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Ligand Binding Sites

Ligand Binding Sites

Proteins are dynamic macromolecules that carry out a wide variety of essential processes; however, the activities of most proteins depend on their interactions with other molecules or ions, known as ligands.
Protein-ligand interactions are quite specific; even though numerous potential ligands surround a cellular protein at any given time, only a particular ligand can bind to that protein. Moreover, a ligand binds only to a dedicated area on the surface of the protein, known as the...

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Detection of Heterodimerization of Protein Isoforms Using an in Situ Proximity Ligation Assay

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Published on: October 20, 2018

PAL-Mediated Ligation for Protein and Cell-Surface Modification.

Zhen Wang¹, Dingpeng Zhang¹, Side Hu¹

¹School of Biological Science, Nanyang Technological University, Singapore, Singapore.

Methods in Molecular Biology (Clifton, N.J.)

|June 27, 2022

Summary

Peptidyl Asx-specific ligases (PALs) enable efficient protein modification through transpeptidation. This study details methods for Asp- and Asn-directed ligations, including dual labeling and cell-surface applications.

Keywords:

Asparaginyl endopeptidase Bio-orthogonal ligation Butelase-1 Protein backbone cyclization Protein labeling Protein theranostics VyPAL2

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Area of Science:

Biochemistry
Molecular Biology
Biotechnology

Background:

Peptidyl Asx-specific ligases (PALs) catalyze peptide ligation at Asn/Asp residues.
PALs, part of the asparaginyl endopeptidase (AEP) superfamily, exhibit transpeptidase activity.
They offer efficient, mild aqueous conditions for protein manipulation.

Purpose of the Study:

To describe methods for protein macrocyclization and labeling at Asp residues using VyPAL2.
To demonstrate dual labeling via orthogonal Asp- and Asn-directed ligations.
To present a novel method for cell-surface protein modification using butelase-1.

Main Methods:

Utilizing VyPAL2 for Asp-specific protein macrocyclization and labeling.
Implementing orthogonal Asp- and Asn-directed ligations for dual labeling.
Applying butelase-1 for cell-surface protein modification.

Main Results:

Successful protein macrocyclization and labeling at Asp residues with VyPAL2.
Efficient dual labeling achieved through orthogonal ligation strategies.
Demonstrated utility of butelase-1 for cell-surface protein modification, highlighting its advantages.

Conclusions:

PALs are versatile tools for diverse protein engineering applications.
VyPAL2 enables Asp-directed modifications and dual labeling.
Butelase-1 offers an improved method for cell-surface protein functionalization.