1
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Cai W, Wong K, Huang Q. Isolation, structural features, rheological properties and bioactivities of polysaccharides from Lignosus rhinocerotis: A review. Int J Biol Macromol 2023; 242:124818. [PMID: 37178885 DOI: 10.1016/j.ijbiomac.2023.124818] [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: 01/26/2023] [Revised: 05/04/2023] [Accepted: 05/07/2023] [Indexed: 05/15/2023]
Abstract
L. rhinocerotis, an edible and medicinal mushroom, has long been utilized as folk medicine and nutritional food in Southeast Asia and southern China. Polysaccharides are the main bioactive substances of L. rhinocerotis sclerotia, and they have attracted extensive attention of researchers both at home and abroad. In the past few decades, various methods have been applied to extract polysaccharides from L. rhinocerotis (LRPs) and the structural features of LRPs are closely related to the used methods of extraction and purification. Many studies have confirmed that LRPs possess various remarkable bioactivities, including immunomodulatory, prebiotic, antioxidant, anti-inflammatory and anti-tumor activities and intestinal mucosa protective effect. As a natural polysaccharide, LRP has the potential to be a drug and functional material. This paper systematically reviews the recent studies on structural characteristics, modification, rheological properties and bioactivities of LRPs, and provides a theoretical basis for an in-depth study of the structure-activity relationship, and utilization of LRPs as therapeutic agents and functional foods. Additionally, the further research and development of LRPs are also prospected.
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Affiliation(s)
- Wudan Cai
- College of Food Science and Technology, and MOE Key Laboratory of Environment Correlative Dietology, Huazhong Agricultural University, Wuhan 430070, China
| | - Kahing Wong
- Research Institute for Future Food, The Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong, China; Department of Applied Biology and Chemical Technology, The Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong, China
| | - Qilin Huang
- College of Food Science and Technology, and MOE Key Laboratory of Environment Correlative Dietology, Huazhong Agricultural University, Wuhan 430070, China.
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2
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Lisacek F, Tiemeyer M, Mazumder R, Aoki-Kinoshita KF. Worldwide Glycoscience Informatics Infrastructure: The GlySpace Alliance. JACS AU 2023; 3:4-12. [PMID: 36711080 PMCID: PMC9875223 DOI: 10.1021/jacsau.2c00477] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/30/2022] [Revised: 11/04/2022] [Accepted: 11/07/2022] [Indexed: 06/18/2023]
Abstract
The GlySpace Alliance was formed in 2018 among the principal investigators of three major glycoscience portals: Glyco@Expasy, GlyCosmos, and GlyGen, representing Europe, Asia, and the United States, respectively. While each of these portals has its unique user interface, the aim is to provide the same basic data set of glycan-related omics data. These portals will be introduced with the aim to enable users to find their target information in the most efficient manner, in particular, in terms of the chemical structures of glycans and their functions.
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Affiliation(s)
- Frederique Lisacek
- Proteome
Informatics Group, SIB Swiss Institute of Bioinformatics, University of Geneva, Geneva CH-1227, Switzerland
- Computer
Science Department & Section of Biology, University of Geneva, Geneva CH-1227, Switzerland
| | - Michael Tiemeyer
- Complex
Carbohydrate Research Center, University
of Georgia, Athens, Georgia 30602, United States
| | - Raja Mazumder
- George
Washington University, Washington, District of Columbia 20037, United States
| | - Kiyoko F. Aoki-Kinoshita
- Glycan
and Life Systems Integration Center (GaLSIC), Soka University, Hachioji, Tokyo 192-8577, Japan
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3
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Liu Y, Huang Y, Zhu R, Farag MA, Capanoglu E, Zhao C. Structural elucidation approaches in carbohydrates: A comprehensive review on techniques and future trends. Food Chem 2023; 400:134118. [DOI: 10.1016/j.foodchem.2022.134118] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2022] [Accepted: 09/01/2022] [Indexed: 10/14/2022]
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4
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Huang Y, Hu Y, Chan U, Lai P, Sun Y, Dai J, Cheng X, Yang X. Student perceptions toward virtual reality training in dental implant education. PeerJ 2023; 11:e14857. [PMID: 37168535 PMCID: PMC10166074 DOI: 10.7717/peerj.14857] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2022] [Accepted: 01/15/2023] [Indexed: 05/13/2023] Open
Abstract
Objectives Both the shortage of professional teaching resources and the expensive dental implant supplies impede the effective training of dental undergraduate in implantology. Virtual reality (VR) technology may provide solutions to solve these problems. This pilot study was implemented to explore the usability and acceptance of a VR application in the training of dental implant among dental students at the Jinan University School of Stomatology. Methods We designed and developed a VR system with head-mounted displays (HMDs) to assist dental implant training. Undergraduate dental students were invited to experience a 30-minute "Introduction to dental implants" VR-HMDs training module. A total of 119 dental students participated the training. Firstly, the VR interactive training on dental implant was described, illustrated and practiced. Next, a system usability scale (SUS) survey was used to verify the usability and feasibility of the VR application on training dental students. Finally, the participants were given a questionnaire to provide their perceptions and feedback of the usefulness of the VR application for training dental implant skills. Results The SUS score was 82.00 ± 10.79, indicating a top 10 percentage ranking of the system's usabilitys. The participants' answers to the questionnaire reflected most of them exhibited strong interests in the VR system, with a tendency that the female students were more confident than the male in manipulating the VR system. The participants generally acknowledged the usefulness of VR dental implants, ranking VR value above the traditional laboratory operations, and a preference for using the VR system on learning other skills. They also gave valuable suggestions on VR dental implants for substantial improvement. However, some students were not strongly positive about the VR training in this study, the reason might lie in a more theoretical module was selected for testing, which impacted the students' ratings. Conclusions In this study we revealed the feasibility and usability of VR applications on training dental implant among undergraduate dental students. This pilot study showed that the participants benefited from the dental implant VR training by practicing the skills repeatedly. The feedback from student participants affirmed the advantages and their acceptance of the VR application in dental education. Especially, the VR-based technology is highly conducive to clinical operating skills and surgical procedures-focused training in medical education, indicating that the VR system should be combined with the traditional practice approach in improving dental students' practical abilities.
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Affiliation(s)
- Yue Huang
- School of Stomatology, Jinan University, Guangzhou, China
| | - Yingwen Hu
- School of Stomatology, Jinan University, Guangzhou, China
| | - Unman Chan
- School of Stomatology, Jinan University, Guangzhou, China
| | - Pengyu Lai
- School of Stomatology, Jinan University, Guangzhou, China
| | - Yueting Sun
- School of Stomatology, Jinan University, Guangzhou, China
| | - Jun Dai
- Shanghai VR-Sens Intelligent Technology Co., Ltd, Shanghai, China
| | - Xin Cheng
- Division of Histology and Embryology, Key Laboratory for Regenerative Medicine of the Ministry of Education, Medical College, Jinan University, Guangzhou, China
| | - Xuesong Yang
- Division of Histology and Embryology, Key Laboratory for Regenerative Medicine of the Ministry of Education, Medical College, Jinan University, Guangzhou, China
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5
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Abstract
Glycoscience assembles all the scientific disciplines involved in studying various molecules and macromolecules containing carbohydrates and complex glycans. Such an ensemble involves one of the most extensive sets of molecules in quantity and occurrence since they occur in all microorganisms and higher organisms. Once the compositions and sequences of these molecules are established, the determination of their three-dimensional structural and dynamical features is a step toward understanding the molecular basis underlying their properties and functions. The range of the relevant computational methods capable of addressing such issues is anchored by the specificity of stereoelectronic effects from quantum chemistry to mesoscale modeling throughout molecular dynamics and mechanics and coarse-grained and docking calculations. The Review leads the reader through the detailed presentations of the applications of computational modeling. The illustrations cover carbohydrate-carbohydrate interactions, glycolipids, and N- and O-linked glycans, emphasizing their role in SARS-CoV-2. The presentation continues with the structure of polysaccharides in solution and solid-state and lipopolysaccharides in membranes. The full range of protein-carbohydrate interactions is presented, as exemplified by carbohydrate-active enzymes, transporters, lectins, antibodies, and glycosaminoglycan binding proteins. A final section features a list of 150 tools and databases to help address the many issues of structural glycobioinformatics.
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Affiliation(s)
- Serge Perez
- Centre de Recherche sur les Macromolecules Vegetales, University of Grenoble-Alpes, Centre National de la Recherche Scientifique, Grenoble F-38041, France
| | - Olga Makshakova
- FRC Kazan Scientific Center of Russian Academy of Sciences, Kazan Institute of Biochemistry and Biophysics, Kazan 420111, Russia
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6
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Rao RM, Dauchez M, Baud S. How molecular modelling can better broaden the understanding of glycosylations. Curr Opin Struct Biol 2022; 75:102393. [PMID: 35679802 DOI: 10.1016/j.sbi.2022.102393] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2021] [Revised: 03/31/2022] [Accepted: 04/18/2022] [Indexed: 11/03/2022]
Abstract
Glycosylations are among the most ubiquitous post-translational modifications (PTMs) in proteins, and the effects of their perturbations are seen in various diseases such as cancers, diabetes and arthritis to name a few. Yet they remain one of the most enigmatic aspects of protein structure and function. On the other hand, molecular modelling techniques have been rapidly bridging this knowledge gap since the last decade. In this review, we discuss how these techniques have proven to be indispensable for a better understanding of the role of glycosylations in glycoprotein structure and function.
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Affiliation(s)
- Rajas M Rao
- Université de Reims Champagne Ardenne, CNRS UMR 7369, MEDyC, Reims, 51687, France
| | - Manuel Dauchez
- Université de Reims Champagne Ardenne, CNRS UMR 7369, MEDyC, Reims, 51687, France.
| | - Stéphanie Baud
- Université de Reims Champagne Ardenne, CNRS UMR 7369, MEDyC, Reims, 51687, France
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7
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Pujić I, Perreault H. Recent advancements in glycoproteomic studies: Glycopeptide enrichment and derivatization, characterization of glycosylation in SARS CoV2, and interacting glycoproteins. MASS SPECTROMETRY REVIEWS 2022; 41:488-507. [PMID: 33393161 DOI: 10.1002/mas.21679] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/22/2020] [Revised: 12/13/2020] [Accepted: 12/16/2020] [Indexed: 06/12/2023]
Abstract
Proteomics studies allow for the determination of the identity, amount, and interactions of proteins under specific conditions that allow the biological state of an organism to ultimately change. These conditions can be either beneficial or detrimental. Diseases are due to detrimental changes caused by either protein overexpression or underexpression caused by as a result of a mutation or posttranslational modifications (PTM), among other factors. Identification of disease biomarkers through proteomics can be potentially used as clinical information for diagnostics. Common biomarkers to look for include PTM. For example, aberrant glycosylation of proteins is a common marker and will be a focus of interest in this review. A common way to analyze glycoproteins is by glycoproteomics involving mass spectrometry. Due to factors such as micro- and macroheterogeneity which result in a lower abundance of each version of a glycoprotein, it is difficult to obtain meaningful results unless rigorous sample preparation procedures are in place. Microheterogeneity represents the diversity of glycans at a single site, whereas macroheterogeneity depicts glycosylation levels at each site of a protein. Enrichment and derivatization of glycopeptides help to overcome these limitations. Over the time range of 2016 to 2020, several methods have been proposed in the literature and have contributed to drastically improve the outcome of glycosylation analysis, as presented in the sampling surveyed in this review. As a current topic in 2020, glycoproteins carried by pathogens can also cause disease and this is seen with SARS CoV2, causing the COVID-19 pandemic. This review will discuss glycoproteomic studies of the spike glycoprotein and interacting proteins such as the ACE2 receptor.
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Affiliation(s)
- Ivona Pujić
- Chemistry Department, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Hélène Perreault
- Chemistry Department, University of Manitoba, Winnipeg, Manitoba, Canada
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8
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Liu X, Li J, Rolland-Sabaté A, Perez S, Le Bourvellec C, Renard CM. Experimental and theoretical investigation on interactions between xylose-containing hemicelluloses and procyanidins. Carbohydr Polym 2022; 281:119086. [DOI: 10.1016/j.carbpol.2021.119086] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2021] [Revised: 12/29/2021] [Accepted: 12/29/2021] [Indexed: 11/29/2022]
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9
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Huang Y, Cheng X, Chan U, Zheng L, Hu Y, Sun Y, Lai P, Dai J, Yang X. Virtual reality approach for orthodontic education at School of Stomatology, Jinan University. J Dent Educ 2022; 86:1025-1035. [DOI: 10.1002/jdd.12915] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2021] [Revised: 01/24/2022] [Accepted: 02/19/2022] [Indexed: 11/05/2022]
Affiliation(s)
- Yue Huang
- School of Stomatology Jinan University Guangzhou China
| | - Xin Cheng
- Division of Histology and Embryology Key Laboratory for Regenerative Medicine of the Ministry of Education Medical College Jinan University Guangzhou China
| | - Unman Chan
- School of Stomatology Jinan University Guangzhou China
| | - Liyang Zheng
- School of Stomatology Jinan University Guangzhou China
| | - Yingwen Hu
- School of Stomatology Jinan University Guangzhou China
| | - Yueting Sun
- School of Stomatology Jinan University Guangzhou China
| | - Pengyu Lai
- School of Stomatology Jinan University Guangzhou China
| | - Jun Dai
- Shanghai VR‐Sens Intelligent Technology Co., Ltd. Shanghai China
| | - Xuesong Yang
- Division of Histology and Embryology Key Laboratory for Regenerative Medicine of the Ministry of Education Medical College Jinan University Guangzhou China
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10
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Mariethoz J, Alocci D, Karlsson NG, Packer NH, Lisacek F. An Interactive View of Glycosylation. Methods Mol Biol 2022; 2370:41-65. [PMID: 34611864 DOI: 10.1007/978-1-0716-1685-7_3] [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: 06/13/2023]
Abstract
The present chapter focuses on the interactive and explorative aspects of bioinformatics resources that have been recently released in glycobiology. The comparative analysis of data in a field where knowledge is scattered, incomplete, and disconnected from main biology requires efficient visualization, integration, and interactive tools that are currently only partially implemented. This overview highlights converging efforts toward building a consistent picture of protein glycosylation.
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Affiliation(s)
- Julien Mariethoz
- Proteome Informatics Group, SIB Swiss Institute of Bioinformatics, Geneva, Switzerland
- Computer Science Department, University of Geneva, Geneva, Switzerland
| | - Davide Alocci
- Proteome Informatics Group, SIB Swiss Institute of Bioinformatics, Geneva, Switzerland
| | - Niclas G Karlsson
- Department of Medical Biochemistry and Cell Biology, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Nicolle H Packer
- Department of Molecular Sciences and ARC Centre of Excellence for Nanoscale Biophotonics, Macquarie University, Sydney, NSW, Australia
- Institute for Glycomics, Griffith University, Gold Coast, QLD, Australia
| | - Frédérique Lisacek
- Proteome Informatics Group, SIB Swiss Institute of Bioinformatics, University of Geneva, Geneva, Switzerland.
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11
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Taujale R, Soleymani S, Priyadarshi A, Venkat A, Yeung W, Kochut KJ, Kannan N. GTXplorer: A portal to navigate and visualize the evolutionary information encoded in fold a glycosyltransferases. Glycobiology 2021; 31:1472-1477. [PMID: 34351427 DOI: 10.1093/glycob/cwab082] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2021] [Revised: 07/22/2021] [Accepted: 07/22/2021] [Indexed: 11/12/2022] Open
Abstract
Glycosyltransferases (GTs) play a central role in sustaining all forms of life through the biosynthesis of complex carbohydrates. Despite significant strides made in recent years to establish computational resources, databases, and tools to understand the nature and role of carbohydrates and related glycoenzymes, a data analytics framework that connects the sequence-structure-function relationships to the evolution of GTs is currently lacking. This hinders the characterization of understudied GTs and the synthetic design of GTs for medical and biotechnology applications. Here, we present GTXplorer as an integrated platform that presents evolutionary information of GTs adopting a GT-A fold in an intuitive format enabling in silico investigation through comparative sequence analysis to derive informed hypotheses about their function. The tree view mode provides an overview of the evolutionary relationships of GT-A families and allows users to select phylogenetically relevant families for comparisons. The selected families can then be compared in the alignment view at the residue level using annotated weblogo stacks of the GT-A core specific to the selected clade, family, or subfamily. All data are easily accessible and can be downloaded for further analysis. GTXplorer can be accessed at https://vulcan.cs.uga.edu/gtxplorer/ or from GitHub at https://github.com/esbgkannan/GTxplorer to deploy locally. By packaging multiple data streams into an accessible, user-friendly format, GTXplorer presents the first evolutionary data analytics platform for comparative glycomics.
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Affiliation(s)
- Rahil Taujale
- Institute of Bioinformatics.,Complex Carbohydrate Research Center
| | | | | | - Aarya Venkat
- Biochemistry and Molecular Biology, University of Georgia, Athens, GA
| | | | | | - Natarajan Kannan
- Institute of Bioinformatics.,Biochemistry and Molecular Biology, University of Georgia, Athens, GA
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12
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Rao RM, Wong H, Dauchez M, Baud S. Effects of changes in glycan composition on glycoprotein dynamics: example of N-glycans on insulin receptor. Glycobiology 2021; 31:1121-1133. [PMID: 34343291 DOI: 10.1093/glycob/cwab049] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2020] [Revised: 05/21/2021] [Accepted: 05/21/2021] [Indexed: 12/20/2022] Open
Abstract
Glycosylation is among the most common post-translational modifications in proteins, although it is observed in only about 10% of all the protein structures in protein data bank (PDB). Modifications of sugar composition in glycoproteins profoundly impact the overall physiology of the organism. One such example is the development of insulin resistance, which has been attributed to the removal of sialic acid residues from N-glycans of insulin receptor (IR) from various experimental studies. How such modifications affect the glycan-glycoprotein dynamics, and ultimately their function is not clearly understood to date. In this study, we performed molecular dynamics simulations of glycans in different environments. We studied the effects of removal of sialic acid on the glycan, as well as on the dynamics of leucine-rich repeat L1 domain of the IR ectodomain. We observed perturbations in L1 domain dynamics as a result of the removal of sialic acid. The perturbations include an increase in the flexibility of insulin-binding residues, which may affect insulin binding with IR. These changes are accompanied by perturbations in glycan-protein interactions and perturbation of long-range allosteric dynamics. Our observations will further aid in understanding the role of sugars in maintaining homeostasis and how changes in glycan composition may lead to perturbations in homeostasis, ultimately leading to conditions such as insulin resistance.
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Affiliation(s)
- Rajas M Rao
- Université de Reims Champagne Ardenne, CNRS UMR 7369, MEDyC, Reims 51687, France
| | - Hua Wong
- Université de Reims Champagne Ardenne, CNRS UMR 7369, MEDyC, Reims 51687, France
| | - Manuel Dauchez
- Université de Reims Champagne Ardenne, CNRS UMR 7369, MEDyC, Reims 51687, France.,Université de Reims Champagne Ardenne, P3M, Multi-scale Molecular Modeling Plateform, Reims 51687, France
| | - Stéphanie Baud
- Université de Reims Champagne Ardenne, CNRS UMR 7369, MEDyC, Reims 51687, France.,Université de Reims Champagne Ardenne, P3M, Multi-scale Molecular Modeling Plateform, Reims 51687, France
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13
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Kadowaki MAS, Briganti L, Evangelista DE, Echevarría-Poza A, Tryfona T, Pellegrini VOA, Nakayama DG, Dupree P, Polikarpov I. Unlocking the structural features for the xylobiohydrolase activity of an unusual GH11 member identified in a compost-derived consortium. Biotechnol Bioeng 2021; 118:4052-4064. [PMID: 34232504 DOI: 10.1002/bit.27880] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2021] [Revised: 06/28/2021] [Accepted: 07/04/2021] [Indexed: 11/08/2022]
Abstract
The heteropolysaccharide xylan is a valuable source of sustainable chemicals and materials from renewable biomass sources. A complete hydrolysis of this major hemicellulose component requires a diverse set of enzymes including endo-β-1,4-xylanases, β-xylosidases, acetylxylan esterases, α-l-arabinofuranosidases, and α-glucuronidases. Notably, the most studied xylanases from glycoside hydrolase family 11 (GH11) have exclusively been endo-β-1,4- and β-1,3-xylanases. However, a recent analysis of a metatranscriptome library from a microbial lignocellulose community revealed GH11 enzymes capable of releasing solely xylobiose from xylan. Although initial biochemical studies clearly indicated their xylobiohydrolase mode of action, the structural features that drive this new activity still remained unclear. It was also not clear whether the enzymes acted on the reducing or nonreducing end of the substrate. Here, we solved the crystal structure of MetXyn11 in the apo and xylobiose-bound forms. The structure of MetXyn11 revealed the molecular features that explain the observed pattern on xylooligosaccharides released by this nonreducing end xylobiohydrolase.
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Affiliation(s)
- Marco A S Kadowaki
- Grupo de Biotecnologia Molecular, Instituto de Física de São Carlos, Universidade de São Paulo, São Carlos, São Paulo, Brazil.,PhotoBioCatalysis-Biomass transformation Lab (BTL), École Interfacultaire de Bioingénieurs (EIB), Université Libre de Bruxelles, Brussels, Belgium
| | - Lorenzo Briganti
- Grupo de Biotecnologia Molecular, Instituto de Física de São Carlos, Universidade de São Paulo, São Carlos, São Paulo, Brazil
| | - Danilo E Evangelista
- Grupo de Biotecnologia Molecular, Instituto de Física de São Carlos, Universidade de São Paulo, São Carlos, São Paulo, Brazil.,Instituto de Criminalística de Andradina, Superintendência da Polícia Técnico Científica de São Paulo, Andradina, São Paulo, Brazil
| | | | - Theodora Tryfona
- Department of Biochemistry, University of Cambridge, Cambridge, UK
| | - Vanessa O A Pellegrini
- Grupo de Biotecnologia Molecular, Instituto de Física de São Carlos, Universidade de São Paulo, São Carlos, São Paulo, Brazil
| | - Darlan G Nakayama
- Grupo de Biotecnologia Molecular, Instituto de Física de São Carlos, Universidade de São Paulo, São Carlos, São Paulo, Brazil
| | - Paul Dupree
- Department of Biochemistry, University of Cambridge, Cambridge, UK
| | - Igor Polikarpov
- Grupo de Biotecnologia Molecular, Instituto de Física de São Carlos, Universidade de São Paulo, São Carlos, São Paulo, Brazil
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14
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Insausti A, Alonso ER, Tercero B, Santos JI, Calabrese C, Vogt N, Corzana F, Demaison J, Cernicharo J, Cocinero EJ. Laboratory Observation of, Astrochemical Search for, and Structure of Elusive Erythrulose in the Interstellar Medium. J Phys Chem Lett 2021; 12:1352-1359. [PMID: 33507076 DOI: 10.1021/acs.jpclett.0c03050] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Rotational spectroscopy provides the most powerful means of identifying molecules of biological interest in the interstellar medium (ISM), but despite their importance, the detection of carbohydrates has remained rather elusive. Here, we present a comprehensive Fourier transform rotational spectroscopic study of elusive erythrulose, a sugar building block likely to be present in the ISM, employing a novel method of transferring the hygroscopic oily carbohydrate into the gas phase. The high sensitivity of the experiment allowed the rotational spectra of all monosubstituted isotopologue species of 13C-12C3H8O4 to be recorded, which, together with quantum chemical calculations, enabled us to determine their equilibrium geometries (reSE) with great precision. Searches employing the new experimental data for erythrulose have been undertaken in different ISM regions, so far including the cold areas Barnard 1, the pre-stellar core TMC-1, Sagittarius B2. Although no lines of erythrulose were found, this data will serve to enable future searches and possible detections in other ISM regions.
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Affiliation(s)
- Aran Insausti
- Departamento de Química Física, Facultad de Ciencia y Tecnología, Universidad del País Vasco (UPV/EHU), Barrio Sarriena s/n, 48940 Leioa, Spain
- Instituto Biofisika (UPV/EHU, CSIC), University of the Basque Country, 48940 Leioa, Spain
| | - Elena R Alonso
- Departamento de Química Física, Facultad de Ciencia y Tecnología, Universidad del País Vasco (UPV/EHU), Barrio Sarriena s/n, 48940 Leioa, Spain
- Instituto Biofisika (UPV/EHU, CSIC), University of the Basque Country, 48940 Leioa, Spain
- Fundación Biofísica Bizkaia/Biofisika Bizkaia Fundazioa (FBB), Barrio Sarriena s/n, 48940 Leioa, Spain
| | - Belen Tercero
- Observatorio Astronómico Nacional (OAN-IGN), c/Alfonso XII, 3, 28014 Madrid, Spain
- Observatorio de Yebes (IGN), Cerro de la Palera, s/n, 19141 Yebes, Guadalajara Spain
| | - José I Santos
- SGIker UPV/EHU, Centro Joxe Mari Korta, Tolosa Hiribidea 72, 20018 Donostia, Spain
| | - Camilla Calabrese
- Departamento de Química Física, Facultad de Ciencia y Tecnología, Universidad del País Vasco (UPV/EHU), Barrio Sarriena s/n, 48940 Leioa, Spain
- Instituto Biofisika (UPV/EHU, CSIC), University of the Basque Country, 48940 Leioa, Spain
- Fundación Biofísica Bizkaia/Biofisika Bizkaia Fundazioa (FBB), Barrio Sarriena s/n, 48940 Leioa, Spain
| | - Natalja Vogt
- Chemical Information Systems, Faculty of Sciences, University of Ulm, 89069 Ulm, Germany
- Department of Chemistry, Lomonosov Moscow State University, 119992 Moscow, Russian Federation
| | - Francisco Corzana
- Departamento de Química, Centro de Investigación en Síntesis Química, Universidad de La Rioja, 26006 Logroño, Spain
| | - Jean Demaison
- Chemical Information Systems, Faculty of Sciences, University of Ulm, 89069 Ulm, Germany
| | - Jose Cernicharo
- Instituto de Física Fundamental (IFF-CSIC), Group of Molecular Astrophysics, c/Serrano 123, 28006 Madrid, Spain
| | - Emilio J Cocinero
- Departamento de Química Física, Facultad de Ciencia y Tecnología, Universidad del País Vasco (UPV/EHU), Barrio Sarriena s/n, 48940 Leioa, Spain
- Instituto Biofisika (UPV/EHU, CSIC), University of the Basque Country, 48940 Leioa, Spain
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15
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GAG-DB, the New Interface of the Three-Dimensional Landscape of Glycosaminoglycans. Biomolecules 2020; 10:biom10121660. [PMID: 33322545 PMCID: PMC7763844 DOI: 10.3390/biom10121660] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2020] [Revised: 12/03/2020] [Accepted: 12/09/2020] [Indexed: 12/18/2022] Open
Abstract
Glycosaminoglycans (GAGs) are complex linear polysaccharides. GAG-DB is a curated database that classifies the three-dimensional features of the six mammalian GAGs (chondroitin sulfate, dermatan sulfate, heparin, heparan sulfate, hyaluronan, and keratan sulfate) and their oligosaccharides complexed with proteins. The entries are structures of GAG and GAG-protein complexes determined by X-ray single-crystal diffraction methods, X-ray fiber diffractometry, solution NMR spectroscopy, and scattering data often associated with molecular modeling. We designed the database architecture and the navigation tools to query the database with the Protein Data Bank (PDB), UniProtKB, and GlyTouCan (universal glycan repository) identifiers. Special attention was devoted to the description of the bound glycan ligands using simple graphical representation and numerical format for cross-referencing to other databases in glycoscience and functional data. GAG-DB provides detailed information on GAGs, their bound protein ligands, and features their interactions using several open access applications. Binding covers interactions between monosaccharides and protein monosaccharide units and the evaluation of quaternary structure. GAG-DB is freely available.
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16
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Fu Y, Huang X, Zhou Z. Insight into the Assembling Mechanism of Cryptococcus Capsular Glucuronoxylomannan Based on Molecular Dynamics Simulations. ACS OMEGA 2020; 5:29351-29356. [PMID: 33225166 PMCID: PMC7676341 DOI: 10.1021/acsomega.0c04164] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/28/2020] [Accepted: 10/21/2020] [Indexed: 06/11/2023]
Abstract
Cryptococcus spp. is an invasive fungal pathogen and causes life-threatening cryptococcosis. Opportunistic cryptococcal infections among the immunocompromised population are mostly caused by Cryptococcus neoformans, whereas the geographical dissemination of Cryptococcus gattii in recent years has threatened lives of even immunocompetent people. The capsule, mainly composed of glucuronoxylomannan (GXM) polysaccharides, plays important roles in the virulence of Cryptococcus spp. The assembling mechanism of GXM polysaccharides into the capsule is little understood because of insufficient experimental data. Molecular modeling and molecular dynamics simulation provide insight into the assembling process. We first built GXM oligosaccharide models of serotypes D, A, B, and C and extracted their secondary structure information from simulation trajectories. All the four mainchains tend to take the nearly twofold helical conformation, whereas peripheral sidechains prefer to form left-handed helices, which are further stabilized by intramolecular hydrogen bonds. Based on the obtained secondary structure information, GXM polysaccharide arrays were built to simulate capsule-assembling processes of C. neoformans and C. gattii using serotypes A and C as representatives, respectively. Trajectory analysis illustrates that electrostatic neutralization of acidic sidechain residues of GXM is a prerequisite for capsule assembling, followed by formation of intermolecular hydrogen bond networks. Further insight into the assembling mechanism of GXM polysaccharides provides the possibility to develop novel treatment and prevention solutions for cryptococcosis.
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Affiliation(s)
- Yankai Fu
- Key
Laboratory of Bioactive Materials, Ministry of Education, College
of Life Sciences, and State Key Laboratory of Medicinal Chemical Biology, Nankai University, Tianjin 300071, China
- Beijing
Key Laboratory for Mechanism Study and Precision Diagnosis of Invasive
Fungal Diseases, Dynamiker Biotechnology
Sub-Center, Tianjin 300467, China
| | - Xinglu Huang
- Key
Laboratory of Bioactive Materials, Ministry of Education, College
of Life Sciences, and State Key Laboratory of Medicinal Chemical Biology, Nankai University, Tianjin 300071, China
| | - Zeqi Zhou
- Beijing
Key Laboratory for Mechanism Study and Precision Diagnosis of Invasive
Fungal Diseases, Dynamiker Biotechnology
Sub-Center, Tianjin 300467, China
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17
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Scherbinina SI, Toukach PV. Three-Dimensional Structures of Carbohydrates and Where to Find Them. Int J Mol Sci 2020; 21:E7702. [PMID: 33081008 PMCID: PMC7593929 DOI: 10.3390/ijms21207702] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2020] [Revised: 10/15/2020] [Accepted: 10/16/2020] [Indexed: 02/06/2023] Open
Abstract
Analysis and systematization of accumulated data on carbohydrate structural diversity is a subject of great interest for structural glycobiology. Despite being a challenging task, development of computational methods for efficient treatment and management of spatial (3D) structural features of carbohydrates breaks new ground in modern glycoscience. This review is dedicated to approaches of chemo- and glyco-informatics towards 3D structural data generation, deposition and processing in regard to carbohydrates and their derivatives. Databases, molecular modeling and experimental data validation services, and structure visualization facilities developed for last five years are reviewed.
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Affiliation(s)
- Sofya I. Scherbinina
- N.D. Zelinsky Institute of Organic Chemistry, Russian Academy of Science, Leninsky prospect 47, 119991 Moscow, Russia
- Higher Chemical College, D. Mendeleev University of Chemical Technology of Russia, Miusskaya Square 9, 125047 Moscow, Russia
| | - Philip V. Toukach
- N.D. Zelinsky Institute of Organic Chemistry, Russian Academy of Science, Leninsky prospect 47, 119991 Moscow, Russia
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18
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Lal K, Bermeo R, Perez S. Computational tools for drawing, building and displaying carbohydrates: a visual guide. Beilstein J Org Chem 2020; 16:2448-2468. [PMID: 33082879 PMCID: PMC7537382 DOI: 10.3762/bjoc.16.199] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2020] [Accepted: 09/17/2020] [Indexed: 01/08/2023] Open
Abstract
Drawing and visualisation of molecular structures are some of the most common tasks carried out in structural glycobiology, typically using various software. In this perspective article, we outline developments in the computational tools for the sketching, visualisation and modelling of glycans. The article also provides details on the standard representation of glycans, and glycoconjugates, which helps the communication of structure details within the scientific community. We highlight the comparative analysis of the available tools which could help researchers to perform various tasks related to structure representation and model building of glycans. These tools can be useful for glycobiologists or any researcher looking for a ready to use, simple program for the sketching or building of glycans.
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Affiliation(s)
- Kanhaya Lal
- Univ. Grenoble Alpes, CNRS, CERMAV, 38000 Grenoble, France
- Dipartimento di Chimica, Università Degli Studi di Milano, via Golgi 19, I-20133, Italy
| | - Rafael Bermeo
- Univ. Grenoble Alpes, CNRS, CERMAV, 38000 Grenoble, France
- Dipartimento di Chimica, Università Degli Studi di Milano, via Golgi 19, I-20133, Italy
| | - Serge Perez
- Univ. Grenoble Alpes, CNRS, CERMAV, 38000 Grenoble, France
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19
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Calvelo M, Piñeiro Á, Garcia-Fandino R. An immersive journey to the molecular structure of SARS-CoV-2: Virtual reality in COVID-19. Comput Struct Biotechnol J 2020; 18:2621-2628. [PMID: 32983399 PMCID: PMC7500438 DOI: 10.1016/j.csbj.2020.09.018] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2020] [Revised: 09/11/2020] [Accepted: 09/12/2020] [Indexed: 02/04/2023] Open
Abstract
The era of the explosion of immersive technologies has bumped head-on with the coronavirus disease 2019 (COVID-19) global pandemic caused by the severe acute respiratory syndrome–coronavirus 2 (SARS-CoV-2). The proper understanding of the three-dimensional structures that compose the virus, as well as of those involved in the infection process and in treatments, is expected to contribute to the advance of fundamental and applied research against this pandemic, including basic molecular biology studies and drug design. Virtual reality (VR) is a powerful technology to visualize the biomolecular structures that are currently being identified for SARS-CoV-2 infection, opening possibilities to significant advances in the understanding of the disease-associate mechanisms and thus to boost new therapies and treatments. The present availability of VR for a large variety of practical applications together with the increasingly easiness, quality and economic access of this technology is transforming the way we interact with digital information. Here, we review the software implementations currently available for VR visualization of SARS-CoV-2 molecular structures, covering a range of virtual environments: CAVEs, desktop software, and cell phone applications, all of them combined with head-mounted devices like cardboards, Oculus Rift or the HTC Vive. We aim to impulse and facilitate the use of these emerging technologies in research against COVID-19 trying to increase the knowledge and thus minimizing risks before placing huge amounts of money for the development of potential treatments.
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Affiliation(s)
- Martín Calvelo
- Centro Singular de Investigación en Química Biolóxica e Materiais Moleculares (CIQUS), Departamento de Química Orgánica, Universidade de Santiago de Compostela, Spain
| | - Ángel Piñeiro
- Departamento de Física Aplicada, Facultade de Física, Universidade de Santiago de Compostela, Spain
| | - Rebeca Garcia-Fandino
- Centro Singular de Investigación en Química Biolóxica e Materiais Moleculares (CIQUS), Departamento de Química Orgánica, Universidade de Santiago de Compostela, Spain.,Departamento de Química e Bioquímica, Faculdade de Ciências da Universidade do Porto, Porto, Portugal
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20
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Zhu Q, Shen Z, Chiodo F, Nicolardi S, Molinaro A, Silipo A, Yu B. Chemical synthesis of glycans up to a 128-mer relevant to the O-antigen of Bacteroides vulgatus. Nat Commun 2020; 11:4142. [PMID: 32811831 PMCID: PMC7434892 DOI: 10.1038/s41467-020-17992-x] [Citation(s) in RCA: 56] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2020] [Accepted: 07/29/2020] [Indexed: 12/21/2022] Open
Abstract
Glycans are involved in various life processes and represent critical targets of biomedical developments. Nevertheless, the accessibility to long glycans with precise structures remains challenging. Here we report on the synthesis of glycans consisting of [→4)-α-Rha-(1 → 3)-β-Man-(1 → ] repeating unit, which are relevant to the O-antigen of Bacteroides vulgatus, a common component of gut microbiota. The optimal combination of assembly strategy, protecting group arrangement, and glycosylation reaction has enabled us to synthesize up to a 128-mer glycan. The synthetic glycans are accurately characterized by advanced NMR and MS approaches, the 3D structures are defined, and their potent binding activity with human DC-SIGN, a receptor associated with the gut lymphoid tissue, is disclosed.
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Affiliation(s)
- Qian Zhu
- State Key Laboratory of Bioorganic and Natural Products Chemistry, Center for Excellence in Molecular Synthesis, Shanghai Institute of Organic Chemistry, University of Chinese Academy of Sciences, Chinese Academy of Sciences, 345 Lingling Road, Shanghai, 200032, China
| | - Zhengnan Shen
- School of Physical Science and Technology, ShanghaiTech University, 393 Huaxia Middle Road, Shanghai, 201210, China
| | - Fabrizio Chiodo
- Department of Molecular Cell Biology and Immunology, Amsterdam Infection and Immunity Institute, De Boelelaan 1108, 1081HZ, Amsterdam, The Netherlands
| | - Simone Nicolardi
- Center for Proteomics and Metabolomics, Leiden University Medical Center, Leiden, 2333 ZA, The Netherlands
| | - Antonio Molinaro
- Department of Chemical Sciences, University of Naples Federico II, Via Cintia 4, 80126, Napoli, Italy
| | - Alba Silipo
- Department of Chemical Sciences, University of Naples Federico II, Via Cintia 4, 80126, Napoli, Italy.
| | - Biao Yu
- State Key Laboratory of Bioorganic and Natural Products Chemistry, Center for Excellence in Molecular Synthesis, Shanghai Institute of Organic Chemistry, University of Chinese Academy of Sciences, Chinese Academy of Sciences, 345 Lingling Road, Shanghai, 200032, China.
- School of Chemistry and Materials Science, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, 1 Sub-Lane Xiangshan, Hangzhou, 310024, China.
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21
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Atanasova M, Bagdonas H, Agirre J. Structural glycobiology in the age of electron cryo-microscopy. Curr Opin Struct Biol 2020; 62:70-78. [DOI: 10.1016/j.sbi.2019.12.003] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2019] [Revised: 11/20/2019] [Accepted: 12/02/2019] [Indexed: 01/05/2023]
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22
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Besançon C, Guillot A, Blaise S, Dauchez M, Belloy N, Prévoteau-Jonquet J, Baud S. Umbrella Visualization: A method of analysis dedicated to glycan flexibility with UnityMol. Methods 2020; 173:94-104. [PMID: 31302178 PMCID: PMC7128144 DOI: 10.1016/j.ymeth.2019.07.010] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2019] [Revised: 05/09/2019] [Accepted: 07/09/2019] [Indexed: 01/17/2023] Open
Abstract
N-glycosylation is a post-translational modification heavily impacting protein functions. Some alterations of glycosylation, such as sialic acid hydrolysis, are related to protein dysfunction. Because of their high flexibility and the many reactive groups of the glycan chains, studying glycans with in vitro methods is a challenging task. Molecular dynamics is a useful tool and probably the only one in biology able to overcome this problem and gives access to conformational information through exhaustive sampling. To better decipher the impact of N-glycans, the analysis and visualization of their influence over time on protein structure is a prerequisite. We developed the Umbrella Visualization, a graphical method that assigns the glycan intrinsic flexibility during a molecular dynamics trajectory. The density plot generated by this method brought relevant informations regarding glycans dynamics and flexibility, but needs further development in order to integrate an accurate description of the protein topology and its interactions. We propose here to transform this analysis method into a visualization mode in UnityMol. UnityMol is a molecular editor, viewer and prototyping platform, coded in C#. The new representation of glycan chains presented in this study takes into account both the main positions adopted by each antenna of a glycan and their statistical relevance. By displaying the collected data on the protein surface, one is then able to investigate the protein/glycan interactions.
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Affiliation(s)
- Camille Besançon
- Université de Reims Champagne Ardenne, CNRS, MEDyC UMR 7369, 51097 Reims, France.
| | - Alexandre Guillot
- Université de Reims Champagne Ardenne, CNRS, MEDyC UMR 7369, 51097 Reims, France
| | - Sébastien Blaise
- Université de Reims Champagne Ardenne, CNRS, MEDyC UMR 7369, 51097 Reims, France
| | - Manuel Dauchez
- Université de Reims Champagne Ardenne, CNRS, MEDyC UMR 7369, 51097 Reims, France; Université de Reims Champagne Ardenne, Plateau de Modélisation Moléculaire Multi-Echelle (P3M), Maison de la Simulation de Champagne Ardenne (MaSCA), 51097 Reims, France
| | - Nicolas Belloy
- Université de Reims Champagne Ardenne, CNRS, MEDyC UMR 7369, 51097 Reims, France; Université de Reims Champagne Ardenne, Plateau de Modélisation Moléculaire Multi-Echelle (P3M), Maison de la Simulation de Champagne Ardenne (MaSCA), 51097 Reims, France
| | | | - Stéphanie Baud
- Université de Reims Champagne Ardenne, CNRS, MEDyC UMR 7369, 51097 Reims, France; Université de Reims Champagne Ardenne, Plateau de Modélisation Moléculaire Multi-Echelle (P3M), Maison de la Simulation de Champagne Ardenne (MaSCA), 51097 Reims, France
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23
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Blatzer M, Beauvais A, Henrissat B, Latgé JP. Revisiting Old Questions and New Approaches to Investigate the Fungal Cell Wall Construction. Curr Top Microbiol Immunol 2020; 425:331-369. [PMID: 32418033 DOI: 10.1007/82_2020_209] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
The beginning of our understanding of the cell wall construction came from the work of talented biochemists in the 70-80's. Then came the era of sequencing. Paradoxically, the accumulation of fungal genomes complicated rather than solved the mystery of cell wall construction, by revealing the involvement of a much higher number of proteins than originally thought. The situation has become even more complicated since it is now recognized that the cell wall is an organelle whose composition continuously evolves with the changes in the environment or with the age of the fungal cell. The use of new and sophisticated technologies to observe cell wall construction at an almost atomic scale should improve our knowledge of the cell wall construction. This essay will present some of the major and still unresolved questions to understand the fungal cell wall biosynthesis and some of these exciting futurist approaches.
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Affiliation(s)
- Michael Blatzer
- Experimental Neuropathology Unit, Institut Pasteur, 25 rue du Docteur Roux, 75015, Paris, France
| | - Anne Beauvais
- Mycology Department, Institut Pasteur, 25 rue du Docteur Roux, 75015, Paris, France
| | - Bernard Henrissat
- Architecture et Fonction des Macromolécules Biologiques, UMR 7257-CNRS & Aix-Marseille Université, 13288, Marseille cedex 9, France.,Department of Biological Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Jean-Paul Latgé
- Institute of Molecular Biology and Biotechnology of the Foundation for Research and Technology Hellas (IMBB-FORTH), Heraklion, Greece.
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24
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Puzzarini C, Bloino J, Tasinato N, Barone V. Accuracy and Interpretability: The Devil and the Holy Grail. New Routes across Old Boundaries in Computational Spectroscopy. Chem Rev 2019; 119:8131-8191. [DOI: 10.1021/acs.chemrev.9b00007] [Citation(s) in RCA: 114] [Impact Index Per Article: 22.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Affiliation(s)
- Cristina Puzzarini
- Dipartimento di Chimica “Giacomo Ciamician”, Università di Bologna, Via F. Selmi 2, I-40126 Bologna, Italy
| | - Julien Bloino
- Scuola Normale Superiore, Piazza dei Cavalieri 7, I-56126 Pisa, Italy
| | - Nicola Tasinato
- Scuola Normale Superiore, Piazza dei Cavalieri 7, I-56126 Pisa, Italy
| | - Vincenzo Barone
- Scuola Normale Superiore, Piazza dei Cavalieri 7, I-56126 Pisa, Italy
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25
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Visualizing Biological Membrane Organization and Dynamics. J Mol Biol 2019; 431:1889-1919. [DOI: 10.1016/j.jmb.2019.02.018] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2018] [Revised: 02/02/2019] [Accepted: 02/13/2019] [Indexed: 11/22/2022]
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26
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Zhang JF, Paciorkowski AR, Craig PA, Cui F. BioVR: a platform for virtual reality assisted biological data integration and visualization. BMC Bioinformatics 2019; 20:78. [PMID: 30767777 PMCID: PMC6376704 DOI: 10.1186/s12859-019-2666-z] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2018] [Accepted: 01/31/2019] [Indexed: 12/01/2022] Open
Abstract
Background Functional characterization of single nucleotide variants (SNVs) involves two steps, the first step is to convert DNA to protein and the second step is to visualize protein sequences with their structures. As massively parallel sequencing has emerged as a leading technology in genomics, resulting in a significant increase in data volume, direct visualization of SNVs together with associated protein sequences/structures in a new user interface (UI) would be a more effective way to assess their potential effects on protein function. Results We have developed BioVR, an easy-to-use interactive, virtual reality (VR)-assisted platform for integrated visual analysis of DNA/RNA/protein sequences and protein structures using Unity3D and the C# programming language. It utilizes the cutting-edge Oculus Rift, and Leap Motion hand detection, resulting in intuitive navigation and exploration of various types of biological data. Using Gria2 and its associated gene product as an example, we present this proof-of-concept software to integrate protein and nucleic acid data. For any amino acid or nucleotide of interest in the Gria2 sequence, it can be quickly linked to its corresponding location on Gria2 protein structure and visualized within VR. Conclusions Using innovative 3D techniques, we provide a VR-based platform for visualization of DNA/RNA sequences and protein structures in aggregate, which can be extended to view omics data. Electronic supplementary material The online version of this article (10.1186/s12859-019-2666-z) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Jimmy F Zhang
- Thomas H. Gosnell School of Life Sciences, Rochester Institute of Technology, One Lomb Memorial Drive, Rochester, NY, 14623, USA.
| | - Alex R Paciorkowski
- Departments of Neurology, Pediatrics, Biomedical Genetics, and Neuroscience, University of Rochester Medical Center, 601 Elmwood Ave, Rochester, NY, 14642, USA
| | - Paul A Craig
- School of Chemistry and Materials Science, Rochester Institute of Technology, One Lomb Memorial Drive, Rochester, NY, 14623, USA
| | - Feng Cui
- Thomas H. Gosnell School of Life Sciences, Rochester Institute of Technology, One Lomb Memorial Drive, Rochester, NY, 14623, USA.
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27
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Birch J, Van Calsteren MR, Pérez S, Svensson B. The exopolysaccharide properties and structures database: EPS-DB. Application to bacterial exopolysaccharides. Carbohydr Polym 2019; 205:565-570. [DOI: 10.1016/j.carbpol.2018.10.063] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2018] [Revised: 10/19/2018] [Accepted: 10/21/2018] [Indexed: 11/27/2022]
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28
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Abstract
The representation of carbohydrates in 3D space using symbols is a powerful visualization method, but such representations are lacking in currently available visualization software. The work presented here allows researchers to display carbohydrate 3D structures as 3D-SNFG symbols using LiteMol from a web browser (e.g., v.litemol.org/?loadFromCS=5T3X ). Any PDB ID can be substituted at the end of the URL. Alternatively, the user may enter a PDB ID or upload a structure. LiteMol is available at https://v.litemol.org and automatically depicts any carbohydrate residues as 3D-SNFG symbols. To embed LiteMol in a webpage, visit https://github.com/dsehnal/LiteMol .
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Affiliation(s)
- David Sehnal
- CEITEC - Central European Institute of Technology , Masaryk University Brno , Kamenice 5 , 625 00 Brno-Bohunice , Czech Republic.,National Centre for Biomolecular Research , Faculty of Science , Kamenice 5 , 625 00 Brno-Bohunice , Czech Republic.,Protein Data Bank in Europe (PDBe), European Molecular Biology Laboratory , European Bioinformatics Institute (EMBL-EBI) , Wellcome Genome Campus , Hinxton , Cambridgeshire CB10 1SD , United Kingdom
| | - Oliver C Grant
- Complex Carbohydrate Research Center , University of Georgia , Athens , Georgia 30602 , United States
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29
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Maes A, Martinez X, Druart K, Laurent B, Guégan S, Marchand CH, Lemaire SD, Baaden M. MinOmics, an Integrative and Immersive Tool for Multi-Omics Analysis. J Integr Bioinform 2018; 15:/j/jib.ahead-of-print/jib-2018-0006/jib-2018-0006.xml. [PMID: 29927748 PMCID: PMC6167043 DOI: 10.1515/jib-2018-0006] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2018] [Accepted: 05/09/2018] [Indexed: 12/15/2022] Open
Abstract
Proteomic and transcriptomic technologies resulted in massive biological datasets, their interpretation requiring sophisticated computational strategies. Efficient and intuitive real-time analysis remains challenging. We use proteomic data on 1417 proteins of the green microalga Chlamydomonas reinhardtii to investigate physicochemical parameters governing selectivity of three cysteine-based redox post translational modifications (PTM): glutathionylation (SSG), nitrosylation (SNO) and disulphide bonds (SS) reduced by thioredoxins. We aim to understand underlying molecular mechanisms and structural determinants through integration of redox proteome data from gene- to structural level. Our interactive visual analytics approach on an 8.3 m2 display wall of 25 MPixel resolution features stereoscopic three dimensions (3D) representation performed by UnityMol WebGL. Virtual reality headsets complement the range of usage configurations for fully immersive tasks. Our experiments confirm that fast access to a rich cross-linked database is necessary for immersive analysis of structural data. We emphasize the possibility to display complex data structures and relationships in 3D, intrinsic to molecular structure visualization, but less common for omics-network analysis. Our setup is powered by MinOmics, an integrated analysis pipeline and visualization framework dedicated to multi-omics analysis. MinOmics integrates data from various sources into a materialized physical repository. We evaluate its performance, a design criterion for the framework.
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Affiliation(s)
- Alexandre Maes
- Laboratoire de Biologie Moléculaire et Cellulaire des Eucaryotes, Institut de Biologie Physico-Chimique, UMR8226, CNRS, Sorbonne Université, 13 rue Pierre et Marie Curie, 75005, Paris, France
| | - Xavier Martinez
- Laboratoire de Biochimie Théorique, CNRS, UPR9080, Institut de Biologie Physico-Chimique, Univ Paris Diderot, Sorbonne Paris Cité, PSL Research University, 13 rue Pierre et Marie Curie, 75005, Paris, France
| | - Karen Druart
- Laboratoire de Biochimie Théorique, CNRS, UPR9080, Institut de Biologie Physico-Chimique, Univ Paris Diderot, Sorbonne Paris Cité, PSL Research University, 13 rue Pierre et Marie Curie, 75005, Paris, France
| | - Benoist Laurent
- Institut de Biologie Physico-Chimique, FRC 550, CNRS, Paris, France
| | - Sean Guégan
- Laboratoire de Biochimie Théorique, CNRS, UPR9080, Institut de Biologie Physico-Chimique, Univ Paris Diderot, Sorbonne Paris Cité, PSL Research University, 13 rue Pierre et Marie Curie, 75005, Paris, France
| | - Christophe H Marchand
- Laboratoire de Biologie Moléculaire et Cellulaire des Eucaryotes, Institut de Biologie Physico-Chimique, UMR8226, CNRS, Sorbonne Université, 13 rue Pierre et Marie Curie, 75005, Paris, France
| | - Stéphane D Lemaire
- Laboratoire de Biologie Moléculaire et Cellulaire des Eucaryotes, Institut de Biologie Physico-Chimique, UMR8226, CNRS, Sorbonne Université, 13 rue Pierre et Marie Curie, 75005, Paris, France
| | - Marc Baaden
- Laboratoire de Biochimie Théorique, CNRS, UPR9080, Institut de Biologie Physico-Chimique, Univ Paris Diderot, Sorbonne Paris Cité, PSL Research University, 13 rue Pierre et Marie Curie, 75005, Paris, France
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30
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Distributed, Immersive and Multi-platform Molecular Visualization for Chemistry Learning. ACTA ACUST UNITED AC 2017. [DOI: 10.1007/978-3-319-62392-4_41] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/25/2023]
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31
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Abstract
Inspired by the recent success of scientific-discovery games for predicting protein tertiary and RNA secondary structures, we have developed an open software for coarse-grained RNA folding simulations, guided by human intuition. To determine the extent to which interactive simulations can accurately predict 3D RNA structures of increasing complexity and lengths (four RNAs with 22-47 nucleotides), an interactive experiment was conducted with 141 participants who had very little knowledge of nucleic acids systems and computer simulations, and had received only a brief description of the important forces stabilizing RNA structures. Their structures and full trajectories have been analyzed statistically and compared to standard replica exchange molecular dynamics simulations. Our analyses show that participants gain easily chemical intelligence to fold simple and nontrivial topologies, with little computer time, and this result opens the door for the use of human-guided simulations to RNA folding. Our experiment shows that interactive simulations have better chances of success when the user widely explores the conformational space. Interestingly, providing on-the-fly feedback of the root mean square deviation with respect to the experimental structure did not improve the quality of the proposed models.
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McNicholas S, Agirre J. Glycoblocks: a schematic three-dimensional representation for glycans and their interactions. Acta Crystallogr D Struct Biol 2017; 73:187-194. [PMID: 28177314 PMCID: PMC5297921 DOI: 10.1107/s2059798316013553] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2016] [Accepted: 08/23/2016] [Indexed: 02/08/2023] Open
Abstract
The close-range interactions provided by covalently linked glycans are essential for the correct folding of glycoproteins and also play a pivotal role in recognition processes. Being able to visualise protein-glycan and glycan-glycan contacts in a clear way is thus of great importance for the understanding of these biological processes. In structural terms, glycosylation sugars glue the protein together via hydrogen bonds, whereas non-covalently bound glycans frequently harness additional stacking interactions. Finding an unobscured molecular view of these multipartite scenarios is usually far from trivial; in addition to the need to show the interacting protein residues, glycans may contain many branched sugars, each composed of more than ten non-H atoms and offering more than three potential bonding partners. With structural glycoscience finally gaining popularity and steadily increasing the deposition rate of three-dimensional structures of glycoproteins, the need for a clear way of depicting these interactions is more pressing than ever. Here a schematic representation, named Glycoblocks, is introduced which combines a simplified bonding-network depiction (covering hydrogen bonds and stacking interactions) with the familiar two-dimensional glycan notation used by the glycobiology community, brought into three dimensions by the CCP4 molecular graphics project (CCP4mg).
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Affiliation(s)
- Stuart McNicholas
- York Structural Biology Laboratory, Department of Chemistry, The University of York, York YO10 5DD, England
| | - Jon Agirre
- York Structural Biology Laboratory, Department of Chemistry, The University of York, York YO10 5DD, England
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Metrics of rhamnogalacturonan I with β-(1→4)-linked galactan side chains and structural basis for its self-aggregation. Carbohydr Polym 2017; 158:93-101. [DOI: 10.1016/j.carbpol.2016.11.082] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2016] [Revised: 11/28/2016] [Accepted: 11/29/2016] [Indexed: 11/18/2022]
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Agirre J, Davies GJ, Wilson KS, Cowtan KD. Carbohydrate structure: the rocky road to automation. Curr Opin Struct Biol 2016; 44:39-47. [PMID: 27940408 DOI: 10.1016/j.sbi.2016.11.011] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2016] [Revised: 10/26/2016] [Accepted: 11/10/2016] [Indexed: 11/29/2022]
Abstract
With the introduction of intuitive graphical software, structural biologists who are not experts in crystallography are now able to build complete protein or nucleic acid models rapidly. In contrast, carbohydrates are in a wholly different situation: scant automation exists, with manual building attempts being sometimes toppled by incorrect dictionaries or refinement problems. Sugars are the most stereochemically complex family of biomolecules and, as pyranose rings, have clear conformational preferences. Despite this, all refinement programs may produce high-energy conformations at medium to low resolution, without any support from the electron density. This problem renders the affected structures unusable in glyco-chemical terms. Bringing structural glycobiology up to 'protein standards' will require a total overhaul of the methodology. Time is of the essence, as the community is steadily increasing the production rate of glycoproteins, and electron cryo-microscopy has just started to image them in precisely that resolution range where crystallographic methods falter most.
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Affiliation(s)
- Jon Agirre
- York Structural Biology Laboratory, Department of Chemistry, University of York, York YO10 5DD, UK.
| | - Gideon J Davies
- York Structural Biology Laboratory, Department of Chemistry, University of York, York YO10 5DD, UK
| | - Keith S Wilson
- York Structural Biology Laboratory, Department of Chemistry, University of York, York YO10 5DD, UK
| | - Kevin D Cowtan
- York Structural Biology Laboratory, Department of Chemistry, University of York, York YO10 5DD, UK.
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35
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Thieker DF, Hadden JA, Schulten K, Woods RJ. 3D implementation of the symbol nomenclature for graphical representation of glycans. Glycobiology 2016; 26:786-7. [PMID: 27514939 DOI: 10.1093/glycob/cww076] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2016] [Indexed: 11/13/2022] Open
Affiliation(s)
- David F Thieker
- Complex Carbohydrate Research Center, University of Georgia, Athens, GA, USA
| | - Jodi A Hadden
- Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Klaus Schulten
- Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Robert J Woods
- Complex Carbohydrate Research Center, University of Georgia, Athens, GA, USA
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36
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Topin J, Lelimousin M, Arnaud J, Audfray A, Pérez S, Varrot A, Imberty A. The Hidden Conformation of Lewis x, a Human Histo-Blood Group Antigen, Is a Determinant for Recognition by Pathogen Lectins. ACS Chem Biol 2016; 11:2011-20. [PMID: 27198630 DOI: 10.1021/acschembio.6b00333] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Histo-blood group epitopes are fucosylated branched oligosaccharides with well-defined conformations in solution that are recognized by receptors, such as lectins from pathogens. We report here the results of a series of experimental and computational endeavors revealing the unusual distortion of histo-blood group antigens by bacterial and fungal lectins. The Lewis x trisaccharide adopts a rigid closed conformation in solution, while crystallography and molecular dynamics reveal several higher energy open conformations when bound to the Ralstonia solanacearum lectin, which is in agreement with thermodynamic and kinetic measurements. Extensive molecular dynamics simulations confirm rare transient Le(x) openings in solution, frequently assisted by distortion of the central N-acetyl-glucosamine ring. Additional directed molecular dynamic trajectories revealed the role of a conserved tryptophan residue in guiding the fucose into the binding site. Our findings show that conformational adaptation of oligosaccharides is of paramount importance in cell recognition and should be considered when designing anti-infective glyco-compounds.
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Affiliation(s)
- Jérémie Topin
- CERMAV UPR5301,
CNRS, and Université Grenoble Alpes, BP 53, 38041 Grenoble cedex 9, France
| | - Mickaël Lelimousin
- CERMAV UPR5301,
CNRS, and Université Grenoble Alpes, BP 53, 38041 Grenoble cedex 9, France
| | - Julie Arnaud
- CERMAV UPR5301,
CNRS, and Université Grenoble Alpes, BP 53, 38041 Grenoble cedex 9, France
| | - Aymeric Audfray
- CERMAV UPR5301,
CNRS, and Université Grenoble Alpes, BP 53, 38041 Grenoble cedex 9, France
| | - Serge Pérez
- DPM UMR5063, Université Grenoble Alpes, and CNRS, BP 53, 38041 Grenoble cedex 9, France
| | - Annabelle Varrot
- CERMAV UPR5301,
CNRS, and Université Grenoble Alpes, BP 53, 38041 Grenoble cedex 9, France
| | - Anne Imberty
- CERMAV UPR5301,
CNRS, and Université Grenoble Alpes, BP 53, 38041 Grenoble cedex 9, France
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37
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Mariethoz J, Khatib K, Alocci D, Campbell MP, Karlsson NG, Packer NH, Mullen EH, Lisacek F. SugarBindDB, a resource of glycan-mediated host-pathogen interactions. Nucleic Acids Res 2016; 44:D1243-50. [PMID: 26578555 PMCID: PMC4702881 DOI: 10.1093/nar/gkv1247] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2015] [Revised: 10/22/2015] [Accepted: 10/31/2015] [Indexed: 12/16/2022] Open
Abstract
The SugarBind Database (SugarBindDB) covers knowledge of glycan binding of human pathogen lectins and adhesins. It is a curated database; each glycan-protein binding pair is associated with at least one published reference. The core data element of SugarBindDB is a set of three inseparable components: the pathogenic agent, a lectin/adhesin and a glycan ligand. Each entity (agent, lectin or ligand) is described by a range of properties that are summarized in an entity-dedicated page. Several search, navigation and visualisation tools are implemented to investigate the functional role of glycans in pathogen binding. The database is cross-linked to protein and glycan-relaled resources such as UniProtKB and UniCarbKB. It is tightly bound to the latter via a substructure search tool that maps each ligand to full structures where it occurs. Thus, a glycan-lectin binding pair of SugarBindDB can lead to the identification of a glycan-mediated protein-protein interaction, that is, a lectin-glycoprotein interaction, via substructure search and the knowledge of site-specific glycosylation stored in UniCarbKB. SugarBindDB is accessible at: http://sugarbind.expasy.org.
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Affiliation(s)
- Julien Mariethoz
- Proteome Informatics Group, SIB Swiss Institute of Bioinformatics, Geneva, Switzerland
| | | | - Davide Alocci
- Proteome Informatics Group, SIB Swiss Institute of Bioinformatics, Geneva, Switzerland Department of Computer Science, University of Geneva, Geneva, Switzerland
| | - Matthew P Campbell
- Biomolecular Frontiers Research Centre, Macquarie University, North Ryde, NSW, Australia
| | - Niclas G Karlsson
- University of Gothenburg, Sahlgrenska Academy, Institute of Biomedicine, Department of Medical Biochemistry and Cell Biology, Gothenburg, Sweden
| | - Nicolle H Packer
- Biomolecular Frontiers Research Centre, Macquarie University, North Ryde, NSW, Australia
| | | | - Frederique Lisacek
- Proteome Informatics Group, SIB Swiss Institute of Bioinformatics, Geneva, Switzerland Department of Computer Science, University of Geneva, Geneva, Switzerland
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Sarkar A, Drouillard S, Rivet A, Perez S. Databases of Conformations and NMR Structures of Glycan Determinants. Glycobiology 2015; 25:1480-90. [PMID: 26240168 DOI: 10.1093/glycob/cwv054] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2015] [Accepted: 07/15/2015] [Indexed: 11/13/2022] Open
Abstract
The present study reports a comprehensive nuclear magnetic resonance (NMR) characterization and a systematic conformational sampling of the conformational preferences of 170 glycan moieties of glycosphingolipids as produced in large-scale quantities by bacterial fermentation. These glycans span across a variety of families including the blood group antigens (A, B and O), core structures (Types 1, 2 and 4), fucosylated oligosaccharides (core and lacto-series), sialylated oligosaccharides (Types 1 and 2), Lewis antigens, GPI-anchors and globosides. A complementary set of about 100 glycan determinants occurring in glycoproteins and glycosaminoglycans has also been structurally characterized using molecular mechanics-based computation. The experimental and computational data generated are organized in two relational databases that can be queried by the user through a user-friendly search engine. The NMR ((1)H and (13)C, COSY, TOCSY, HMQC, HMBC correlation) spectra and 3D structures are available for visualization and download in commonly used structure formats. Emphasis has been given to the use of a common nomenclature for the structural encoding of the carbohydrates and each glycan molecule is described by four different types of representations in order to cope with the different usages in chemistry and biology. These web-based databases were developed with non-proprietary software and are open access for the scientific community available at http://glyco3d.cermav.cnrs.fr.
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Affiliation(s)
- Anita Sarkar
- Centre de Recherches sur les Macromolécules Végétales, UPR5301 CNRS-Université Grenoble Alpes, BP53, 38041 Grenoble cédex 09, France
| | - Sophie Drouillard
- Centre de Recherches sur les Macromolécules Végétales, UPR5301 CNRS-Université Grenoble Alpes, BP53, 38041 Grenoble cédex 09, France
| | - Alain Rivet
- Centre de Recherches sur les Macromolécules Végétales, UPR5301 CNRS-Université Grenoble Alpes, BP53, 38041 Grenoble cédex 09, France
| | - Serge Perez
- Centre de Recherches sur les Macromolécules Végétales, UPR5301 CNRS-Université Grenoble Alpes, BP53, 38041 Grenoble cédex 09, France Département de Pharmacochimie Moléculaire, UMR5063 CNRS-Université Grenoble Alpes, BP53, 38041 Grenoble cédex 09, France
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