulations, we reveal Siglec-15 binding mode to α(2,3)- and α(2,6)-linked sialic acids and the cancer-associated sialyl-Tn (STn) glycoform. We demonstrate that binding of Siglec-15 to T cells, which lack STn expression, depends on the presence of α(2,3)- and α(2,6)-linked sialoglycans. Furthermore, we identify the leukocyte integrin CD11b as a Siglec-15 binding partner on human T cells. Collectively, our findings provide an integrated understanding of the structural features of Siglec-15 and emphasize glycosylation as a crucial factor in controlling T cell responses.
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Affiliation(s)
- Maria Pia Lenza
- Chemical Glycobiology lab, Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Bizkaia Technology Park, Building 800, 48160, Derio, Bizkaia, Spain
| | - Leire Egia-Mendikute
- Cancer Immunology and Immunotherapy Lab, Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Bizkaia Technology Park, Building 801A, 48160, Derio, Bizkaia, Spain
| | - Asier Antoñana-Vildosola
- Cancer Immunology and Immunotherapy Lab, Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Bizkaia Technology Park, Building 801A, 48160, Derio, Bizkaia, Spain
| | - Cátia O Soares
- Associate Laboratory i4HB-Institute for Health and Bioeconomy, NOVA School of Science and Technology, Caparica campus, 2829-516, Caparica, Portugal
- UCIBIO, Department of Chemistry, NOVA School of Science and Technology, Caparica campus, 2829-516, Caparica, Portugal
| | - Helena Coelho
- Associate Laboratory i4HB-Institute for Health and Bioeconomy, NOVA School of Science and Technology, Caparica campus, 2829-516, Caparica, Portugal
- UCIBIO, Department of Chemistry, NOVA School of Science and Technology, Caparica campus, 2829-516, Caparica, Portugal
| | - Francisco Corzana
- Department of Chemistry, University of La Rioja, The Center for Research in Chemical Synthesis, Madre de Dios 53, E-26006, Logroño, Spain
| | - Alexandre Bosch
- Cancer Immunology and Immunotherapy Lab, Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Bizkaia Technology Park, Building 801A, 48160, Derio, Bizkaia, Spain
| | - Prodhi Manisha
- Cancer Immunology and Immunotherapy Lab, Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Bizkaia Technology Park, Building 801A, 48160, Derio, Bizkaia, Spain
| | - Jon Imanol Quintana
- Chemical Glycobiology lab, Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Bizkaia Technology Park, Building 800, 48160, Derio, Bizkaia, Spain
| | - Iker Oyenarte
- Chemical Glycobiology lab, Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Bizkaia Technology Park, Building 800, 48160, Derio, Bizkaia, Spain
| | - Luca Unione
- Chemical Glycobiology lab, Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Bizkaia Technology Park, Building 800, 48160, Derio, Bizkaia, Spain
- Ikerbasque, Basque Foundation for Science, Bilbao, Spain
| | - María Jesús Moure
- Chemical Glycobiology lab, Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Bizkaia Technology Park, Building 800, 48160, Derio, Bizkaia, Spain
| | - Mikel Azkargorta
- Proteomics Platform, CIC bioGUNE, CIBERehd, Basque Research and Technology Alliance (BRTA), Bizkaia Technology Park, Building 800, 48160, Derio, Spain
| | - Unai Atxabal
- Chemical Glycobiology lab, Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Bizkaia Technology Park, Building 800, 48160, Derio, Bizkaia, Spain
| | - Klaudia Sobczak
- Chemical Glycobiology lab, Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Bizkaia Technology Park, Building 800, 48160, Derio, Bizkaia, Spain
| | - Felix Elortza
- Proteomics Platform, CIC bioGUNE, CIBERehd, Basque Research and Technology Alliance (BRTA), Bizkaia Technology Park, Building 800, 48160, Derio, Spain
| | - James D Sutherland
- Ubiquitin-likes and Development Lab, Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Bizkaia Technology Park, Building 801A, 48160, Derio, Bizkaia, Spain
| | - Rosa Barrio
- Ubiquitin-likes and Development Lab, Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Bizkaia Technology Park, Building 801A, 48160, Derio, Bizkaia, Spain
| | - Filipa Marcelo
- Associate Laboratory i4HB-Institute for Health and Bioeconomy, NOVA School of Science and Technology, Caparica campus, 2829-516, Caparica, Portugal
- UCIBIO, Department of Chemistry, NOVA School of Science and Technology, Caparica campus, 2829-516, Caparica, Portugal
| | - Jesús Jiménez-Barbero
- Chemical Glycobiology lab, Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Bizkaia Technology Park, Building 800, 48160, Derio, Bizkaia, Spain.
- Ikerbasque, Basque Foundation for Science, Bilbao, Spain.
- Department of Organic & Inorganic Chemistry, Faculty of Science and Technology, University of the Basque Country, EHU-UPV, 48940, Leioa, Bizkaia, Spain.
- Centro de Investigacion Biomedica En Red de Enfermedades Respiratorias, 28029, Madrid, Spain.
| | - Asis Palazon
- Cancer Immunology and Immunotherapy Lab, Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Bizkaia Technology Park, Building 801A, 48160, Derio, Bizkaia, Spain.
- Ikerbasque, Basque Foundation for Science, Bilbao, Spain.
| | - June Ereño-Orbea
- Chemical Glycobiology lab, Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Bizkaia Technology Park, Building 800, 48160, Derio, Bizkaia, Spain.
- Ikerbasque, Basque Foundation for Science, Bilbao, Spain.
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153
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Deubler M, Weißenborn L, Leukel S, Horn AHC, Eichler J, Sticht H. Computational Characterization of the Binding Properties of the HIV1-Neutralizing Antibody PG16 and Design of PG16-Derived CDRH3 Peptides. BIOLOGY 2023; 12:824. [PMID: 37372110 DOI: 10.3390/biology12060824] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/28/2023] [Revised: 05/28/2023] [Accepted: 06/02/2023] [Indexed: 06/29/2023]
Abstract
PG16 is a broadly neutralizing antibody that binds to the gp120 subunit of the HIV-1 Env protein. The major interaction site is formed by the unusually long complementarity determining region (CDR) H3. The CDRH3 residue Tyr100H is known to represent a tyrosine sulfation site; however, this modification is not present in the experimental complex structure of PG16 with full-length HIV-1 Env. To investigate the role of sulfation for this complex, we modeled the sulfation of Tyr100H and compared the dynamics and energetics of the modified and unmodified complex by molecular dynamics simulations at the atomic level. Our results show that sulfation does not affect the overall conformation of CDRH3, but still enhances gp120 interactions both at the site of modification and for the neighboring residues. This stabilization affects not only protein-protein contacts, but also the interactions between PG16 and the gp120 glycan shield. Furthermore, we also investigated whether PG16-CDRH3 is a suitable template for the development of peptide mimetics. For a peptide spanning residues 93-105 of PG16, we obtained an experimental EC50 value of 3nm for the binding of gp120 to the peptide. This affinity can be enhanced by almost one order of magnitude by artificial disulfide bonding between residues 99 and 100F. In contrast, any truncation results in significantly lower affinity, suggesting that the entire peptide segment is involved in gp120 recognition. Given their high affinity, it should be possible to further optimize the PG16-derived peptides as potential inhibitors of HIV invasion.
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Affiliation(s)
- Manuel Deubler
- Division of Bioinformatics, Institute of Biochemistry, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), 91054 Erlangen, Germany
| | - Lucas Weißenborn
- Department of Chemistry and Pharmacy, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), 91058 Erlangen, Germany
| | - Simon Leukel
- Department of Chemistry and Pharmacy, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), 91058 Erlangen, Germany
| | - Anselm H C Horn
- Division of Bioinformatics, Institute of Biochemistry, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), 91054 Erlangen, Germany
- Erlangen National High Performance Computing Center (NHR@FAU), Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), 91058 Erlangen, Germany
| | - Jutta Eichler
- Department of Chemistry and Pharmacy, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), 91058 Erlangen, Germany
| | - Heinrich Sticht
- Division of Bioinformatics, Institute of Biochemistry, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), 91054 Erlangen, Germany
- Erlangen National High Performance Computing Center (NHR@FAU), Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), 91058 Erlangen, Germany
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154
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Le HT, Liu M, Grimes CL. Application of bioanalytical and computational methods in decoding the roles of glycans in host-pathogen interactions. Curr Opin Chem Biol 2023; 74:102301. [PMID: 37080155 PMCID: PMC10296625 DOI: 10.1016/j.cbpa.2023.102301] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2022] [Revised: 03/09/2023] [Accepted: 03/14/2023] [Indexed: 04/22/2023]
Abstract
Host-pathogen interactions (HPIs) are complex processes that require tight regulation. A common regulatory mechanism of HPIs is through glycans of either host cells or pathogens. Due to their diverse sequences, complex structures, and conformations, studies of glycans require highly sensitive and powerful tools. Recent improvements in technology have enabled the application of many bioanalytical techniques and modeling methods to investigate glycans and their mechanisms in HPIs. This mini-review highlights how these advances have been used to understand the role glycans play in HPIs in the past 2 years.
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Affiliation(s)
- Ha T Le
- Department of Chemistry and Biochemistry, University of Delaware, Newark, DE, USA
| | - Min Liu
- Department of Chemistry and Biochemistry, University of Delaware, Newark, DE, USA
| | - Catherine L Grimes
- Department of Chemistry and Biochemistry, University of Delaware, Newark, DE, USA; Department of Biological Sciences, University of Delaware, Newark, DE, USA.
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155
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Momont C, Dang HV, Zatta F, Hauser K, Wang C, di Iulio J, Minola A, Czudnochowski N, De Marco A, Branch K, Donermeyer D, Vyas S, Chen A, Ferri E, Guarino B, Powell AE, Spreafico R, Yim SS, Balce DR, Bartha I, Meury M, Croll TI, Belnap DM, Schmid MA, Schaiff WT, Miller JL, Cameroni E, Telenti A, Virgin HW, Rosen LE, Purcell LA, Lanzavecchia A, Snell G, Corti D, Pizzuto MS. A pan-influenza antibody inhibiting neuraminidase via receptor mimicry. Nature 2023:10.1038/s41586-023-06136-y. [PMID: 37258672 DOI: 10.1038/s41586-023-06136-y] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2022] [Accepted: 04/26/2023] [Indexed: 06/02/2023]
Abstract
Rapidly evolving influenza A viruses (IAVs) and influenza B viruses (IBVs) are major causes of recurrent lower respiratory tract infections. Current influenza vaccines elicit antibodies predominantly to the highly variable head region of haemagglutinin and their effectiveness is limited by viral drift1 and suboptimal immune responses2. Here we describe a neuraminidase-targeting monoclonal antibody, FNI9, that potently inhibits the enzymatic activity of all group 1 and group 2 IAVs, as well as Victoria/2/87-like, Yamagata/16/88-like and ancestral IBVs. FNI9 broadly neutralizes seasonal IAVs and IBVs, including the immune-evading H3N2 strains bearing an N-glycan at position 245, and shows synergistic activity when combined with anti-haemagglutinin stem-directed antibodies. Structural analysis reveals that D107 in the FNI9 heavy chain complementarity-determinant region 3 mimics the interaction of the sialic acid carboxyl group with the three highly conserved arginine residues (R118, R292 and R371) of the neuraminidase catalytic site. FNI9 demonstrates potent prophylactic activity against lethal IAV and IBV infections in mice. The unprecedented breadth and potency of the FNI9 monoclonal antibody supports its development for the prevention of influenza illness by seasonal and pandemic viruses.
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Affiliation(s)
| | - Ha V Dang
- Vir Biotechnology, San Francisco, CA, USA
| | - Fabrizia Zatta
- Humabs Biomed SA, a subsidiary of Vir Biotechnology, Bellinzona, Switzerland
| | | | | | | | - Andrea Minola
- Humabs Biomed SA, a subsidiary of Vir Biotechnology, Bellinzona, Switzerland
| | | | - Anna De Marco
- Humabs Biomed SA, a subsidiary of Vir Biotechnology, Bellinzona, Switzerland
| | | | | | | | - Alex Chen
- Vir Biotechnology, San Francisco, CA, USA
| | | | - Barbara Guarino
- Humabs Biomed SA, a subsidiary of Vir Biotechnology, Bellinzona, Switzerland
| | | | | | | | | | | | | | - Tristan I Croll
- Cambridge Institute for Medical Research, Department of Haematology, University of Cambridge, Cambridge, UK
| | - David M Belnap
- School of Biological Sciences, Department of Biochemistry, University of Utah, Salt Lake City, UT, USA
| | - Michael A Schmid
- Humabs Biomed SA, a subsidiary of Vir Biotechnology, Bellinzona, Switzerland
| | | | | | - Elisabetta Cameroni
- Humabs Biomed SA, a subsidiary of Vir Biotechnology, Bellinzona, Switzerland
| | | | - Herbert W Virgin
- Vir Biotechnology, San Francisco, CA, USA
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO, USA
| | | | | | | | | | - Davide Corti
- Humabs Biomed SA, a subsidiary of Vir Biotechnology, Bellinzona, Switzerland.
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156
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Verzeaux L, Rao R, Vyumvuhore R, Belloy N, Aymard E, Baud S, Manfait M, Dauchez M, Closs B. Highlighting the hygroscopic capacities of apiogalacturonans. J Mol Graph Model 2023; 123:108527. [PMID: 37270896 DOI: 10.1016/j.jmgm.2023.108527] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2023] [Revised: 04/28/2023] [Accepted: 05/12/2023] [Indexed: 06/06/2023]
Abstract
To meet the needs of dehydrated skin, molecules with a high hygroscopic potential are necessary to hydrate it effectively and durably. In this context, we were interested in pectins, and more precisely in apiogalacturonans (AGA), a singular one that is currently only found in a few species of aquatic plants. As key structures in water regulation of these aquatic plants and thanks to their molecular composition and conformations, we hypothesized that they could have beneficial role for skin hydration. Spirodela polyrhiza is a duckweed known to be naturally rich in AGA. The aim of this study was to investigate the hygroscopic potential of AGA. Firstly, AGA models were built based on structural information obtained from previous experimental studies. Molecular dynamics (MD) simulations were performed, and the hygroscopic potential was predicted in silico by analyzing the frequency of interaction of water molecules with each AGA residue. Quantification of interactions identified the presence of 23 water molecules on average in contact with each residue of AGA. Secondly, the hygroscopic properties were investigated directly in vivo. Indeed, the water capture in the skin was measured in vivo by Raman microspectroscopy thanks to the deuterated water (D20) tracking. Investigations revealed that AGA significantly capture and retain more water in the epidermis and deeper than a placebo control. Not only do these original natural molecules interact with water molecules, but they capture and retain them efficiently in the skin.
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Affiliation(s)
| | - Rajas Rao
- Université de Reims Champagne Ardenne, CNRS, MEDyC,UMR 7369, 51097, Reims, France
| | | | - Nicolas Belloy
- Université de Reims Champagne Ardenne, CNRS, MEDyC,UMR 7369, 51097, Reims, France
| | | | - Stéphanie Baud
- Université de Reims Champagne Ardenne, CNRS, MEDyC,UMR 7369, 51097, Reims, France
| | - Michel Manfait
- BioSpecT (Translational BioSpectroscopy), EA 7506, University of Reims Champagne-Ardenne, Reims, France
| | - Manuel Dauchez
- Université de Reims Champagne Ardenne, CNRS, MEDyC,UMR 7369, 51097, Reims, France
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157
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Lete M, Hoffmann M, Schomann N, Martínez-Castillo A, Peccati F, Konietzny PB, Delgado S, Snyder NL, Jiménez-Oses G, Abrescia NGA, Ardá A, Hartmann L, Jiménez-Barbero J. Molecular Recognition of Glycan-Bearing Glycomacromolecules Presented at Membrane Surfaces by Lectins: An NMR View. ACS OMEGA 2023; 8:16883-16895. [PMID: 37214724 PMCID: PMC10193412 DOI: 10.1021/acsomega.3c00634] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Accepted: 04/18/2023] [Indexed: 05/24/2023]
Abstract
Lectin-glycan interactions are at the heart of a multitude of biological events. Glycans are usually presented in a multivalent manner on the cell surface as part of the so-called glycocalyx, where they interact with other entities. This multivalent presentation allows us to overcome the typical low affinities found for individual glycan-lectin interactions. Indeed, the presentation of glycans may drastically impact their binding by lectins, highly affecting the corresponding binding affinity and even selectivity. In this context, we herein present the study of the interaction of a variety of homo- and heteromultivalent lactose-functionalized glycomacromolecules and their lipid conjugates with two human galectins. We have employed as ligands the glycomacromolecules, as well as liposomes decorated with those structures, to evaluate their interactions in a cell-mimicking environment. Key details of the interaction have been unravelled by NMR experiments, both from the ligand and receptor perspectives, complemented by cryo-electron microscopy methods and molecular dynamics simulations.
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Affiliation(s)
- Marta
G. Lete
- CIC
bioGUNE, Basque Research
& Technology Alliance (BRTA), Bizkaia Technology Park, Building 800, Derio 48160, Bizkaia, Spain
| | - Miriam Hoffmann
- Department
of Organic and Macromolecular Chemistry, Heinrich-Heine-University Düsseldorf, Universitätsstraße 1, Düsseldorf 40225, Germany
| | - Nils Schomann
- Department
of Organic and Macromolecular Chemistry, Heinrich-Heine-University Düsseldorf, Universitätsstraße 1, Düsseldorf 40225, Germany
| | - Ane Martínez-Castillo
- CIC
bioGUNE, Basque Research
& Technology Alliance (BRTA), Bizkaia Technology Park, Building 800, Derio 48160, Bizkaia, Spain
| | - Francesca Peccati
- CIC
bioGUNE, Basque Research
& Technology Alliance (BRTA), Bizkaia Technology Park, Building 800, Derio 48160, Bizkaia, Spain
| | - Patrick B. Konietzny
- Department
of Organic and Macromolecular Chemistry, Heinrich-Heine-University Düsseldorf, Universitätsstraße 1, Düsseldorf 40225, Germany
| | - Sandra Delgado
- CIC
bioGUNE, Basque Research
& Technology Alliance (BRTA), Bizkaia Technology Park, Building 800, Derio 48160, Bizkaia, Spain
| | - Nicole L. Snyder
- Department
of Chemistry, Davidson College, Davidson, North Carolina 28035, United States
| | - Gonzalo Jiménez-Oses
- CIC
bioGUNE, Basque Research
& Technology Alliance (BRTA), Bizkaia Technology Park, Building 800, Derio 48160, Bizkaia, Spain
- Ikerbasque,
Basque Foundation for Science, Plaza Euskadi 5, Bilbao 48009, Bizkaia, Spain
| | - Nicola G. A. Abrescia
- CIC
bioGUNE, Basque Research
& Technology Alliance (BRTA), Bizkaia Technology Park, Building 800, Derio 48160, Bizkaia, Spain
- Ikerbasque,
Basque Foundation for Science, Plaza Euskadi 5, Bilbao 48009, Bizkaia, Spain
- Centro
de Investigación Biomédica en Red de Enfermedades Hepáticas
y Digestivas, Instituto de Salud Carlos
III, Madrid 28029, Spain
| | - Ana Ardá
- CIC
bioGUNE, Basque Research
& Technology Alliance (BRTA), Bizkaia Technology Park, Building 800, Derio 48160, Bizkaia, Spain
- Ikerbasque,
Basque Foundation for Science, Plaza Euskadi 5, Bilbao 48009, Bizkaia, Spain
| | - Laura Hartmann
- Department
of Organic and Macromolecular Chemistry, Heinrich-Heine-University Düsseldorf, Universitätsstraße 1, Düsseldorf 40225, Germany
| | - Jesús Jiménez-Barbero
- CIC
bioGUNE, Basque Research
& Technology Alliance (BRTA), Bizkaia Technology Park, Building 800, Derio 48160, Bizkaia, Spain
- Ikerbasque,
Basque Foundation for Science, Plaza Euskadi 5, Bilbao 48009, Bizkaia, Spain
- Department
of Organic and Inorganic Chemistry, Faculty of Science and Technology, University of the Basque Country, EHU-UPV, 48940 Leioa, Spain
- Centro
de Investigación Biomédica En Red de Enfermedades Respiratorias, Madrid 28029, Spain
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158
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Pengthaisong S, Piniello B, Davies GJ, Rovira C, Ketudat Cairns JR. Reaction Mechanism of Glycoside Hydrolase Family 116 Utilizes Perpendicular Protonation. ACS Catal 2023; 13:5850-5863. [PMID: 37180965 PMCID: PMC10167657 DOI: 10.1021/acscatal.3c00620] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2023] [Revised: 03/15/2023] [Indexed: 05/16/2023]
Abstract
Retaining glycoside hydrolases use acid/base catalysis with an enzymatic acid/base protonating the glycosidic bond oxygen to facilitate leaving-group departure alongside attack by a catalytic nucleophile to form a covalent intermediate. Generally, this acid/base protonates the oxygen laterally with respect to the sugar ring, which places the catalytic acid/base and nucleophile carboxylates within about 4.5-6.5 Å of each other. However, in glycoside hydrolase (GH) family 116, including disease-related human acid β-glucosidase 2 (GBA2), the distance between the catalytic acid/base and the nucleophile is around 8 Å (PDB: 5BVU) and the catalytic acid/base appears to be above the plane of the pyranose ring, rather than being lateral to that plane, which could have catalytic consequences. However, no structure of an enzyme-substrate complex is available for this GH family. Here, we report the structures of Thermoanaerobacterium xylanolyticum β-glucosidase (TxGH116) D593N acid/base mutant in complexes with cellobiose and laminaribiose and its catalytic mechanism. We confirm that the amide hydrogen bonding to the glycosidic oxygen is in a perpendicular rather than lateral orientation. Quantum mechanics/molecular mechanics (QM/MM) simulations of the glycosylation half-reaction in wild-type TxGH116 indicate that the substrate binds with the nonreducing glucose residue in an unusual relaxed 4C1 chair at the -1 subsite. Nevertheless, the reaction can still proceed through a 4H3 half-chair transition state, as in classical retaining β-glucosidases, as the catalytic acid D593 protonates the perpendicular electron pair. The glucose C6OH is locked in a gauche, trans orientation with respect to the C5-O5 and C4-C5 bonds to facilitate perpendicular protonation. These data imply a unique protonation trajectory in Clan-O glycoside hydrolases, which has strong implications for the design of inhibitors specific to either lateral protonators, such as human GBA1, or perpendicular protonators, such as human GBA2.
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Affiliation(s)
- Salila Pengthaisong
- School
of Chemistry, Institute of Science, Suranaree
University of Technology, Nakhon
Ratchasima 30000, Thailand
- Center
for Biomolecular Structure, Function and Application, Suranaree University of Technology, Nakhon Ratchasima 30000, Thailand
| | - Beatriz Piniello
- Departament
de Quımica Inorgánica i Orgànica (Secció
de Química Orgànica) and Institut de Química
Teòrica i Computacional (IQTCUB), Universitat de Barcelona, 08028 Barcelona, Spain
| | - Gideon J. Davies
- Department
of Chemistry, University of York, Heslington, York YO10
5DD, U.K.
| | - Carme Rovira
- Departament
de Quımica Inorgánica i Orgànica (Secció
de Química Orgànica) and Institut de Química
Teòrica i Computacional (IQTCUB), Universitat de Barcelona, 08028 Barcelona, Spain
- Institució
Catalana de Recerca i Estudis Avancats (ICREA), 08010 Barcelona, Spain
| | - James R. Ketudat Cairns
- School
of Chemistry, Institute of Science, Suranaree
University of Technology, Nakhon
Ratchasima 30000, Thailand
- Center
for Biomolecular Structure, Function and Application, Suranaree University of Technology, Nakhon Ratchasima 30000, Thailand
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159
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Bojarski KK, Samsonov SA. In silico insights into procathepsin S maturation mediated by glycosaminoglycans. J Mol Graph Model 2023; 120:108406. [PMID: 36707295 DOI: 10.1016/j.jmgm.2023.108406] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2022] [Revised: 11/24/2022] [Accepted: 01/10/2023] [Indexed: 01/15/2023]
Abstract
Procathepsins, inactive precursors of cathepsins are present in the extracellular matrix (ECM) and in lysosomes. Their active forms are involved in a number of biologically relevant processes, including bone resorption, intracellular proteolysis and regulation of programmed cell death. These processes might be mediated by glycosaminoglycans (GAGs), long unbranched periodic negatively charged polysaccharides. GAGs are also present in ECM and play important role in anticoagulation, angiogenesis and tissue regeneration. GAGs not only mediate the enzymatic activity of cathepsins but can also regulate the process of procathepsin maturation, as it was shown for procathepsin B and S. In this study, we propose the molecular mechanism underlying the biological role of GAGs in procathepsin S maturation and compare our findings with computational data obtained for procathepsin B. We rigorously analyse procathepsin S-GAG complexes in terms of their dynamics, free energy and potential allosteric regulation. We conclude that the GAG binding region might have an effect on the dynamics of procathepsin S structure and so affect its maturation by two different mechanisms.
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Affiliation(s)
- Krzysztof K Bojarski
- Department of Physical Chemistry, Gdansk University of Technology, Narutowicza 11/12, Gdansk, 80-233, Poland.
| | - Sergey A Samsonov
- Department of Theoretical Chemistry, University of Gdansk, Wita Stwosza 63, Gdansk, 80-308, Poland
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160
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Arend LB, Verli H. Revisiting the structural basis for biological activity of GMI-1070, a sialyl Lewis x mimetic. Carbohydr Res 2023; 529:108829. [PMID: 37182470 DOI: 10.1016/j.carres.2023.108829] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2022] [Revised: 04/26/2023] [Accepted: 04/27/2023] [Indexed: 05/16/2023]
Abstract
When it comes to the treatment of pathologies in which aberrant cell adhesion and extravasation from the bloodstream have been implicated, the selectins represent a central therapeutic target. In this context, the present work investigates the conformational landscape of two prototypes for the design of new antineoplasic and anti-inflammatory agents: the natural selectin ligand sialyl Lewisx and its mimetic GMI-1070. Accordingly, a series of unbiased molecular dynamics simulations at the microsecond scale using GROMOS 53A6 (GLYC), CHARMM36m and GLYCAM06 force fields were employed, together with ConfID, an analytical method for the characterization of conformational populations of small molecules. Our results for sialyl Lewisx are in agreement with and expand upon prior work. As for the mimetic, our results indicate that, in spite of its conformational restriction, GMI-1070's behavior in solution deviates from what had been proposed, highlighting thus some features that could be optimized, as the development of sialyl Lewisx mimetics continues, and new candidates emerge.
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Affiliation(s)
- Laís B Arend
- Centro de Biotecnologia, Universidade Federal do Rio Grande do Sul, Av Bento Gonçalves, 9500, CP 15005, Porto Alegre, 91500-970, RS, Brazil
| | - Hugo Verli
- Centro de Biotecnologia, Universidade Federal do Rio Grande do Sul, Av Bento Gonçalves, 9500, CP 15005, Porto Alegre, 91500-970, RS, Brazil.
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161
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Sakai S, Hirano Y, Kobayashi Y, Arai N. Effect of temperature on the structure and drug-release behaviour of inclusion complex of β-cyclodextrin with cyclophosphamide: a molecular dynamics study. SOFT MATTER 2023; 19:2902-2907. [PMID: 36987748 DOI: 10.1039/d2sm01542k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/17/2023]
Abstract
Cyclodextrins (CDs) are suitable drug carriers because of their doughnut-shaped cavities with hydrophilic outer and hydrophobic inner surfaces. Temperature-responsive CD-based drug carriers are expected to be one of the most promising candidates for drug delivery systems. In this study, we performed molecular dynamics simulations of the inclusion complex of β-CD with cyclophosphamide (CP) at temperatures from 300 K to 400 K to investigate the temperature dependency of the release behaviour of CP and structural changes of β-CD in an aqueous solution. We analysed the distance between the centres of mass of β-CD and CP and the radius of gyration of β-CD. The CP molecule was released from the β-CD cavity at 400 K, whereas two different inclusion complexes, partially and completely, were observed at T < 400 K. β-CD encapsulating a CP molecule had a more spherical shape and rigidity than β-CD without a CP, and the rigidity of their inclusion complex decreased with increasing temperature. Our findings provide fundamental insights into the behaviours of the β-CD/CP complex and drug release at the molecular level and can facilitate the development of new temperature-responsive drug delivery systems with CD nanocarriers triggered by localised temperature increases using focused ultrasound.
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Affiliation(s)
- Seiga Sakai
- Department of Mechanical Engineering, Keio University, Yokohama, Kanagawa 223-8522, Japan.
| | - Yoshinori Hirano
- Department of Mechanical Engineering, Keio University, Yokohama, Kanagawa 223-8522, Japan.
| | - Yusei Kobayashi
- Department of Mechanical Engineering, Keio University, Yokohama, Kanagawa 223-8522, Japan.
| | - Noriyoshi Arai
- Department of Mechanical Engineering, Keio University, Yokohama, Kanagawa 223-8522, Japan.
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162
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Yamazaki M, Yabe M, Iijima K. Specific ion effects on the aggregation of polysaccharide-based polyelectrolyte complex particles induced by monovalent ions within Hofmeister series. J Colloid Interface Sci 2023; 643:305-317. [PMID: 37075539 DOI: 10.1016/j.jcis.2023.04.030] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2022] [Revised: 03/14/2023] [Accepted: 04/08/2023] [Indexed: 04/21/2023]
Abstract
Polysaccharide-based polyelectrolyte complex (PEC) particles have been utilized as carriers for drug delivery systems (DDS) and as building components for material development. Despite their versatility, the aggregation mechanism of PEC particles in the presence of salts remains unclear. To clarify the aggregation mechanism, the specific ion effects of monovalent salts within the Hofmeister series on the aggregation behavior of PEC particles composed of chitosan and chondroitin sulfate C, which are often used as DDS carriers and materials, were studied. Here, we found that weakly hydrated chaotropic anions promoted the aggregation of positively charged PEC particles. The hydrophobicity of the PEC particles was increased by these ions. Strongly hydrated ions such as Cl- are less likely to accumulate in these particles, whereas weakly hydrated chaotropic ions such as SCN- are more likely to accumulate. Molecular dynamics simulations suggested that the hydrophobicity of PECs might be strengthened by ions due to changes in intrinsic and extrinsic ion pairs and hydrophobic interactions. Based on our results, it is expected that the control of surface hydrophilicity or hydrophobicity is an effective approach for controlling the stability of PEC particles in the presence of ions.
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Affiliation(s)
- Makoto Yamazaki
- Graduate School of Engineering Science, Yokohama National University, Tokiwadai 79-5, Hodogaya-ku, Yokohama 240-8501, Japan
| | - Makoto Yabe
- Mol Processing, 1015 1-9-7 Kitashinagawa, Shinagawa-ku, Tokyo 140-0001, Japan
| | - Kazutoshi Iijima
- Faculty of Engineering, Yokohama National University, Tokiwadai 79-5, Hodogaya-ku, Yokohama 240-8501, Japan.
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163
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Svilenov HL, Delhommel F, Siebenmorgen T, Rührnößl F, Popowicz GM, Reiter A, Sattler M, Brockmeyer C, Buchner J. Extrinsic stabilization of antiviral ACE2-Fc fusion proteins targeting SARS-CoV-2. Commun Biol 2023; 6:386. [PMID: 37031320 PMCID: PMC10082628 DOI: 10.1038/s42003-023-04762-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2022] [Accepted: 03/24/2023] [Indexed: 04/10/2023] Open
Abstract
The angiotensin-converting enzyme 2 (ACE2) is a viral receptor used by sarbecoviruses to infect cells. Fusion proteins comprising extracellular ACE2 domains and the Fc part of immunoglobulins exhibit high virus neutralization efficiency, but the structure and stability of these molecules are poorly understood. We show that although the hinge between the ACE2 and the IgG4-Fc is highly flexible, the conformational dynamics of the two ACE2 domains is restricted by their association. Interestingly, the conformational stability of the ACE2 moiety is much lower than that of the Fc part. We found that chemical compounds binding to ACE2, such as DX600 and MLN4760, can be used to strongly increase the thermal stability of the ACE2 by different mechanisms. Together, our findings reveal a general concept for stabilizing the labile receptor segments of therapeutic antiviral fusion proteins by chemical compounds.
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Affiliation(s)
- Hristo L Svilenov
- Center for Functional Protein Assemblies (CPA) and School of Natural Sciences, Department of Bioscience, Technical University of Munich, 85748, Garching, Germany.
- Faculty of Pharmaceutical Sciences, Ghent University, Ottergemsesteenweg 460, 9000, Ghent, Belgium.
| | - Florent Delhommel
- Institute of Structural Biology, Helmholtz Zentrum München, Neuherberg, Germany
- Bavarian NMR Center, School of Natural Sciences, Department of Bioscience, Technical University of Munich, Garching, 85748, Munich, Germany
| | - Till Siebenmorgen
- Institute of Structural Biology, Helmholtz Zentrum München, Neuherberg, Germany
- Bavarian NMR Center, School of Natural Sciences, Department of Bioscience, Technical University of Munich, Garching, 85748, Munich, Germany
| | - Florian Rührnößl
- Center for Functional Protein Assemblies (CPA) and School of Natural Sciences, Department of Bioscience, Technical University of Munich, 85748, Garching, Germany
| | - Grzegorz M Popowicz
- Institute of Structural Biology, Helmholtz Zentrum München, Neuherberg, Germany
- Bavarian NMR Center, School of Natural Sciences, Department of Bioscience, Technical University of Munich, Garching, 85748, Munich, Germany
| | | | - Michael Sattler
- Institute of Structural Biology, Helmholtz Zentrum München, Neuherberg, Germany
- Bavarian NMR Center, School of Natural Sciences, Department of Bioscience, Technical University of Munich, Garching, 85748, Munich, Germany
| | | | - Johannes Buchner
- Center for Functional Protein Assemblies (CPA) and School of Natural Sciences, Department of Bioscience, Technical University of Munich, 85748, Garching, Germany.
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164
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Anso I, Naegeli A, Cifuente JO, Orrantia A, Andersson E, Zenarruzabeitia O, Moraleda-Montoya A, García-Alija M, Corzana F, Del Orbe RA, Borrego F, Trastoy B, Sjögren J, Guerin ME. Turning universal O into rare Bombay type blood. Nat Commun 2023; 14:1765. [PMID: 36997505 PMCID: PMC10063614 DOI: 10.1038/s41467-023-37324-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2022] [Accepted: 03/09/2023] [Indexed: 04/01/2023] Open
Abstract
AbstractRed blood cell antigens play critical roles in blood transfusion since donor incompatibilities can be lethal. Recipients with the rare total deficiency in H antigen, the Oh Bombay phenotype, can only be transfused with group Oh blood to avoid serious transfusion reactions. We discover FucOB from the mucin-degrading bacteria Akkermansia muciniphila as an α-1,2-fucosidase able to hydrolyze Type I, Type II, Type III and Type V H antigens to obtain the afucosylated Bombay phenotype in vitro. X-ray crystal structures of FucOB show a three-domain architecture, including a GH95 glycoside hydrolase. The structural data together with site-directed mutagenesis, enzymatic activity and computational methods provide molecular insights into substrate specificity and catalysis. Furthermore, using agglutination tests and flow cytometry-based techniques, we demonstrate the ability of FucOB to convert universal O type into rare Bombay type blood, providing exciting possibilities to facilitate transfusion in recipients/patients with Bombay phenotype.
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165
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Marcisz M, Samsonov SA. Solvent Model Benchmark for Molecular Dynamics of Glycosaminoglycans. J Chem Inf Model 2023; 63:2147-2157. [PMID: 36989082 PMCID: PMC10091405 DOI: 10.1021/acs.jcim.2c01472] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/30/2023]
Abstract
In computational studies of glycosaminoglycans (GAGs), a group of anionic, periodic linear polysaccharides, so far there has been very little discussion about the role of solvent models in the molecular dynamics simulations of these molecules. Predominantly, the TIP3P water model is commonly used as one of the most popular explicit water models in general. However, there are numerous alternative explicit and implicit water models that are neglected in the computational research of GAGs. Since solvent-mediated interactions are particularly important for GAG dynamic and structural properties, it would be of great interest for the GAG community to establish the solvent model that is suited the best in terms of the quality of theoretically obtained GAG parameters and, at the same time, would be reasonably demanding in terms of computational resources required. In this study, heparin (HP) was simulated using five implicit and six explicit solvent models with the aim to find out how different solvent models influence HP's molecular descriptors in the molecular dynamics simulations. Here, we initiate the search for the most appropriate solvent representation for GAG systems and we hope to encourage other groups to contribute to this highly relevant subject.
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Affiliation(s)
- Mateusz Marcisz
- Faculty of Chemistry, University of Gdańsk, ul. Wita Stwosza 63, 80-308 Gdańsk, Poland
- Intercollegiate Faculty of Biotechnology of UG and MUG, ul. Abrahama 58, 80-307 Gdańsk, Poland
| | - Sergey A Samsonov
- Faculty of Chemistry, University of Gdańsk, ul. Wita Stwosza 63, 80-308 Gdańsk, Poland
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166
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Trastoy B, Du JJ, Cifuente JO, Rudolph L, García-Alija M, Klontz EH, Deredge D, Sultana N, Huynh CG, Flowers MW, Li C, Sastre DE, Wang LX, Corzana F, Mallagaray A, Sundberg EJ, Guerin ME. Mechanism of antibody-specific deglycosylation and immune evasion by Streptococcal IgG-specific endoglycosidases. Nat Commun 2023; 14:1705. [PMID: 36973249 PMCID: PMC10042849 DOI: 10.1038/s41467-023-37215-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2022] [Accepted: 03/03/2023] [Indexed: 03/29/2023] Open
Abstract
Bacterial pathogens have evolved intricate mechanisms to evade the human immune system, including the production of immunomodulatory enzymes. Streptococcus pyogenes serotypes secrete two multi-modular endo-β-N-acetylglucosaminidases, EndoS and EndoS2, that specifically deglycosylate the conserved N-glycan at Asn297 on IgG Fc, disabling antibody-mediated effector functions. Amongst thousands of known carbohydrate-active enzymes, EndoS and EndoS2 represent just a handful of enzymes that are specific to the protein portion of the glycoprotein substrate, not just the glycan component. Here, we present the cryoEM structure of EndoS in complex with the IgG1 Fc fragment. In combination with small-angle X-ray scattering, alanine scanning mutagenesis, hydrolytic activity measurements, enzyme kinetics, nuclear magnetic resonance and molecular dynamics analyses, we establish the mechanisms of recognition and specific deglycosylation of IgG antibodies by EndoS and EndoS2. Our results provide a rational basis from which to engineer novel enzymes with antibody and glycan selectivity for clinical and biotechnological applications.
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Affiliation(s)
- Beatriz Trastoy
- Structural Glycobiology Laboratory, Biocruces Health Research Institute, Barakaldo, Bizkaia, 48903, Spain.
- Structural Glycobiology Laboratory, Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Bizkaia Technology Park, Building 801A, 48160, Derio, Spain.
- Ikerbasque, Basque Foundation for Science, 48009, Bilbao, Spain.
| | - Jonathan J Du
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA, 30322, USA
| | - Javier O Cifuente
- Structural Glycobiology Laboratory, Biocruces Health Research Institute, Barakaldo, Bizkaia, 48903, Spain
- Structural Glycobiology Laboratory, Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Bizkaia Technology Park, Building 801A, 48160, Derio, Spain
| | - Lorena Rudolph
- University of Lübeck, Center of Structural and Cell Biology in Medicine (CSCM), Institute of Chemistry and Metabolomics, Ratzeburger Allee 160, 23562, Lübeck, Germany
| | - Mikel García-Alija
- Structural Glycobiology Laboratory, Biocruces Health Research Institute, Barakaldo, Bizkaia, 48903, Spain
- Structural Glycobiology Laboratory, Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Bizkaia Technology Park, Building 801A, 48160, Derio, Spain
| | - Erik H Klontz
- Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, MD, 21201, USA
- Institute of Human Virology, University of Maryland School of Medicine, Baltimore, MD, 21201, USA
| | - Daniel Deredge
- Department of Pharmaceutical Sciences, University of Maryland School of Pharmacy, Baltimore, MD, 21201, USA
| | - Nazneen Sultana
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA, 30322, USA
| | - Chau G Huynh
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA, 30322, USA
| | - Maria W Flowers
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA, 30322, USA
| | - Chao Li
- Department of Chemistry and Biochemistry, University of Maryland, College Park, MD, 20742, USA
| | - Diego E Sastre
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA, 30322, USA
| | - Lai-Xi Wang
- Department of Chemistry and Biochemistry, University of Maryland, College Park, MD, 20742, USA
| | - Francisco Corzana
- Departamento Química and Centro de Investigación en Síntesis Quı́mica, Universidad de La Rioja, 26006, Rioja, Spain
| | - Alvaro Mallagaray
- University of Lübeck, Center of Structural and Cell Biology in Medicine (CSCM), Institute of Chemistry and Metabolomics, Ratzeburger Allee 160, 23562, Lübeck, Germany.
| | - Eric J Sundberg
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA, 30322, USA.
| | - Marcelo E Guerin
- Structural Glycobiology Laboratory, Biocruces Health Research Institute, Barakaldo, Bizkaia, 48903, Spain.
- Structural Glycobiology Laboratory, Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Bizkaia Technology Park, Building 801A, 48160, Derio, Spain.
- Ikerbasque, Basque Foundation for Science, 48009, Bilbao, Spain.
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167
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Natesan R, Agrawal NJ. IgG1 and IgG4 antibodies sample initial structure dependent local conformational states and exhibit non-identical Fab dynamics. Sci Rep 2023; 13:4791. [PMID: 36959284 PMCID: PMC10036467 DOI: 10.1038/s41598-023-32067-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2022] [Accepted: 03/22/2023] [Indexed: 03/25/2023] Open
Abstract
We have investigated the dynamics of two [Formula: see text]-immunoglobulin molecules, IgG1 and IgG4, using long all atom molecular dynamics simulations. We first show that the de novo structures of IgG1 and IgG4 predicted using AlphaFold, with no interactions between the fragment crystallizable (Fc) domain and the antigen fragment binding domain (Fab), eventually relaxes to a state with persistent Fc-Fab interactions that mirrors experimentally resolved structures. We quantified the conformational space sampled by antibody trajectories spawned from six different initial structures and show that the individual trajectories only sample states bound by a local minimum and display very little mixing in their conformational states. Furthermore, the dynamics of the individual Fab domains are strongly dependent on the initial crystal structure and isotype. In all conditions, we observe non-identical dynamics between the Fab arms in an antibody. For a six-bead coarse grained model, we show that non-covalent Fc-Fab interactions can modulate the stiffnesses associated with Fc-Fab distances, angles, and dihedral angles by up to three orders of magnitude. Our results clearly illustrate the inherent complexities in studying antibody dynamics and highlight the need to include non-identical Fab dynamics as an inherent feature in computational models of therapeutic antibodies.
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Affiliation(s)
| | - Neeraj J Agrawal
- Process Development, Amgen Inc., 360 Binney St, Cambridge, MA, 02141, USA.
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168
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Mehranfar A, Khavani M, Mofrad MRK. Adsorption Process of Various Antimicrobial Peptides on Different Surfaces of Cellulose. ACS APPLIED BIO MATERIALS 2023; 6:1041-1053. [PMID: 36935640 DOI: 10.1021/acsabm.2c00905] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/11/2023]
Abstract
Current antimicrobial challenges in hospitals, pharmaceutical production units, and food packaging have motivated the development of antimicrobial agents, among them the antimicrobial compounds based on cellulose and peptides. Herein, we develop molecular dynamics (MD) models to dissect and characterize the adsorption process of antimicrobial peptides (AMPs) such as protegrin 1, magainin 2, and cyclic indolicidin on various surfaces of cellulose including [-1-10], [1-10], [-100], [100], [-110], and [110]. Our results suggest that the magainin 2 antimicrobial peptide loses most of its initial helix form, spreads on the cellulose surface, and makes the most rigid structure with [110] surface. The cyclic indolicidin peptide has the lowest affinity to adsorb on the cellulose surfaces, and the protegrin 1 peptide successfully adsorbs on all the proposed cellulose surfaces. Our MD simulations confirmed that cellulose can improve the corresponding peptides' structural stability and change their secondary structures during adsorption. The [-1-10] and [100] surfaces of cellulose show considerable affinity against the AMPs, exhibiting greater interactions with and adsorption to the peptides. Our data imply that the stronger adsorptions are caused by a set of H-bonds, van der Waals, and electrostatic interactions, where van der Waals interactions play a prominent role in the stability of the AMP-cellulose structures. Our energy analysis results suggest that glutamic acid and arginine amino acids have key roles in the stability of AMPs on cellulose surfaces due largely to stronger interactions with the cellulose surfaces as compared with other residues. Our results can provide useful insight at the molecular level that can help design better antimicrobial biomaterials based on cellulose.
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Affiliation(s)
- Aliyeh Mehranfar
- Molecular Cell Biomechanics Laboratory, Departments of Bioengineering and Mechanical Engineering, University of California Berkeley, Berkeley, California 94720, United States
| | - Mohammad Khavani
- Molecular Cell Biomechanics Laboratory, Departments of Bioengineering and Mechanical Engineering, University of California Berkeley, Berkeley, California 94720, United States
| | - Mohammad R K Mofrad
- Molecular Cell Biomechanics Laboratory, Departments of Bioengineering and Mechanical Engineering, University of California Berkeley, Berkeley, California 94720, United States
- Molecular Biophysics and Integrative Bioimaging Division, Lawrence Berkeley National Lab, Berkeley, California 94720, United States
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169
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Kříž P, Beránek J, Spiwok V. Free Energy Differences from Molecular Simulations: Exact Confidence Intervals from Transition Counts. J Chem Theory Comput 2023; 19:2102-2108. [PMID: 36926862 PMCID: PMC10100533 DOI: 10.1021/acs.jctc.2c01237] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/18/2023]
Abstract
Here, we demonstrate a method to estimate the uncertainty (confidence intervals and standard errors) of free energy differences calculated by molecular simulations. The widths of confidence intervals and standard errors can be calculated solely from temperature and the number of transitions between states. Uncertainty (95% confidence interval) lower than ±1 kcal/mol can be achieved by a simulation with four forward and four reverse transitions. For a two-state Markovian system, the confidence interval is exact, regardless the number of transitions.
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Affiliation(s)
- Pavel Kříž
- Faculty of Mathematics and Physics, Charles University, 186 75 Prague, Czech Republic
| | - Jan Beránek
- Department of Biochemistry and Microbiology, University of Chemistry and Technology, 166 28 Prague, Czech Republic
| | - Vojtěch Spiwok
- Department of Biochemistry and Microbiology, University of Chemistry and Technology, 166 28 Prague, Czech Republic
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170
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Triveri A, Casali E, Frasnetti E, Doria F, Frigerio F, Cinquini F, Pavoni S, Moroni E, Marchetti F, Serapian SA, Colombo G. Conformational Behavior of SARS-Cov-2 Spike Protein Variants: Evolutionary Jumps in Sequence Reverberate in Structural Dynamic Differences. J Chem Theory Comput 2023; 19:2120-2134. [PMID: 36926878 PMCID: PMC10029694 DOI: 10.1021/acs.jctc.3c00077] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/18/2023]
Abstract
SARS-CoV-2 has evolved rapidly in the first 3 years of pandemic diffusion. The initial evolution of the virus appeared to proceed through big jumps in sequence changes rather than through the stepwise accumulation of point mutations on already established variants. Here, we examine whether this nonlinear mutational process reverberates in variations of the conformational dynamics of the SARS-CoV-2 Spike protein (S-protein), the first point of contact between the virus and the human host. We run extensive microsecond-scale molecular dynamics simulations of seven distinct variants of the protein in their fully glycosylated state and set out to elucidate possible links between the mutational spectrum of the S-protein and the structural dynamics of the respective variant, at global and local levels. The results reveal that mutation-dependent structural and dynamic modulations mostly consist of increased coordinated motions in variants that acquire stability and in an increased internal flexibility in variants that are less stable. Importantly, a limited number of functionally important substructures (the receptor binding domain, in particular) share the same time of movements in all variants, indicating efficient preorganization for functional regions dedicated to host interactions. Our results support a model in which the internal dynamics of the S-proteins from different strains varies in a way that reflects the observed random and non-stepwise jumps in sequence evolution, while conserving the functionally oriented traits of conformational dynamics necessary to support productive interactions with host receptors.
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Affiliation(s)
- Alice Triveri
- Dipartimento di Chimica,
Università di Pavia, via Taramelli 12, 27100 Pavia,
Italy
| | - Emanuele Casali
- Dipartimento di Chimica,
Università di Pavia, via Taramelli 12, 27100 Pavia,
Italy
| | - Elena Frasnetti
- Dipartimento di Chimica,
Università di Pavia, via Taramelli 12, 27100 Pavia,
Italy
| | - Filippo Doria
- Dipartimento di Chimica,
Università di Pavia, via Taramelli 12, 27100 Pavia,
Italy
| | - Francesco Frigerio
- Department of Physical Chemistry, R&D
Eni SpA, via Maritano 27, 20097 San Donato Milanese (Mi),
Italy
| | - Fabrizio Cinquini
- Upstream & Technical
Services—TECS/STES—Eni Spa, via Emilia 1, 20097 San Donato
Milanese (Mi), Italy
| | - Silvia Pavoni
- Department of Physical Chemistry, R&D
Eni SpA, via Maritano 27, 20097 San Donato Milanese (Mi),
Italy
| | | | - Filippo Marchetti
- Dipartimento di Chimica,
Università di Pavia, via Taramelli 12, 27100 Pavia,
Italy
| | - Stefano A. Serapian
- Dipartimento di Chimica,
Università di Pavia, via Taramelli 12, 27100 Pavia,
Italy
| | - Giorgio Colombo
- Dipartimento di Chimica,
Università di Pavia, via Taramelli 12, 27100 Pavia,
Italy
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171
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Solhi L, Guccini V, Heise K, Solala I, Niinivaara E, Xu W, Mihhels K, Kröger M, Meng Z, Wohlert J, Tao H, Cranston ED, Kontturi E. Understanding Nanocellulose-Water Interactions: Turning a Detriment into an Asset. Chem Rev 2023; 123:1925-2015. [PMID: 36724185 PMCID: PMC9999435 DOI: 10.1021/acs.chemrev.2c00611] [Citation(s) in RCA: 41] [Impact Index Per Article: 41.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
Modern technology has enabled the isolation of nanocellulose from plant-based fibers, and the current trend focuses on utilizing nanocellulose in a broad range of sustainable materials applications. Water is generally seen as a detrimental component when in contact with nanocellulose-based materials, just like it is harmful for traditional cellulosic materials such as paper or cardboard. However, water is an integral component in plants, and many applications of nanocellulose already accept the presence of water or make use of it. This review gives a comprehensive account of nanocellulose-water interactions and their repercussions in all key areas of contemporary research: fundamental physical chemistry, chemical modification of nanocellulose, materials applications, and analytical methods to map the water interactions and the effect of water on a nanocellulose matrix.
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Affiliation(s)
- Laleh Solhi
- Department of Bioproducts and Biosystems, Aalto University, EspooFI-00076, Finland
| | - Valentina Guccini
- Department of Bioproducts and Biosystems, Aalto University, EspooFI-00076, Finland
| | - Katja Heise
- Department of Bioproducts and Biosystems, Aalto University, EspooFI-00076, Finland
| | - Iina Solala
- Department of Bioproducts and Biosystems, Aalto University, EspooFI-00076, Finland
| | - Elina Niinivaara
- Department of Bioproducts and Biosystems, Aalto University, EspooFI-00076, Finland.,Department of Wood Science, University of British Columbia, Vancouver, British ColumbiaV6T 1Z4, Canada
| | - Wenyang Xu
- Department of Bioproducts and Biosystems, Aalto University, EspooFI-00076, Finland.,Laboratory of Natural Materials Technology, Åbo Akademi University, TurkuFI-20500, Finland
| | - Karl Mihhels
- Department of Bioproducts and Biosystems, Aalto University, EspooFI-00076, Finland
| | - Marcel Kröger
- Department of Bioproducts and Biosystems, Aalto University, EspooFI-00076, Finland
| | - Zhuojun Meng
- Department of Bioproducts and Biosystems, Aalto University, EspooFI-00076, Finland.,Wenzhou Institute, University of Chinese Academy of Sciences, Wenzhou325001, China
| | - Jakob Wohlert
- Wallenberg Wood Science Centre (WWSC), Department of Fibre and Polymer Technology, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH Royal Institute of Technology, 10044Stockholm, Sweden
| | - Han Tao
- Department of Bioproducts and Biosystems, Aalto University, EspooFI-00076, Finland
| | - Emily D Cranston
- Department of Wood Science, University of British Columbia, Vancouver, British ColumbiaV6T 1Z4, Canada.,Department of Chemical and Biological Engineering, University of British Columbia, Vancouver, British ColumbiaV6T 1Z3, Canada
| | - Eero Kontturi
- Department of Bioproducts and Biosystems, Aalto University, EspooFI-00076, Finland
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172
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Hsu YP, Frank M, Mukherjee D, Shchurik V, Makarov A, Mann BF. Structural remodeling of SARS-CoV-2 spike protein glycans reveals the regulatory roles in receptor-binding affinity. Glycobiology 2023; 33:126-137. [PMID: 36370046 PMCID: PMC9990995 DOI: 10.1093/glycob/cwac077] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2021] [Revised: 10/12/2022] [Accepted: 11/04/2022] [Indexed: 11/14/2022] Open
Abstract
Glycans of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) spike protein are speculated to play functional roles in the infection processes as they extensively cover the protein surface and are highly conserved across the variants. The spike protein has been the principal target for vaccine and therapeutic development while the exact effects of its glycosylation remain elusive. Analytical reports have described the glycan heterogeneity of the spike protein. Subsequent molecular simulation studies provided a knowledge basis of the glycan functions. However, experimental data on the role of discrete glycoforms on the spike protein pathobiology remains scarce. Building an understanding of their roles in SARS-CoV-2 is important as we continue to develop effective medicines and vaccines to combat the disease. Herein, we used designed combinations of glycoengineering enzymes to simplify and control the glycosylation profile of the spike protein receptor-binding domain (RBD). Measurements of the receptor-binding affinity revealed opposite regulatory effects of the RBD glycans with and without sialylation, which presents a potential strategy for modulating the spike protein behaviors through glycoengineering. Moreover, we found that the reported anti-SARS-CoV-(2) antibody, S309, neutralizes the impact of different RBD glycoforms on the receptor-binding affinity. In combination with molecular dynamics simulation, this work reports the regulatory roles that glycosylation plays in the interaction between the viral spike protein and host receptor, providing new insights into the nature of SARS-CoV-2. Beyond this study, enzymatic glycan remodeling offers the opportunity to understand the fundamental role of specific glycoforms on glycoconjugates across molecular biology.
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Affiliation(s)
- Yen-Pang Hsu
- Merck & Co., Inc., Merck Research Laboratories, Discovery Biologics, 320 Bent St., Cambridge, MA 02141, United States
| | | | - Debopreeti Mukherjee
- Merck & Co., Inc., Merck Research Laboratories, Analytical Research and Development, 90 E. Scott Ave., Rahway, NJ 07065, United States
| | - Vladimir Shchurik
- Merck & Co., Inc., Merck Research Laboratories, Analytical Research and Development, 90 E. Scott Ave., Rahway, NJ 07065, United States
| | - Alexey Makarov
- Merck & Co., Inc., Merck Research Laboratories, Analytical Research and Development, 90 E. Scott Ave., Rahway, NJ 07065, United States
| | - Benjamin F Mann
- Merck & Co., Inc., Merck Research Laboratories, Analytical Research and Development, 90 E. Scott Ave., Rahway, NJ 07065, United States
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173
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Charge-changing point mutations in the E protein of tick-borne encephalitis virus. Arch Virol 2023; 168:100. [PMID: 36871232 DOI: 10.1007/s00705-023-05728-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2022] [Accepted: 02/19/2023] [Indexed: 03/06/2023]
Abstract
Introduction of point mutations is one of the forces enabling arboviruses to rapidly adapt in a changing environment. The influence of these mutations on the properties of the virus is not always obvious. In this study, we attempted to clarify this influence using an in silico approach. Using molecular dynamics (MD) simulations, we investigated how the position of charge-changing point mutations influences the structure and conformational stability of the E protein for a set of variants of a single TBEV strain. The computational findings were supported by experimental evaluation of relevant properties of virions, such as binding to heparan sulfate, thermostability, and susceptibility of the viral hemagglutinating activity to detergents. Our results also point to relationships between E protein dynamics and viral neuroinvasiveness.
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174
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Meier M, Gupta M, Akgül S, McDougall M, Imhof T, Nikodemus D, Reuten R, Moya-Torres A, To V, Ferens F, Heide F, Padilla-Meier GP, Kukura P, Huang W, Gerisch B, Mörgelin M, Poole K, Antebi A, Koch M, Stetefeld J. The dynamic nature of netrin-1 and the structural basis for glycosaminoglycan fragment-induced filament formation. Nat Commun 2023; 14:1226. [PMID: 36869049 PMCID: PMC9984387 DOI: 10.1038/s41467-023-36692-w] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2021] [Accepted: 02/13/2023] [Indexed: 03/05/2023] Open
Abstract
Netrin-1 is a bifunctional chemotropic guidance cue that plays key roles in diverse cellular processes including axon pathfinding, cell migration, adhesion, differentiation, and survival. Here, we present a molecular understanding of netrin-1 mediated interactions with glycosaminoglycan chains of diverse heparan sulfate proteoglycans (HSPGs) and short heparin oligosaccharides. Whereas interactions with HSPGs act as platform to co-localise netrin-1 close to the cell surface, heparin oligosaccharides have a significant impact on the highly dynamic behaviour of netrin-1. Remarkably, the monomer-dimer equilibrium of netrin-1 in solution is abolished in the presence of heparin oligosaccharides and replaced with highly hierarchical and distinct super assemblies leading to unique, yet unknown netrin-1 filament formation. In our integrated approach we provide a molecular mechanism for the filament assembly which opens fresh paths towards a molecular understanding of netrin-1 functions.
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Affiliation(s)
- Markus Meier
- Department of Chemistry, University of Manitoba, Winnipeg, Canada
| | - Monika Gupta
- Department of Chemistry, University of Manitoba, Winnipeg, Canada
| | - Serife Akgül
- Center for Biochemistry II, Faculty of Medicine and University Hospital Cologne, University of Cologne, 50931, Cologne, Germany.,Max Planck Institute for Biology of Ageing, Cologne, Germany
| | | | - Thomas Imhof
- Center for Biochemistry II, Faculty of Medicine and University Hospital Cologne, University of Cologne, 50931, Cologne, Germany
| | - Denise Nikodemus
- Faculty of Biology, Institute of Biology II, Albert Ludwigs University of Freiburg, Freiburg, Germany
| | - Raphael Reuten
- Institute of Experimental and Clinical Pharmacology and Toxicology, Medical Faculty, University of Freiburg, Freiburg, Germany.,Department of Obsterics and Gynecology, Medical Center, University of Freiburg, Freiburg, Germany
| | | | - Vu To
- Department of Chemistry, University of Manitoba, Winnipeg, Canada
| | - Fraser Ferens
- Department of Chemistry, University of Manitoba, Winnipeg, Canada
| | - Fabian Heide
- Department of Chemistry, University of Manitoba, Winnipeg, Canada
| | | | - Philipp Kukura
- Physical and Theoretical Chemistry Laboratory, Department of Chemistry, University of Oxford, South Parks Road, Oxford, OX1 3QZ, UK
| | - Wenming Huang
- Max Planck Institute for Biology of Ageing, Cologne, Germany
| | - Birgit Gerisch
- Max Planck Institute for Biology of Ageing, Cologne, Germany
| | | | - Kate Poole
- Max Delbrück Center for Molecular Medicine, Robert Roessle Str 10, Berlin-Buch, Germany.,EMBL Australia Node in Single Molecule Science, School of Medical Sciences, Faculty of Medicine, University of New South Wales, Sydney, NSW, Australia
| | - Adam Antebi
- Max Planck Institute for Biology of Ageing, Cologne, Germany. .,Cologne Excellence Cluster on Cellular Stress Responses in Aging Associated Diseases, University of Cologne, Cologne, 50931, Germany.
| | - Manuel Koch
- Center for Biochemistry II, Faculty of Medicine and University Hospital Cologne, University of Cologne, 50931, Cologne, Germany. .,Institute for Dental Research and Oral Musculoskeletal Biology, Faculty of Medicine and University Hospital Cologne, University of Cologne, 50931, Cologne, Germany. .,Center for Molecular Medicine Cologne, Faculty of Medicine and University Hospital Cologne, University of Cologne, 50931, Cologne, Germany.
| | - Jörg Stetefeld
- Department of Chemistry, University of Manitoba, Winnipeg, Canada.
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175
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Ma B, Wang R, Chen B, Liu W, Zhou S, Li X, Gong J, Shang S, Li Y, Xu D, Tan Z. Insights into the effect of protein glycosylation on carbohydrate substrate binding. Int J Biol Macromol 2023; 235:123833. [PMID: 36870654 DOI: 10.1016/j.ijbiomac.2023.123833] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2022] [Revised: 02/20/2023] [Accepted: 02/21/2023] [Indexed: 03/06/2023]
Abstract
The role of glycosylation in the binding of glycoproteins to carbohydrate substrates has not been well understood. The present study addresses this knowledge gap by elucidating the links between the glycosylation patterns of a model glycoprotein, a Family 1 carbohydrate-binding module (TrCBM1), and the thermodynamic and structural properties of its binding to different carbohydrate substrates using isothermal titration calorimetry and computational simulation. The variations in glycosylation patterns cause a gradual transition of the binding to soluble cellohexaose from an entropy-driven process to an enthalpy-driven one, a trend closely correlated with the glycan-induced shift of the predominant binding force from hydrophobic interactions to hydrogen bonding. However, when binding to a large surface of solid cellulose, glycans on TrCBM1 have a more dispersed distribution and thus have less adverse impact on the hydrophobic interaction forces, leading to overall improved binding. Unexpectedly, our simulation results also suggest an evolutionary role of O-mannosylation in transforming the substrate binding features of TrCBM1 from those of type A CBMs to those of type B CBMs. Taken together, these findings provide new fundamental insights into the molecular basis of the role of glycosylation in protein-carbohydrate interactions and are expected to better facilitate further studies in this area.
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Affiliation(s)
- Bo Ma
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100050, China
| | - Ruihan Wang
- MOE Key Laboratory of Green Chemistry and Technology, College of Chemistry, Sichuan University, Sichuan 610064, China
| | - Baoquan Chen
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100050, China
| | - Wenqiang Liu
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100050, China
| | - Sen Zhou
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100050, China
| | - Xue Li
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100050, China
| | - Jinyuan Gong
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100050, China
| | - Shiying Shang
- Center of Pharmaceutical Technology, School of Pharmaceutical Sciences, Tsinghua University, Beijing 100084, China
| | - Yaohao Li
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100050, China.
| | - Dingguo Xu
- MOE Key Laboratory of Green Chemistry and Technology, College of Chemistry, Sichuan University, Sichuan 610064, China.
| | - Zhongping Tan
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100050, China.
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176
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Gaardløsa M, Lervikb A, Samsonova SA. Computational modeling of the molecular basis for the calcium-dependence of the mannuronan C-5 epimerase AvAlgE6 from Azotobacter vinelandii. Comput Struct Biotechnol J 2023; 21:2188-2196. [PMID: 37013001 PMCID: PMC10066508 DOI: 10.1016/j.csbj.2023.03.021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2022] [Revised: 03/13/2023] [Accepted: 03/13/2023] [Indexed: 03/17/2023] Open
Abstract
The mannuronan C-5 epimerases catalyze epimerization of β-d-mannuronic acid to α-l-guluronic acid in alginate polymers. The seven extracellular Azotobacter vinelandii epimerases (AvAlgE1-7) are calcium-dependent, and calcium is essential for the structural integrity of their carbohydrate binding R-modules. Ca2+ is also found in the crystal structures of the A-modules, where it is suggested to play a structural role. In this study, the structure of the catalytic A-module of the A. vinelandii mannuronan C-5 epimerase AvAlgE6 is used to investigate the role of this Ca2+. Molecular dynamics (MD) simulations with and without calcium reveal the possible importance of the bound Ca2+ in the hydrophobic packing of β-sheets. In addition, a putative calcium binding site is found in the active site, indicating a potential direct role of this calcium in the catalysis. According to the literature, two of the residues coordinating calcium in this site are essential for the activity. MD simulations of the interaction with bound substrate indicate that the presence of a calcium ion in this binding site increases the binding strength. Further, explicit calculations of the substrate dissociation pathways with umbrella sampling simulations show and energetically higher dissociation barrier when calcium is present. The present study eludes to a putative catalytic role of calcium in the charge neutralizing first step of the enzymatic reaction. In addition to the importance for understanding these enzymes' molecular mechanisms, this could have implications for engineering strategies of the epimerases in industrial alginate processing.
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177
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Pang J, Mehandzhiyski AY, Zozoulenko I. A computational study of cellulose regeneration: Coarse-grained molecular dynamics simulations. Carbohydr Polym 2023; 313:120853. [PMID: 37182953 DOI: 10.1016/j.carbpol.2023.120853] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2023] [Revised: 03/22/2023] [Accepted: 03/25/2023] [Indexed: 04/03/2023]
Abstract
Understanding the microscopic mechanisms of regeneration of cellulose is prerequisite for engineering and controlling its material properties. In this paper, we performed coarse-grained Martini 3 molecular dynamics simulations of cellulose regeneration at a scale comparable to the experiments. The X-ray diffraction (XRD) curves were monitored to follow the structural changes of regenerated cellulose and trace formation of cellulose sheets and crystallites. The calculated coarse-grained morphologies of regenerated cellulose were backmapped to atomistic ones. After the backmapping we find that the regenerated coarse-grained cellulose structures calculated for both topology parameters of cellulose Iβ and cellulose II/III, are transformed to cellulose II, where the calculated XRD curves exhibit the main peak at approximately 20-21 degrees, corresponding to the (110)/(020) planes of cellulose II. This result is in good quantitative agreement with the available experimental observations.
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Affiliation(s)
- Jiu Pang
- Laboratory of Organic Electronics and Wallenberg Wood Science Center, Department of Science and Technology, Linköping University, Norrköping SE-60174, Sweden
| | - Aleksandar Y Mehandzhiyski
- Laboratory of Organic Electronics and Wallenberg Wood Science Center, Department of Science and Technology, Linköping University, Norrköping SE-60174, Sweden
| | - Igor Zozoulenko
- Laboratory of Organic Electronics and Wallenberg Wood Science Center, Department of Science and Technology, Linköping University, Norrköping SE-60174, Sweden.
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178
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Erichsen A, Peters GHJ, Beeren SR. Templated Enzymatic Synthesis of δ-Cyclodextrin. J Am Chem Soc 2023; 145:4882-4891. [PMID: 36802551 DOI: 10.1021/jacs.3c00341] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/22/2023]
Abstract
While α-, β-, and γ-cyclodextrin (CD) are ubiquitous hosts employed by supramolecular chemists, δ-CD (formed from nine α-1,4-linked glucopyranose units) has received very little attention. α-, β-, and γ-CD are the major products of the enzymatic breakdown of starch by cyclodextrin glucanotransferase (CGTase), but δ-CD forms only transiently in this reaction, as a minor component of a complex mixture of linear and cyclic glucans. In this work, we show how δ-CD can be synthesized in unprecedented yields by employing a bolaamphiphile template in an enzyme-mediated dynamic combinatorial library of cyclodextrins. NMR spectroscopy studies revealed that δ-CD can thread up to three bolaamphiphiles forming [2]-, [3]-, or [4]-pseudorotaxanes, depending on the size of the hydrophilic headgroup and the length of the alkyl chain axle. Threading of the first bolaamphiphile occurs in fast exchange on the NMR chemical shift time scale, while subsequent threading occurs in slow exchange. To extract quantitative information for 1:2 and 1:3 binding events occurring in mixed exchange regimes, we derived equations for nonlinear curve fitting that take into consideration both the chemical shift changes for species in fast exchange and the integrals for species in slow exchange to determine Ka1, Ka2, and Ka3. Template T1 could be used to direct the enzymatic synthesis of δ-CD due to the cooperative formation of a 1:2 complex─the [3]-pseudorotaxane δ-CD·T12. Importantly, T1 is recyclable. It can be readily recovered from the enzymatic reaction by precipitation and reused in subsequent syntheses enabling preparative-scale synthesis of δ-CD.
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Affiliation(s)
- Andreas Erichsen
- Department of Chemistry, Technical University of Denmark, 2800 Kgs. Lyngby, Denmark
| | - Günther H J Peters
- Department of Chemistry, Technical University of Denmark, 2800 Kgs. Lyngby, Denmark
| | - Sophie R Beeren
- Department of Chemistry, Technical University of Denmark, 2800 Kgs. Lyngby, Denmark
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179
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Ruiz-Gómez G, Salbach-Hirsch J, Dürig JN, Köhler L, Balamurugan K, Rother S, Heidig SL, Moeller S, Schnabelrauch M, Furesi G, Pählig S, Guillem-Gloria PM, Hofbauer C, Hintze V, Pisabarro MT, Rademann J, Hofbauer LC. Rational engineering of glycosaminoglycan-based Dickkopf-1 scavengers to improve bone regeneration. Biomaterials 2023; 297:122105. [PMID: 37031548 DOI: 10.1016/j.biomaterials.2023.122105] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2022] [Revised: 03/13/2023] [Accepted: 03/27/2023] [Indexed: 04/03/2023]
Abstract
The WNT signaling pathway is a central regulator of bone development and regeneration. Functional alterations of WNT ligands and inhibitors are associated with a variety of bone diseases that affect bone fragility and result in a high medical and socioeconomic burden. Hence, this cellular pathway has emerged as a novel target for bone-protective therapies, e.g. in osteoporosis. Here, we investigated glycosaminoglycan (GAG) recognition by Dickkopf-1 (DKK1), a potent endogenous WNT inhibitor, and the underlying functional implications in order to develop WNT signaling regulators. In a multidisciplinary approach we applied in silico structure-based de novo design strategies and molecular dynamics simulations combined with synthetic chemistry and surface plasmon resonance spectroscopy to Rationally Engineer oligomeric Glycosaminoglycan derivatives (REGAG) with improved neutralizing properties for DKK1. In vitro and in vivo assays show that the GAG modification to obtain REGAG translated into increased WNT pathway activity and improved bone regeneration in a mouse calvaria defect model with critical size bone lesions. Importantly, the developed REGAG outperformed polymeric high-sulfated hyaluronan (sHA3) in enhancing bone healing up to 50% due to their improved DKK1 binding properties. Thus, rationally engineered GAG variants may represent an innovative strategy to develop novel therapeutic approaches for regenerative medicine.
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Affiliation(s)
- Gloria Ruiz-Gómez
- Structural Bioinformatics, BIOTEC, Technische Universität Dresden, Tatzberg 47/51, D-01307, Dresden, Germany
| | - Juliane Salbach-Hirsch
- Division of Endocrinology, Diabetes and Bone Diseases & Center for Healthy Aging, Department of Medicine III, Technische Universität Dresden Medical Center, Fetscherstraße 74, D-01307, Dresden, Germany
| | - Jan-Niklas Dürig
- Institute of Pharmacy - Medicinal Chemistry, Freie Universität Berlin, Königin-Luise-Str. 2+4, D-14195, Berlin, Germany
| | - Linda Köhler
- Institute of Materials Science, Max Bergmann Center of Biomaterials, Technische Universität Dresden, Budapester Str. 27, D-01069, Dresden, Germany
| | - Kanagasabai Balamurugan
- Structural Bioinformatics, BIOTEC, Technische Universität Dresden, Tatzberg 47/51, D-01307, Dresden, Germany
| | - Sandra Rother
- Institute of Materials Science, Max Bergmann Center of Biomaterials, Technische Universität Dresden, Budapester Str. 27, D-01069, Dresden, Germany
| | - Sophie-Luise Heidig
- Structural Bioinformatics, BIOTEC, Technische Universität Dresden, Tatzberg 47/51, D-01307, Dresden, Germany
| | | | | | - Giulia Furesi
- Division of Endocrinology, Diabetes and Bone Diseases & Center for Healthy Aging, Department of Medicine III, Technische Universität Dresden Medical Center, Fetscherstraße 74, D-01307, Dresden, Germany
| | - Sophie Pählig
- Division of Endocrinology, Diabetes and Bone Diseases & Center for Healthy Aging, Department of Medicine III, Technische Universität Dresden Medical Center, Fetscherstraße 74, D-01307, Dresden, Germany
| | - Pedro M Guillem-Gloria
- Structural Bioinformatics, BIOTEC, Technische Universität Dresden, Tatzberg 47/51, D-01307, Dresden, Germany
| | - Christine Hofbauer
- National Center for Tumor Diseases/University Cancer Center Dresden, Technische Universität Dresden Medical Center, Fetscherstraße 74, D-01307, Dresden, Germany
| | - Vera Hintze
- Institute of Materials Science, Max Bergmann Center of Biomaterials, Technische Universität Dresden, Budapester Str. 27, D-01069, Dresden, Germany.
| | - M Teresa Pisabarro
- Structural Bioinformatics, BIOTEC, Technische Universität Dresden, Tatzberg 47/51, D-01307, Dresden, Germany.
| | - Jörg Rademann
- Institute of Pharmacy - Medicinal Chemistry, Freie Universität Berlin, Königin-Luise-Str. 2+4, D-14195, Berlin, Germany.
| | - Lorenz C Hofbauer
- Division of Endocrinology, Diabetes and Bone Diseases & Center for Healthy Aging, Department of Medicine III, Technische Universität Dresden Medical Center, Fetscherstraße 74, D-01307, Dresden, Germany; Center for Regenerative Therapies Dresden, Technische Universität Dresden, Fetscherstraße 105, D-01307, Dresden, Germany.
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180
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Li Y, Yu T, Wang Z, Li Q, Rao L, Zhao L, Wang Y, Liao X. The influence mechanism of pH and hydrothermal processing on the interaction between cyanidin-3-O-glucoside and starch. Food Hydrocoll 2023. [DOI: 10.1016/j.foodhyd.2022.108234] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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181
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Khavani M, Mehranfar A, Mofrad MRK. On the potentials of sialic acid derivatives as inhibitors for the mumps virus: A molecular dynamics and quantum chemistry investigation. Virus Res 2023; 326:199050. [PMID: 36682462 DOI: 10.1016/j.virusres.2023.199050] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2022] [Revised: 12/21/2022] [Accepted: 01/18/2023] [Indexed: 01/22/2023]
Abstract
Mumps virus is an infectious pathogen causing major health problems for humans such as encephalitis, orchitis, and parotitis. Therefore, designing an inhibitor for this virus is of great medical and public health importance. With this goal in mind, we investigate the affinity of different sialic acid-based compounds (ligands) against the hemagglutinin-neuraminidase (HN) protein of the mumps virus, using a combination of molecular dynamics (MD) simulations and quantum chemistry calculations. Our MD simulation results indicate that the ligands form stable complexes with the HN protein through a combination of electrostatic, van der Waals (vdW), and hydrogen bond (H-bond) interactions, which the electrostatic interactions play a more important role in the complexation process. Based on the obtained results from the structural analysis Arg381, Arg291, and Arg49 play a key role in the binding site interactions with the different ligands, in comparison with other residues. There are some candidates such as Neu5Acα2-6Galβ1-4GlcNAcβ, Neu5Acα2-3Galβ1-3GlcNacβ1-3Galβ1-4Glc, and Neu5Acα2-6Galβ1-4GlcNAcβ1-3Galβ1-4Glc that form more stable complexes with the HN than the α2-3-Sialyllactose confirmed by the calculated Gibbs binding energies (-39.65, -46.93, and -36.49 kcal.mol-1, respectively). To investigate the relationship between the molecular properties of the selected compounds and their affinity to the HN receptor, density functional theory dispersion corrected (DFT-D3) calculations were employed. According to our DFT-D3 results, neutral sialic acid-based compounds have lower reactivity to the mumps virus than the negativity charge structures. Moreover, by increasing the electronic chemical potential (μ) the vdW and H-bond interactions between drugs and the HN protein increase. In other words, by elevating the electron tendency of the selected ligands their affinity to the mumps virus increases. Our quantum chemistry calculations reveal that in addition to the structural features the molecular properties of the drugs can play important roles in their affinity and reactivity against the virus. The results of this study can provide useful details to design new compounds or improve their properties against the mumps virus.
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Affiliation(s)
- Mohammad Khavani
- Departments of Bioengineering and Mechanical Engineering, Molecular Cell Biomechanics Laboratory, University of California Berkeley, Berkeley, CA 94720, USA
| | - Aliyeh Mehranfar
- Departments of Bioengineering and Mechanical Engineering, Molecular Cell Biomechanics Laboratory, University of California Berkeley, Berkeley, CA 94720, USA
| | - Mohammad R K Mofrad
- Departments of Bioengineering and Mechanical Engineering, Molecular Cell Biomechanics Laboratory, University of California Berkeley, Berkeley, CA 94720, USA.
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182
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El-Barghouthi MI, Assaf KI, Bodoor K, Alhamed DF, Alnajjar MA. Computational Study on the Encapsulation of Glucosamine Anomers by Cucurbit[6]uril and Cucurbit[8]uril in Aqueous Solution. ARAB J CHEM 2023. [DOI: 10.1016/j.arabjc.2023.104779] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/09/2023] Open
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183
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Yousef FO, Ghanem R, El-Barghouthi MI, Abu-Shattal ED, Al-Sa'doni HH, Bodoor K. Heptakis(2,6-di-O-methyl)-β-CD as a host of olanzapine: Experimental and computational study. J Mol Struct 2023. [DOI: 10.1016/j.molstruc.2022.134812] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
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184
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Wang R, Pu Z, Janke JJ, Zheng YC, Kong XD, Niu T, Zhao S, Yang L, Wang Z, Xu JH. Engineered Glycosidase for Significantly Improved Production of Naturally Rare Vina-Ginsenoside R7. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2023; 71:3852-3861. [PMID: 36790033 DOI: 10.1021/acs.jafc.2c09115] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Abstract
Ginsenosides are the main bioactive ingredients in plants of the genus Panax. Vina-ginsenoside R7 (VG-R7) is one of the rare high-value ginsenosides with health benefits. The only reported method for preparing VG-R7 involves inefficient and low-yield isolation from highly valuable natural resources. Notoginsenoside Fc (NG-Fc) isolated in the leaves and stems of Panax notoginseng is a suitable substrate for the preparation of VG-R7 via specific hydrolysis of the outside xylose at the C-20 position. Here, we first screened putative enzymes belonging to the glycoside hydrolase (GH) families 1, 3, and 43 and found that KfGH01 can specifically hydrolyze the β-d-xylopyranosyl-(1 → 6)-β-d-glucopyranoside linkage of NG-Fc to form VG-R7. The I248F/Y410R variant of KfGH01 obtained by protein engineering displayed a kcat/KM value (305.3 min-1 mM-1) for the reaction enhanced by approximately 270-fold compared with wild-type KfGH01. A change in the shape of the substrate binding pockets in the mutant allows the substrate to sit closer to the catalytic residues which may explain the enhanced catalytic efficiency of the engineered enzyme. This study identifies the first glycosidase for bioconversion of a ginsenoside with more than four sugar units, and it will inspire efforts to investigate other promising enzymes to obtain valuable natural products.
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Affiliation(s)
- Rufeng Wang
- The MOE Key Laboratory for Standardization of Chinese Medicines and the SATCM Key Laboratory for New Resources and Quality Evaluation of Chinese Medicines, Institute of Chinese Materia Medica, Shanghai University of Traditional Chinese Medicine, Shanghai 201203, China
- State Key Laboratory of Bioreactor Engineering, Shanghai Collaborative Innovation Center for Biomanufacturing, East China University of Science and Technology, Shanghai 200237, China
| | - Zhongji Pu
- Hangzhou Global Scientific and Technological Innovation Center, Zhejiang University, Hangzhou 311200, China
- School of Bioengineering, Dalian University of Technology, Dalian 116024, China
| | - Jonathan Joel Janke
- Department of Biomedical Engineering, Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, New York 12180, United States
| | - Yu-Cong Zheng
- State Key Laboratory of Bioreactor Engineering, Shanghai Collaborative Innovation Center for Biomanufacturing, East China University of Science and Technology, Shanghai 200237, China
| | - Xu-Dong Kong
- State Key Laboratory of Bioreactor Engineering, Shanghai Collaborative Innovation Center for Biomanufacturing, East China University of Science and Technology, Shanghai 200237, China
| | - Tengfei Niu
- The MOE Key Laboratory for Standardization of Chinese Medicines and the SATCM Key Laboratory for New Resources and Quality Evaluation of Chinese Medicines, Institute of Chinese Materia Medica, Shanghai University of Traditional Chinese Medicine, Shanghai 201203, China
| | - Shujuan Zhao
- The MOE Key Laboratory for Standardization of Chinese Medicines and the SATCM Key Laboratory for New Resources and Quality Evaluation of Chinese Medicines, Institute of Chinese Materia Medica, Shanghai University of Traditional Chinese Medicine, Shanghai 201203, China
| | - Li Yang
- The MOE Key Laboratory for Standardization of Chinese Medicines and the SATCM Key Laboratory for New Resources and Quality Evaluation of Chinese Medicines, Institute of Chinese Materia Medica, Shanghai University of Traditional Chinese Medicine, Shanghai 201203, China
| | - Zhengtao Wang
- The MOE Key Laboratory for Standardization of Chinese Medicines and the SATCM Key Laboratory for New Resources and Quality Evaluation of Chinese Medicines, Institute of Chinese Materia Medica, Shanghai University of Traditional Chinese Medicine, Shanghai 201203, China
| | - Jian-He Xu
- State Key Laboratory of Bioreactor Engineering, Shanghai Collaborative Innovation Center for Biomanufacturing, East China University of Science and Technology, Shanghai 200237, China
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185
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Newby ML, Fogarty CA, Allen JD, Butler J, Fadda E, Crispin M. Variations within the Glycan Shield of SARS-CoV-2 Impact Viral Spike Dynamics. J Mol Biol 2023; 435:167928. [PMID: 36565991 PMCID: PMC9769069 DOI: 10.1016/j.jmb.2022.167928] [Citation(s) in RCA: 21] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2022] [Revised: 11/25/2022] [Accepted: 12/15/2022] [Indexed: 12/24/2022]
Abstract
The emergence of SARS-CoV-2 variants alters the efficacy of existing immunity, whether arisen naturally or through vaccination. Understanding the structure of the viral spike assists in determining the impact of mutations on the antigenic surface. One class of mutation impacts glycosylation attachment sites, which have the capacity to influence the antigenic structure beyond the immediate site of attachment. Here, we compare the site-specific glycosylation of recombinant viral spike mimetics of B.1.351 (Beta), P.1 (Gamma), B.1.617.2 (Delta), B.1.1.529 (Omicron). The P.1 strain exhibits two additional N-linked glycan sites compared to the other variants analyzed and we investigate the impact of these glycans by molecular dynamics. The acquired N188 site is shown to exhibit very limited glycan maturation, consistent with limited enzyme accessibility. Structural modeling and molecular dynamics reveal that N188 is located within a cavity by the receptor binding domain, which influences the dynamics of these attachment domains. These observations suggest a mechanism whereby mutations affecting viral glycosylation sites have a structural impact across the protein surface.
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Affiliation(s)
- Maddy L Newby
- School of Biological Sciences, University of Southampton, Southampton, UK. https://twitter.com/Maddy_Newby
| | - Carl A Fogarty
- Department of Chemistry and Hamilton Institute, Maynooth University, Maynooth, Kildare, Ireland. https://twitter.com/2016Carl
| | - Joel D Allen
- School of Biological Sciences, University of Southampton, Southampton, UK. https://twitter.com/JoelDalllen
| | - John Butler
- School of Biological Sciences, University of Southampton, Southampton, UK
| | - Elisa Fadda
- Department of Chemistry and Hamilton Institute, Maynooth University, Maynooth, Kildare, Ireland.
| | - Max Crispin
- School of Biological Sciences, University of Southampton, Southampton, UK.
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186
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Sangkhawasi M, Kerdpol K, Ismail A, Nutho B, Hanpiboon C, Wolschann P, Krusong K, Rungrotmongkol T, Hannongbua S. In Vitro and In Silico Study on the Molecular Encapsulation of α-Tocopherol in a Large-Ring Cyclodextrin. Int J Mol Sci 2023; 24:ijms24054425. [PMID: 36901859 PMCID: PMC10002136 DOI: 10.3390/ijms24054425] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2023] [Revised: 02/17/2023] [Accepted: 02/22/2023] [Indexed: 02/25/2023] Open
Abstract
α-tocopherol is the physiologically most active form of vitamin E, with numerous biological activities, such as significant antioxidant activity, anticancer capabilities, and anti-aging properties. However, its low water solubility has limited its potential use in the food, cosmetic, and pharmaceutical industries. One possible strategy for addressing this issue is the use of a supramolecular complex with large-ring cyclodextrins (LR-CDs). In this study, the phase solubility of the CD26/α-tocopherol complex was investigated to assess the possible ratios between host and guest in the solution phase. Next, the host-guest association of the CD26/α-tocopherol complex at different ratios of 1:2, 1:4, 1:6, 2:1, 4:1, and 6:1 was studied by all-atom molecular dynamics (MD) simulations. At 1:2 ratio, two α-tocopherol units interact spontaneously with CD26, forming an inclusion complex, as supported by the experimental data. In the 2:1 ratio, a single α-tocopherol unit was encapsulated by two CD26 molecules. In comparison, increasing the number of α-tocopherol or CD26 molecules above two led to self-aggregation and consequently limited the solubility of α-tocopherol. The computational and experimental results indicate that a 1:2 ratio could be the most suitable stoichiometry to use in the CD26/α-tocopherol complex to improve α-tocopherol solubility and stability in inclusion complex formation.
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Affiliation(s)
- Mattanun Sangkhawasi
- Center of Excellence in Computational Chemistry (CECC), Department of Chemistry, Faculty of Science, Chulalongkorn University, Bangkok 10330, Thailand
- Center of Excellence in Structural and Computational Biology, Department of Biochemistry, Faculty of Science, Chulalongkorn University, Bangkok 10330, Thailand
| | - Khanittha Kerdpol
- Center of Excellence in Computational Chemistry (CECC), Department of Chemistry, Faculty of Science, Chulalongkorn University, Bangkok 10330, Thailand
| | - Abbas Ismail
- Center of Excellence in Structural and Computational Biology, Department of Biochemistry, Faculty of Science, Chulalongkorn University, Bangkok 10330, Thailand
| | - Bodee Nutho
- Department of Pharmacology, Faculty of Science, Mahidol University, Bangkok 10400, Thailand
| | - Chonnikan Hanpiboon
- Center of Excellence in Structural and Computational Biology, Department of Biochemistry, Faculty of Science, Chulalongkorn University, Bangkok 10330, Thailand
| | - Peter Wolschann
- Institute of Theoretical Chemistry, University of Vienna, 1090 Vienna, Austria
| | - Kuakarun Krusong
- Center of Excellence in Structural and Computational Biology, Department of Biochemistry, Faculty of Science, Chulalongkorn University, Bangkok 10330, Thailand
| | - Thanyada Rungrotmongkol
- Center of Excellence in Structural and Computational Biology, Department of Biochemistry, Faculty of Science, Chulalongkorn University, Bangkok 10330, Thailand
- Program in Bioinformatics and Computational Biology, Graduate School, Chulalongkorn University, Bangkok 10330, Thailand
- Correspondence: (T.R.); (S.H.); Tel.: +66-2218-5426 (T.R.); +66-8163-61957 (S.H.)
| | - Supot Hannongbua
- Center of Excellence in Computational Chemistry (CECC), Department of Chemistry, Faculty of Science, Chulalongkorn University, Bangkok 10330, Thailand
- Correspondence: (T.R.); (S.H.); Tel.: +66-2218-5426 (T.R.); +66-8163-61957 (S.H.)
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187
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Karna NK, Wohlert J, Hjorth A, Theliander H. Capillary forces exerted by a water bridge on cellulose nanocrystals: the effect of an external electric field. Phys Chem Chem Phys 2023; 25:6326-6332. [PMID: 36779301 DOI: 10.1039/d2cp05563e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
Capillary forces play an important role during the dewatering and drying of nanocellulosic materials. Traditional moisture removal techniques, such as heating, have been proved to be deterimental to the properties of these materials and hence, there is a need to develop novel dewatering techniques without affecting the desired properties of materials. It is, therefore, important to explore novel methods for dewatering these high-added-value materials without negatively influencing their properties. In this context, we explore the effect of electric field on the capillary forces developed by a liquid-water bridge between two cellulosic surfaces, which may be formed during the water removal process following its displacement from the interfibrillar spaces. All-atom molecular dynamics (MD) simulations have been used to study the influence of an externally applied electric field on the capillary force exerted by a water bridge. Our results suggest that the equilibrium contact angle of water and the capillary force exerted by the water bridge between two nanocellulosic surfaces depend on the magnitude and direction of the externally applied electric fields. Hence, an external electric field can be applied to manipulate the capillary forces between two particles. The close agreement between the capillary forces measured through MD simulations and those calculated through classical equations indicates that, within the range of the electric field applied in this study, Young-Laplace equations can be safely employed to predict the capillary forces between two particles. The present study provides insights into the use of electric fields for drying of nanocellulosic materials.
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Affiliation(s)
- Nabin Kumar Karna
- Chalmers University of Technology, Chalmersplatsen-4, Sweden. .,Wallenberg Wood Science Center, The Royal Institute of Technology, Chalmers University of Technology and Linköping University, SE-10044 Stockholm, Sweden
| | - Jakob Wohlert
- Wallenberg Wood Science Center, The Royal Institute of Technology, Chalmers University of Technology and Linköping University, SE-10044 Stockholm, Sweden.,KTH Royal Institute of Technology, Stockholm, Sweden
| | - Anna Hjorth
- Chalmers University of Technology, Chalmersplatsen-4, Sweden. .,Wallenberg Wood Science Center, The Royal Institute of Technology, Chalmers University of Technology and Linköping University, SE-10044 Stockholm, Sweden
| | - Hans Theliander
- Chalmers University of Technology, Chalmersplatsen-4, Sweden.
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188
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Couves EC, Gardner S, Voisin TB, Bickel JK, Stansfeld PJ, Tate EW, Bubeck D. Structural basis for membrane attack complex inhibition by CD59. Nat Commun 2023; 14:890. [PMID: 36797260 PMCID: PMC9935631 DOI: 10.1038/s41467-023-36441-z] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2022] [Accepted: 02/01/2023] [Indexed: 02/18/2023] Open
Abstract
CD59 is an abundant immuno-regulatory receptor that protects human cells from damage during complement activation. Here we show how the receptor binds complement proteins C8 and C9 at the membrane to prevent insertion and polymerization of membrane attack complex (MAC) pores. We present cryo-electron microscopy structures of two inhibited MAC precursors known as C5b8 and C5b9. We discover that in both complexes, CD59 binds the pore-forming β-hairpins of C8 to form an intermolecular β-sheet that prevents membrane perforation. While bound to C8, CD59 deflects the cascading C9 β-hairpins, rerouting their trajectory into the membrane. Preventing insertion of C9 restricts structural transitions of subsequent monomers and indirectly halts MAC polymerization. We combine our structural data with cellular assays and molecular dynamics simulations to explain how the membrane environment impacts the dual roles of CD59 in controlling pore formation of MAC, and as a target of bacterial virulence factors which hijack CD59 to lyse human cells.
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Affiliation(s)
- Emma C Couves
- Department of Life Sciences, Sir Ernst Chain Building, Imperial College London, London, SW7 2AZ, United Kingdom
| | - Scott Gardner
- Department of Life Sciences, Sir Ernst Chain Building, Imperial College London, London, SW7 2AZ, United Kingdom
| | - Tomas B Voisin
- Department of Life Sciences, Sir Ernst Chain Building, Imperial College London, London, SW7 2AZ, United Kingdom
| | - Jasmine K Bickel
- Department of Life Sciences, Sir Ernst Chain Building, Imperial College London, London, SW7 2AZ, United Kingdom
- Department of Chemistry, Molecular Sciences Research Hub, Imperial College London, London, W12 0BZ, United Kingdom
| | - Phillip J Stansfeld
- School of Life Sciences and Department of Chemistry, Gibbet Hill Campus, The University of Warwick, Coventry, CV4 7AL, United Kingdom
| | - Edward W Tate
- Department of Chemistry, Molecular Sciences Research Hub, Imperial College London, London, W12 0BZ, United Kingdom
| | - Doryen Bubeck
- Department of Life Sciences, Sir Ernst Chain Building, Imperial College London, London, SW7 2AZ, United Kingdom.
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189
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Westberry BP, Mansel BW, Lundin L, Williams MAK. Molecular dynamics simulations and X-ray scattering show the κ-carrageenan disorder-to-order transition to be the formation of double-helices. Carbohydr Polym 2023; 302:120417. [PMID: 36604079 DOI: 10.1016/j.carbpol.2022.120417] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2022] [Revised: 10/20/2022] [Accepted: 11/23/2022] [Indexed: 12/12/2022]
Abstract
Recent molecular dynamics simulations, verified experimentally by solution-state x-ray scattering experiments, have found that κ-carrageenan chains contain helical secondary structure, akin to that found in the solid-state, even in aqueous solution. Furthermore, upon the addition of ions to single chains the simulations found no evidence that any conformational transitions take place. These findings challenge the long-held assumption that the so-called disorder-to-order transition in carrageenan systems involves a uni-molecular 'coil-to-helix transition'. Herein, the results of further molecular dynamics simulations undertaken using pairs of κ-carrageenan chains in 0.1 M NaI solutions are reported, and are validated experimentally using state-of-the-art solution-state WAXS experiments. From initially separated chains double-helices are shown to form, leading the authors to propose 'two single helices-to-stabilized double-helix' as a description of the molecular events taking place during the disorder-to-order transition.
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Affiliation(s)
- Benjamin P Westberry
- School of Natural Sciences, Massey University, Palmerston North, New Zealand; MacDiarmid Institute for Advanced Materials and Nanotechnology, Wellington, New Zealand.
| | - Bradley W Mansel
- National Synchrotron Radiation Research Center, 101 Hsin-Ann Road, Hsinchu Science Park, Hsinchu, 30076, Taiwan, ROC
| | - Leif Lundin
- CSIRO Agriculture and Food, 671 Sneydes Road, Werribee, Victoria 3030, Australia
| | - M A K Williams
- School of Natural Sciences, Massey University, Palmerston North, New Zealand; MacDiarmid Institute for Advanced Materials and Nanotechnology, Wellington, New Zealand
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190
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Young M, Tang M, Li H, Richard DJ, McLeod DSA, d'Emden MC, Richard K. Transthyretin binds soluble endoglin and increases its uptake by hepatocytes: A possible role for transthyretin in preeclampsia? Mol Cell Endocrinol 2023; 562:111851. [PMID: 36634839 DOI: 10.1016/j.mce.2023.111851] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/25/2022] [Revised: 01/05/2023] [Accepted: 01/09/2023] [Indexed: 01/11/2023]
Abstract
BACKGROUND Preeclampsia is a common but life-threatening condition of pregnancy. It is caused by poor placentation resulting in release of trophoblast material (including soluble endoglin (sEng)) into the maternal circulation leading to maternal vascular dysfunction and to the life-threatening condition of eclampsia. The only cure is early delivery, which can have lifelong consequences for the premature child. The thyroid hormone binding protein transthyretin is dysregulated in preeclampsia, however it is not known if this plays a role in disease pathology. We hypothesised that transthyretin may bind sEng and abrogate its negative effects by removing it from the maternal serum. METHODS The effect of transthyretin on hepatocyte uptake of Alexa-labelled sEng was measured using live cell imaging. Interactions between transthyretin, and sEng were investigated using molecular modelling, direct binding on CnBr Sepharose columns, confocal imaging, and measurement of fluorescence resonance energy transfer. RESULTS Transthyretin directly bound to sEng and increased its uptake by hepatocytes. This uptake was altered in the presence of transforming growth factor-β1 (TGF-β1). Molecular modelling predicted that transthyretin and TGF-β1 bind at the same site in sEng and may compete for binding. Endocytosed transthyretin and endoglin entered cells together and co-localised inside hepatocyte cells. CONCLUSION Transthyretin can bind sEng and increase its uptake from the extracellular medium. This suggests that increasing transthyretin levels or developing drugs that normalise or mimic transthyretin, may provide treatment options to reduce sEng induced vascular dysfunction.
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Affiliation(s)
- Melanie Young
- Conjoint Internal Medicine Laboratory, Chemical Pathology, Pathology Queensland, Queensland Health, Brisbane, Australia
| | - Ming Tang
- Queensland University of Technology (QUT), Cancer & Ageing Research Program, Centre for Genomics and Personalised Health, Translational Research Institute (TRI), Brisbane, Australia
| | - Huika Li
- Conjoint Internal Medicine Laboratory, Chemical Pathology, Pathology Queensland, Queensland Health, Brisbane, Australia
| | - Derek J Richard
- Queensland University of Technology (QUT), Cancer & Ageing Research Program, Centre for Genomics and Personalised Health, Translational Research Institute (TRI), Brisbane, Australia
| | - Donald S A McLeod
- Department of Endocrinology and Diabetes, Royal Brisbane and Women's Hospital, Brisbane, Australia; QIMR Berghofer Medical Research Institute, Brisbane, Australia
| | - Michael C d'Emden
- Department of Endocrinology and Diabetes, Royal Brisbane and Women's Hospital, Brisbane, Australia; School of Medicine, University of Queensland, Herston, Qld, 4029, Australia
| | - Kerry Richard
- Conjoint Internal Medicine Laboratory, Chemical Pathology, Pathology Queensland, Queensland Health, Brisbane, Australia; Queensland University of Technology (QUT), Cancer & Ageing Research Program, Centre for Genomics and Personalised Health, Translational Research Institute (TRI), Brisbane, Australia; Department of Endocrinology and Diabetes, Royal Brisbane and Women's Hospital, Brisbane, Australia; School of Medicine, University of Queensland, Herston, Qld, 4029, Australia.
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191
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Dhurua S, Jana M. Understanding Conformational Properties and Role of Hydrogen Bonds in Glycosaminoglycans-Interleukin8 Complexes in Aqueous Medium by Molecular Dynamics Simulation. Chemphyschem 2023; 24:e202200440. [PMID: 36239153 DOI: 10.1002/cphc.202200440] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2022] [Revised: 10/13/2022] [Indexed: 11/11/2022]
Abstract
Atomistic molecular dynamics simulations were performed under ambient conditions to explore the conformational features and binding affinities of hexameric glycosaminoglycans (GAGs) with chemokine Interleukin8 (IL8) in an aqueous medium. We tried to understand the role of hydrogen bonds (HBs) involving conserved water in mediating the interactions. The Luzar-Chandler model was adopted to study the kinetics of HB breaking and formation concerning different water-mediated HBs. The conformational flexibilities of bound GAGs are due to the flexible glycosidic linkages than the occasional/rare ring pucker conformation. The free energy landscape constructed with ϕ, and ψ, depicted that different conformational minima associated with the glycosidic linkage flexibility of the GAGs in bound states are separated by energy barriers. The binding affinities of IL8 towards GAGs are favored through the electrostatic and non-polar solvation interactions. 4-different types of conserved water were explored in the solvent-mediated binding of GAGs with IL8. The average lifetime of the IL8-GAG direct HB pairs was ∼ten times less than the IL8-GAG-shared water HBs. This is due to the rapid establishment of HB breaking and reformation kinetics involving water of a shared layer. We find that despite the highly negatively charged surface of GAGs, the IL8 surface populated by non-cationic amino acids could serve as a promising binding site in addition to the cationic surface of the protein.
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Affiliation(s)
- Shakuntala Dhurua
- Molecular Simulation Laboratory, Department of Chemistry, National Institute of Technology, 769008, Rourkela, India
| | - Madhurima Jana
- Molecular Simulation Laboratory, Department of Chemistry, National Institute of Technology, 769008, Rourkela, India
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192
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Verma P, Kwansa AL, Ho R, Yingling YG, Zimmer J. Insights into substrate coordination and glycosyl transfer of poplar cellulose synthase-8. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.02.07.527505. [PMID: 36798277 PMCID: PMC9934533 DOI: 10.1101/2023.02.07.527505] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/10/2023]
Abstract
Cellulose is an abundant cell wall component of land plants. It is synthesized from UDP-activated glucose molecules by cellulose synthase, a membrane-integrated processive glycosyltransferase. Cellulose synthase couples the elongation of the cellulose polymer with its translocation across the plasma membrane. Here, we present substrate and product-bound cryogenic electron microscopy structures of the homotrimeric cellulose synthase isoform-8 (CesA8) from hybrid aspen (poplar). UDP-glucose binds to a conserved catalytic pocket adjacent to the entrance to a transmembrane channel. The substrate's glucosyl unit is coordinated by conserved residues of the glycosyltransferase domain and amphipathic interface helices. Site-directed mutagenesis of a conserved gating loop capping the active site reveals its critical function for catalytic activity. Molecular dynamics simulations reveal prolonged interactions of the gating loop with the substrate molecule, particularly across its central conserved region. These transient interactions likely facilitate the proper positioning of the substrate molecule for glycosyl transfer and cellulose translocation. Highlights Cryo-EM structures of substrate and product bound poplar cellulose synthase provide insights into substrate selectivitySite directed mutagenesis signifies a critical function of the gating loop for catalysisMolecular dynamics simulations support persistent gating loop - substrate interactionsGating loop helps in positioning the substrate molecule to facilitate cellulose elongationConserved cellulose synthesis substrate binding mechanism across the kingdoms.
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Affiliation(s)
- Preeti Verma
- Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, VA, 22903, USA
| | - Albert L. Kwansa
- Department of Materials Science and Engineering, North Carolina State University, Raleigh, NC 27695, USA
| | - Ruoya Ho
- Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, VA, 22903, USA
- Howard Hughes Medical Institute, University of Virginia, Charlottesville, VA 22903
| | - Yaroslava G. Yingling
- Department of Materials Science and Engineering, North Carolina State University, Raleigh, NC 27695, USA
| | - Jochen Zimmer
- Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, VA, 22903, USA
- Howard Hughes Medical Institute, University of Virginia, Charlottesville, VA 22903
- Lead contact
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193
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Romerio A, Gotri N, Franco AR, Artusa V, Shaik MM, Pasco ST, Atxabal U, Matamoros-Recio A, Mínguez-Toral M, Zalamea JD, Franconetti A, Abrescia NGA, Jimenez-Barbero J, Anguita J, Martín-Santamaría S, Peri F. New Glucosamine-Based TLR4 Agonists: Design, Synthesis, Mechanism of Action, and In Vivo Activity as Vaccine Adjuvants. J Med Chem 2023; 66:3010-3029. [PMID: 36728697 PMCID: PMC9969399 DOI: 10.1021/acs.jmedchem.2c01998] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
We disclose here a panel of small-molecule TLR4 agonists (the FP20 series) whose structure is derived from previously developed TLR4 ligands (FP18 series). The new molecules have increased chemical stability and a shorter, more efficient, and scalable synthesis. The FP20 series showed selective activity as TLR4 agonists with a potency similar to FP18. Interestingly, despite the chemical similarity with the FP18 series, FP20 showed a different mechanism of action and immunofluorescence microscopy showed no NF-κB nor p-IRF-3 nuclear translocation but rather MAPK and NLRP3-dependent inflammasome activation. The computational studies related a 3D shape of FP20 series with agonist binding properties inside the MD-2 pocket. FP20 displayed a CMC value lower than 5 μM in water, and small unilamellar vesicle (SUV) formation was observed in the biological activity concentration range. FP20 showed no toxicity in mouse vaccination experiments with OVA antigen and induced IgG production, thus indicating a promising adjuvant activity.
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Affiliation(s)
- Alessio Romerio
- Department
of Biotechnology and Biosciences, University
of Milano-Bicocca, Piazza della Scienza, 2, 20126 Milano, Italy
| | - Nicole Gotri
- Department
of Biotechnology and Biosciences, University
of Milano-Bicocca, Piazza della Scienza, 2, 20126 Milano, Italy
| | - Ana Rita Franco
- Department
of Biotechnology and Biosciences, University
of Milano-Bicocca, Piazza della Scienza, 2, 20126 Milano, Italy
| | - Valentina Artusa
- Department
of Biotechnology and Biosciences, University
of Milano-Bicocca, Piazza della Scienza, 2, 20126 Milano, Italy
| | - Mohammed Monsoor Shaik
- Department
of Biotechnology and Biosciences, University
of Milano-Bicocca, Piazza della Scienza, 2, 20126 Milano, Italy
| | - Samuel T. Pasco
- Center
for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), 48160 Derio, Bizkaia, Spain
| | - Unai Atxabal
- Center
for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), 48160 Derio, Bizkaia, Spain
| | - Alejandra Matamoros-Recio
- Centro
de Investigaciones Biológicas Margarita Salas CSIC, C/Ramiro de Maeztu, 9, 28040 Madrid, Spain
| | - Marina Mínguez-Toral
- Centro
de Investigaciones Biológicas Margarita Salas CSIC, C/Ramiro de Maeztu, 9, 28040 Madrid, Spain
| | - Juan Diego Zalamea
- Center
for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), 48160 Derio, Bizkaia, Spain
| | - Antonio Franconetti
- Center
for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), 48160 Derio, Bizkaia, Spain
| | - Nicola G. A. Abrescia
- Center
for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), 48160 Derio, Bizkaia, Spain,Ikerbasque,
Basque Foundation for Science, Plaza Euskadi 5, 48009 Bilbao, Bizkaia, Spain
| | - Jesus Jimenez-Barbero
- Center
for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), 48160 Derio, Bizkaia, Spain,Ikerbasque,
Basque Foundation for Science, Plaza Euskadi 5, 48009 Bilbao, Bizkaia, Spain,Department
of Organic Chemistry, II Faculty of Science and Technology, EHU-UPV, 48940 Leioa, Spain,Centro
de Investigación Biomédica En Red de Enfermedades Respiratorias, 28029 Madrid, Spain
| | - Juan Anguita
- Center
for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), 48160 Derio, Bizkaia, Spain,Ikerbasque,
Basque Foundation for Science, Plaza Euskadi 5, 48009 Bilbao, Bizkaia, Spain
| | | | - Francesco Peri
- Department
of Biotechnology and Biosciences, University
of Milano-Bicocca, Piazza della Scienza, 2, 20126 Milano, Italy,
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194
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Zou Y, Wang R, Du M, Wang X, Xu D. Identifying Protein-Ligand Interactions via a Novel Distance Self-Feedback Biomolecular Interaction Network. J Phys Chem B 2023; 127:899-911. [PMID: 36657025 DOI: 10.1021/acs.jpcb.2c07592] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
Efficient and accurate characterizations of protein-ligand interactions are key to understanding biology at the molecular level. They are particularly useful in pharmaceutical industry applications. They are usually computationally demanding for those widely applied dynamics-based methods in identifying important residues or calculating ligand binding free energy. In this work, we proposed a graph deep learning (DL) framework, namely, the distance self-feedback biomolecular interaction network (DSBIN), in which the relationship between the complex structure and binding affinity can be established by means of a carefully designed distance self-feedback module and interaction layer. Our model can directly provide a quantitative evaluation of inhibitor binding affinities (pKd). More importantly, the DSBIN model efficiently identifies key interactions for inhibitor binding and thus intrinsically bears the interpretability. Its generalization performance was further verified using 1405 unseen structures. The predicted binding free energies' deviations were calculated to be less than 1.37 kcal/mol for more than 55% structures. Moreover, we also compared the DSBIN model with a commonly used theoretical method in calculating the substrate binding free energy, MM/GBSA. Our results show that the current DL model has generally better performance in predicting the binding free energy. For a specific complex system, mannopentaose/TmCBM27, the DSBIN predicted binding free energy is -8.21 kcal/mol, which is very close to experimentally measured -7.76 kcal/mol and MM/GBSA calculated -7.16 kcal/mol. Meanwhile, all important aromatic residues around the binding pocket can be identified by our DL model. Considering the accuracy and efficiency of the newly developed DL model, it may be very helpful in the field of drug design and molecular recognition.
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Affiliation(s)
- Yurong Zou
- MOE Key Laboratory of Green Chemistry and Technology, College of Chemistry, Sichuan University, Chengdu, Sichuan610064, PR China
| | - Ruihan Wang
- MOE Key Laboratory of Green Chemistry and Technology, College of Chemistry, Sichuan University, Chengdu, Sichuan610064, PR China
| | - Meng Du
- MOE Key Laboratory of Green Chemistry and Technology, College of Chemistry, Sichuan University, Chengdu, Sichuan610064, PR China
| | - Xin Wang
- MOE Key Laboratory of Green Chemistry and Technology, College of Chemistry, Sichuan University, Chengdu, Sichuan610064, PR China
| | - Dingguo Xu
- MOE Key Laboratory of Green Chemistry and Technology, College of Chemistry, Sichuan University, Chengdu, Sichuan610064, PR China.,Research Center for Materials Genome Engineering, Sichuan University, Chengdu, Sichuan610065, PR China
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195
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Torres-Arteaga I, Blanco-Labra A, Mendiola-Olaya E, García-Gasca T, Aguirre-Mancilla C, Ortega-de-Santiago AL, Barboza M, Lebrilla CB, Castro-Guillén JL. Comparative study, homology modelling and molecular docking with cancer associated glycans of two non-fetuin-binding Tepary bean lectins. Glycoconj J 2023; 40:69-84. [PMID: 36385669 DOI: 10.1007/s10719-022-10091-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2022] [Revised: 10/19/2022] [Accepted: 11/02/2022] [Indexed: 11/18/2022]
Abstract
We present the purification and characterization of the two most abundant isoforms of lectins isolated from Tepary bean (Phaseolus acutifolius) seeds, which have been shown to differentially affect the survival of different cancer cells. They were separated by concanavalin A-affinity chromatography. After purification, to release the N-glycans, they were digested with the endoglycosidases PNGase and Glycanase A. Fractions resulted from the hydrolysis products were analyzed to determine their carbohydrate composition. Mass spectrometry data indicated that both isoforms contained high mannose glycans being mannose 6 the most abundant form. Furthermore, based on sequence Ans-X-Ser/Thr, where X is any amino acid except proline, a glycosylation site was determined on asparagine 36. When their metal requirement to preserve their biological activity was determined, the lectins showed differences. While lectin A (LA) agglutination activity was best in the presence of magnesium, lectin B (LB) was best with calcium. Additionally, only LA exhibited affinity to human type-A erythrocytes. Although both lectins showed small differences in their properties, an identical structure-model for both lectins was generated by the homology modelling process. Also, the analysis of ligand binding sites and in silico glycosylation were achieved. Molecular docking with colon adenocarcinoma associated-N-glycans revealed some highly possible interactions and, on the other hand, that N-glycan interaction zones of Tepary bean lectins is not restricted to the carbohydrate binding domain but to an extended part of their surface, which could lead new strategies to explain their biological activity.
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Affiliation(s)
- Iovanna Torres-Arteaga
- Centro de Investigación y de Estudios Avanzados. Unidad Irapuato. Departamento de Biotecnología y Bioquímica., Libramiento Norte. Carretera Irapuato-León. Km. 9.6, 36824, Irapuato, Guanajuato, México
| | - Alejandro Blanco-Labra
- Centro de Investigación y de Estudios Avanzados. Unidad Irapuato. Departamento de Biotecnología y Bioquímica., Libramiento Norte. Carretera Irapuato-León. Km. 9.6, 36824, Irapuato, Guanajuato, México
| | - Elizabeth Mendiola-Olaya
- Centro de Investigación y de Estudios Avanzados. Unidad Irapuato. Departamento de Biotecnología y Bioquímica., Libramiento Norte. Carretera Irapuato-León. Km. 9.6, 36824, Irapuato, Guanajuato, México
| | - Teresa García-Gasca
- Universidad Autónoma de Querétaro. Campus Juriquilla. Facultad de Ciencias Naturales., Av. de las Ciencias s/n, Juriquilla, 76230, Santiago de Querétaro, Querétaro, México
| | - Cesar Aguirre-Mancilla
- Tecnológico Nacional de México / Instituto Tecnológico de Roque., Carretera Celaya-Juventino Rosas Km. 8., 38110, Celaya, Guanajuato, México
| | - Alondra L Ortega-de-Santiago
- Centro de Investigación y de Estudios Avanzados. Unidad Irapuato. Departamento de Biotecnología y Bioquímica., Libramiento Norte. Carretera Irapuato-León. Km. 9.6, 36824, Irapuato, Guanajuato, México
| | - Mariana Barboza
- University of California. Davis campus. Department of Chemistry, One Shields Ave. Chemistry Department 2465. Chemistry Annex., 95616, CA, Davis, USA
| | - Carlito B Lebrilla
- University of California. Davis campus. Department of Chemistry, One Shields Ave. Chemistry Department 2465. Chemistry Annex., 95616, CA, Davis, USA
| | - José Luis Castro-Guillén
- Tecnológico Nacional de México / Instituto Tecnológico Superior de Irapuato, Carretera Irapuato-Silao Km. 12.5. Colonia El Copal, 36821, Irapuato, Guanajuato, México.
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196
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Rivet R, Rao RM, Nizet P, Belloy N, Huber L, Dauchez M, Ramont L, Baud S, Brézillon S. Differential MMP-14 targeting by biglycan, decorin, fibromodulin, and lumican unraveled by in silico approach. Am J Physiol Cell Physiol 2023; 324:C353-C365. [PMID: 36534501 DOI: 10.1152/ajpcell.00429.2022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Small leucine-rich proteoglycans (SLRPs) are major regulators of extracellular matrix assembly and cell signaling. Lumican, a member of the SLRPs family, and its derived peptides were shown to possess antitumor activity by interacting directly with the catalytic domain of MMP-14 leading to the inhibition of its activity. The aim of the present report was to characterize by in silico three-dimensional (3D) modeling the structure and the dynamics of four SLRPs including their core protein and their specific polysaccharide chains to assess their capacity to bind to MMP-14 and to regulate its activity. Molecular docking experiments were performed to identify the specific amino acids of MMP-14 interacting with each of the four SLRPs. The inhibition of each SLRP (100 nM) on MMP-14 activity was measured and the constants of inhibition (Ki) were evaluated. The impact of the number of glycan chains, structures, and dynamics of lumican on the interaction with MMP-14 was assessed by molecular dynamics simulations. Molecular docking analysis showed that all SLRPs bind to MMP-14 through their concave face, but in different regions of the catalytic domain of MMP-14. Each SLRPs inhibited significantly the MMP-14 activity. Finally, molecular dynamics showed the role of glycan chains in interaction with MMP-14 and shielding effect of SLRPs. Altogether, the results demonstrated that each SLRP exhibited inhibition of MMP-14 activity. However, the differential targeting of MMP-14 by the SLRPs was shown to be related not only to the core protein conformation but also to the glycan chain structures and dynamics.
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Affiliation(s)
- Romain Rivet
- CNRS UMR 7369, Matrice Extracellulaire et Dynamique Cellulaire (MEDyC), Université de Reims Champagne Ardenne, Reims, France
| | - Rajas Mallenahalli Rao
- CNRS UMR 7369, Matrice Extracellulaire et Dynamique Cellulaire (MEDyC), Université de Reims Champagne Ardenne, Reims, France.,P3M, Multi-Scale-Molecular Modeling Platform, Université de Reims Champagne Ardenne, Reims, France
| | - Pierre Nizet
- CNRS UMR 7369, Matrice Extracellulaire et Dynamique Cellulaire (MEDyC), Université de Reims Champagne Ardenne, Reims, France
| | - Nicolas Belloy
- CNRS UMR 7369, Matrice Extracellulaire et Dynamique Cellulaire (MEDyC), Université de Reims Champagne Ardenne, Reims, France.,P3M, Multi-Scale-Molecular Modeling Platform, Université de Reims Champagne Ardenne, Reims, France
| | - Louise Huber
- CNRS UMR 7369, Matrice Extracellulaire et Dynamique Cellulaire (MEDyC), Université de Reims Champagne Ardenne, Reims, France
| | - Manuel Dauchez
- CNRS UMR 7369, Matrice Extracellulaire et Dynamique Cellulaire (MEDyC), Université de Reims Champagne Ardenne, Reims, France.,P3M, Multi-Scale-Molecular Modeling Platform, Université de Reims Champagne Ardenne, Reims, France
| | - Laurent Ramont
- CNRS UMR 7369, Matrice Extracellulaire et Dynamique Cellulaire (MEDyC), Université de Reims Champagne Ardenne, Reims, France.,CHU Reims, Service Biochimie Pharmacologie-Toxicologie, Reims, France
| | - Stéphanie Baud
- CNRS UMR 7369, Matrice Extracellulaire et Dynamique Cellulaire (MEDyC), Université de Reims Champagne Ardenne, Reims, France.,P3M, Multi-Scale-Molecular Modeling Platform, Université de Reims Champagne Ardenne, Reims, France
| | - Stéphane Brézillon
- CNRS UMR 7369, Matrice Extracellulaire et Dynamique Cellulaire (MEDyC), Université de Reims Champagne Ardenne, Reims, France
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197
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Kikuchi K, Kaneko K, Seonju J, Fukaya R, Yamada M, Ishii H, Inoue T, Shimizu A. Influence of gelation temperature on physicochemical properties of cellulose hydrogels prepared from ionic liquid/DMSO solution. J Mol Liq 2023. [DOI: 10.1016/j.molliq.2023.121465] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/17/2023]
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198
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Kim SB, Farrag M, Mishra SK, Misra SK, Sharp JS, Doerksen RJ, Pomin VH. Selective 2-desulfation of tetrasaccharide-repeating sulfated fucans during oligosaccharide production by mild acid hydrolysis. Carbohydr Polym 2023; 301:120316. [PMID: 36436858 PMCID: PMC9745898 DOI: 10.1016/j.carbpol.2022.120316] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2022] [Revised: 11/03/2022] [Accepted: 11/04/2022] [Indexed: 11/10/2022]
Abstract
Sulfated fucans (SFs) from echinoderms, such as sea cucumbers and sea urchins, present linear and regular sulfation patterns within defined oligosaccharide building blocks. The high molecular weights of these polymers pose a problem in advanced structure-activity relationship studies for which derived oligosaccharides are more appropriate tools for investigation. However, enzymes capable of specifically depolymerizing SFs, fucanases, are not very common. Scarce abundance and unknown catalytic activities are additional barriers to exploiting fucanases. Oligosaccharide production by controlled chemical reactions such as mild acid hydrolysis then becomes a convenient strategy. As a consequence, physicochemical studies are necessary to understand the structural modifications caused on SFs by this chemical hydrolysis. Hence, in this work, we subjected three tetrasaccharide-repeating SFs from sea cucumbers, Isostichopus badionotus (IbSF), Holothuria floridana (HfSF), and Lytechinus variegatus (LvSF) to mild acid hydrolysis for oligosaccharide production. Interestingly, selective 2-desulfation reaction was observed in all three SFs. Through our study, we indicate that selective 2-desulfation is a common and expected phenomenon in oligosaccharide production by mild acid hydrolysis of SFs, including those composed of tetrasaccharide-repeating units.
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Affiliation(s)
- Seon Beom Kim
- Department of BioMolecular Sciences, University of Mississippi, Oxford, MS, United States; Department of Food Science & Technology, College of Natural Resources and Life Science, Pusan National University, Miryang, Republic of Korea
| | - Marwa Farrag
- Department of BioMolecular Sciences, University of Mississippi, Oxford, MS, United States; Department of Pharmacognosy, Faculty of Pharmacy, Assiut University, Assiut, Egypt
| | - Sushil K Mishra
- Department of BioMolecular Sciences, University of Mississippi, Oxford, MS, United States
| | - Sandeep K Misra
- Department of BioMolecular Sciences, University of Mississippi, Oxford, MS, United States
| | - Joshua S Sharp
- Department of BioMolecular Sciences, University of Mississippi, Oxford, MS, United States; Department of Chemistry and Biochemistry, University of Mississippi, Oxford, MS, United States
| | - Robert J Doerksen
- Department of BioMolecular Sciences, University of Mississippi, Oxford, MS, United States; Research Institute of Pharmaceutical Sciences, School of Pharmacy, University of Mississippi, Oxford, MS, United States
| | - Vitor H Pomin
- Department of BioMolecular Sciences, University of Mississippi, Oxford, MS, United States; Research Institute of Pharmaceutical Sciences, School of Pharmacy, University of Mississippi, Oxford, MS, United States.
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199
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Vemula D, Jayasurya P, Sushmitha V, Kumar YN, Bhandari V. CADD, AI and ML in drug discovery: A comprehensive review. Eur J Pharm Sci 2023; 181:106324. [PMID: 36347444 DOI: 10.1016/j.ejps.2022.106324] [Citation(s) in RCA: 31] [Impact Index Per Article: 31.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2022] [Revised: 10/26/2022] [Accepted: 11/03/2022] [Indexed: 11/06/2022]
Abstract
Computer-aided drug design (CADD) is an emerging field that has drawn a lot of interest because of its potential to expedite and lower the cost of the drug development process. Drug discovery research is expensive and time-consuming, and it frequently took 10-15 years for a drug to be commercially available. CADD has significantly impacted this area of research. Further, the combination of CADD with Artificial Intelligence (AI), Machine Learning (ML), and Deep Learning (DL) technologies to handle enormous amounts of biological data has reduced the time and cost associated with the drug development process. This review will discuss how CADD, AI, ML, and DL approaches help identify drug candidates and various other steps of the drug discovery process. It will also provide a detailed overview of the different in silico tools used and how these approaches interact.
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Affiliation(s)
- Divya Vemula
- National Institute of Pharmaceutical Education and Research- Hyderabad, India
| | - Perka Jayasurya
- National Institute of Pharmaceutical Education and Research- Hyderabad, India
| | - Varthiya Sushmitha
- National Institute of Pharmaceutical Education and Research- Hyderabad, India
| | | | - Vasundhra Bhandari
- National Institute of Pharmaceutical Education and Research- Hyderabad, India.
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200
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Pągielska M, Samsonov SA. Molecular Dynamics-Based Comparative Analysis of Chondroitin and Dermatan Sulfates. Biomolecules 2023; 13:biom13020247. [PMID: 36830616 PMCID: PMC9953526 DOI: 10.3390/biom13020247] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2022] [Revised: 01/20/2023] [Accepted: 01/26/2023] [Indexed: 01/31/2023] Open
Abstract
Glycosaminoglycans (GAGs) are a class of linear anionic periodic polysaccharides containing disaccharide repetitive units. These molecules interact with a variety of proteins in the extracellular matrix and so participate in biochemically crucial processes such as cell signalling affecting tissue regeneration as well as the onset of cancer, Alzheimer's or Parkinson's diseases. Due to their flexibility, periodicity and chemical heterogeneity, often termed "sulfation code", GAGs are challenging molecules both for experiments and computation. One of the key questions in the GAG research is the specificity of their intermolecular interactions. In this study, we make a step forward to deciphering the "sulfation code" of chondroitin sulfates-4,6 (CS4, CS6, where the numbers correspond to the position of sulfation in NAcGal residue) and dermatan sulfate (DS), which is different from CSs by the presence of IdoA acid instead of GlcA. We rigorously investigate two sets of these GAGs in dimeric, tetrameric and hexameric forms with molecular dynamics-based descriptors. Our data clearly suggest that CS4, CS6 and DS are substantially different in terms of their structural, conformational and dynamic properties, which contributes to the understanding of how these molecules can be different when they bind proteins, which could have practical implications for the GAG-based drug design strategies in the regenerative medicine.
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