C-type lectin-(like) fold – Protein-protein interaction patterns and utilization

Dohnálek, Jan; Skálová, Tereza

doi:10.1016/j.biotechadv.2022.107944

Cited by 6 publications

(13 citation statements)

References 83 publications

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“…The protein data bank ID code for the carbohydrate domain of C-type lectin mincle was obtained [3]. After downloading the protein receptor, the file was saved in the exact format (.…”

Section: Methodsmentioning

confidence: 99%

“…However, Trehalose Dimycolate, a glycolipid found on the cell surface, and its derivative analog trehalose dimycolate, have been shown to elicit an immunogenic response as they are bioactive and can react with mincle receptors on neighboring macrophages [3][4][5]. In this project, we visually and statistically examined how exactly these glycolipids/ligands bind to the carbohydrate domain of the c-type lectin molecule using a process called molecular docking [6][7][8][9].…”

Section: Introductionmentioning

confidence: 99%

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It Is Possible Molecular Docking of Carbohydrates to a Mycobacterium tuberculosis Molecule?

Soodeen,

Justiz-Vaillant,

Jalsa

2023

Preprint

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Mincle, a C-type lectin, is expressed predominantly in macrophages, where it plays a role in the macrophage response to various microorganisms such as mycobacteria. Docking is a computational procedure in which various software packages generate different positions at which ligands bind to their receptors. Discovery Studio docking was used in Molegro Virtual Studios. ChemDraw and ChemDraw3D were used for ligand preparation and construction because the protein preparation performed using docking software was a very lengthy process. Mincle plays a novel and non-redundant role in the induction of inflammatory signaling in response to mycobacteria. One disadvantage of Molegro studio docking is that it does not show the metallic atoms with which it interacts but rather shows hydrogen bonding and amino acid interactions. Hypothetically, trehalose dimycolate (TDM) and trehalose dibenzenate (TDB) detected by macrophages ultimately lead to CARD9 signaling, thereby producing pro-inflammatory cytokines and chemokines that have the potential to be used therapeutically.

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“…The protein data bank ID code for the carbohydrate domain of C-type lectin mincle was obtained [3]. After downloading the protein receptor, the file was saved in the exact format (.…”

Section: Methodsmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

It Is Possible Molecular Docking of Carbohydrates to a Mycobacterium tuberculosis Molecule?

Soodeen,

Justiz-Vaillant,

Jalsa

2023

Preprint

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show abstract

“…[250,252,253] In a meta-analysis of the crystal structures of CTLD-containing proteins involved in protein-protein interaction, Dohnálek and Skálová found that most protein-protein interactions are mediated by a surface in the upper lobe of the domain that overlaps with the protein-protein interaction interface of NKG2D. [107] While the residues constituting this surface are not particularly well conserved between different CTLDs, amino acids mapping to the Y152 were found to be involved in protein-protein interactions in 15 CTLD crystal structures. Their analysis concluded that ~77 % of the CTLD surface is, to some extent, involved in the binding of protein ligands, highlighting the high adaptability of the CTLD fold, allowing for the recognition of a diverse array of ligands.…”

Section: Example 6: Nkg2dmentioning

confidence: 99%

“…The distinct protein‐protein interactions of NKG2D are not based on induced fit but on ‘rigid body adaptation’ [250,252,253] . In a meta‐analysis of the crystal structures of CTLD‐containing proteins involved in protein‐protein interaction, Dohnálek and Skálová found that most protein‐protein interactions are mediated by a surface in the upper lobe of the domain that overlaps with the protein‐protein interaction interface of NKG2D [107] . While the residues constituting this surface are not particularly well conserved between different CTLDs, amino acids mapping to the Y152 were found to be involved in protein‐protein interactions in 15 CTLD crystal structures.…”

Section: Example 6: Nkg2dmentioning

confidence: 99%

“…While the residues constituting this surface are not particularly well conserved between different CTLDs, amino acids mapping to the Y152 were found to be involved in protein‐protein interactions in 15 CTLD crystal structures. Their analysis concluded that ~77 % of the CTLD surface is, to some extent, involved in the binding of protein ligands, highlighting the high adaptability of the CTLD fold, allowing for the recognition of a diverse array of ligands [107] …”

Section: Example 6: Nkg2dmentioning

confidence: 99%

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Secondary Sites of the C‐type Lectin‐Like Fold

Lefèbre,

Falk,

Ning

et al. 2024

Chemistry A European J

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C‐type lectins are a large superfamily of proteins involved in a multitude of biological processes. In particular, their involvement in immunity and homeostasis has rendered them attractive targets for diverse therapeutic interventions. They share a characteristic C‐type lectin‐like domain whose adaptability enables them to bind a broad spectrum of ligands beyond the originally defined canonical Ca2+‐dependent carbohydrate binding. Together with variable domain architecture and high‐level conformational plasticity, this enables C‐type lectins to meet diverse functional demands. Secondary sites provide another layer of regulation and are often intricately linked to functional diversity. Located remote from the canonical primary binding site, secondary sites can accommodate ligands with other physicochemical properties and alter protein dynamics, thus enhancing selectivity and enabling fine‐tuning of the biological response. In this review, we outline the structural determinants allowing C‐type lectins to perform a large variety of tasks and to accommodate the ligands associated with it. Using the six well‐characterized Ca2+‐dependent and Ca2+‐independent C‐type lectin receptors DC‐SIGN, langerin, MGL, dectin‐1, CLEC‐2 and NKG2D as examples, we focus on the characteristics of non‐canonical interactions and secondary sites and their potential use in drug discovery endeavors.

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A potent anticoagulant hybrid of snake venom derived FIX-binding protein and anti-factor IX RNA aptamer: Assessed by in-silico and electrochemical analyses

Krishnan

Gopinath

2023

International Journal of Biological Macromolecules

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C-type lectin-(like) fold – Protein-protein interaction patterns and utilization

Cited by 6 publications

References 83 publications

It Is Possible Molecular Docking of Carbohydrates to a Mycobacterium tuberculosis Molecule?

It Is Possible Molecular Docking of Carbohydrates to a Mycobacterium tuberculosis Molecule?

Secondary Sites of the C‐type Lectin‐Like Fold

A potent anticoagulant hybrid of snake venom derived FIX-binding protein and anti-factor IX RNA aptamer: Assessed by in-silico and electrochemical analyses

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