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Cited by 2Protein Structure and DynamicsTuberculosis Research and EpidemiologyLipid Membrane Structure and Behavior

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Coarse-Graining the Recognition of a Glycolipid by the C-Type Lectin Mincle Receptor

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Noriega, Maxime, Corey, Robin A., Haanappel, Evert, Demange, Pascal, Czaplicki, Georges, Atkinson, R. Andrew, Chavent, Matthieu·2024·The Journal of Physical Chemistry B
DOI 10.1021/acs.jpcb.4c03242

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Abstract

Abstract Macrophage inducible Ca 2+ -dependent lectin (Mincle) receptor recognizes Mycobacterium tuberculosis glycolipids to trigger an immune response. This host membrane receptor is thus a key player in the modulation of the immune response to infection by M. tuberculosis , and has emerged as a promising target for the development of new vaccines for tuberculosis. The recent development of the Martini 3 force field for coarse-grained (CG) molecular modeling allow the study of interactions of soluble proteins with small ligands but its use for the study of interactions with lipids remains less explored. Here, we present a refined approach detailing a protocol for modeling such interactions at a CG level using the Martini 3 force field. Using this approach, we studied Mincle and identified critical parameters governing ligand recognition, such as loop flexibility and the regulation of hydrophobic groove formation by calcium ions. In addition, we assessed ligand affinity using free energy perturbation calculations. Our results offer mechanistic insight into the interactions between Mincle and glycolipids, providing a basis for rational design of molecules targeting this type of membrane receptors.

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Metadata

Authors
Noriega, M., Corey, R. A., Haanappel, E., Demange, P., Czaplicki, G., Atkinson, R. A., & Chavent, M.
Affiliations
  • Centre National de la Recherche Scientifique (FR)
  • University of Bristol (GB)
Corresponding author
  • Atkinson, R. Andrew
  • Chavent, Matthieu
ORCID
Venue
The Journal of Physical Chemistry B
Publisher
American Chemical Society (ACS)
Published
2024-10-05
Volume
128
Issue
41
Pages
9935-9946
ISSN
  • 1520-5207 (ISSN-L)
  • 1520-6106
DOI
10.1021/acs.jpcb.4c03242
OpenAlex
W4403154719
Cited by
2
References
6
Citations by year
2025: 2
FWCI
0.27
Type
journal article
Language
en
Open access
Licence
Locations
  • The Journal of Physical Chemistry B (publishedVersion)
  • bioRxiv (Cold Spring Harbor Laboratory) (acceptedVersion, cc-by)
  • PubMed (publishedVersion)
  • Explore Bristol Research (publishedVersion, cc-by)
  • Bristol Research (University of Bristol) (acceptedVersion, cc-by)
  • HAL (submittedVersion, other-oa)
Funders
  • Grand ?quipement National De Calcul Intensif (A0130712941)
  • Universit? Toulouse III - Paul Sabatier (P16015)
Topics
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Protein Structure and Dynamics
  • Health Sciences › Medicine › Infectious Diseases › Tuberculosis Research and Epidemiology
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Lipid Membrane Structure and Behavior
Keywords
C-type lectin, glycolipid recognition, Mycobacterium tuberculosis, Martini 3 force field, ligand-receptor interactions, calcium-dependent binding, hydrophobic groove, loop flexibility, free energy perturbation, host immune response
MeSH terms
Calcium, Glycolipids, Humans, Ligands, Mycobacterium tuberculosis, Receptors, Immunologic, Thermodynamics, Lectins, C-Type, Molecular Dynamics Simulation

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