Unravelling the Glycan Code: Molecular Dynamics and Quantum Chemistry Reveal How O-Glycan Functional Groups Govern OgpA Selectivity in Mucin Degradation by Akkermansia muciniphila

Khavani, Mohammad; Mehranfar, Aliyeh; Mofrad, Mohammad K.

doi:10.1111/1751-7915.70091

Unravelling the Glycan Code: Molecular Dynamics and Quantum Chemistry Reveal How O-Glycan Functional Groups Govern OgpA Selectivity in Mucin Degradation by Akkermansia muciniphila

Journal Article · Thu Apr 03 00:00:00 EDT 2025 · Microbial Biotechnology (Online)

DOI:https://doi.org/10.1111/1751-7915.70091· OSTI ID:2565634

Khavani, Mohammad ^[1]; Mehranfar, Aliyeh ^[1]; ^[2]

University of California, Berkeley, CA (United States)
University of California, Berkeley, CA (United States); Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States)

Mucins, heavily O-glycosylated glycoproteins, are a key component of mucus, and certain gut microbiota, including Akkermansia muciniphila, can utilise mucin glycans as a carbon source. Akkermansia muciniphila produces the O-glycopeptidase enzyme OgpA, which cleaves peptide bonds at the N-terminus of serine (Ser) or threonine (Thr) residues carrying O-glycan substitutions, with selectivity influenced by the O-glycan functional groups. Using molecular dynamics (MD) simulations and quantum chemistry calculations, we explored how different O-glycan groups affect OgpA's selectivity. Our results show that peptides bind to the enzyme via hydrogen bonds, π–π interactions, van der Waals forces and electrostatic interactions, with key residues, including Tyr90, Val138, Gly176, Tyr210 and Glu91, playing important roles. The primary determinant of selectivity is the interaction between the peptide's functional group and the enzyme's binding cavity, while peptide–enzyme interface interactions are secondary. Quantum chemistry calculations reveal that OgpA prefers peptides with a lower electrophilic character. This study provides new insights into mucin degradation by gut microbiota enzymes, advancing our understanding of this critical biological process.

View Accepted Manuscript (DOE)

Research Organization:: Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States)

Sponsoring Organization:: USDOE Office of Science (SC), Basic Energy Sciences (BES)

Grant/Contract Number:: AC02-05CH11231

OSTI ID:: 2565634

Journal Information:: Microbial Biotechnology (Online), Journal Name: Microbial Biotechnology (Online) Journal Issue: 4 Vol. 18; ISSN 1751-7915

Publisher:: WileyCopyright Statement

Country of Publication:: United States

Language:: English

References (60)

GLYCAM06: A generalizable biomolecular force field. Carbohydrates: GLYCAM06 Kirschner, Karl N.; Yongye, Austin B.; Tschampel, Sarah M. Journal of Computational Chemistry, Vol. 29, Issue 4 https://doi.org/10.1002/jcc.20820	journal	September 2007
AutoDock Vina: Improving the speed and accuracy of docking with a new scoring function, efficient optimization, and multithreading Trott, Oleg; Olson, Arthur J. Journal of Computational Chemistry https://doi.org/10.1002/jcc.21334	journal	January 2009
The M06 suite of density functionals for main group thermochemistry, thermochemical kinetics, noncovalent interactions, excited states, and transition elements: two new functionals and systematic testing of four M06-class functionals and 12 other functionals Zhao, Yan; Truhlar, Donald G. Theoretical Chemistry Accounts, Vol. 120, Issue 1-3 https://doi.org/10.1007/s00214-007-0310-x	journal	July 2007
Ab initio study of solvated molecules: a new implementation of the polarizable continuum model Cossi, Maurizio; Barone, Vincenzo; Cammi, Roberto Chemical Physics Letters, Vol. 255, Issue 4-6 https://doi.org/10.1016/0009-2614(96)00349-1	journal	June 1996
Numerical integration of the cartesian equations of motion of a system with constraints: molecular dynamics of n-alkanes Ryckaert, Jean-Paul; Ciccotti, Giovanni; Berendsen, Herman J. C. Journal of Computational Physics, Vol. 23, Issue 3 https://doi.org/10.1016/0021-9991(77)90098-5	journal	March 1977
Interrogating gut bacterial genomes for discovery of novel carbohydrate degrading enzymes Luis, Ana S.; Martens, Eric C. Current Opinion in Chemical Biology, Vol. 47 https://doi.org/10.1016/j.cbpa.2018.09.012	journal	December 2018
A Dietary Fiber-Deprived Gut Microbiota Degrades the Colonic Mucus Barrier and Enhances Pathogen Susceptibility Desai, Mahesh S.; Seekatz, Anna M.; Koropatkin, Nicole M. Cell, Vol. 167, Issue 5 https://doi.org/10.1016/j.cell.2016.10.043	journal	November 2016
IL-22 promotes the formation of a MUC17 glycocalyx barrier in the postnatal small intestine during weaning Layunta, Elena; Jäverfelt, Sofia; Dolan, Brendan Cell Reports, Vol. 34, Issue 7 https://doi.org/10.1016/j.celrep.2021.108757	journal	February 2021
Mucosal Glycan Foraging Enhances Fitness and Transmission of a Saccharolytic Human Gut Bacterial Symbiont Martens, Eric C.; Chiang, Herbert C.; Gordon, Jeffrey I. Cell Host & Microbe, Vol. 4, Issue 5 https://doi.org/10.1016/j.chom.2008.09.007	journal	November 2008
Bifidobacteria or Fiber Protects against Diet-Induced Microbiota-Mediated Colonic Mucus Deterioration Schroeder, Bjoern O.; Birchenough, George M. H.; Ståhlman, Marcus Cell Host & Microbe, Vol. 23, Issue 1 https://doi.org/10.1016/j.chom.2017.11.004	journal	January 2018
A previously uncharacterized O-glycopeptidase from Akkermansia muciniphila requires the Tn-antigen for cleavage of the peptide bond Medley, Brendon J.; Leclaire, Leif; Thompson, Nicole Journal of Biological Chemistry, Vol. 298, Issue 10 https://doi.org/10.1016/j.jbc.2022.102439	journal	October 2022
A combined MD/QM study on the sensing mechanism of Pb2+ by glutathione functionalized gold nanoparticles Khavani, Mohammad; Izadyar, Mohammad; Housaindokht, Mohammad Reza Journal of Molecular Liquids, Vol. 280 https://doi.org/10.1016/j.molliq.2019.02.034	journal	April 2019
Deciphering Protein O-Glycosylation: Solid-Phase Chemoenzymatic Cleavage and Enrichment Yang, Shuang; Onigman, Philip; Wu, Wells W. Analytical Chemistry, Vol. 90, Issue 13 https://doi.org/10.1021/acs.analchem.8b01834	journal	June 2018
ff14SB: Improving the Accuracy of Protein Side Chain and Backbone Parameters from ff99SB Maier, James A.; Martinez, Carmenza; Kasavajhala, Koushik Journal of Chemical Theory and Computation, Vol. 11, Issue 8 https://doi.org/10.1021/acs.jctc.5b00255	journal	July 2015
Sensing Ability of Hybrid Cyclic Nanopeptides Based on Thiourea Cryptands for Different Ions, A Joint DFT-D3/MD Study Izadyar, Mohammad; Khavani, Mohammad; Housaindokht, Mohammad Reza The Journal of Physical Chemistry A, Vol. 121, Issue 1 https://doi.org/10.1021/acs.jpca.6b09738	journal	January 2017
Free-Energy Landscape of Protein–Ligand Interactions Coupled with Protein Structural Changes Moritsugu, Kei; Terada, Tohru; Kidera, Akinori The Journal of Physical Chemistry B, Vol. 121, Issue 4 https://doi.org/10.1021/acs.jpcb.6b11696	journal	January 2017
MMPBSA.py : An Efficient Program for End-State Free Energy Calculations Miller, Bill R.; McGee, T. Dwight; Swails, Jason M. Journal of Chemical Theory and Computation, Vol. 8, Issue 9 https://doi.org/10.1021/ct300418h	journal	August 2012
Bad Seeds Sprout Perilous Dynamics: Stochastic Thermostat Induced Trajectory Synchronization in Biomolecules Sindhikara, Daniel J.; Kim, Seonah; Voter, Arthur F. Journal of Chemical Theory and Computation, Vol. 5, Issue 6 https://doi.org/10.1021/ct800573m	journal	April 2009
Human gut microbes associated with obesity Ley, Ruth E.; Turnbaugh, Peter J.; Klein, Samuel Nature, Vol. 444, Issue 7122 https://doi.org/10.1038/4441022a	journal	December 2006
Mucolytic Bacteria With Increased Prevalence in IBD Mucosa Augment In Vitro Utilization of Mucin by Other Bacteria Png, Chin Wen; Lindén, Sara K.; Gilshenan, Kristen S. American Journal of Gastroenterology, Vol. 105, Issue 11 https://doi.org/10.1038/ajg.2010.281	journal	January 2010
Mucins in the mucosal barrier to infection Linden, S. K.; Sutton, P.; Karlsson, N. G. Mucosal Immunology, Vol. 1, Issue 3 https://doi.org/10.1038/mi.2008.5	journal	May 2008
New developments in goblet cell mucus secretion and function Birchenough, G. M. H.; Johansson, M. Ev; Gustafsson, J. K. Mucosal Immunology, Vol. 8, Issue 4 https://doi.org/10.1038/mi.2015.32	journal	July 2015
Diet–microbiota interactions as moderators of human metabolism Sonnenburg, Justin L.; Bäckhed, Fredrik Nature, Vol. 535, Issue 7610 https://doi.org/10.1038/nature18846	journal	July 2016
A purified membrane protein from Akkermansia muciniphila or the pasteurized bacterium improves metabolism in obese and diabetic mice Plovier, Hubert; Everard, Amandine; Druart, Céline Nature Medicine, Vol. 23, Issue 1 https://doi.org/10.1038/nm.4236	journal	November 2016
Role of gut microbiota in atherosclerosis Jonsson, Annika Lindskog; Bäckhed, Fredrik Nature Reviews Cardiology, Vol. 14, Issue 2 https://doi.org/10.1038/nrcardio.2016.183	journal	December 2016
The gastrointestinal mucus system in health and disease Johansson, Malin E. V.; Sjövall, Henrik; Hansson, Gunnar C. Nature Reviews Gastroenterology & Hepatology, Vol. 10, Issue 6 https://doi.org/10.1038/nrgastro.2013.35	journal	March 2013
How glycan metabolism shapes the human gut microbiota Koropatkin, Nicole M.; Cameron, Elizabeth A.; Martens, Eric C. Nature Reviews Microbiology, Vol. 10, Issue 5 https://doi.org/10.1038/nrmicro2746	journal	April 2012
Structural basis of mammalian mucin processing by the human gut O-glycopeptidase OgpA from Akkermansia muciniphila Trastoy, Beatriz; Naegeli, Andreas; Anso, Itxaso Nature Communications, Vol. 11, Issue 1 https://doi.org/10.1038/s41467-020-18696-y	journal	September 2020
Structural and mechanistic insights into the cleavage of clustered O-glycan patches-containing glycoproteins by mucinases of the human gut Taleb, Víctor; Liao, Qinghua; Narimatsu, Yoshiki Nature Communications, Vol. 13, Issue 1 https://doi.org/10.1038/s41467-022-32021-9	journal	July 2022
Towards personalized microbial substrates for metabolic health Canfora, Emanuel E.; Blaak, Ellen E. Nature Reviews Endocrinology, Vol. 16, Issue 11 https://doi.org/10.1038/s41574-020-00416-7	journal	September 2020
Intestinal epithelial glycosylation in homeostasis and gut microbiota interactions in IBD Kudelka, Matthew R.; Stowell, Sean R.; Cummings, Richard D. Nature Reviews Gastroenterology & Hepatology, Vol. 17, Issue 10 https://doi.org/10.1038/s41575-020-0331-7	journal	July 2020
Interactions of commensal and pathogenic microorganisms with the intestinal mucosal barrier Martens, Eric C.; Neumann, Mareike; Desai, Mahesh S. Nature Reviews Microbiology, Vol. 16, Issue 8 https://doi.org/10.1038/s41579-018-0036-x	journal	June 2018
Structural diversity and specific distribution of O-glycans in normal human mucins along the intestinal tract Robbe, Catherine; Capon, Calliope; Coddeville, Bernadette Biochemical Journal, Vol. 384, Issue 2 https://doi.org/10.1042/BJ20040605	journal	November 2004
Mucin utilization by gut microbiota: recent advances on characterization of key enzymes Raba, Grete; Luis, Ana S. Essays in Biochemistry, Vol. 67, Issue 3 https://doi.org/10.1042/EBC20220121	journal	April 2023
Synchronization of trajectories in canonical molecular-dynamics simulations: Observation, explanation, and exploitation Uberuaga, Blas P.; Anghel, Marian; Voter, Arthur F. The Journal of Chemical Physics, Vol. 120, Issue 14 https://doi.org/10.1063/1.1667473	journal	April 2004
A consistent and accurate ab initio parametrization of density functional dispersion correction (DFT-D) for the 94 elements H-Pu Grimme, Stefan; Antony, Jens; Ehrlich, Stephan The Journal of Chemical Physics, Vol. 132, Issue 15 https://doi.org/10.1063/1.3382344	journal	April 2010
Comparison of simple potential functions for simulating liquid water Jorgensen, William L.; Chandrasekhar, Jayaraman; Madura, Jeffry D. The Journal of Chemical Physics, Vol. 79, Issue 2 https://doi.org/10.1063/1.445869	journal	July 1983
Density‐functional thermochemistry. I. The effect of the exchange‐only gradient correction Becke, Axel D. The Journal of Chemical Physics, Vol. 96, Issue 3 https://doi.org/10.1063/1.462066	journal	February 1992
Particle mesh Ewald: An N ⋅log( N ) method for Ewald sums in large systems Darden, Tom; York, Darrin; Pedersen, Lee The Journal of Chemical Physics, Vol. 98, Issue 12 https://doi.org/10.1063/1.464397	journal	June 1993
Comparison of some dispersion-corrected and traditional functionals with CCSD(T) and MP2 ab initio methods: Dispersion, induction, and basis set superposition error Roy, Dipankar; Marianski, Mateusz; Maitra, Neepa T. The Journal of Chemical Physics, Vol. 137, Issue 13 https://doi.org/10.1063/1.4755990	journal	October 2012
The inner of the two Muc2 mucin-dependent mucus layers in colon is devoid of bacteria Johansson, M. E. V.; Phillipson, M.; Petersson, J. Proceedings of the National Academy of Sciences, Vol. 105, Issue 39 https://doi.org/10.1073/pnas.0803124105	journal	September 2008
Cross-talk between Akkermansia muciniphila and intestinal epithelium controls diet-induced obesity Everard, A.; Belzer, C.; Geurts, L. Proceedings of the National Academy of Sciences, Vol. 110, Issue 22 https://doi.org/10.1073/pnas.1219451110	journal	May 2013
The N Terminus of the MUC2 Mucin Forms Trimers That Are Held Together within a Trypsin-resistant Core Fragment Godl, Klaus; Johansson, Malin E. V.; Lidell, Martin E. Journal of Biological Chemistry, Vol. 277, Issue 49 https://doi.org/10.1074/jbc.M208483200	journal	October 2002
Increased susceptibility to colitis and colorectal tumors in mice lacking core 3–derived O-glycans An, Guangyu; Wei, Bo; Xia, Baoyun The Journal of Experimental Medicine, Vol. 204, Issue 6 https://doi.org/10.1084/jem.20061929	journal	May 2007
All in the family: the UDP-GalNAc:polypeptide N-acetylgalactosaminyltransferases Ten Hagen, K. G. Glycobiology, Vol. 13, Issue 1 https://doi.org/10.1093/glycob/cwg007	journal	November 2002
Mucin-type O-glycans and their roles in intestinal homeostasis Bergstrom, K. S. B.; Xia, L. Glycobiology, Vol. 23, Issue 9 https://doi.org/10.1093/glycob/cwt045	journal	June 2013
H++ 3.0: automating pK prediction and the preparation of biomolecular structures for atomistic molecular modeling and simulations Anandakrishnan, R.; Aguilar, B.; Onufriev, A. V. Nucleic Acids Research, Vol. 40, Issue W1 https://doi.org/10.1093/nar/gks375	journal	May 2012
Akkermansia muciniphila gen. nov., sp. nov., a human intestinal mucin-degrading bacterium Derrien, M. INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY, Vol. 54, Issue 5 https://doi.org/10.1099/ijs.0.02873-0	journal	September 2004
Cultivating complexity: Advancements in establishing in vitro models for the mucus‐adhering gut microbiota Calvigioni, Marco; Mazzantini, Diletta; Celandroni, Francesco Microbial Biotechnology, Vol. 17, Issue 10 https://doi.org/10.1111/1751-7915.70036	journal	October 2024
Home, sweet home: how mucus accommodates our microbiota Wang, Benjamin X.; Wu, Chloe M.; Ribbeck, Katharina The FEBS Journal, Vol. 288, Issue 6 https://doi.org/10.1111/febs.15504	journal	August 2020
Gut Microbiota from Twins Discordant for Obesity Modulate Metabolism in Mice Ridaura, V. K.; Faith, J. J.; Rey, F. E. Science, Vol. 341, Issue 6150 https://doi.org/10.1126/science.1241214	journal	September 2013
The Mucin Degrader Akkermansia muciniphila Is an Abundant Resident of the Human Intestinal Tract Derrien, M.; Collado, M. C.; Ben-Amor, K. Applied and Environmental Microbiology, Vol. 74, Issue 5 https://doi.org/10.1128/AEM.01226-07	journal	December 2007
Intestinal Integrity and Akkermansia muciniphila, a Mucin-Degrading Member of the Intestinal Microbiota Present in Infants, Adults, and the Elderly Collado, M. C.; Derrien, M.; Isolauri, E. Applied and Environmental Microbiology, Vol. 73, Issue 23 https://doi.org/10.1128/AEM.01477-07	journal	October 2007
Bacteria penetrate the normally impenetrable inner colon mucus layer in both murine colitis models and patients with ulcerative colitis Johansson, Malin E. V.; Gustafsson, Jenny K.; Holmén-Larsson, Jessica Gut, Vol. 63, Issue 2 https://doi.org/10.1136/gutjnl-2012-303207	journal	February 2013
Akkermansia muciniphila and improved metabolic health during a dietary intervention in obesity: relationship with gut microbiome richness and ecology Dao, Maria Carlota; Everard, Amandine; Aron-Wisnewsky, Judith Gut, Vol. 65, Issue 3 https://doi.org/10.1136/gutjnl-2014-308778	journal	June 2015
Mucins and the Microbiome Hansson, Gunnar C. Annual Review of Biochemistry, Vol. 89, Issue 1 https://doi.org/10.1146/annurev-biochem-011520-105053	journal	June 2020
Gastrointestinal expression and partial cDNA cloning of murine Muc2 Van Klinken, B. Jan-Willem; Einerhand, Alexandra W. C.; Duits, Louise A. American Journal of Physiology-Gastrointestinal and Liver Physiology, Vol. 276, Issue 1 https://doi.org/10.1152/ajpgi.1999.276.1.G115	journal	January 1999
Altered Mucus Glycosylation in Core 1 O-Glycan-Deficient Mice Affects Microbiota Composition and Intestinal Architecture Sommer, Felix; Adam, Nina; Johansson, Malin E. V. PLoS ONE, Vol. 9, Issue 1 https://doi.org/10.1371/journal.pone.0085254	journal	January 2014
Mucin glycan foraging in the human gut microbiome Tailford, Louise E.; Crost, Emmanuelle H.; Kavanaugh, Devon Frontiers in Genetics, Vol. 6 https://doi.org/10.3389/fgene.2015.00081	journal	March 2015
Mucins in Intestinal Mucosal Defense and Inflammation: Learning From Clinical and Experimental Studies Grondin, Jensine A.; Kwon, Yun Han; Far, Parsa Mehraban Frontiers in Immunology, Vol. 11 https://doi.org/10.3389/fimmu.2020.02054	journal	September 2020

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37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CHEMISTRY
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Unravelling the Glycan Code: Molecular Dynamics and Quantum Chemistry Reveal How O-Glycan Functional Groups Govern OgpA Selectivity in Mucin Degradation by Akkermansia muciniphila

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