Photoaffinity glycoprobes-a new tool for the identification of lectins

Switching of Photocatalytic Tyrosine/Histidine Labeling and Application to Photocatalytic Proximity Labeling

Weak and transient protein interactions are involved in dynamic biological responses and are an important research subject; however, methods to elucidate such interactions are lacking. Proximity labeling is a promising technique for labeling transient ligand–binding proteins and protein–protein interaction partners of analytes via an irreversible covalent bond. Expanding chemical tools for proximity labeling is required to analyze the interactome. We developed several photocatalytic proximity-labeling reactions mediated by two different mechanisms. We found that numerous dye molecules can function as catalysts for protein labeling. We also identified catalysts that selectively modify tyrosine and histidine residues and evaluated their mechanisms. Model experiments using HaloTag were performed to demonstrate photocatalytic proximity labeling. We found that both ATTO465, which catalyzes labeling by a single electron transfer, and BODIPY, which catalyzes labeling by singlet oxygen, catalyze proximity labeling in cells.

Photocrosslinking probes for capture of carbohydrate interactions

Glycan-mediated interactions are essential in many biological processes and regulate a wide variety of cellular functions. However, characterizing these interactions is difficult because glycan biosynthesis is not template driven and because carbohydrate recognition events are usually of low affinity and transient. Photocrosslinking carbohydrate probes can form a covalent bond with molecules in close proximity on UV irradiation and are capable of capturing interactions between glycans and glycan-binding proteins in situ. Because of these advantages, multiple photocrosslinking carbohydrate probes have been designed and applied to study the biological functions of glycans. This review will discuss recent advances in the development of novel photocrosslinking functional groups and the design of photocrosslinking probes to detect interactions mediated by glycolipids, peptidoglycan, and multivalent carbohydrate ligands. These probes have demonstrated the potential to address some of the major challenges in the study of glycan-mediated interactions in both model systems and in more complex biological settings.

Catalyst-proximity protein chemical labelling on affinity beads targeting endogenous lectins

Catalyst-proximity labelling on affinity beads enables the identification of ligand-binding proteins such as lectins, which cannot be analyzed by conventional techniques. 1-Methyl-4-arylurazole (MAUra) efficiently labels proteins bound to the beads.

Chemical Glycoproteomics

Chemical tools have accelerated progress in glycoscience, reducing experimental barriers to studying protein glycosylation, the most widespread and complex form of posttranslational modification. For example, chemical glycoproteomics technologies have enabled the identification of specific glycosylation sites and glycan structures that modulate protein function in a number of biological processes. This field is now entering a stage of logarithmic growth, during which chemical innovations combined with mass spectrometry advances could make it possible to fully characterize the human glycoproteome. In this review, we describe the important role that chemical glycoproteomics methods are playing in such efforts. We summarize developments in four key areas: enrichment of glycoproteins and glycopeptides from complex mixtures, emphasizing methods that exploit unique chemical properties of glycans or introduce unnatural functional groups through metabolic labeling and chemoenzymatic tagging; identification of sites of protein glycosylation; targeted glycoproteomics; and functional glycoproteomics, with a focus on probing interactions between glycoproteins and glycan-binding proteins. Our goal with this survey is to provide a foundation on which continued technological advancements can be made to promote further explorations of protein glycosylation.

Gold nanoparticle-based multivalent carbohydrate probes: selective photoaffinity labeling of carbohydrate-binding proteins

Multivalent carbohydrate photoaffinity probes were developed based on gold nanoparticles (AuNPs) to provide a streamlined approach toward identification of carbohydrate-binding proteins. By using AuNPs as scaffolds, a carbohydrate ligand and a photoreactive group could be readily assembled on a probe in a modular fashion, which greatly accelerated the process of optimizing the probe design. The novel AuNP-based probes serve dual functions by facilitating photoaffinity labeling and by directly enriching the crosslinked proteins by centrifugation. We demonstrated that their ability to enhance the affinity and to stringently remove nonspecific proteins allowed selective photoaffinity labeling and isolation of a low affinity carbohydrate-binding protein in cell lysate.

Photoaffinity probes for studying carbohydrate biology

Carbohydrates and carbohydrate-containing biomolecules engage in binding events that underlie many essential biological processes. Yet these carbohydrate-mediated interactions are often poorly characterized, due to their low affinities and heterogenous natures. The use of photocrosslinking functional groups offers a way to photochemically capture carbohydrate-containing complexes, which can be isolated for further analysis. Here we survey progress in the synthesis and use of carbohydrate-based photoprobes, reagents that incorporate carbohydrates or their analogs, photocrosslinking moieties, and affinity purification handles. Carbohydrate photoprobes, used in combination with modern mass spectrometry methods, can provide important new insights into the cellular roles of carbohydrates and glycosylated molecules.

Photoaffinity labeling and its application in structural biology

This review contains a brief consideration of some theoretical aspects of photoaffinity (photoreactive) labeling (PAL), and the most widely used photoreactive groups, such as arylazide, benzophenone, and 3-(trifluoromethyl)-3-phenyldiazirine, are characterized in comparison. Experimental methodology is described, including modern approaches of mass spectrometry for analysis of cross-linking products between the photoreactive probes and biomolecules. Examples of PAL application in diverse fields of structural biology during the last five-ten years are presented. Potential drug targets, transport processes, stereochemistry of interaction of G-protein-coupled receptors with ligands, as well as structural changes in nicotinic acetylcholine receptor are considered. Applications of photoaffinity ganglioside and phospholipid probes for studying biological membranes and of nucleotide probes in investigations of replicative and transcriptional complexes, as well as photoaffinity glycoconjugates for detecting carbohydrate-binding proteins are covered. In combination with modern techniques of instrumental analysis and computer-aided modeling, PAL remains the most important approach in studies on the organization of biological systems.

A new chemical probe for the detection of the cancer-linked galectin-3

A chemical probe was developed for the detection of the emerging cancer marker galectin-3. The probe contains a benzophenone moiety which covalently attaches itself to the protein upon binding and irradiation. Introduction of a fluorescent label via'click' chemistry allows the labelled proteins to be visualized in a gel. With the probe, selective visualization of galectin-3 in protein mixtures was shown and remarkably even in cell lysates.

Photochemical Fishing Approaches for Identifying Target Proteins and Elucidating the Structure of a Ligand-binding Region Using Carbene-generating Photoreactive Probes

Photoaffinity labeling enables the direct probing of a target protein through a covalent bond between a ligand and its binding protein, and even a complex formed by weak interactions can be isolated by the method. The photochemical fishing approach accelerates the throughput, isolating crosslinked complexes and analyzing the structure of the ligand binding site within the protein. We used carbene-generating phenyldiazirine for this approach because practical examinations had shown that the phenyldiazirine functioned as the powerful barb on the hook. Improving the synthetic pathways of the photoprobes and using chemoselective-integrated photoreactive units makes possible the easy and rapid preparation of carbene-generating photoreactive probes including the derivatives in peptides, proteins, DNAs, and carbohydrates. This review also shows several recent impacts of photoaffinity labeling, including the in vivo preparation of photoreactive proteins in living cells.