Rapid simulation of glycoprotein structures by grafting and steric exclusion of glycan conformer libraries

Cell, Journal Year: 2024, Volume and Issue: 187(5), P. 1296 - 1311.e26

Published: Feb. 1, 2024

Most membrane proteins are modified by covalent addition of complex sugars through N- and O-glycosylation. Unlike proteins, glycans do not typically adopt specific secondary structures remain very mobile, shielding potentially large fractions protein surface. High glycan conformational freedom hinders complete structural elucidation glycoproteins. Computer simulations may be used to model glycosylated but require hundreds thousands computing hours on supercomputers, thus limiting routine use. Here, we describe GlycoSHIELD, a reductionist method that can implemented personal computers graft realistic ensembles conformers onto static in minutes. Using molecular dynamics simulation, small-angle X-ray scattering, cryoelectron microscopy, mass spectrometry, show this open-access toolkit provides enhanced models glycoprotein structures. Focusing N-cadherin, human coronavirus spike gamma-aminobutyric acid receptors, GlycoSHIELD shed light the impact conformation activity

Language: Английский

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Site specific N- and O-glycosylation mapping of the spike proteins of SARS-CoV-2 variants of concern

Scientific Reports, Journal Year: 2023, Volume and Issue: 13(1)

Published: June 21, 2023

The glycosylation on the spike (S) protein of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), virus that causes COVID-19, modulates viral infection by altering conformational dynamics, receptor interaction and host immune responses. Several variants concern (VOCs) SARS-CoV-2 have evolved during pandemic, crucial mutations S led to increased transmissibility escape. In this study, we compare site-specific overall glycomic profiles wild type Wuhan-Hu-1 strain (WT) five VOCs SARS-CoV-2: Alpha, Beta, Gamma, Delta Omicron. Interestingly, both N- O-glycosylation sites are highly conserved among mutant variants, particularly at receptor-binding domain (RBD). conservation is noteworthy, as over million sequences been reported with various amino acid mutations. Our detailed profiling each individual across revealed intriguing possible association pattern their previously infectivity. While conserved, observed changes in profile variants. newly emerged which showed higher resistance neutralizing antibodies vaccines, displayed a decrease abundance complex-type glycans fucosylation sialylation an increase oligomannose-type sites. Among significant glycan were N-terminal RBD protein, Omicron showing highest deviation. happens sequentially from Alpha through Delta. does not contain more compared but WT other VOCs. lower occupancy comparison WT. study proteins may help understand how trick system. also highlights has O- most successful even after undergoing extensive mutations, suggesting correlation between infectivity/ glycosylation.

Language: Английский

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Water–glycan interactions drive the SARS-CoV-2 spike dynamics: insights into glycan-gate control and camouflage mechanisms

Chemical Science, Journal Year: 2024, Volume and Issue: 15(35), P. 14177 - 14187

Published: Jan. 1, 2024

To develop therapeutic strategies against COVID-19, we introduce a high-resolution all-atom polarizable model capturing many-body effects of protein, glycan, solvent, and membrane components in SARS-CoV-2 spike protein open closed states. Employing μs-long molecular dynamics simulations powered by high-performance cloud-computing unsupervised density-driven adaptive sampling, investigated the differences bulk-solvent-glycan protein-solvent-glycan interfaces between these We unraveled sophisticated solvent-glycan polarization interaction network involving N165/N343 glycan-gate patterns that provide structural support for state identified key water molecules could potentially be targeted to destabilize this configuration. In state, reduced solvent diminishes overall dipoles, yet internal interactions reorganized sugar coat stabilize state. Despite variations, our glycan-solvent accessibility analysis reveals glycan shield capability conserve constant with effectively camouflaging virus from immune detection both The presented insights advance comprehension viral pathogenesis at an atomic level, offering potential combat COVID-19.

Language: Английский

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Restoring Protein Glycosylation with GlycoShape

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2023, Volume and Issue: unknown

Published: Dec. 11, 2023

Abstract During the past few years, we have been witnessing a revolution in structural biology. Leveraging on technological and computational advances, scientists can now resolve biomolecular structures at atomistic level of detail by cryogenic electron microscopy (cryo-EM) predict 3D from sequence alone machine learning (ML). One technique often supports other to provide view atoms molecules required capture function molecular machines. An example extraordinary impact these advances scientific discovery public health is given how information supported rapid development COVID-19 vaccines based SARS-CoV-2 spike (S) glycoprotein. Yet, none new technologies details dense coat glycans covering S, which responsible for its natural, biologically active structure ultimately viral evasion. Indeed, glycosylation, most abundant post-translational modification proteins, largely invisible through experimental biology turn it cannot be reproduced ML, because lack data learn from. Molecular simulations high-performance computing (HPC) fill this crucial gap, yet resources, users’ skills long timescales involved limit applications modelling single study cases. To broaden access glycans, here introduce GlycoShape ( https://glycoshape.org ) an open (OA) glycan database toolbox designed restore glycoproteins their native functional form supplementing available proteins repositories, such as RCSB PDB www.rcsb.org AlphaFold Protein Structure Database https://alphafold.ebi.ac.uk/ ), with missing derived over 1 ms cumulative sampling dynamics (MD) simulations. The Glycan (GDB) currently counts 435 unique principally human glycome additional structures, fragments, epitopes eukaryotic prokaryotic organisms. GDB feeds into Re-Glyco, bespoke algorithm rapidly natural glycosylation protein N- occupancy, where unknown. Ultimately, integration OA databases step-change discovery, characterization biomolecules, all way down pharmacological drug discovery.

Language: Английский

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Restoring protein glycosylation with GlycoShape

Nature Methods, Journal Year: 2024, Volume and Issue: 21(11), P. 2117 - 2127

Published: Oct. 14, 2024

Abstract Despite ground-breaking innovations in experimental structural biology and protein structure prediction techniques, capturing the of glycans that functionalize proteins remains a challenge. Here we introduce GlycoShape ( https://glycoshape.org ), an open-access glycan database toolbox designed to restore glycoproteins their native functional form seconds. The counts over 500 unique so far, covering human glycome augmented by elements from wide range organisms, obtained 1 ms cumulative sampling molecular dynamics simulations. These structures can be linked with robust algorithm named Re-Glyco, directly compatible data repositories, such as Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB) AlphaFold Structure Database, or own. quality, performance broad applicability is demonstrated its ability predict N-glycosylation occupancy, scoring 93% agreement experiment, based on screening all PDB corresponding glycoproteomics profile, total 4,259 N - glycosylation sequons.

Language: Английский

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Analysis of the N-glycosylation profiles of the spike proteins from the Alpha, Beta, Gamma, and Delta variants of SARS-CoV-2

Analytical and Bioanalytical Chemistry, Journal Year: 2023, Volume and Issue: 415(19), P. 4779 - 4793

Published: June 24, 2023

N-Glycosylation plays an important role in the structure and function of membrane secreted proteins. Viral proteins used cell entry are often extensively glycosylated to assist protein folding, provide stability, shield virus from immune recognition by its host (described as a "glycan shield"). The SARS-CoV-2 spike (S) is prime example, having 22 potential sites N-glycosylation per protomer, predicted primary sequence. In this report, we conducted mass spectrometric analysis profiles recombinant derived four common variants classified Variant Concern, including Alpha, Beta, Gamma, Delta along with D614G variant control. Our data reveal that amino acid substitutions deletions between impact abundance type glycans on glycosylation protein. Some sequons S show differences distribution glycan forms. comparison our previously reported site-specific S-D614G ancestral protein, types later showed high similarity content S-D614G. Additionally, applied multiple digestion methods each sample, confirmed results for individual different experiment conditions improve identification quantification glycopeptides. Detailed wide variety provides useful information toward understanding viral development effective vaccines therapeutics.

Language: Английский

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Influence of glycosylation on the immunogenicity and antigenicity of viral immunogens

Biotechnology Advances, Journal Year: 2023, Volume and Issue: 70, P. 108283 - 108283

Published: Nov. 14, 2023

A key aspect of successful viral vaccine design is the elicitation neutralizing antibodies targeting attachment and fusion glycoproteins that embellish particles. This observation has catalyzed development numerous glycoprotein mimetics as vaccines. Glycans can dominate surface such, glycome influence antigenicity immunogenicity a candidate vaccine. In one extreme, glycans form an integral part epitopes targeted by are therefore considered to be important feature immunogens within immunization regimen. other existence peptide bacterially expressed protein vaccines shows glycosylation dispensable in some cases. However, native-like indicate folding presence conformational epitopes. Furthermore, going beyond native glycan mimicry, either occupancy sites or processing state, may offer opportunities for enhancing associated protection elicited immunogen. Here, we review determinants how recombinant recapitulate these signatures across range enveloped viruses, including HIV-1, Ebola virus, SARS-CoV-2, Influenza Lassa virus. The emerging understanding immunogen its control will help guide future both protein- nucleic acid-based technologies.

Language: Английский

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Evolving spike-proteinN-glycosylation in SARS-CoV-2 variants

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2023, Volume and Issue: unknown

Published: May 9, 2023

Since >3 years, SARS-CoV-2 has plunged humans into a colossal pandemic. Henceforth, multiple waves of infection have swept through the human population, led by variants that were able to partially evade acquired immunity. The co-evolution with immunity provides an excellent opportunity study interaction between viral pathogens and their hosts. heavily

Language: Английский

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Analysis of N‐ and O‐linked site‐specific glycosylation by ion mobility mass spectrometry: State of the art and future directions

PROTEOMICS, Journal Year: 2024, Volume and Issue: 24(12-13)

Published: Jan. 3, 2024

Abstract Glycosylation, the major post‐translational modification of proteins, significantly increases diversity proteoforms. Glycans are involved in a variety pivotal structural and functional roles changes glycosylation profoundly connected to progression numerous diseases. Mass spectrometry (MS) has emerged as gold standard for glycan glycopeptide analysis because its high sensitivity wealth fragmentation information that can be obtained. Various separation techniques have been employed resolve isomers at front end MS. However, differentiating structures isobaric isomeric glycopeptides constitutes challenge MS‐based characterization. Many reports described use various ion mobility–mass (IM–MS) glycomic analyses. Nevertheless, very few studies focused on N ‐ O ‐linked site‐specific glycopeptidomic analysis. Unlike glycomics, glycoproteomics presents multitude inherent challenges microheterogeneity, which further exacerbated by lack dedicated bioinformatics tools. In this review, we cover recent advances made towards growing field using IM–MS with specific emphasis MS capabilities resolving peptidoglycan structures. Furthermore, discuss commonly used software supports data glycopeptides.

Language: Английский

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Combinatorial Approach with Mass Spectrometry and Lectin Microarray Dissected Site-Specific Glycostem and Glycoleaf Features of the Virion-Derived Spike Protein of Ancestral and γ Variant SARS-CoV-2 Strains

Journal of Proteome Research, Journal Year: 2024, Volume and Issue: 23(4), P. 1408 - 1419

Published: March 27, 2024

The coronavirus disease (COVID-19) pandemic, caused by severe acute respiratory syndrome 2 (SARS-CoV-2), has impacted public health globally. As the glycosylation of viral envelope glycoproteins is strongly associated with their immunogenicity, intensive studies have been conducted on glycans glycoprotein SARS-CoV-2, spike (S) protein. Here, we glycoproteomic analyses SARS-CoV-2 S protein ancestral and γ-variant strains using a combinatorial approach two different technologies: mass spectrometry (MS) lectin microarrays (LMA). Our unique MS1-based technique, Glyco-RIDGE, in addition to MS2-based Byonic search, identified 1448 (ancestral strain) 1785 (γ-variant site-specific glycan compositions, respectively. Asparagine at amino acid position 20 (N20) mainly glycosylated within successive potential sites, N17 N20, protein; however, found low-frequency N17. novel approaches, glycostem mapping glycoleaf scoring, also illustrate moderately branched/extended, highly fucosylated, less sialylated natures glycoforms proteins. Subsequent LMA analysis emphasized end-capping Lewis fucoses, which complemented features. These results high-resolution features protein, contributing vaccine design understanding synthesis.

Language: Английский

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