Using Covalent Labeling and Mass Spectrometry To Study Protein Binding Sites of Amyloid Inhibiting Molecules

Liu, Tianying; Marcinko, Tyler M.; Kiefer, Patrick A.; Vachet, Richard W.

doi:10.1021/acs.analchem.7b02915

Cited by 37 publications

(54 citation statements)

References 35 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…It should be noted that there are numerous examples in the literature in which nothing is done to ensure a protein’s structural integrity during CL. This approach can be successful if “single-hit” conditions are achieved [81]. In other words, as long as there is one label per protein on average, the labeling chemistry should have successfully probed the original protein structure.…”

Section: Using Covalent Labeling With Mass Spectrometry Detectionmentioning

confidence: 99%

Covalent labeling-mass spectrometry with non-specific reagents for studying protein structure and interactions

Limpikirati

Liu

Vachet

2018

Methods

Self Cite

148

View full text Add to dashboard Cite

Using mass spectrometry (MS) to obtain information about a higher order structure of protein requires that a protein's structural properties are encoded into the mass of that protein. Covalent labeling (CL) with reagents that can irreversibly modify solvent accessible amino acid side chains is an effective way to encode structural information into the mass of a protein, as this information can be read-out in a straightforward manner using standard MS-based proteomics techniques. The differential reactivity of proteins under two or more conditions can be used to distinguish protein topologies, conformations, and/or binding sites. CL-MS methods have been effectively used for the structural analysis of proteins and protein complexes, particularly for systems that are difficult to study by other more traditional biochemical techniques. This review provides an overview of the non-specific CL approaches that have been combined with MS with a particular emphasis on the reagents that are commonly used, including hydroxyl radicals, carbenes, and diethylpyrocarbonate. We describe the reagent and protein factors that affect the reactivity of amino acid side chains. We also include details about experimental design and workflow, data analysis, recent applications, and some future prospects of CL-MS methods.

show abstract

Section: Using Covalent Labeling With Mass Spectrometry Detectionmentioning

confidence: 99%

Covalent labeling-mass spectrometry with non-specific reagents for studying protein structure and interactions

Limpikirati

Liu

Vachet

2018

Methods

Self Cite

148

View full text Add to dashboard Cite

show abstract

“…Apparently, tetracyclines not only bind mature fibrils, but can also interact with soluble precursors of insoluble amyloid fibrils: monomers and oligomers. In the case of the Aβ peptide, tetracyclines bind oligomers, but not the monomer [ 38 ]; in the case of the globular protein β2-m the binding not only involves oligomers but also the monomer through a binding site highly influenced by the physical-chemical properties of the environment [ 39 ]; furthermore, in the case of ataxin-3 (ATX3), tetracycline only binds oligomers via functional groups, mostly hydrophobic, located on one edge of the molecule, probably shielding to some extent the aggregate from the medium [ 87 , 88 ]. It is worth noting that also fibrils, upon binding to tetracyclines, deeply rearrange their structure resulting in the formation of disordered insoluble material lacking the typical features of amyloid fibrils [ 40 ].…”

Section: The Main Classes Of Anti-amyloid Compoundsmentioning

confidence: 99%

Targeting Amyloid Aggregation: An Overview of Strategies and Mechanisms

Giorgetti

Greco

Tortora

et al. 2018

IJMS

131

View full text Add to dashboard Cite

Amyloids result from the aggregation of a set of diverse proteins, due to either specific mutations or promoting intra- or extra-cellular conditions. Structurally, they are rich in intermolecular β-sheets and are the causative agents of several diseases, both neurodegenerative and systemic. It is believed that the most toxic species are small aggregates, referred to as oligomers, rather than the final fibrillar assemblies. Their mechanisms of toxicity are mostly mediated by aberrant interactions with the cell membranes, with resulting derangement of membrane-related functions. Much effort is being exerted in the search for natural antiamyloid agents, and/or in the development of synthetic molecules. Actually, it is well documented that the prevention of amyloid aggregation results in several cytoprotective effects. Here, we portray the state of the art in the field. Several natural compounds are effective antiamyloid agents, notably tetracyclines and polyphenols. They are generally non-specific, as documented by their partially overlapping mechanisms and the capability to interfere with the aggregation of several unrelated proteins. Among rationally designed molecules, we mention the prominent examples of β-breakers peptides, whole antibodies and fragments thereof, and the special case of drugs with contrasting transthyretin aggregation. In this framework, we stress the pivotal role of the computational approaches. When combined with biophysical methods, in several cases they have helped clarify in detail the protein/drug modes of interaction, which makes it plausible that more effective drugs will be developed in the future.

show abstract

“…102 There have been multiple applications using DEPC to study protein structure and protein–protein interactions such as studying protein-binding sites of amyloid inhibiting molecules. 103 The advantage of using a specific covalent label is that it reduces the complexity of data analysis. A recently developed nonspecific covalent label is the use of carbenes that are photoreactive.…”

Section: Covalent Labelingmentioning

confidence: 99%