The Application of Fluorine‐Containing Reagents in Structural Proteomics

Abstract

Structural proteomics refers to large‐scale mapping of protein structures in order to understand the relationship between protein sequence, structure, and function. Chemical labeling, in combination with mass‐spectrometry (MS) analysis, have emerged as powerful tools to enable a broad range of biological applications in structural proteomics. The key to success is a biocompatible reagent that modifies a protein without affecting its high‐order structure. Fluorine, well‐known to exert profound effects on the physical and chemical properties of reagents, should have an impact on structural proteomics. In this Minireview, we describe several fluorine‐containing reagents that can be applied in structural proteomics. We organize their applications around four MS‐based techniques: a) affinity labeling, b) activity‐based protein profiling (ABPP), c) protein footprinting, and d) protein cross‐linking. Our aim is to provide an overview of the research, development, and application of fluorine‐containing reagents in protein structural studies.

Free‐Radical Membrane Protein Footprinting by Photolysis of Perfluoroisopropyl Iodide Partitioned to Detergent Micelle by Sonication

“…The outcome extends, considerably, a novel paradigm suggested in previous articles in this journal on footprinting membrane proteins [15] and on the use of fluorine chemistry in structural proteomics [19, 24, 32] . Our design steps include 1) reagent selection in terms of Log P , 2) reagent transfer to the membrane domain, 3) reagent photochemistry in the lipid‐like medium to give free radicals (or other reactive species), and 4) tailored radical specificity/reactivity design to address the biochemical question at hand.…”

“…We reasoned that photolyzable reagents with high partition coefficients (P) into nonpolar solvents would be well‐suited for transmembrane labeling. We chose PFIPI because it has a high positive log P (Figure 1), small size, ready availability, and suitability to form radicals upon 248 nm laser photolysis on the fast photochemical oxidation of proteins (FPOP) platform [19] . FPOP, in its original conception, is a hydroxyl radical ( .…”

Perfluorocarbons in Chemical Biology

“…[131,132] Fluorous tags installed through direct radical trifluoromethylation of proteins can also be used for MS protein profiling applications. [133,134] Recently, noncovalent fluoroustagging has been explored for isolating proteins, however this has yet to be demonstrated in a complex biological environment. [135]…”

“…This approach has been extended to the enrichment of peptides with other side chain functionalities and small‐molecule metabolites by using perfluoroalkyl chains with different functional handles, [130] many of which are now commercially available or have additional functionality, such as photo‐crosslinkers [131,132] . Fluorous tags installed through direct radical trifluoromethylation of proteins can also be used for MS protein profiling applications [133,134] . Recently, noncovalent fluorous‐tagging has been explored for isolating proteins, however this has yet to be demonstrated in a complex biological environment [135] …”

Environmentally Compatible Access to α‐Trifluoromethylseleno‐Enones

“…Nowadays, fluorinated molecules find more and more uses in a wide panel of applications, mainly due to their peculiar properties [1–13] . In the race of the development of molecules dedicated to targeted applications, fine tuning of physico‐chemical properties is highly investigated.…”