Exploring multivalent carbohydrate–protein interactions by NMR

Quintana, Jon Imanol; Atxabal, Unai; Unione, Luca; Ardá, Ana; Jiménez‐Barbero, Jesús

doi:10.1039/d2cs00983h

Cited by 19 publications

(13 citation statements)

References 143 publications

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“…A ligand-based NMR approach (applied to both proton or fluorine nuclei) used the NOE effect or the analysis of transverse and longitudinal relaxation to identify the exchange between the bound and free state of a ligand . Competition ligand-based NMR experiments were developed to avoid many of the limitations associated with the ligand-based NMR experiments, such as the lack of information about the protein binding site.…”

Section: Nmr-based Approachmentioning

confidence: 99%

Biophysical Assays for Investigating Modulators of Macromolecular Complexes: An Overview

Garbagnoli,

Linciano,

Listro

et al. 2024

ACS Omega

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Drug discovery is a lengthy and intricate process, and in its early stage, crucial steps are the selection of the therapeutic target and the identification of novel ligands. Most targets are dysregulated in pathogenic cells; typically, their activation or deactivation leads to the desired effect, while in other cases, interfering with the target-natural binder complex achieves the therapeutic results. Biophysical assays are a suitable strategy for finding new ligands or interferent agents, being able to evaluate ligand−protein interactions and assessing the effect of small molecules (SMols) on macromolecular complexes. This mini-review provides a detailed analysis of widely used biophysical methods, including fluorescence-based approaches, circular dichroism, isothermal titration calorimetry, microscale thermophoresis, and NMR spectroscopy. After a brief description of the methodologies, examples of interaction and competition experiments are described, together with an analysis of the advantages and disadvantages of each technique. This mini-review provides an overview of the most relevant biophysical technologies that can help in identifying SMols able not only to bind proteins but also to interfere with macromolecular complexes.

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Section: Nmr-based Approachmentioning

confidence: 99%

Biophysical Assays for Investigating Modulators of Macromolecular Complexes: An Overview

Garbagnoli,

Linciano,

Listro

et al. 2024

ACS Omega

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“…In contrast to peptides, the rules that regulate glycan folding are much more obscure, because these compounds exist in a dynamic ensemble of conformers separated by low energy barriers . In addition, the lack of synthetic standards and the complexity of glycan analysis have hampered systematic structural studies. , Nevertheless, insights into the fundamentals of glycan folding are extremely valuable to understand glycan properties and design synthetic analogues capable of performing a particular function …”

Section: Introductionmentioning

confidence: 99%

Dissecting the Conformational Stability of a Glycan Hairpin

Yadav,

Djalali,

Poveda

et al. 2024

J. Am. Chem. Soc.

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Systematic structural studies of model oligopeptides revealed important aspects of protein folding and offered design principles to access non-natural materials. In the same way, the rules that regulate glycan folding could be established by studying synthetic oligosaccharide models. However, their analysis is often limited due to the synthetic and analytical complexity. By utilizing a glycan capable of spontaneously folding into a hairpin conformation as a model system, we investigated the factors that contribute to its conformational stability in aqueous solution. The modular design of the hairpin model featured a trisaccharide turn unit and two β-1,4-oligoglucoside stacking strands that allowed for systematic chemical modifications of the glycan sequence, including the introduction of NMR labels and staples. Nuclear magnetic resonance assisted by molecular dynamics simulations revealed that stereoelectronic effects and multiple glycan−glycan interactions are the major determinants of folding stabilization. Chemical modifications in the glycan primary sequence (e.g., strand elongation) can be employed to fine-tune the rigidity of structural motifs distant from the modification sites. These results could inspire the design of other glycan architectures, with implications in glycobiology and material sciences.

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“…21 Among antibacterial polymers that are not prone to drug resistance, guanidine polymers are a good choice with certain advantages: the guanidine group can be ionized in a wider pH range, and it can bind to the cell membrane in the form of dihydro bonds, making the bacterial cell membrane firmly bound and the antibacterial ability stronger. 22 Carbohydrates play a significant role in biological processes such as recognition and signaling, [23][24][25][26][27] and they have a high affinity for proteins, making them suitable for applications that require target-specific binding. [28][29][30][31] Different carbohydrates have been used to identify bacteria.…”

Section: Introductionmentioning

confidence: 99%

In situ PET-RAFT polymerization to prepare guanidine-and-carbohydrate modified ZnO nanoparticles

Zhao,

Rao,

Zhang

et al. 2024

Polym. Chem.

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Exploring multivalent carbohydrate–protein interactions by NMR

Abstract: Nuclear Magnetic Resonance (NMR) has been widely employed to assess diverse features of glycan–protein molecular recognition events.

Cited by 19 publications

References 143 publications

Biophysical Assays for Investigating Modulators of Macromolecular Complexes: An Overview

Biophysical Assays for Investigating Modulators of Macromolecular Complexes: An Overview

Dissecting the Conformational Stability of a Glycan Hairpin

In situ PET-RAFT polymerization to prepare guanidine-and-carbohydrate modified ZnO nanoparticles

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