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Wang D, Zhang Z, Baudys J, Haynes C, Osman SH, Zhou B, Barr JR, Gumbart JC. Enhanced Surface Accessibility of SARS-CoV-2 Omicron Spike Protein Due to an Altered Glycosylation Profile. ACS Infect Dis 2024; 10:2032-2046. [PMID: 38728322 PMCID: PMC11184558 DOI: 10.1021/acsinfecdis.4c00015] [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: 01/08/2024] [Revised: 04/27/2024] [Accepted: 04/30/2024] [Indexed: 05/12/2024]
Abstract
SARS-CoV-2 spike (S) proteins undergo extensive glycosylation, aiding in proper folding, enhancing stability, and evading host immune surveillance. In this study, we used mass spectrometric analysis to elucidate the N-glycosylation characteristics and disulfide bonding of recombinant spike proteins derived from the SARS-CoV-2 Omicron variant (B.1.1.529) in comparison with the D614G spike variant. Furthermore, we conducted microsecond-long molecular dynamics simulations on spike proteins to resolve how the different N-glycans impact spike conformational sampling in the two variants. Our findings reveal that the Omicron spike protein maintains an overall resemblance to the D614G spike variant in terms of site-specific glycan processing and disulfide bond formation. Nonetheless, alterations in glycans were observed at certain N-glycosylation sites. These changes, in synergy with mutations within the Omicron spike protein, result in increased surface accessibility of the macromolecule, including the ectodomain, receptor-binding domain, and N-terminal domain. Additionally, mutagenesis and pull-down assays reveal the role of glycosylation of a specific sequon (N149); furthermore, the correlation of MD simulation and HDX-MS identified several high-dynamic areas of the spike proteins. These insights contribute to our understanding of the interplay between structure and function, thereby advancing effective vaccination and therapeutic strategies.
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Affiliation(s)
- Dongxia Wang
- National
Center for Environmental Health, Division of Laboratory Sciences, Centers for Disease Control and Prevention (CDC), Atlanta, Georgia 30322 United States
| | - Zijian Zhang
- School
of Physics, Georgia Institute of Technology, Atlanta, Georgia 30332 United States
| | - Jakub Baudys
- National
Center for Environmental Health, Division of Laboratory Sciences, Centers for Disease Control and Prevention (CDC), Atlanta, Georgia 30322 United States
| | - Christopher Haynes
- National
Center for Environmental Health, Division of Laboratory Sciences, Centers for Disease Control and Prevention (CDC), Atlanta, Georgia 30322 United States
| | - Sarah H. Osman
- National
Center for Environmental Health, Division of Laboratory Sciences, Centers for Disease Control and Prevention (CDC), Atlanta, Georgia 30322 United States
| | - Bin Zhou
- National
Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention (CDC), Atlanta, Georgia 30322 United States
| | - John R. Barr
- National
Center for Environmental Health, Division of Laboratory Sciences, Centers for Disease Control and Prevention (CDC), Atlanta, Georgia 30322 United States
| | - James C. Gumbart
- School
of Physics, Georgia Institute of Technology, Atlanta, Georgia 30332 United States
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2
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Cisar JO, Wang X, Woods RJ, Cain KD, Wiens GD. Structural and genetic basis for the binding of a mouse monoclonal antibody to Flavobacterium psychrophilum lipopolysaccharide. JOURNAL OF FISH DISEASES 2024:e13958. [PMID: 38837770 DOI: 10.1111/jfd.13958] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/12/2024] [Revised: 03/20/2024] [Accepted: 04/08/2024] [Indexed: 06/07/2024]
Abstract
A mouse monoclonal antibody (mAb FL100A) previously prepared against Flavobacterium psychrophilum (Fp) CSF259-93 has now been examined for binding to lipopolysaccharides (LPS) of this strain and Fp 950106-1/1. The corresponding O-polysaccharides (O-PS) of these strains are formed by identical trisaccharide repeats composed of l-Rhamnose (l-Rha), 2-acetamido-2-deoxy-l-fucose (l-FucNAc) and 2-acetamido-4-R1-2,4-dideoxy-d-quinovose (d-Qui2NAc4NR1) where R1 represents a dihydroxyhexanamido moiety. The O-PS loci of these strains are also identical except for the gene (wzy1 or wzy2) that encodes the polysaccharide polymerase. Accordingly, adjacent O-PS repeats are joined through d-Qui2NAc4NR1 and l-Rha by wzy2-dependent α(1-2) linkages in Fp CSF259-93 versus wzy1-dependent β(1-3) linkages in Fp 950106-1/1. mAb FL100A reacted strongly with Fp CSF259-93 O-PS and LPS but weakly or not at all with Fp 950106-1/1 LPS and O-PS. Importantly, it also labelled cell surface blebs on the former but not the latter strain. Additionally, mAb binding was approximately 5-times stronger to homologous Fp CSF259-93 LPS than to LPS from a strain with a different R-group gene. A conformational epitope for mAb FL100A binding was suggested from molecular dynamic simulations of each O-PS. Thus, Fp CSF259-93 O-PS formed a stable well-defined compact helix in which the R1 groups were displayed in a regular pattern on the helix exterior while unreactive Fp 950106-1/1 O-PS adopted a flexible extended linear conformation. Taken together, the findings establish the specificity of mAb FL100A for Wzy2-linked F. psychrophilum O-PS and LPS.
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Affiliation(s)
- John O Cisar
- United States Department of Agricultural Research Service, National Center for Cool and Cold Water Aquaculture, Kearneysville, West Virginia, USA
| | - Xiaocong Wang
- Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University, Wuhan, Hubei, China
- Complex Carbohydrate Research Center, University of Georgia, Athens, Georgia, USA
| | - Robert J Woods
- Complex Carbohydrate Research Center, University of Georgia, Athens, Georgia, USA
| | - Kenneth D Cain
- Department of Fish and Wildlife Resources and the Aquaculture Research Institute, University of Idaho, Moscow, Idaho, USA
- Manchester Research Station, Northwest Fisheries Science Center, NOAA - Fisheries, Port Orchard, Washington, USA
| | - Gregory D Wiens
- United States Department of Agricultural Research Service, National Center for Cool and Cold Water Aquaculture, Kearneysville, West Virginia, USA
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3
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Cummings RD. A periodic table of monosaccharides. Glycobiology 2024; 34:cwad088. [PMID: 37935401 DOI: 10.1093/glycob/cwad088] [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: 09/11/2023] [Revised: 10/23/2023] [Accepted: 10/31/2023] [Indexed: 11/09/2023] Open
Abstract
It is important to recognize the great diversity of monosaccharides commonly encountered in animals, plants, and microbes, as well as to organize them in a visually interesting style that also emphasizes their similarities and relatedness. This article discusses the nature of building blocks, monosaccharides, and monosaccharide derivatives-terms commonly used in discussing "glycomolecules" found in nature. To aid in awareness of monosaccharide diversity, here is presented a Periodic Table of Monosaccharides. The rationale is given for construction of the Table and the selection of 103 monosaccharides, which is largely based on those presented in the KEGG and SNFG websites of monosaccharides, and includes room to enlarge as new discoveries are made. The Table should have educational value and is intended to capture the attention and foster imagination of those not very familiar with glycosciences, and encourage researchers to delve deeper into this fascinating area.
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Affiliation(s)
- Richard D Cummings
- Department of Surgery, Beth Israel Deaconess Medical Center, Harvard Medical School, CLS 11087-3 Blackfan Circle, Boston, MA 02115, United States
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4
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Maity S, Acharya A. Many Roles of Carbohydrates: A Computational Spotlight on the Coronavirus S Protein Binding. ACS APPLIED BIO MATERIALS 2024; 7:646-656. [PMID: 36947738 PMCID: PMC10880061 DOI: 10.1021/acsabm.2c01064] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2022] [Accepted: 03/08/2023] [Indexed: 03/24/2023]
Abstract
Glycosylation is one of the post-translational modifications with more than 50% of human proteins being glycosylated. The exact nature and chemical composition of glycans are inaccessible to X-ray or cryo-electron microscopy imaging techniques. Therefore, computational modeling studies and molecular dynamics must be used as a "computational microscope". The spike (S) protein of SARS-CoV-2 is heavily glycosylated, and a few glycans play a more functional role "beyond shielding". In this mini-review, we discuss computational investigations of the roles of specific S-protein and ACE2 glycans in the overall ACE2-S protein binding. We highlight different functions of specific glycans demonstrated in myriad computational models and simulations in the context of the SARS-CoV-2 virus binding to the receptor. We also discuss interactions between glycocalyx and the S protein, which may be utilized to design prophylactic polysaccharide-based therapeutics targeting the S protein. In addition, we underline the recent emergence of coronavirus variants and their impact on the S protein and its glycans.
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Affiliation(s)
- Suman Maity
- Department
of Chemistry, Syracuse University, Syracuse, New York 13244, United States
| | - Atanu Acharya
- Department
of Chemistry, Syracuse University, Syracuse, New York 13244, United States
- BioInspired
Syracuse, Syracuse University, Syracuse, New York 13244, United States
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5
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Wang Y, Peng Y, Long R, Shi P, Zhang Y, Kong DX, Zheng J, Wang X. Sequence variety in the CC' loop of Siglec-8/9/3 determines the recognitions to sulfated oligosaccharides. Comput Struct Biotechnol J 2023; 21:4159-4171. [PMID: 37675287 PMCID: PMC10477811 DOI: 10.1016/j.csbj.2023.08.014] [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: 04/18/2023] [Revised: 08/18/2023] [Accepted: 08/18/2023] [Indexed: 09/08/2023] Open
Abstract
Siglecs are important lectins found in different types of immune cells and function as regulatory molecules by recognizing self-associated glycans and converting extracellular interactions into signals for inhibiting immune cell functions. Although many Siglecs have been found to show broad specificities and recognize different types of sulfated oligosaccharides, Siglec-8 and Siglec-9 displayed a high degree of specificity for sialyl N-acetyllactosamine (sLacNAc) with sulfations at O6-positions of the galactose (6'-sulfation) and N-acetylglucosamine (6-sulfation), respectively. Siglec-3 was recently discovered to bind sLacNAc both sulfations. In addition to a conserved arginine residue for binding to sialic acid residue, the sequence variety in the CC' loop may provide binding specificities to sulfated oligosaccharides in Siglecs. Thus, the present study employed molecular models to study the impact of different residues in the CC' loops of Siglec-8/9/3 to the recognitions of 6-sulfations in Gal and/or GlcNAc of sLacNAc. The negatively charged residues in the CC' loop of Siglec-9 formed unfavorable electrostatic repulsions with the 6-sulfate in Gal and resulted no recognitions, in contrast to the favorable interactions formed between the positively charged residues in the CC' loop of Siglec-8 and the 6-sulfate in Gal resulting strong specificity. A two-state binding model was proposed for Siglec-3 recognizing 6-sulfations in Gal and GlcNAc of sLacNAc, as the neutral residues in the CC' loop of Siglec-3 could not form strong favorable interactions to lock the 6-sulfate in Gal within a single binding pose or strong unfavorable interactions to repel the 6-sulfate in Gal. The oligosaccharide adopted two distinctive binding poses and oriented the sulfate groups to form interactions with residues in the CC' loop and G-strand. The present study provided a structural mechanism for the sequence variety in the CC' loop of Siglec-8/9/3 determining the recognitions to the sulfated oligosaccharides and offered insights into the binding specificities for Siglecs.
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Affiliation(s)
- Yucheng Wang
- Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University, Wuhan, Hubei 430070, China
| | - Yujie Peng
- Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University, Wuhan, Hubei 430070, China
- National Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, Hubei 430070, China
| | - Rui Long
- Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University, Wuhan, Hubei 430070, China
- National Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, Hubei 430070, China
| | - Peiting Shi
- Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University, Wuhan, Hubei 430070, China
| | - Yinghao Zhang
- Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University, Wuhan, Hubei 430070, China
| | - De-Xin Kong
- Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University, Wuhan, Hubei 430070, China
| | - Jinshui Zheng
- Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University, Wuhan, Hubei 430070, China
- National Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, Hubei 430070, China
| | - Xiaocong Wang
- Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University, Wuhan, Hubei 430070, China
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6
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Abstract
Glycans, carbohydrate molecules in the realm of biology, are present as biomedically important glycoconjugates and a characteristic aspect is that their structures in many instances are branched. In determining the primary structure of a glycan, the sugar components including the absolute configuration and ring form, anomeric configuration, linkage(s), sequence, and substituents should be elucidated. Solution state NMR spectroscopy offers a unique opportunity to resolve all these aspects at atomic resolution. During the last two decades, advancement of both NMR experiments and spectrometer hardware have made it possible to unravel carbohydrate structure more efficiently. These developments applicable to glycans include, inter alia, NMR experiments that reduce spectral overlap, use selective excitations, record tilted projections of multidimensional spectra, acquire spectra by multiple receivers, utilize polarization by fast-pulsing techniques, concatenate pulse-sequence modules to acquire several spectra in a single measurement, acquire pure shift correlated spectra devoid of scalar couplings, employ stable isotope labeling to efficiently obtain homo- and/or heteronuclear correlations, as well as those that rely on dipolar cross-correlated interactions for sequential information. Refined computer programs for NMR spin simulation and chemical shift prediction aid the structural elucidation of glycans, which are notorious for their limited spectral dispersion. Hardware developments include cryogenically cold probes and dynamic nuclear polarization techniques, both resulting in enhanced sensitivity as well as ultrahigh field NMR spectrometers with a 1H NMR resonance frequency higher than 1 GHz, thus improving resolution of resonances. Taken together, the developments have made and will in the future make it possible to elucidate carbohydrate structure in great detail, thereby forming the basis for understanding of how glycans interact with other molecules.
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Affiliation(s)
- Carolina Fontana
- Departamento
de Química del Litoral, CENUR Litoral Norte, Universidad de la República, Paysandú 60000, Uruguay
| | - Göran Widmalm
- Department
of Organic Chemistry, Arrhenius Laboratory, Stockholm University, S-106 91 Stockholm, Sweden,
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7
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Harvey DJ. Analysis of carbohydrates and glycoconjugates by matrix-assisted laser desorption/ionization mass spectrometry: An update for 2019-2020. MASS SPECTROMETRY REVIEWS 2022:e21806. [PMID: 36468275 DOI: 10.1002/mas.21806] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/17/2023]
Abstract
This review is the tenth update of the original article published in 1999 on the application of matrix-assisted laser desorption/ionization (MALDI) mass spectrometry to the analysis of carbohydrates and glycoconjugates and brings coverage of the literature to the end of 2020. Also included are papers that describe methods appropriate to analysis by MALDI, such as sample preparation techniques, even though the ionization method is not MALDI. The review is basically divided into three sections: (1) general aspects such as theory of the MALDI process, matrices, derivatization, MALDI imaging, fragmentation, quantification and the use of arrays. (2) Applications to various structural types such as oligo- and polysaccharides, glycoproteins, glycolipids, glycosides and biopharmaceuticals, and (3) other areas such as medicine, industrial processes and glycan synthesis where MALDI is extensively used. Much of the material relating to applications is presented in tabular form. The reported work shows increasing use of incorporation of new techniques such as ion mobility and the enormous impact that MALDI imaging is having. MALDI, although invented nearly 40 years ago is still an ideal technique for carbohydrate analysis and advancements in the technique and range of applications show little sign of diminishing.
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Affiliation(s)
- David J Harvey
- Nuffield Department of Medicine, Target Discovery Institute, University of Oxford, Oxford, UK
- Department of Chemistry, University of Oxford, Oxford, Oxfordshire, United Kingdom
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8
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Pang YT, Acharya A, Lynch DL, Pavlova A, Gumbart JC. SARS-CoV-2 spike opening dynamics and energetics reveal the individual roles of glycans and their collective impact. Commun Biol 2022; 5:1170. [PMID: 36329138 PMCID: PMC9631587 DOI: 10.1038/s42003-022-04138-6] [Citation(s) in RCA: 32] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2021] [Accepted: 10/20/2022] [Indexed: 11/06/2022] Open
Abstract
The trimeric spike (S) glycoprotein, which protrudes from the SARS-CoV-2 viral envelope, binds to human ACE2, initiated by at least one protomer's receptor binding domain (RBD) switching from a "down" (closed) to an "up" (open) state. Here, we used large-scale molecular dynamics simulations and two-dimensional replica exchange umbrella sampling calculations with more than a thousand windows and an aggregate total of 160 μs of simulation to investigate this transition with and without glycans. We find that the glycosylated spike has a higher barrier to opening and also energetically favors the down state over the up state. Analysis of the S-protein opening pathway reveals that glycans at N165 and N122 interfere with hydrogen bonds between the RBD and the N-terminal domain in the up state, while glycans at N165 and N343 can stabilize both the down and up states. Finally, we estimate how epitope exposure for several known antibodies changes along the opening path. We find that the BD-368-2 antibody's epitope is continuously exposed, explaining its high efficacy.
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Affiliation(s)
- Yui Tik Pang
- School of Physics, Georgia Institute of Technology, Atlanta, GA, 30332, USA
| | - Atanu Acharya
- School of Physics, Georgia Institute of Technology, Atlanta, GA, 30332, USA.,BioInspired Syracuse and Department of Chemistry, Syracuse University, Syracuse, NY, 13244, USA
| | - Diane L Lynch
- School of Physics, Georgia Institute of Technology, Atlanta, GA, 30332, USA
| | - Anna Pavlova
- School of Physics, Georgia Institute of Technology, Atlanta, GA, 30332, USA
| | - James C Gumbart
- School of Physics, Georgia Institute of Technology, Atlanta, GA, 30332, USA.
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9
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Computationally guided conversion of the specificity of E-selectin to mimic that of Siglec-8. Proc Natl Acad Sci U S A 2022; 119:e2117743119. [PMID: 36191232 PMCID: PMC9564326 DOI: 10.1073/pnas.2117743119] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Sulfated glycans have been found to be associated with various diseases and therefore have significant potential in molecular pathology as biomarkers. Although lectins are useful reagents for detecting glycans, there is a paucity of sulfate-recognizing lectins, and those that exist, such as from Maackia amurensis, display mixed specificities. Recombinant lectin engineering offers an emerging tool for creating novel glycan recognition by altering and/or enhancing endogenous specificities. The present study demonstrated the use of computational approaches in the engineering of a mutated form of E-selectin that displayed highly specific recognition of 6'-sulfo-sialyl Lewis X (6'-sulfo-sLex), with negligible binding to its endogenous nonsulfated ligand, sLex. This new specificity mimics that of the unrelated protein Siglec-8, for which 6'-sulfo-sLex is its preferred ligand. Molecular dynamics simulations and energy calculations predicted that two point mutations (E92A/E107A) would be required to stabilize binding to the sulfated oligosaccharide with E-selectin. In addition to eliminating putative repulsions between the negatively charged side chains and the sulfate moiety, the mutations also abolished favorable interactions with the endogenous ligand. Glycan microarray screening of the recombinantly expressed proteins confirmed the predicted specificity change but also identified the introduction of unexpected affinity for the unfucosylated form of 6'-sulfo-sLex (6'-sulfo-sLacNAc). Three key requirements were demonstrated in this case for engineering specificity for sulfated oligosaccharide: 1) removal of unfavorable interactions with the 6'-sulfate, 2) introduction of favorable interactions for the sulfate, and 3) removal of favorable interactions with the endogenous ligand.
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10
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Grothaus IL, Bussi G, Colombi Ciacchi L. Exploration, Representation, and Rationalization of the Conformational Phase Space of N-Glycans. J Chem Inf Model 2022; 62:4992-5008. [PMID: 36179122 DOI: 10.1021/acs.jcim.2c01049] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Despite their fundamental biological relevance, structure-property relationships in N-glycans are fundamentally lacking, and their highly multidimensional compositional and conformational phase spaces remain largely unexplored. The torsional flexibility of the glycosidic linkages and the ring dynamics result in wide, rugged free-energy landscapes that are difficult to sample in molecular dynamics simulations. We show that a novel enhanced-sampling scheme combining replica exchange with solute and collective-variable tempering, enabling transitions over all relevant energy barriers, delivers converged distributions of solvated N-glycan conformers. Several dimensionality-reduction algorithms are compared and employed to generate conformational free-energy maps in two dimensions. Together with an originally developed conformation-based nomenclature scheme that uniquely identifies glycan conformers, our modeling procedure is applied to reveal the effect of chemical substitutions on the conformational ensemble of selected high-mannose-type and complex glycans. Moreover, the structure-prediction capabilities of two commonly used glycan force fields are assessed via the theoretical prediction of experimentally available nuclear magnetic resonance J-coupling constants. The results especially confirm the key role of ω and ψ torsion angles in discriminating between different conformational states and suggest an intriguing correlation between the torsional and ring-puckering degrees of freedom that may be biologically relevant.
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Affiliation(s)
- Isabell Louise Grothaus
- Hybrid Materials Interfaces Group, Bremen Center for Computational Materials Science and MAPEX Center for Materials and Processes, University of Bremen, 28359Bremen, Germany
| | - Giovanni Bussi
- Scuola Internazionale Superiore di Studi Avanzati (SISSA), 34136Trieste, Italy
| | - Lucio Colombi Ciacchi
- Hybrid Materials Interfaces Group, Bremen Center for Computational Materials Science and MAPEX Center for Materials and Processes, University of Bremen, 28359Bremen, Germany
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11
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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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12
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Wang X, Bie L, Gao J. Structural Insights into the Cofactor Role of Heparin/Heparan Sulfate in Binding between the SARS-CoV-2 Spike Protein and Host Angiotensin-Converting Enzyme II. J Chem Inf Model 2022; 62:656-667. [PMID: 35060381 PMCID: PMC8791032 DOI: 10.1021/acs.jcim.1c01484] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2021] [Indexed: 02/07/2023]
Abstract
The viral entry process of the novel severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) requires heparin and heparan sulfates from the cell surface, functioning as a cofactor for human angiotensin-converting enzyme 2 (ACE2) for recognizing the receptor-binding domain (RBD) of the spike (S) protein on the surface of the virion. In the present study, the binding poses of an oligosaccharide with four repeating units of GlcNS6S-IdoA2S (octa) predicted by Vina-Carb in the RBD binding site were employed in molecular dynamics (MD) simulations to provide atomic details for studying the cofactor mechanism. The molecular model in the MD simulations reproduced the length- and sequence-dependent behavior observed from the microarray experiments and revealed an important planar U-turn shape for HP/HS binding to RBD. The model for octa with this shape in the ACE2-RBD complex enhanced the interactions in the binding interface. The comparisons with the ACE2-RBD complex suggested that the presence of octa in the RBD binding site blocked the movements in a loop region at the distal end of the RBD binding interface and promoted the contacts of this loop region with the ACE2 N-terminus helix. This study shed light on the atomic and dynamic details for HP/HS interacting with RBD and provided insights into their cofactor role in the ACE2-RBD interactions.
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Affiliation(s)
- Xiaocong Wang
- Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics,
Huazhong Agricultural University, Wuhan 430070, Hubei,
China
| | - Lihua Bie
- Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics,
Huazhong Agricultural University, Wuhan 430070, Hubei,
China
| | - Jun Gao
- Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics,
Huazhong Agricultural University, Wuhan 430070, Hubei,
China
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13
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Hu Z, Bie L, Gao J, Wang X. Insights into Selectin Inhibitor Design from Endogenous Isomeric Ligands of SLe a and SLe x. J Chem Inf Model 2021; 61:6085-6093. [PMID: 34905361 DOI: 10.1021/acs.jcim.1c01356] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
Selectins interact with cell-surface glycans to promote the initial tethering and rolling of leukocytes, and these interactions are targets for designs of inhibitors to neutralize diseases related to excessive inflammatory responses in many cardiovascular and immune dysfunctions, as well as tumor markers in different cancers. The isomeric endogenous tetrasaccharides, sialyl Lewis X (sLex) and sialyl Lewis A (sLea), are minimal sugar structures required for selectin binding. Understanding their subtle structural variances and significant advanced binding strengths of sLea over sLex could benefit the rational designs for selectin inhibitors. Modeling based on the E-selectin-sLex crystal structure in the present study demonstrated that the N-acetyl group of GlcNAc in sLex could form steric hindrances in the E-selectin-sLex complex, but the hydroxy methylene group of GlcNAc in sLea at the same position allows for stronger binding interactions. The subsequent designed inhibitor with a synthetic accessible linker molecule that has no exo-cyclic moieties replacing GlcNAc displayed comparable dynamic and energetic binding features to sLea. The present study deciphered the clues from endogenous isomeric sLea and sLex and provided insights into designing selectin inhibitors with simplified synthesis.
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Affiliation(s)
- Zhicheng Hu
- Cardiac Arrhythmia Center, Fuwai Hospital, National Center for Cardiovascular Diseases, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100037, China
| | - Lihua Bie
- Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University, Wuhan, Hubei 430070, China
| | - Jun Gao
- Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University, Wuhan, Hubei 430070, China
| | - Xiaocong Wang
- Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University, Wuhan, Hubei 430070, China
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14
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Akinbiyi EO, Abramowitz LK, Bauer BL, Stoll MSK, Hoppel CL, Hsiao CP, Hanover JA, Mears JA. Blocked O-GlcNAc cycling alters mitochondrial morphology, function, and mass. Sci Rep 2021; 11:22106. [PMID: 34764359 PMCID: PMC8586252 DOI: 10.1038/s41598-021-01512-y] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2021] [Accepted: 10/18/2021] [Indexed: 12/24/2022] Open
Abstract
O-GlcNAcylation is a prevalent form of glycosylation that regulates proteins within the cytosol, nucleus, and mitochondria. The O-GlcNAc modification can affect protein cellular localization, function, and signaling interactions. The specific impact of O-GlcNAcylation on mitochondrial morphology and function has been elusive. In this manuscript, the role of O-GlcNAcylation on mitochondrial fission, oxidative phosphorylation (Oxphos), and the activity of electron transport chain (ETC) complexes were evaluated. In a cellular environment with hyper O-GlcNAcylation due to the deletion of O-GlcNAcase (OGA), mitochondria showed a dramatic reduction in size and a corresponding increase in number and total mitochondrial mass. Because of the increased mitochondrial content, OGA knockout cells exhibited comparable coupled mitochondrial Oxphos and ATP levels when compared to WT cells. However, we observed reduced protein levels for complex I and II when comparing normalized mitochondrial content and reduced linked activity for complexes I and III when examining individual ETC complex activities. In assessing mitochondrial fission, we observed increased amounts of O-GlcNAcylated dynamin-related protein 1 (Drp1) in cells genetically null for OGA and in glioblastoma cells. Individual regions of Drp1 were evaluated for O-GlcNAc modifications, and we found that this post-translational modification (PTM) was not limited to the previously characterized residues in the variable domain (VD). Additional modification sites are predicted in the GTPase domain, which may influence enzyme activity. Collectively, these results highlight the impact of O-GlcNAcylation on mitochondrial dynamics and ETC function and mimic the changes that may occur during glucose toxicity from hyperglycemia.
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Affiliation(s)
- Elizabeth O Akinbiyi
- Department of Pathology, Case Western Reserve University School of Medicine, Cleveland, OH, 44106, USA
| | - Lara K Abramowitz
- Laboratory of Cellular and Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Brianna L Bauer
- Department of Pharmacology, Case Western Reserve University School of Medicine, Cleveland, OH, 44106, USA
| | - Maria S K Stoll
- Center for Mitochondrial Diseases, Case Western Reserve University School of Medicine, Cleveland, OH, 44106, USA
| | - Charles L Hoppel
- Department of Pharmacology, Case Western Reserve University School of Medicine, Cleveland, OH, 44106, USA
- Center for Mitochondrial Diseases, Case Western Reserve University School of Medicine, Cleveland, OH, 44106, USA
| | - Chao-Pin Hsiao
- Center for Mitochondrial Diseases, Case Western Reserve University School of Medicine, Cleveland, OH, 44106, USA
- Frances Payne Bolton School of Nursing, Case Western Reserve University, Cleveland, OH, 44106, USA
| | - John A Hanover
- Laboratory of Cellular and Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Jason A Mears
- Department of Pharmacology, Case Western Reserve University School of Medicine, Cleveland, OH, 44106, USA.
- Center for Mitochondrial Diseases, Case Western Reserve University School of Medicine, Cleveland, OH, 44106, USA.
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15
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Gao M, Li H, Ye C, Chen K, Jiang H, Yu K. Glycan Epitopes and Potential Glycoside Antagonists of DC-SIGN Involved in COVID-19: In Silico Study. Biomolecules 2021; 11:1586. [PMID: 34827585 PMCID: PMC8615854 DOI: 10.3390/biom11111586] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2021] [Revised: 10/19/2021] [Accepted: 10/19/2021] [Indexed: 12/28/2022] Open
Abstract
Glycosylation is an important post-translational modification that affects a wide variety of physiological functions. DC-SIGN (Dendritic Cell-Specific Intercellular adhesion molecule-3-Grabbing Non-integrin) is a protein expressed in antigen-presenting cells that recognizes a variety of glycan epitopes. Until now, the binding of DC-SIGN to SARS-CoV-2 Spike glycoprotein has been reported in various articles and is regarded to be a factor in systemic infection and cytokine storm. The mechanism of DC-SIGN recognition offers an alternative method for discovering new medication for COVID-19 treatment. Here, we discovered three potential pockets that hold different glycan epitopes by performing molecular dynamics simulations of previously reported oligosaccharides. The "EPN" motif, "NDD" motif, and Glu354 form the most critical pocket, which is known as the Core site. We proposed that the type of glycan epitopes, rather than the precise amino acid sequence, determines the recognition. Furthermore, we deduced that oligosaccharides could occupy an additional site, which adds to their higher affinity than monosaccharides. Based on our findings and previously described glycoforms on the SARS-CoV-2 Spike, we predicted the potential glycan epitopes for DC-SIGN. It suggested that glycan epitopes could be recognized at multiple sites, not just Asn234, Asn149 and Asn343. Subsequently, we found that Saikosaponin A and Liquiritin, two plant glycosides, were promising DC-SIGN antagonists in silico.
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Affiliation(s)
- Meina Gao
- School of Chinese Materia Medica, Nanjing University of Chinese Medicine, Nanjing 210023, China; (M.G.); (K.C.); (H.J.)
- Drug Discovery and Design Center, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 200031, China;
| | - Hui Li
- Drug Discovery and Design Center, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 200031, China;
- University of Chinese Academy of Sciences, Beijing 100049, China
- Shanghai Institute for Advanced Immunochemical Studies, School of Life Science and Technology, ShanghaiTech University, Shanghai 200031, China
| | - Chenghao Ye
- Department of Chemistry, Shantou University, Shantou 515063, China;
| | - Kaixian Chen
- School of Chinese Materia Medica, Nanjing University of Chinese Medicine, Nanjing 210023, China; (M.G.); (K.C.); (H.J.)
- Drug Discovery and Design Center, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 200031, China;
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Hualiang Jiang
- School of Chinese Materia Medica, Nanjing University of Chinese Medicine, Nanjing 210023, China; (M.G.); (K.C.); (H.J.)
- Drug Discovery and Design Center, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 200031, China;
- University of Chinese Academy of Sciences, Beijing 100049, China
- Shanghai Institute for Advanced Immunochemical Studies, School of Life Science and Technology, ShanghaiTech University, Shanghai 200031, China
| | - Kunqian Yu
- Drug Discovery and Design Center, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 200031, China;
- University of Chinese Academy of Sciences, Beijing 100049, China
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16
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Shao C, Feng Z, Westbrook JD, Peisach E, Berrisford J, Ikegawa Y, Kurisu G, Velankar S, Burley SK, Young JY. Modernized uniform representation of carbohydrate molecules in the Protein Data Bank. Glycobiology 2021; 31:1204-1218. [PMID: 33978738 PMCID: PMC8457362 DOI: 10.1093/glycob/cwab039] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2021] [Revised: 04/05/2021] [Accepted: 04/25/2021] [Indexed: 12/12/2022] Open
Abstract
Since 1971, the Protein Data Bank (PDB) has served as the single global archive for experimentally determined 3D structures of biological macromolecules made freely available to the global community according to the FAIR principles of Findability-Accessibility-Interoperability-Reusability. During the first 50 years of continuous PDB operations, standards for data representation have evolved to better represent rich and complex biological phenomena. Carbohydrate molecules present in more than 14,000 PDB structures have recently been reviewed and remediated to conform to a new standardized format. This machine-readable data representation for carbohydrates occurring in the PDB structures and the corresponding reference data improves the findability, accessibility, interoperability and reusability of structural information pertaining to these molecules. The PDB Exchange MacroMolecular Crystallographic Information File data dictionary now supports (i) standardized atom nomenclature that conforms to International Union of Pure and Applied Chemistry-International Union of Biochemistry and Molecular Biology (IUPAC-IUBMB) recommendations for carbohydrates, (ii) uniform representation of branched entities for oligosaccharides, (iii) commonly used linear descriptors of carbohydrates developed by the glycoscience community and (iv) annotation of glycosylation sites in proteins. For the first time, carbohydrates in PDB structures are consistently represented as collections of standardized monosaccharides, which precisely describe oligosaccharide structures and enable improved carbohydrate visualization, structure validation, robust quantitative and qualitative analyses, search for dendritic structures and classification. The uniform representation of carbohydrate molecules in the PDB described herein will facilitate broader usage of the resource by the glycoscience community and researchers studying glycoproteins.
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Affiliation(s)
- Chenghua Shao
- Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB), Institute for Quantitative Biomedicine, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
| | - Zukang Feng
- Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB), Institute for Quantitative Biomedicine, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
| | - John D Westbrook
- Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB), Institute for Quantitative Biomedicine, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
- Rutgers Cancer Institute of New Jersey, Robert Wood Johnson Medical School, New Brunswick, NJ 08903, USA
| | - Ezra Peisach
- Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB), Institute for Quantitative Biomedicine, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
| | - John Berrisford
- Protein Data Bank in Europe (PDBe), European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK
| | - Yasuyo Ikegawa
- Protein Data Bank Japan (PDBj), Institute for Protein Research, Osaka University, Osaka 565-0871, Japan
| | - Genji Kurisu
- Protein Data Bank Japan (PDBj), Institute for Protein Research, Osaka University, Osaka 565-0871, Japan
| | - Sameer Velankar
- Protein Data Bank in Europe (PDBe), European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK
| | - Stephen K Burley
- Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB), Institute for Quantitative Biomedicine, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
- Rutgers Cancer Institute of New Jersey, Robert Wood Johnson Medical School, New Brunswick, NJ 08903, USA
- Research Collaboratory for Structural Bioinformatics Protein Data Bank, San Diego Supercomputer Center, University of California, La Jolla, San Diego, CA 92093, USA
- Department of Chemistry and Chemical Biology, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
| | - Jasmine Y Young
- Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB), Institute for Quantitative Biomedicine, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
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17
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Harvey DJ. ANALYSIS OF CARBOHYDRATES AND GLYCOCONJUGATES BY MATRIX-ASSISTED LASER DESORPTION/IONIZATION MASS SPECTROMETRY: AN UPDATE FOR 2015-2016. MASS SPECTROMETRY REVIEWS 2021; 40:408-565. [PMID: 33725404 DOI: 10.1002/mas.21651] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/06/2020] [Accepted: 07/24/2020] [Indexed: 06/12/2023]
Abstract
This review is the ninth update of the original article published in 1999 on the application of matrix-assisted laser desorption/ionization (MALDI) mass spectrometry to the analysis of carbohydrates and glycoconjugates and brings coverage of the literature to the end of 2016. Also included are papers that describe methods appropriate to analysis by MALDI, such as sample preparation techniques, even though the ionization method is not MALDI. Topics covered in the first part of the review include general aspects such as theory of the MALDI process, matrices, derivatization, MALDI imaging, fragmentation and arrays. The second part of the review is devoted to applications to various structural types such as oligo- and poly-saccharides, glycoproteins, glycolipids, glycosides and biopharmaceuticals. Much of this material is presented in tabular form. The third part of the review covers medical and industrial applications of the technique, studies of enzyme reactions and applications to chemical synthesis. The reported work shows increasing use of combined new techniques such as ion mobility and the enormous impact that MALDI imaging is having. MALDI, although invented over 30 years ago is still an ideal technique for carbohydrate analysis and advancements in the technique and range of applications show no sign of deminishing. © 2020 Wiley Periodicals, Inc.
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Affiliation(s)
- David J Harvey
- Nuffield Department of Medicine, Target Discovery Institute, University of Oxford, Roosevelt Drive, Oxford, OX3 7FZ, United Kingdom
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18
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Prestegard JH. A perspective on the PDB's impact on the field of glycobiology. J Biol Chem 2021; 296:100556. [PMID: 33744289 PMCID: PMC8058564 DOI: 10.1016/j.jbc.2021.100556] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2020] [Revised: 03/07/2021] [Accepted: 03/16/2021] [Indexed: 12/12/2022] Open
Abstract
Structures deposited in the Protein Data Bank (PDB) facilitate our understanding of many biological processes including those that fall under the general category of glycobiology. However, structure-based studies of how glycans affect protein structure, how they are synthesized, and how they regulate other biological processes remain challenging. Despite the abundant presence of glycans on proteins and the dense layers of glycans that surround most of our cells, structures containing glycans are underrepresented in the PDB. There are sound reasons for this, including difficulties in producing proteins with well-defined glycosylation and the tendency of mobile and heterogeneous glycans to inhibit crystallization. Nevertheless, the structures we do find in the PDB, even some of the earliest deposited structures, have had an impact on our understanding of function. I highlight a few examples in this review and point to some promises for the future. Promises include new structures from methodologies, such as cryo-EM, that are less affected by the presence of glycans and experiment-aided computational methods that build on existing structures to provide insight into the many ways glycans affect biological function.
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Affiliation(s)
- James H Prestegard
- Complex Carbohydrate Research Center, University of Georgia, Athens, Georgia, USA.
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19
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Benicky J, Sanda M, Brnakova Kennedy Z, Grant OC, Woods RJ, Zwart A, Goldman R. PD-L1 Glycosylation and Its Impact on Binding to Clinical Antibodies. J Proteome Res 2020; 20:485-497. [PMID: 33073996 DOI: 10.1021/acs.jproteome.0c00521] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Immune checkpoint inhibitors, including PD-L1/PD-1, are key regulators of the immune response and promising targets in cancer immunotherapy. N-glycosylation of PD-L1 affects its interaction with PD-1, but little is known about the distribution of glycoforms at its four NXS/T sequons. We optimized LC-MS/MS methods using collision energy modulation for the site-specific resolution of specific glycan motifs. We demonstrate that PD-L1 on the surface of breast cancer cell line carries mostly complex glycans with a high proportion of polyLacNAc structures at the N219 sequon. Contrary to the full-length protein, the secreted form of PD-L1 expressed in breast MDA-MB-231 or HEK293 cells demonstrated minimum N219 occupancy and low contribution of the polyLacNAc structures. Molecular modeling of PD-L1/PD-1 interaction with N-glycans suggests that glycans at the N219 site of PD-L1 and N74 and N116 of PD-1 may be involved in glycan-glycan interactions, but the impact of this potential interaction on the protein function remains at this point unknown. The interaction of PD-L1 with clinical antibodies is also affected by glycosylation. In conclusion, PD-L1 expressed in the MDA-MB-231 breast cancer cell line carries polyLacNAc glycans mostly at the N219 sequon, which displays the highest variability in occupancy and is most likely to influence the interaction with PD-1.
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Affiliation(s)
- Julius Benicky
- Department of Oncology, Lombardi Comprehensive Cancer Center, Georgetown University, Washington, D.C. 20057, United States.,Clinical and Translational Glycoscience Research Center, Georgetown University, Washington, D.C. 20057, United States
| | - Miloslav Sanda
- Department of Oncology, Lombardi Comprehensive Cancer Center, Georgetown University, Washington, D.C. 20057, United States.,Clinical and Translational Glycoscience Research Center, Georgetown University, Washington, D.C. 20057, United States
| | - Zuzana Brnakova Kennedy
- Department of Oncology, Lombardi Comprehensive Cancer Center, Georgetown University, Washington, D.C. 20057, United States.,Clinical and Translational Glycoscience Research Center, Georgetown University, Washington, D.C. 20057, United States
| | - Oliver C Grant
- Department of Biochemistry and Molecular Biology, Complex Carbohydrate Research Center, University of Georgia, Athens, Georgia 30602, United States
| | - Robert J Woods
- Department of Biochemistry and Molecular Biology, Complex Carbohydrate Research Center, University of Georgia, Athens, Georgia 30602, United States
| | - Alan Zwart
- Department of Oncology, Lombardi Comprehensive Cancer Center, Georgetown University, Washington, D.C. 20057, United States
| | - Radoslav Goldman
- Department of Oncology, Lombardi Comprehensive Cancer Center, Georgetown University, Washington, D.C. 20057, United States.,Department of Biochemistry and Molecular & Cellular Biology, Georgetown University, Washington, D.C. 20057, United States.,Clinical and Translational Glycoscience Research Center, Georgetown University, Washington, D.C. 20057, United States
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20
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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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21
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Zhao P, Praissman JL, Grant OC, Cai Y, Xiao T, Rosenbalm KE, Aoki K, Kellman BP, Bridger R, Barouch DH, Brindley MA, Lewis NE, Tiemeyer M, Chen B, Woods RJ, Wells L. Virus-Receptor Interactions of Glycosylated SARS-CoV-2 Spike and Human ACE2 Receptor. Cell Host Microbe 2020; 28:586-601.e6. [PMID: 32841605 PMCID: PMC7443692 DOI: 10.1016/j.chom.2020.08.004] [Citation(s) in RCA: 289] [Impact Index Per Article: 72.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2020] [Revised: 07/22/2020] [Accepted: 08/10/2020] [Indexed: 12/13/2022]
Abstract
The SARS-CoV-2 betacoronavirus uses its highly glycosylated trimeric Spike protein to bind to the cell surface receptor angiotensin converting enzyme 2 (ACE2) glycoprotein and facilitate host cell entry. We utilized glycomics-informed glycoproteomics to characterize site-specific microheterogeneity of glycosylation for a recombinant trimer Spike mimetic immunogen and for a soluble version of human ACE2. We combined this information with bioinformatics analyses of natural variants and with existing 3D structures of both glycoproteins to generate molecular dynamics simulations of each glycoprotein both alone and interacting with one another. Our results highlight roles for glycans in sterically masking polypeptide epitopes and directly modulating Spike-ACE2 interactions. Furthermore, our results illustrate the impact of viral evolution and divergence on Spike glycosylation, as well as the influence of natural variants on ACE2 receptor glycosylation. Taken together, these data can facilitate immunogen design to achieve antibody neutralization and inform therapeutic strategies to inhibit viral infection.
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Affiliation(s)
- Peng Zhao
- Complex Carbohydrate Research Center, Department of Biochemistry and Molecular Biology, and Department of Chemistry, University of Georgia, Athens, GA 30602, USA
| | - Jeremy L Praissman
- Complex Carbohydrate Research Center, Department of Biochemistry and Molecular Biology, and Department of Chemistry, University of Georgia, Athens, GA 30602, USA
| | - Oliver C Grant
- Complex Carbohydrate Research Center, Department of Biochemistry and Molecular Biology, and Department of Chemistry, University of Georgia, Athens, GA 30602, USA
| | - Yongfei Cai
- Division of Molecular Medicine, Children's Hospital and Department of Pediatrics, Harvard Medical School, Boston, MA 02115, USA
| | - Tianshu Xiao
- Division of Molecular Medicine, Children's Hospital and Department of Pediatrics, Harvard Medical School, Boston, MA 02115, USA
| | - Katelyn E Rosenbalm
- Complex Carbohydrate Research Center, Department of Biochemistry and Molecular Biology, and Department of Chemistry, University of Georgia, Athens, GA 30602, USA
| | - Kazuhiro Aoki
- Complex Carbohydrate Research Center, Department of Biochemistry and Molecular Biology, and Department of Chemistry, University of Georgia, Athens, GA 30602, USA
| | - Benjamin P Kellman
- Departments of Pediatrics and Bioengineering, University of California, San Diego, La Jolla, CA 92093, USA
| | - Robert Bridger
- Complex Carbohydrate Research Center, Department of Biochemistry and Molecular Biology, and Department of Chemistry, University of Georgia, Athens, GA 30602, USA
| | - Dan H Barouch
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02215, USA
| | - Melinda A Brindley
- Department of Infectious Diseases, Department of Population Health, Center for Vaccines and Immunology, College of Veterinary Medicine, University of Georgia, Athens, GA 30602, USA
| | - Nathan E Lewis
- Departments of Pediatrics and Bioengineering, University of California, San Diego, La Jolla, CA 92093, USA; Novo Nordisk Foundation Center for Biosustainability at UC San Diego, La Jolla, CA 92093, USA
| | - Michael Tiemeyer
- Complex Carbohydrate Research Center, Department of Biochemistry and Molecular Biology, and Department of Chemistry, University of Georgia, Athens, GA 30602, USA
| | - Bing Chen
- Division of Molecular Medicine, Children's Hospital and Department of Pediatrics, Harvard Medical School, Boston, MA 02115, USA
| | - Robert J Woods
- Complex Carbohydrate Research Center, Department of Biochemistry and Molecular Biology, and Department of Chemistry, University of Georgia, Athens, GA 30602, USA.
| | - Lance Wells
- Complex Carbohydrate Research Center, Department of Biochemistry and Molecular Biology, and Department of Chemistry, University of Georgia, Athens, GA 30602, USA.
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22
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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: 12] [Impact Index Per Article: 3.0] [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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23
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Zhao P, Praissman JL, Grant OC, Cai Y, Xiao T, Rosenbalm KE, Aoki K, Kellman BP, Bridger R, Barouch DH, Brindley MA, Lewis NE, Tiemeyer M, Chen B, Woods RJ, Wells L. Virus-Receptor Interactions of Glycosylated SARS-CoV-2 Spike and Human ACE2 Receptor. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2020:2020.06.25.172403. [PMID: 32743578 PMCID: PMC7386495 DOI: 10.1101/2020.06.25.172403] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
The current COVID-19 pandemic is caused by the SARS-CoV-2 betacoronavirus, which utilizes its highly glycosylated trimeric Spike protein to bind to the cell surface receptor ACE2 glycoprotein and facilitate host cell entry. We utilized glycomics-informed glycoproteomics to characterize site-specific microheterogeneity of glycosylation for a recombinant trimer Spike mimetic immunogen and for a soluble version of human ACE2. We combined this information with bioinformatic analyses of natural variants and with existing 3D-structures of both glycoproteins to generate molecular dynamics simulations of each glycoprotein alone and interacting with one another. Our results highlight roles for glycans in sterically masking polypeptide epitopes and directly modulating Spike-ACE2 interactions. Furthermore, our results illustrate the impact of viral evolution and divergence on Spike glycosylation, as well as the influence of natural variants on ACE2 receptor glycosylation that, taken together, can facilitate immunogen design to achieve antibody neutralization and inform therapeutic strategies to inhibit viral infection.
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Affiliation(s)
- Peng Zhao
- Complex Carbohydrate Research Center, Department of Biochemistry and Molecular Biology, and Department of Chemistry, University of Georgia, Athens, Georgia, 30602, USA
| | - Jeremy L. Praissman
- Complex Carbohydrate Research Center, Department of Biochemistry and Molecular Biology, and Department of Chemistry, University of Georgia, Athens, Georgia, 30602, USA
| | - Oliver C. Grant
- Complex Carbohydrate Research Center, Department of Biochemistry and Molecular Biology, and Department of Chemistry, University of Georgia, Athens, Georgia, 30602, USA
| | - Yongfei Cai
- Division of Molecular Medicine, Children’s Hospital and Department of Pediatrics, Harvard Medical School, Boston, Massachusetts, 02115, USA
| | - Tianshu Xiao
- Division of Molecular Medicine, Children’s Hospital and Department of Pediatrics, Harvard Medical School, Boston, Massachusetts, 02115, USA
| | - Katelyn E. Rosenbalm
- Complex Carbohydrate Research Center, Department of Biochemistry and Molecular Biology, and Department of Chemistry, University of Georgia, Athens, Georgia, 30602, USA
| | - Kazuhiro Aoki
- Complex Carbohydrate Research Center, Department of Biochemistry and Molecular Biology, and Department of Chemistry, University of Georgia, Athens, Georgia, 30602, USA
| | - Benjamin P. Kellman
- Departments of Pediatrics and Bioengineering, University of California, San Diego, La Jolla, California, 92093, USA
| | - Robert Bridger
- Complex Carbohydrate Research Center, Department of Biochemistry and Molecular Biology, and Department of Chemistry, University of Georgia, Athens, Georgia, 30602, USA
| | - Dan H. Barouch
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, Massachusetts, 02215, USA
| | - Melinda A. Brindley
- Department of Infectious Diseases, Department of Population Health, Center for Vaccines and Immunology, College of Veterinary Medicine, University of Georgia, Athens, GA 30602, USA
| | - Nathan E. Lewis
- Departments of Pediatrics and Bioengineering, University of California, San Diego, La Jolla, California, 92093, USA
- Novo Nordisk Foundation Center for Biosustainability at UC San Diego, La Jolla, California, 92093, USA
| | - Michael Tiemeyer
- Complex Carbohydrate Research Center, Department of Biochemistry and Molecular Biology, and Department of Chemistry, University of Georgia, Athens, Georgia, 30602, USA
| | - Bing Chen
- Division of Molecular Medicine, Children’s Hospital and Department of Pediatrics, Harvard Medical School, Boston, Massachusetts, 02115, USA
| | - Robert J. Woods
- Complex Carbohydrate Research Center, Department of Biochemistry and Molecular Biology, and Department of Chemistry, University of Georgia, Athens, Georgia, 30602, USA
| | - Lance Wells
- Complex Carbohydrate Research Center, Department of Biochemistry and Molecular Biology, and Department of Chemistry, University of Georgia, Athens, Georgia, 30602, USA
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24
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Mandalasi M, Kim HW, Thieker D, Sheikh MO, Gas-Pascual E, Rahman K, Zhao P, Daniel NG, van der Wel H, Ichikawa HT, Glushka JN, Wells L, Woods RJ, Wood ZA, West CM. A terminal α3-galactose modification regulates an E3 ubiquitin ligase subunit in Toxoplasma gondii. J Biol Chem 2020; 295:9223-9243. [PMID: 32414843 PMCID: PMC7335778 DOI: 10.1074/jbc.ra120.013792] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2020] [Revised: 05/14/2020] [Indexed: 12/29/2022] Open
Abstract
Skp1, a subunit of E3 Skp1/Cullin-1/F-box protein ubiquitin ligases, is modified by a prolyl hydroxylase that mediates O2 regulation of the social amoeba Dictyostelium and the parasite Toxoplasma gondii The full effect of hydroxylation requires modification of the hydroxyproline by a pentasaccharide that, in Dictyostelium, influences Skp1 structure to favor assembly of Skp1/F-box protein subcomplexes. In Toxoplasma, the presence of a contrasting penultimate sugar assembled by a different glycosyltransferase enables testing of the conformational control model. To define the final sugar and its linkage, here we identified the glycosyltransferase that completes the glycan and found that it is closely related to glycogenin, an enzyme that may prime glycogen synthesis in yeast and animals. However, the Toxoplasma enzyme catalyzes formation of a Galα1,3Glcα linkage rather than the Glcα1,4Glcα linkage formed by glycogenin. Kinetic and crystallographic experiments showed that the glycosyltransferase Gat1 is specific for Skp1 in Toxoplasma and also in another protist, the crop pathogen Pythium ultimum The fifth sugar is important for glycan function as indicated by the slow-growth phenotype of gat1Δ parasites. Computational analyses indicated that, despite the sequence difference, the Toxoplasma glycan still assumes an ordered conformation that controls Skp1 structure and revealed the importance of nonpolar packing interactions of the fifth sugar. The substitution of glycosyltransferases in Toxoplasma and Pythium by an unrelated bifunctional enzyme that assembles a distinct but structurally compatible glycan in Dictyostelium is a remarkable case of convergent evolution, which emphasizes the importance of the terminal α-galactose and establishes the phylogenetic breadth of Skp1 glycoregulation.
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Affiliation(s)
- Msano Mandalasi
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, Georgia, USA; Center for Tropical and Emerging Global Diseases, University of Georgia, Athens, Georgia, USA
| | - Hyun W Kim
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, Georgia, USA
| | - David Thieker
- Complex Carbohydrate Research Center, University of Georgia, Athens, Georgia, USA
| | - M Osman Sheikh
- Complex Carbohydrate Research Center, University of Georgia, Athens, Georgia, USA
| | - Elisabet Gas-Pascual
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, Georgia, USA; Center for Tropical and Emerging Global Diseases, University of Georgia, Athens, Georgia, USA
| | - Kazi Rahman
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, Georgia, USA
| | - Peng Zhao
- Complex Carbohydrate Research Center, University of Georgia, Athens, Georgia, USA
| | - Nitin G Daniel
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, Georgia, USA
| | - Hanke van der Wel
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, Georgia, USA
| | - H Travis Ichikawa
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, Georgia, USA
| | - John N Glushka
- Complex Carbohydrate Research Center, University of Georgia, Athens, Georgia, USA
| | - Lance Wells
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, Georgia, USA; Complex Carbohydrate Research Center, University of Georgia, Athens, Georgia, USA
| | - Robert J Woods
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, Georgia, USA; Complex Carbohydrate Research Center, University of Georgia, Athens, Georgia, USA
| | - Zachary A Wood
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, Georgia, USA
| | - Christopher M West
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, Georgia, USA; Center for Tropical and Emerging Global Diseases, University of Georgia, Athens, Georgia, USA; Complex Carbohydrate Research Center, University of Georgia, Athens, Georgia, USA.
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25
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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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26
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Kang X, Zhao W, Dickwella Widanage MC, Kirui A, Ozdenvar U, Wang T. CCMRD: a solid-state NMR database for complex carbohydrates. JOURNAL OF BIOMOLECULAR NMR 2020; 74:239-245. [PMID: 32125579 DOI: 10.1007/s10858-020-00304-2] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/24/2019] [Accepted: 01/27/2020] [Indexed: 05/03/2023]
Abstract
Carbohydrates are essential to various life activities in living organisms and serve as the central component in many biomaterials. As an emerging technique with steadily improving resolution, solid-state Nuclear Magnetic Resonance (NMR) spectroscopy has the unique capability in revealing the polymorphic structure and heterogeneous dynamics of insoluble complex carbohydrates. Here, we report the first solid-state NMR database for complex carbohydrates, Complex Carbohydrates Magnetic Resonance Database (CCMRD). This database currently holds the chemical shift information of more than four hundred solid-state NMR compounds and expects rapid expansion. CCMRD provides open portals for data deposition and supports search options based on NMR chemical shifts, carbohydrate names, and compound classes. With the timely implementation, this platform will facilitate spectral analysis and structure determination of carbohydrates and promote software development to benefit the research community. The database is freely accessible at www.ccmrd.org.
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Affiliation(s)
- Xue Kang
- Department of Chemistry, Louisiana State University, Baton Rouge, LA, 70803, USA.
| | - Wancheng Zhao
- Department of Chemistry, Louisiana State University, Baton Rouge, LA, 70803, USA
| | | | - Alex Kirui
- Department of Chemistry, Louisiana State University, Baton Rouge, LA, 70803, USA
| | - Uluc Ozdenvar
- Department of Chemistry, Louisiana State University, Baton Rouge, LA, 70803, USA
| | - Tuo Wang
- Department of Chemistry, Louisiana State University, Baton Rouge, LA, 70803, USA.
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27
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Neelamegham S, Aoki-Kinoshita K, Bolton E, Frank M, Lisacek F, Lütteke T, O'Boyle N, Packer NH, Stanley P, Toukach P, Varki A, Woods RJ. Updates to the Symbol Nomenclature for Glycans guidelines. Glycobiology 2020; 29:620-624. [PMID: 31184695 DOI: 10.1093/glycob/cwz045] [Citation(s) in RCA: 257] [Impact Index Per Article: 64.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2019] [Revised: 05/15/2019] [Accepted: 06/06/2019] [Indexed: 11/14/2022] Open
Abstract
The Symbol Nomenclature for Glycans (SNFG) is a community-curated standard for the depiction of monosaccharides and complex glycans using various colored-coded, geometric shapes, along with defined text additions. It is hosted by the National Center for Biotechnology Information (NCBI) at the NCBI-Glycans Page (www.ncbi.nlm.nih.gov/glycans/snfg.html). Several changes have been made to the SNFG page in the past year to update the rules for depicting glycans using the SNFG, to include more examples of use, particularly for non-mammalian organisms, and to provide guidelines for the depiction of ambiguous glycan structures. This Glycoforum article summarizes these recent changes.
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Affiliation(s)
- Sriram Neelamegham
- Department of Chemical & Biological Engineering and Medicine, State University of New York, 906 Furnas Hall, Buffalo, NY 14260, USA
| | - Kiyoko Aoki-Kinoshita
- Glycan & Life System Integration Center (GaLSIC), Faculty of Science and Engineering, Soka University, 1-236 Tangi-machi, Hachioji, Tokyo 192-8577, Japan
| | - Evan Bolton
- National Library of Medicine, 8600 Rockville Pike, Bldg. 38A, Room 8S810, Bethesda, MD 20896, USA
| | - Martin Frank
- Biognos AB, Generatorsgatan 1 / Box 8963, 402 74 Göteborg, Sweden
| | - Frederique Lisacek
- Proteome Informatics Group, SIB Swiss Institute of Bioinformatics, Computer Science Department, University of Geneva, route de Drize 7, CH - 1227 Geneva Switzerland, and also Section of Biology, University of Geneva, Geneva, Switzerland
| | - Thomas Lütteke
- GIP GmbH, Strahlenberger Str. 112, 63067 Offenbach, Germany
| | - Noel O'Boyle
- NextMove Software, Innovation Centre, Cambridge Science Park, Milton Road, Cambridge, CB4 0EY, UK
| | - Nicolle H Packer
- Department of Molecular Sciences, Faculty of Science & Engineering, Rm 307, Building E8C, Macquarie University, Sydney, NSW 2109, Australia
| | - Pamela Stanley
- Department of Cell Biology, Albert Einstein College of Medicine, 1300 Morris Park Ave, New York, NY, 10461, USA
| | - Philip Toukach
- Laboratory of Carbohydrate Chemistry, Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences. 119991 Moscow, Leninsky prospect 47, Russia
| | - Ajit Varki
- Glycobiology Research and Training Center, University of California, San Diego, La Jolla, CA 92093, USA
| | - Robert J Woods
- Complex Carbohydrate Research Center, University of Georgia, 315 Riverbend Rd, Athens, GA, 30602, USA
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28
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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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29
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Armstrong DR, Berrisford JM, Conroy MJ, Gutmanas A, Anyango S, Choudhary P, Clark AR, Dana JM, Deshpande M, Dunlop R, Gane P, Gáborová R, Gupta D, Haslam P, Koča J, Mak L, Mir S, Mukhopadhyay A, Nadzirin N, Nair S, Paysan-Lafosse T, Pravda L, Sehnal D, Salih O, Smart O, Tolchard J, Varadi M, Svobodova-Vařeková R, Zaki H, Kleywegt GJ, Velankar S. PDBe: improved findability of macromolecular structure data in the PDB. Nucleic Acids Res 2020; 48:D335-D343. [PMID: 31691821 PMCID: PMC7145656 DOI: 10.1093/nar/gkz990] [Citation(s) in RCA: 58] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2019] [Revised: 10/11/2019] [Accepted: 10/25/2019] [Indexed: 11/23/2022] Open
Abstract
The Protein Data Bank in Europe (PDBe), a founding member of the Worldwide Protein Data Bank (wwPDB), actively participates in the deposition, curation, validation, archiving and dissemination of macromolecular structure data. PDBe supports diverse research communities in their use of macromolecular structures by enriching the PDB data and by providing advanced tools and services for effective data access, visualization and analysis. This paper details the enrichment of data at PDBe, including mapping of RNA structures to Rfam, and identification of molecules that act as cofactors. PDBe has developed an advanced search facility with ∼100 data categories and sequence searches. New features have been included in the LiteMol viewer at PDBe, with updated visualization of carbohydrates and nucleic acids. Small molecules are now mapped more extensively to external databases and their visual representation has been enhanced. These advances help users to more easily find and interpret macromolecular structure data in order to solve scientific problems.
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Affiliation(s)
- David R Armstrong
- Protein Data Bank in Europe, European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - John M Berrisford
- Protein Data Bank in Europe, European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Matthew J Conroy
- Protein Data Bank in Europe, European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Aleksandras Gutmanas
- Protein Data Bank in Europe, European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Stephen Anyango
- Protein Data Bank in Europe, European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Preeti Choudhary
- Protein Data Bank in Europe, European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Alice R Clark
- Protein Data Bank in Europe, European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Jose M Dana
- Protein Data Bank in Europe, European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Mandar Deshpande
- Protein Data Bank in Europe, European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Roisin Dunlop
- Protein Data Bank in Europe, European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Paul Gane
- Protein Data Bank in Europe, European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Romana Gáborová
- CEITEC - Central European Institute of Technology, Masaryk University Brno, Kamenice 5, 625 00 Brno-Bohunice, Czech Republic
| | - Deepti Gupta
- Protein Data Bank in Europe, European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Pauline Haslam
- Protein Data Bank in Europe, European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Jaroslav Koča
- CEITEC - Central European Institute of Technology, Masaryk University Brno, Kamenice 5, 625 00 Brno-Bohunice, Czech Republic
| | - Lora Mak
- Protein Data Bank in Europe, European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Saqib Mir
- Protein Data Bank in Europe, European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Abhik Mukhopadhyay
- Protein Data Bank in Europe, European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Nurul Nadzirin
- Protein Data Bank in Europe, European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Sreenath Nair
- Protein Data Bank in Europe, European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Typhaine Paysan-Lafosse
- Protein Data Bank in Europe, European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
- InterPro, European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Lukas Pravda
- Protein Data Bank in Europe, European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - David Sehnal
- CEITEC - Central European Institute of Technology, Masaryk University Brno, Kamenice 5, 625 00 Brno-Bohunice, Czech Republic
| | - Osman Salih
- Electron Microscopy Data Bank (EMDB), European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Oliver Smart
- Protein Data Bank in Europe, European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - James Tolchard
- Protein Data Bank in Europe, European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Mihaly Varadi
- Protein Data Bank in Europe, European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Radka Svobodova-Vařeková
- CEITEC - Central European Institute of Technology, Masaryk University Brno, Kamenice 5, 625 00 Brno-Bohunice, Czech Republic
| | - Hossam Zaki
- Protein Data Bank in Europe, European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Gerard J Kleywegt
- Protein Data Bank in Europe, European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
- Electron Microscopy Data Bank (EMDB), European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Sameer Velankar
- Protein Data Bank in Europe, European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
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30
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Copoiu L, Torres PHM, Ascher DB, Blundell TL, Malhotra S. ProCarbDB: a database of carbohydrate-binding proteins. Nucleic Acids Res 2020; 48:D368-D375. [PMID: 31598690 PMCID: PMC6943041 DOI: 10.1093/nar/gkz860] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2019] [Revised: 09/12/2019] [Accepted: 10/05/2019] [Indexed: 02/02/2023] Open
Abstract
Carbohydrate-binding proteins play crucial roles across all organisms and viruses. The complexity of carbohydrate structures, together with inconsistencies in how their 3D structures are reported, has led to difficulties in characterizing the protein-carbohydrate interfaces. In order to better understand protein-carbohydrate interactions, we have developed an open-access database, ProCarbDB, which, unlike the Protein Data Bank (PDB), clearly distinguishes between the complete carbohydrate ligands and their monomeric units. ProCarbDB is a comprehensive database containing over 5200 3D X-ray crystal structures of protein-carbohydrate complexes. In ProCarbDB, the complete carbohydrate ligands are annotated and all their interactions are displayed. Users can also select any protein residue in the proximity of the ligand to inspect its interactions with the carbohydrate ligand and with other neighbouring protein residues. Where available, additional curated information on the binding affinity of the complex and the effects of mutations on the binding have also been provided in the database. We believe that ProCarbDB will be an invaluable resource for understanding protein-carbohydrate interfaces. The ProCarbDB web server is freely available at http://www.procarbdb.science/procarb.
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Affiliation(s)
- Liviu Copoiu
- Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge, CB2 1GA, UK
| | - Pedro H M Torres
- Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge, CB2 1GA, UK
| | - David B Ascher
- Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge, CB2 1GA, UK,Department of Biochemistry, University of Melbourne, Flemington Road, Parkville, Australia
| | - Tom L Blundell
- Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge, CB2 1GA, UK,To whom correspondence should be addressed. Tel: +44 1223 333628;
| | - Sony Malhotra
- Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge, CB2 1GA, UK,Correspondence may also be addressed to Sony Malhotra.
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31
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Abstract
LiteMol suite is an innovative solution that enables near-instant delivery of model and experimental biomacromolecular structural data, providing users with an interactive and responsive experience in all modern web browsers and mobile devices. LiteMol suite is a combination of data delivery services (CoordinateServer and DensityServer), compression format (BinaryCIF), and a molecular viewer (LiteMol Viewer). The LiteMol suite is integrated into Protein Data Bank in Europe (PDBe) and other life science web applications (e.g., UniProt, Ensemble, SIB, and CNRS services), it is freely available at https://litemol.org , and its source code is available via GitHub. LiteMol suite provides advanced functionality (annotations and their visualization, powerful selection features), and this chapter will describe their use for visual inspection of protein structures.
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32
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Abrahams JL, Taherzadeh G, Jarvas G, Guttman A, Zhou Y, Campbell MP. Recent advances in glycoinformatic platforms for glycomics and glycoproteomics. Curr Opin Struct Biol 2019; 62:56-69. [PMID: 31874386 DOI: 10.1016/j.sbi.2019.11.009] [Citation(s) in RCA: 65] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2019] [Revised: 11/05/2019] [Accepted: 11/15/2019] [Indexed: 12/16/2022]
Abstract
Protein glycosylation is the most complex and prevalent post-translation modification in terms of the number of proteins modified and the diversity generated. To understand the functional roles of glycoproteins it is important to gain an insight into the repertoire of oligosaccharides present. The comparison and relative quantitation of glycoforms combined with site-specific identification and occupancy are necessary steps in this direction. Computational platforms have continued to mature assisting researchers with the interpretation of such glycomics and glycoproteomics data sets, but frequently support dedicated workflows and users rely on the manual interpretation of data to gain insights into the glycoproteome. The growth of site-specific knowledge has also led to the implementation of machine-learning algorithms to predict glycosylation which is now being integrated into glycoproteomics pipelines. This short review describes commercial and open-access databases and software with an emphasis on those that are actively maintained and designed to support current analytical workflows.
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Affiliation(s)
- Jodie L Abrahams
- Institute for Glycomics, Griffith University, Gold Coast, QLD, Australia
| | - Ghazaleh Taherzadeh
- School of Information and Communication Technology, Griffith University, Gold Coast, QLD, Australia
| | - Gabor Jarvas
- Translational Glycomics Research Group, Research Institute of Biomolecular and Chemical Engineering, University of Pannonia, Veszprém, Hungary; Horváth Csaba Laboratory of Bioseparation Sciences, Research Centre for Molecular Medicine, Faculty of Medicine, University of Debrecen, Debrecen, Hungary
| | - Andras Guttman
- Translational Glycomics Research Group, Research Institute of Biomolecular and Chemical Engineering, University of Pannonia, Veszprém, Hungary; Horváth Csaba Laboratory of Bioseparation Sciences, Research Centre for Molecular Medicine, Faculty of Medicine, University of Debrecen, Debrecen, Hungary; SCIEX, Brea, CA, USA
| | - Yaoqi Zhou
- School of Information and Communication Technology, Griffith University, Gold Coast, QLD, Australia
| | - Matthew P Campbell
- Institute for Glycomics, Griffith University, Gold Coast, QLD, Australia.
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33
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Martini F, Eckmair B, Štefanić S, Jin C, Garg M, Yan S, Jiménez-Castells C, Hykollari A, Neupert C, Venco L, Varón Silva D, Wilson IBH, Paschinger K. Highly modified and immunoactive N-glycans of the canine heartworm. Nat Commun 2019; 10:75. [PMID: 30622255 PMCID: PMC6325117 DOI: 10.1038/s41467-018-07948-7] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2017] [Accepted: 12/06/2018] [Indexed: 01/05/2023] Open
Abstract
The canine heartworm (Dirofilaria immitis) is a mosquito-borne parasitic nematode whose range is extending due to climate change. In a four-dimensional analysis involving HPLC, MALDI-TOF–MS and MS/MS in combination with chemical and enzymatic digestions, we here reveal an N-glycome of unprecedented complexity. We detect N-glycans of up to 7000 Da, which contain long fucosylated HexNAc-based repeats, as well as glucuronylated structures. While some modifications including LacdiNAc, chitobiose, α1,3-fucose and phosphorylcholine are familiar, anionic N-glycans have previously not been reported in nematodes. Glycan array data show that the neutral glycans are preferentially recognised by IgM in dog sera or by mannose binding lectin when antennal fucose and phosphorylcholine residues are removed; this pattern of reactivity is reversed for mammalian C-reactive protein, which can in turn be bound by the complement component C1q. Thereby, the N-glycans of D. immitis contain features which may either mediate immunomodulation of the host or confer the ability to avoid immune surveillance. The glycome of parasites can have immunomodulatory properties or help to avoid immune surveillance, but details are unknown. Here, Martini et al. characterize the N-glycome of the canine heartworm, reveal an unprecedented complexity, particularly in anionic N-glycans, and determine recognition by components of the immune system.
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Affiliation(s)
| | - Barbara Eckmair
- Department für Chemie, Universität für Bodenkultur, Muthgasse 18, 1190, Wien, Austria
| | - Saša Štefanić
- Institute of Parasitology, Universität Zürich, Winterthurerstraße 266a, 8057, Zürich, Switzerland
| | - Chunsheng Jin
- Institutionen för Biomedicin, Göteborgs Universitet, 405 30, Göteborg, Sweden
| | - Monika Garg
- Max-Planck-Institut für Kolloid- und Grenzflächenforschung, Biomolekulare Systeme, 14424, Potsdam, Germany
| | - Shi Yan
- Department für Chemie, Universität für Bodenkultur, Muthgasse 18, 1190, Wien, Austria.,Institut für Parasitologie, Veterinärmedizinische Universität, 1210, Wien, Austria
| | | | - Alba Hykollari
- Department für Chemie, Universität für Bodenkultur, Muthgasse 18, 1190, Wien, Austria
| | | | - Luigi Venco
- Clinica Veterinaria Lago Maggiore, Arona, 28040, Italy
| | - Daniel Varón Silva
- Max-Planck-Institut für Kolloid- und Grenzflächenforschung, Biomolekulare Systeme, 14424, Potsdam, Germany
| | - Iain B H Wilson
- Department für Chemie, Universität für Bodenkultur, Muthgasse 18, 1190, Wien, Austria.
| | - Katharina Paschinger
- Department für Chemie, Universität für Bodenkultur, Muthgasse 18, 1190, Wien, Austria
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34
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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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35
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Fu X, Liao B, Zhu W, Cai L. New 3D graphical representation for RNA structure analysis and its application in the pre-miRNA identification of plants. RSC Adv 2018; 8:30833-30841. [PMID: 35548744 PMCID: PMC9085476 DOI: 10.1039/c8ra04138e] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2018] [Accepted: 08/24/2018] [Indexed: 11/26/2022] Open
Abstract
MicroRNAs (miRNAs) are a family of short non-coding RNAs that play significant roles as post-transcriptional regulators. Consequently, various methods have been proposed to identify precursor miRNAs (pre-miRNAs), among which the comparative studies of miRNA structures are the most important. To measure and classify the structural similarity of miRNAs, we propose a new three-dimensional (3D) graphical representation of the secondary structure of miRNAs, in which an miRNA secondary structure is initially transformed into a characteristic sequence based on physicochemical properties and frequency of base. A numerical characterization of the 3D graph is used to represent the miRNA secondary structure. We then utilize a novel Euclidean distance method based on this expression to compute the distance of different miRNA sequences for the sequence similarity analysis. Finally, we use this sequence similarity analysis method to identify plant pre-miRNAs among three commonly used datasets. Results show that the method is reasonable and effective.
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Affiliation(s)
- Xiangzheng Fu
- College of Information Science and Engineering, Hunan University Changsha Hunan 410082 China
| | - Bo Liao
- College of Information Science and Engineering, Hunan University Changsha Hunan 410082 China
| | - Wen Zhu
- College of Information Science and Engineering, Hunan University Changsha Hunan 410082 China
| | - Lijun Cai
- College of Information Science and Engineering, Hunan University Changsha Hunan 410082 China
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36
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Abstract
Complex carbohydrates are ubiquitous in nature, and together with proteins and nucleic acids they comprise the building blocks of life. But unlike proteins and nucleic acids, carbohydrates form nonlinear polymers, and they are not characterized by robust secondary or tertiary structures but rather by distributions of well-defined conformational states. Their molecular flexibility means that oligosaccharides are often refractory to crystallization, and nuclear magnetic resonance (NMR) spectroscopy augmented by molecular dynamics (MD) simulation is the leading method for their characterization in solution. The biological importance of carbohydrate-protein interactions, in organismal development as well as in disease, places urgency on the creation of innovative experimental and theoretical methods that can predict the specificity of such interactions and quantify their strengths. Additionally, the emerging realization that protein glycosylation impacts protein function and immunogenicity places the ability to define the mechanisms by which glycosylation impacts these features at the forefront of carbohydrate modeling. This review will discuss the relevant theoretical approaches to studying the three-dimensional structures of this fascinating class of molecules and interactions, with reference to the relevant experimental data and techniques that are key for validation of the theoretical predictions.
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Affiliation(s)
- Robert J Woods
- Complex Carbohydrate Research Center and Department of Biochemistry and Molecular Biology , University of Georgia , 315 Riverbend Road , Athens , Georgia 30602 , United States
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37
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Thieker DF, Xu Y, Chapla D, Nora C, Qiu H, Felix T, Wang L, Moremen KW, Liu J, Esko JD, Woods RJ. Downstream Products are Potent Inhibitors of the Heparan Sulfate 2-O-Sulfotransferase. Sci Rep 2018; 8:11832. [PMID: 30087361 PMCID: PMC6081452 DOI: 10.1038/s41598-018-29602-4] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2018] [Accepted: 07/09/2018] [Indexed: 12/31/2022] Open
Abstract
Heparan Sulfate (HS) is a cell signaling molecule linked to pathological processes ranging from cancer to viral entry, yet fundamental aspects of its biosynthesis remain incompletely understood. Here, the binding preferences of the uronyl 2-O-sulfotransferase (HS2ST) are examined with variably-sulfated hexasaccharides. Surprisingly, heavily sulfated oligosaccharides formed by later-acting sulfotransferases bind more tightly to HS2ST than those corresponding to its natural substrate or product. Inhibition assays also indicate that the IC50 values correlate simply with degree of oligosaccharide sulfation. Structural analysis predicts a mode of inhibition in which 6-O-sulfate groups located on glucosamine residues present in highly-sulfated oligosaccharides occupy the canonical binding site of the nucleotide cofactor. The unexpected finding that oligosaccharides associated with later stages in HS biosynthesis inhibit HS2ST indicates that the enzyme must be separated temporally and/or spatially from downstream products during biosynthesis in vivo, and highlights a challenge for the enzymatic synthesis of lengthy HS chains in vitro.
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Affiliation(s)
- David F Thieker
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA, 30602, USA
- Complex Carbohydrate Research Center, University of Georgia, Athens, GA, 30602, USA
| | - Yongmei Xu
- Division of Chemical Biology and Medicinal Chemistry, Eshelman School of Pharmacy, University of North Carolina, Rm 1044, Genetic Medicine Building, Chapel Hill, USA
| | - Digantkumar Chapla
- Complex Carbohydrate Research Center, University of Georgia, Athens, GA, 30602, USA
| | - Chelsea Nora
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, California, USA
| | - Hong Qiu
- Complex Carbohydrate Research Center, University of Georgia, Athens, GA, 30602, USA
| | - Thomas Felix
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA, 30602, USA
- Complex Carbohydrate Research Center, University of Georgia, Athens, GA, 30602, USA
| | - Lianchun Wang
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA, 30602, USA
- Complex Carbohydrate Research Center, University of Georgia, Athens, GA, 30602, USA
| | - Kelley W Moremen
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA, 30602, USA
- Complex Carbohydrate Research Center, University of Georgia, Athens, GA, 30602, USA
| | - Jian Liu
- Division of Chemical Biology and Medicinal Chemistry, Eshelman School of Pharmacy, University of North Carolina, Rm 1044, Genetic Medicine Building, Chapel Hill, USA
| | - Jeffrey D Esko
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, California, USA
| | - Robert J Woods
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA, 30602, USA.
- Complex Carbohydrate Research Center, University of Georgia, Athens, GA, 30602, USA.
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Lis-Kuberka J, Orczyk-Pawiłowicz M, Królak-Olejnik B, Berghausen-Mazur M, Barańska K, Kątnik-Prastowska I. Lectin-based analysis of human milk immunoglobulin G fucosylated variants in relation to milk maturation and perinatal risk factors. J Appl Biomed 2018. [DOI: 10.1016/j.jab.2018.02.001] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
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Blaum BS, Neu U, Peters T, Stehle T. Spin ballet for sweet encounters: saturation-transfer difference NMR and X-ray crystallography complement each other in the elucidation of protein-glycan interactions. Acta Crystallogr F Struct Biol Commun 2018; 74:451-462. [PMID: 30084394 PMCID: PMC6096479 DOI: 10.1107/s2053230x18006581] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2018] [Accepted: 04/28/2018] [Indexed: 03/11/2023] Open
Abstract
Biomolecular NMR spectroscopy has limitations in the determination of protein structures: an inherent size limit and the requirement for expensive and potentially difficult isotope labelling pose considerable hurdles. Therefore, structural analysis of larger proteins is almost exclusively performed by crystallography. However, the diversity of biological NMR applications outperforms that of any other structural biology technique. For the characterization of transient complexes formed by proteins and small ligands, notably oligosaccharides, one NMR technique has recently proven to be particularly powerful: saturation-transfer difference NMR (STD-NMR) spectroscopy. STD-NMR experiments are fast and simple to set up, with no general protein size limit and no requirement for isotope labelling. The method performs best in the moderate-to-low affinity range that is of interest in most of glycobiology. With small amounts of unlabelled protein, STD-NMR experiments can identify hits from mixtures of potential ligands, characterize mutant proteins and pinpoint binding epitopes on the ligand side. STD-NMR can thus be employed to complement and improve protein-ligand complex models obtained by other structural biology techniques or by purely computational means. With a set of protein-glycan interactions from our own work, this review provides an introduction to the technique for structural biologists. It exemplifies how crystallography and STD-NMR can be combined to elucidate protein-glycan (and other protein-ligand) interactions in atomic detail, and how the technique can extend structural biology from simplified systems amenable to crystallization to more complex biological entities such as membranes, live viruses or entire cells.
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Affiliation(s)
- Bärbel S. Blaum
- Interfaculty Institute of Biochemistry, University of Tübingen, 72076 Tübingen, Germany
| | - Ursula Neu
- Department of Biomolecular Systems, Max Planck Institute of Colloids and Interfaces, 14424 Potsdam, Germany
| | - Thomas Peters
- Institute of Chemistry and Metabolomics, University of Lübeck, 23562 Lübeck, Germany
| | - Thilo Stehle
- Interfaculty Institute of Biochemistry, University of Tübingen, 72076 Tübingen, Germany
- Department of Pediatrics, Vanderbilt University School of Medicine, Nashville, Tennessee, USA
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40
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Amon R, Grant OC, Leviatan Ben-Arye S, Makeneni S, Nivedha AK, Marshanski T, Norn C, Yu H, Glushka JN, Fleishman SJ, Chen X, Woods RJ, Padler-Karavani V. A combined computational-experimental approach to define the structural origin of antibody recognition of sialyl-Tn, a tumor-associated carbohydrate antigen. Sci Rep 2018; 8:10786. [PMID: 30018351 PMCID: PMC6050261 DOI: 10.1038/s41598-018-29209-9] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2018] [Accepted: 07/06/2018] [Indexed: 12/16/2022] Open
Abstract
Anti-carbohydrate monoclonal antibodies (mAbs) hold great promise as cancer therapeutics and diagnostics. However, their specificity can be mixed, and detailed characterization is problematic, because antibody-glycan complexes are challenging to crystallize. Here, we developed a generalizable approach employing high-throughput techniques for characterizing the structure and specificity of such mAbs, and applied it to the mAb TKH2 developed against the tumor-associated carbohydrate antigen sialyl-Tn (STn). The mAb specificity was defined by apparent KD values determined by quantitative glycan microarray screening. Key residues in the antibody combining site were identified by site-directed mutagenesis, and the glycan-antigen contact surface was defined using saturation transfer difference NMR (STD-NMR). These features were then employed as metrics for selecting the optimal 3D-model of the antibody-glycan complex, out of thousands plausible options generated by automated docking and molecular dynamics simulation. STn-specificity was further validated by computationally screening of the selected antibody 3D-model against the human sialyl-Tn-glycome. This computational-experimental approach would allow rational design of potent antibodies targeting carbohydrates.
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Affiliation(s)
- Ron Amon
- Department of Cell Research and Immunology, The George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, 69978, Israel
| | - Oliver C Grant
- Complex Carbohydrate Research Center, University of Georgia, Athens, 30606, GA, USA
| | - Shani Leviatan Ben-Arye
- Department of Cell Research and Immunology, The George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, 69978, Israel
| | - Spandana Makeneni
- Complex Carbohydrate Research Center, University of Georgia, Athens, 30606, GA, USA
| | - Anita K Nivedha
- Complex Carbohydrate Research Center, University of Georgia, Athens, 30606, GA, USA
| | - Tal Marshanski
- Department of Cell Research and Immunology, The George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, 69978, Israel
| | - Christoffer Norn
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot, 76100, Israel
| | - Hai Yu
- Department of Chemistry, University of California-Davis, Davis, CA, USA
| | - John N Glushka
- Complex Carbohydrate Research Center, University of Georgia, Athens, 30606, GA, USA
| | - Sarel J Fleishman
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot, 76100, Israel
| | - Xi Chen
- Department of Chemistry, University of California-Davis, Davis, CA, USA
| | - Robert J Woods
- Complex Carbohydrate Research Center, University of Georgia, Athens, 30606, GA, USA.
| | - Vered Padler-Karavani
- Department of Cell Research and Immunology, The George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, 69978, Israel.
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41
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Hunter CD, Guo T, Daskhan G, Richards MR, Cairo CW. Synthetic Strategies for Modified Glycosphingolipids and Their Design as Probes. Chem Rev 2018; 118:8188-8241. [DOI: 10.1021/acs.chemrev.8b00070] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Affiliation(s)
- Carmanah D. Hunter
- Alberta Glycomics Centre, Department of Chemistry, University of Alberta, Edmonton, Alberta T6G 2G2, Canada
| | - Tianlin Guo
- Alberta Glycomics Centre, Department of Chemistry, University of Alberta, Edmonton, Alberta T6G 2G2, Canada
| | - Gour Daskhan
- Alberta Glycomics Centre, Department of Chemistry, University of Alberta, Edmonton, Alberta T6G 2G2, Canada
| | - Michele R. Richards
- Alberta Glycomics Centre, Department of Chemistry, University of Alberta, Edmonton, Alberta T6G 2G2, Canada
| | - Christopher W. Cairo
- Alberta Glycomics Centre, Department of Chemistry, University of Alberta, Edmonton, Alberta T6G 2G2, Canada
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42
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Cheng K, Zhou Y, Neelamegham S. DrawGlycan-SNFG: a robust tool to render glycans and glycopeptides with fragmentation information. Glycobiology 2018; 27:200-205. [PMID: 28177454 DOI: 10.1093/glycob/cww115] [Citation(s) in RCA: 50] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2016] [Revised: 11/09/2016] [Accepted: 11/11/2016] [Indexed: 11/13/2022] Open
Abstract
Glycan or carbohydrate structures can be pictorially represented using symbolic nomenclatures. The symbol nomenclature for glycans (SNFG) contains 67 different monosaccharides represented using various colors and geometric shapes. A simple tool to convert International Union of Pure and Applied Chemistry (IUPAC) format text to SNFG will be useful for sketching glycans and glycopeptides. Such code can also enable the development of more sophisticated applications, where the visual representation of carbohydrate structures is necessary. To address this need, the current manuscript describes DrawGlycan-SNFG, a freely available, platform-independent, open-source tool. It allows: i. the display of glycans and glycopeptides from IUPAC-condensed text inputs and ii. the depiction of glycan and glycopeptide fragments. The online version of this program is provided with a user-friendly web interface at www.virtualglycome.org/DrawGlycan. Downloadable, stand-alone GUI (Graphical User Interface) version and the program source code are also available from this repository. DrawGlycan-SNFG will be useful for experimentalists looking for a ready to use, simple program for sketching carbohydrates and for software developers interested in incorporating SNFG into their program suite.
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Affiliation(s)
- Kai Cheng
- Department of Chemical and Biological Engineering, Clinical and Translational Research Center, University at Buffalo, The State University of New York, Buffalo, NY 14260, USA
| | - Yusen Zhou
- Department of Chemical and Biological Engineering, Clinical and Translational Research Center, University at Buffalo, The State University of New York, Buffalo, NY 14260, USA
| | - Sriram Neelamegham
- Department of Chemical and Biological Engineering, Clinical and Translational Research Center, University at Buffalo, The State University of New York, Buffalo, NY 14260, USA
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43
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Zhao Y, Yang JY, Thieker DF, Xu Y, Zong C, Boons GJ, Liu J, Woods RJ, Moremen KW, Amster IJ. A Traveling Wave Ion Mobility Spectrometry (TWIMS) Study of the Robo1-Heparan Sulfate Interaction. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2018; 29:1153-1165. [PMID: 29520710 PMCID: PMC6004239 DOI: 10.1007/s13361-018-1903-4] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/01/2017] [Revised: 01/14/2018] [Accepted: 01/14/2018] [Indexed: 06/10/2023]
Abstract
Roundabout 1 (Robo1) interacts with its receptor Slit to regulate axon guidance, axon branching, and dendritic development in the nervous system and to regulate morphogenesis and many cell functions in the nonneuronal tissues. This interaction is known to be critically regulated by heparan sulfate (HS). Previous studies suggest that HS is required to promote the binding of Robo1 to Slit to form the minimal signaling complex, but the molecular details and the structural requirements of HS for this interaction are still unclear. Here, we describe the application of traveling wave ion mobility spectrometry (TWIMS) to study the conformational details of the Robo1-HS interaction. The results suggest that Robo1 exists in two conformations that differ by their compactness and capability to interact with HS. The results also suggest that the highly flexible interdomain hinge region connecting the Ig1 and Ig2 domains of Robo1 plays an important functional role in promoting the Robo1-Slit interaction. Moreover, variations in the sulfation pattern and size of HS were found to affect its binding affinity and selectivity to interact with different conformations of Robo1. Both MS measurements and CIU experiments show that the Robo1-HS interaction requires the presence of a specific size and pattern of modification of HS. Furthermore, the effect of N-glycosylation on the conformation of Robo1 and its binding modes with HS is reported. Graphical Abstract ᅟ.
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Affiliation(s)
- Yuejie Zhao
- Department of Chemistry, University of Georgia, Athens, GA, 30602, USA
| | - Jeong Yeh Yang
- Complex Carbohydrate Research Center, University of Georgia, Athens, GA, 30602, USA
| | - David F Thieker
- Complex Carbohydrate Research Center, University of Georgia, Athens, GA, 30602, USA
| | - Yongmei Xu
- Eshelman School of Pharmacy, Division of Chemical Biology & Medicinal Chemistry, University of North Carolina, Chapel Hill, NC, USA
| | - Chengli Zong
- Complex Carbohydrate Research Center, University of Georgia, Athens, GA, 30602, USA
| | - Geert-Jan Boons
- Complex Carbohydrate Research Center, University of Georgia, Athens, GA, 30602, USA
| | - Jian Liu
- Eshelman School of Pharmacy, Division of Chemical Biology & Medicinal Chemistry, University of North Carolina, Chapel Hill, NC, USA
| | - Robert J Woods
- Complex Carbohydrate Research Center, University of Georgia, Athens, GA, 30602, USA
| | - Kelley W Moremen
- Complex Carbohydrate Research Center, University of Georgia, Athens, GA, 30602, USA
| | - I Jonathan Amster
- Department of Chemistry, University of Georgia, Athens, GA, 30602, USA.
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44
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Makeneni S, Thieker DF, Woods RJ. Applying Pose Clustering and MD Simulations To Eliminate False Positives in Molecular Docking. J Chem Inf Model 2018; 58:605-614. [PMID: 29431438 PMCID: PMC6067002 DOI: 10.1021/acs.jcim.7b00588] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
In this work, we developed a computational protocol that employs multiple molecular docking experiments, followed by pose clustering, molecular dynamic simulations (10 ns), and energy rescoring to produce reliable 3D models of antibody-carbohydrate complexes. The protocol was applied to 10 antibody-carbohydrate co-complexes and three unliganded (apo) antibodies. Pose clustering significantly reduced the number of potential poses. For each system, 15 or fewer clusters out of 100 initial poses were generated and chosen for further analysis. Molecular dynamics (MD) simulations allowed the docked poses to either converge or disperse, and rescoring increased the likelihood that the best-ranked pose was an acceptable pose. This approach is amenable to automation and can be a valuable aid in determining the structure of antibody-carbohydrate complexes provided there is no major side chain rearrangement or backbone conformational change in the H3 loop of the CDR regions. Further, the basic protocol of docking a small ligand to a known binding site, clustering the results, and performing MD with a suitable force field is applicable to any protein ligand system.
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Affiliation(s)
| | - David F. Thieker
- Complex Carbohydrate Research Center, University of Georgia, 315 Riverbend Road, Athens, Georgia 30602, United States
| | - Robert J. Woods
- Complex Carbohydrate Research Center, University of Georgia, 315 Riverbend Road, Athens, Georgia 30602, United States
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45
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Sheikh MO, Thieker D, Chalmers G, Schafer CM, Ishihara M, Azadi P, Woods RJ, Glushka JN, Bendiak B, Prestegard JH, West CM. O 2 sensing-associated glycosylation exposes the F-box-combining site of the Dictyostelium Skp1 subunit in E3 ubiquitin ligases. J Biol Chem 2017; 292:18897-18915. [PMID: 28928219 PMCID: PMC5704474 DOI: 10.1074/jbc.m117.809160] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2017] [Revised: 09/12/2017] [Indexed: 11/06/2022] Open
Abstract
Skp1 is a conserved protein linking cullin-1 to F-box proteins in SCF (Skp1/Cullin-1/F-box protein) E3 ubiquitin ligases, which modify protein substrates with polyubiquitin chains that typically target them for 26S proteasome-mediated degradation. In Dictyostelium (a social amoeba), Toxoplasma gondii (the agent for human toxoplasmosis), and other protists, Skp1 is regulated by a unique pentasaccharide attached to hydroxylated Pro-143 within its C-terminal F-box-binding domain. Prolyl hydroxylation of Skp1 contributes to O2-dependent Dictyostelium development, but full glycosylation at that position is required for optimal O2 sensing. Previous studies have shown that the glycan promotes organization of the F-box-binding region in Skp1 and aids in Skp1's association with F-box proteins. Here, NMR and MS approaches were used to determine the glycan structure, and then a combination of NMR and molecular dynamics simulations were employed to characterize the impact of the glycan on the conformation and motions of the intrinsically flexible F-box-binding domain of Skp1. Molecular dynamics trajectories of glycosylated Skp1 whose calculated monosaccharide relaxation kinetics and rotational correlation times agreed with the NMR data indicated that the glycan interacts with the loop connecting two α-helices of the F-box-combining site. In these trajectories, the helices separated from one another to create a more accessible and dynamic F-box interface. These results offer an unprecedented view of how a glycan modification influences a disordered region of a full-length protein. The increased sampling of an open Skp1 conformation can explain how glycosylation enhances interactions with F-box proteins in cells.
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Affiliation(s)
- M Osman Sheikh
- From the Department of Biochemistry and Molecular Biology
- the Complex Carbohydrate Research Center, and
- the Department of Biochemistry and Molecular Biology, Oklahoma Center for Medical Glycobiology, University of Oklahoma Health Sciences Center, Oklahoma City, Oklahoma 73104, and
| | | | - Gordon Chalmers
- the Complex Carbohydrate Research Center, and
- the Department of Computer Science, University of Georgia, Athens, Georgia 30602
| | - Christopher M Schafer
- the Department of Biochemistry and Molecular Biology, Oklahoma Center for Medical Glycobiology, University of Oklahoma Health Sciences Center, Oklahoma City, Oklahoma 73104, and
| | | | | | - Robert J Woods
- From the Department of Biochemistry and Molecular Biology
- the Complex Carbohydrate Research Center, and
| | | | - Brad Bendiak
- the Department of Cell and Developmental Biology, School of Medicine, University of Colorado Anschutz Medical Campus, Aurora, Colorado 80045
| | - James H Prestegard
- From the Department of Biochemistry and Molecular Biology
- the Complex Carbohydrate Research Center, and
| | - Christopher M West
- From the Department of Biochemistry and Molecular Biology,
- the Department of Biochemistry and Molecular Biology, Oklahoma Center for Medical Glycobiology, University of Oklahoma Health Sciences Center, Oklahoma City, Oklahoma 73104, and
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Ji Y, White YJ, Hadden JA, Grant OC, Woods RJ. New insights into influenza A specificity: an evolution of paradigms. Curr Opin Struct Biol 2017; 44:219-231. [PMID: 28675835 DOI: 10.1016/j.sbi.2017.06.001] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2017] [Revised: 05/29/2017] [Accepted: 06/02/2017] [Indexed: 02/05/2023]
Abstract
Understanding the molecular origin of influenza receptor specificity is complicated by the paucity of quantitative affinity measurements, and the qualitative and variable nature of glycan array data. Further obstacles arise from the varied impact of viral glycosylation and the relatively narrow spectrum of biologically relevant receptors present on glycan arrays. A survey of receptor conformational properties is presented, leading to the conclusion that conformational entropy plays a key role in defining specificity, as does the newly reported ability of biantennary receptors that terminate in Siaα2-6Gal sequences to form bidentate interactions to two binding sites in a hemagglutinin trimer. Bidentate binding provides a functional explanation for the observation that Siaα2-6 receptors adopt an open-umbrella topology when bound to hemagglutinins from human-infective viruses, and calls for a reassessment of virus avidity and tissue tropism.
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Affiliation(s)
- Ye Ji
- Complex Carbohydrate Research Center, University of Georgia, 315 Riverbend Rd, Athens, GA 30602, United States
| | - Yohanna Jb White
- Complex Carbohydrate Research Center, University of Georgia, 315 Riverbend Rd, Athens, GA 30602, United States
| | - Jodi A Hadden
- Complex Carbohydrate Research Center, University of Georgia, 315 Riverbend Rd, Athens, GA 30602, United States
| | - Oliver C Grant
- Complex Carbohydrate Research Center, University of Georgia, 315 Riverbend Rd, Athens, GA 30602, United States
| | - Robert J Woods
- Complex Carbohydrate Research Center, University of Georgia, 315 Riverbend Rd, Athens, GA 30602, United States.
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47
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Yu J, Grant OC, Pett C, Strahl S, Stahl S, Woods RJ, Westerlind U. Induction of Antibodies Directed Against Branched Core O-Mannosyl Glycopeptides-Selectivity Complimentary to the ConA Lectin. Chemistry 2017; 23:3466-3473. [PMID: 28079948 PMCID: PMC5548291 DOI: 10.1002/chem.201605627] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2016] [Indexed: 01/31/2023]
Abstract
Mammalian protein O-mannosylation, initiated by attachment of α-mannopyranose to Ser or Thr residues, comprise a group of post-translational modifications (PTMs) involved in muscle and brain development. Recent advances in glycoproteomics methodology and the "SimpleCell" strategy have enabled rapid identification of glycoproteins and specific glycosylation sites. Despite the enormous progress made, the biological impact of the mammalian O-mannosyl glycoproteome remains largely unknown to date. Tools are still needed to investigate the structure, role, and abundance of O-mannosyl glycans. Although O-mannosyl branching has been shown to be of relevance in integrin-dependent cell migration, and also plays a role in demyelinating diseases, such as multiple sclerosis, a broader understanding of the biological roles of branched O-mannosyl glycans is lacking in part due to the paucity of detection tools. In this work, a glycopeptide vaccine construct was synthesized and used to generate antibodies against branched O-mannosyl glycans. Glycopeptide microarray screening revealed high selectivity of the induced antibodies for branched glycan core structures presented on different peptide backbones, with no cross-reactivity observed with related linear glycans. For comparison, microarray screening of the mannose-binding lectin concanavalin A (ConA), which is commonly used in glycoproteomics workflows to enrich tryptic O-mannosyl peptides, showed that the ConA lectin did not recognize branched O-mannosyl glycans. The binding preference of ConA for short linear O-mannosyl glycans was rationalized in terms of molecular structure using crystallographic data augmented by molecular modeling. The contrast between the ConA binding specificity and that of the new antibodies indicates a novel role for the antibodies in studies of protein O-mannosylation.
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Affiliation(s)
- Jin Yu
- Gesellschaft zur Förderung der Analytischen Wissenschaften e.V., ISAS-Leibniz Institute for Analytical Sciences, Otto-Hahn-Str. 6b, 44227, Dortmund, Germany
| | - Oliver C Grant
- Complex Carbohydrate Research Center, University of Georgia, 315 Riverbend Rd, Athens, GA, 30602, USA
| | - Christian Pett
- Gesellschaft zur Förderung der Analytischen Wissenschaften e.V., ISAS-Leibniz Institute for Analytical Sciences, Otto-Hahn-Str. 6b, 44227, Dortmund, Germany
| | | | - Sabine Stahl
- Centre for Organismal Studies (COS), Cell Chemistry, Heidelberg University, Im Neuenheimer Feld 360, 69120, Heidelberg, Germany
| | - Robert J Woods
- Complex Carbohydrate Research Center, University of Georgia, 315 Riverbend Rd, Athens, GA, 30602, USA
| | - Ulrika Westerlind
- Gesellschaft zur Förderung der Analytischen Wissenschaften e.V., ISAS-Leibniz Institute for Analytical Sciences, Otto-Hahn-Str. 6b, 44227, Dortmund, Germany
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48
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Li X, Grant OC, Ito K, Wallace A, Wang S, Zhao P, Wells L, Lu S, Woods RJ, Sharp JS. Structural Analysis of the Glycosylated Intact HIV-1 gp120-b12 Antibody Complex Using Hydroxyl Radical Protein Footprinting. Biochemistry 2017; 56:957-970. [PMID: 28102671 PMCID: PMC5319886 DOI: 10.1021/acs.biochem.6b00888] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
![]()
Glycoprotein gp120
is a surface antigen and virulence factor of
human immunodeficiency virus 1. Broadly neutralizing antibodies (bNAbs)
that react to gp120 from a variety of HIV isolates offer hope for
the development of broadly effective immunogens for vaccination purposes,
if the interactions between gp120 and bNAbs can be understood. From
a structural perspective, gp120 is a particularly difficult system
because of its size, the presence of multiple flexible regions, and
the large amount of glycosylation, all of which are important in gp120–bNAb
interactions. Here, the interaction of full-length, glycosylated gp120
with bNAb b12 is probed using high-resolution hydroxyl radical protein
footprinting (HR-HRPF) by fast photochemical oxidation of proteins.
HR-HRPF allows for the measurement of changes in the average solvent
accessible surface area of multiple amino acids without the need for
measures that might alter the protein conformation, such as mutagenesis.
HR-HRPF of the gp120–b12 complex coupled with computational
modeling shows a novel extensive interaction of the V1/V2 domain,
probably with the light chain of b12. Our data also reveal HR-HRPF
protection in the C3 domain caused by interaction of the N330 glycan
with the b12 light chain. In addition to providing information about
the interactions of full-length, glycosylated gp120 with b12, this
work serves as a template for the structural interrogation of full-length
glycosylated gp120 with other bNAbs to better characterize the interactions
that drive the broad specificity of the bNAb.
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Affiliation(s)
- Xiaoyan Li
- Complex Carbohydrate Research Center, University of Georgia , Athens, Georgia 30602, United States
| | - Oliver C Grant
- Complex Carbohydrate Research Center, University of Georgia , Athens, Georgia 30602, United States
| | - Keigo Ito
- Complex Carbohydrate Research Center, University of Georgia , Athens, Georgia 30602, United States
| | - Aaron Wallace
- Department of Medicine, University of Massachusetts Medical School , Worcester, Massachusetts 01605, United States
| | - Shixia Wang
- Department of Medicine, University of Massachusetts Medical School , Worcester, Massachusetts 01605, United States
| | - Peng Zhao
- Complex Carbohydrate Research Center, University of Georgia , Athens, Georgia 30602, United States
| | - Lance Wells
- Complex Carbohydrate Research Center, University of Georgia , Athens, Georgia 30602, United States
| | - Shan Lu
- Department of Medicine, University of Massachusetts Medical School , Worcester, Massachusetts 01605, United States
| | - Robert J Woods
- Complex Carbohydrate Research Center, University of Georgia , Athens, Georgia 30602, United States
| | - Joshua S Sharp
- Department of BioMolecular Sciences, University of Mississippi , University, Mississippi 38677, United States
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49
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Substrate recognition and catalysis by GH47 α-mannosidases involved in Asn-linked glycan maturation in the mammalian secretory pathway. Proc Natl Acad Sci U S A 2016; 113:E7890-E7899. [PMID: 27856750 DOI: 10.1073/pnas.1611213113] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Maturation of Asn-linked oligosaccharides in the eukaryotic secretory pathway requires the trimming of nascent glycan chains to remove all glucose and several mannose residues before extension into complex-type structures on the cell surface and secreted glycoproteins. Multiple glycoside hydrolase family 47 (GH47) α-mannosidases, including endoplasmic reticulum (ER) α-mannosidase I (ERManI) and Golgi α-mannosidase IA (GMIA), are responsible for cleavage of terminal α1,2-linked mannose residues to produce uniquely trimmed oligomannose isomers that are necessary for ER glycoprotein quality control and glycan maturation. ERManI and GMIA have similar catalytic domain structures, but each enzyme cleaves distinct residues from tribranched oligomannose glycan substrates. The structural basis for branch-specific cleavage by ERManI and GMIA was explored by replacing an essential enzyme-bound Ca2+ ion with a lanthanum (La3+) ion. This ion swap led to enzyme inactivation while retaining high-affinity substrate interactions. Cocrystallization of La3+-bound enzymes with Man9GlcNAc2 substrate analogs revealed enzyme-substrate complexes with distinct modes of glycan branch insertion into the respective enzyme active-site clefts. Both enzymes had glycan interactions that extended across the entire glycan structure, but each enzyme engaged a different glycan branch and used different sets of glycan interactions. Additional mutagenesis and time-course studies of glycan cleavage probed the structural basis of enzyme specificity. The results provide insights into the enzyme catalytic mechanisms and reveal structural snapshots of the sequential glycan cleavage events. The data also indicate that full steric access to glycan substrates determines the efficiency of mannose-trimming reactions that control the conversion to complex-type structures in mammalian cells.
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