Conformational Stabilization and Rapid Labeling of a 29-Residue Peptide by a Small Molecule Reaction Partner

Perfluoroaryl and Perfluoroheteroaryl Reagents as Emerging New Tools for Peptide Synthesis, Modification and Bioconjugation

Peptides and proteins are becoming increasingly valuable as medicines, diagnostic agents and as tools for biomedical sciences. Much of this has been underpinned by the emergence of new methods for the manipulation and augmentation of native biomolecules. Perfluoroaromatic reagents are perhaps one of the most diverse and exciting tools with which to modify peptides and proteins, due principally to their nucleophilic substitution chemistry, high electron deficiency and the ability for their reactivity to be tuned towards specific nucleophiles. As discussed in this minireview, in recent years, perfluoroaromatic reagents have found applications as protecting groups or activating groups in peptide synthesis and as orthogonal handles for peptide modification. Furthermore, they have applications in chemoselective ‘tagging’, stapling and bioconjugation of peptides and proteins, as well as tuning of ‘drug‐like’ properties. This review will also explore possible future applications of these reagents in biological chemistry.

A reactive peptide interface for site-selective cysteine bioconjugation

We report aqueous, site-selective modification of proteins using a reactive peptide interface comprising a nine-residue sequence. This interface is the fastest (second-order rate constant of 152 M^-1 s^-1) catalyst-free, cysteine-based method for modifying proteins available to date, and enables near-quantitative labeling of antibodies in cell lysate.

Directed evolution of dibenzocyclooctyne-reactive peptide tags for protein labeling

Protein labeling with a functional molecule is a technique widely used for protein research. The covalent reaction of self-labeling peptide tags with synthetic probe-modified small molecules enables tag-fused protein labeling with chemically diverse molecules, including fluorescent probes. We report the discovery, by in vitro directed evolution, of a novel 23-mer dibenzocyclooctyne (DBCO)-reactive peptide (DRP) tag using Systematic Evolution of Ligands by EXponential enrichment (SELEX) with a combination of a reconstituted cell-free translation system (PURE system) and cDNA display. The N- and C-terminal DRP truncations created a shorter 16-mer DBCO-reactive peptide (sDRP) tag without significant reactivity reduction. By fusing the sDRP tag to a model protein, we showed the chemical labeling and in-gel fluorescence imaging of the sDRP-fused protein using a fluorescent DBCO probe. Results showed that sDRP tag-mediated protein labeling has potential for use as a basic molecular tool in a variety of applications for protein research.

Nucleophilicity of cysteine and related biothiols and the development of fluorogenic probes and other applications

Biothiols such as l-cysteine, l-homocysteine, and glutathione play essential roles in many biological processes, and are directly associated with several health conditions. Therefore, the development of fast, selective, sensitive, and inexpensive methods for quantitatively analyzing biothiols in aqueous solution, but especially in biological samples, is a very attractive research field. In this feature review, we have approached the relevance of biothiols' nucleophilicity to develop selective fluorogenic probes. Since biothiols have considerable structural similarity, relevant strategies are in full development, including several fluorescent molecular platforms, specific receptor sites, reaction conditions, and optical responses. All of these features are properly presented and discussed. Biothiol sensing protocols are based on traditional organic chemistry reactions such as (hetero)aromatic nucleophilic substitution, addition, and substitution at carbonyl carbon, conjugate addition, and nucleophilic substitution at saturated carbon, amongst others including combined processes; furthermore, mechanistic aspects are detailed herein, including some interesting historical contexts. The feasibility of related fluorogenic probes is illustrated by analysis in complex matrices such as serum, cells, tissues, and animal models. Applications of these reactions in more complex systems such as sulfhydryl-based peptides and proteins are also presented, aiming at functionalizing and detecting these nucleophiles. Most literature cited in this review is recent; however, some other prominent works are also detailed. It is believed that this review may be accessible for many academic levels and may efficiently contribute not only to popularizing science but also to the rational development of fluorogenic probes for biothiol sensing.

Quantifying residue-specific conformational dynamics of a highly reactive 29-mer peptide

Understanding structural transitions within macromolecules remains an important challenge in biochemistry, with important implications for drug development and medicine. Insight into molecular behavior often requires residue-specific dynamics measurement at micromolar concentrations. We studied MP01-Gen4, a library peptide selected to rapidly undergo bioconjugation, by using electron paramagnetic resonance (EPR) to measure conformational dynamics. We mapped the dynamics of MP01-Gen4 with residue-specificity and identified the regions involved in a structural transformation related to the conjugation reaction. Upon reaction, the conformational dynamics of residues near the termini slow significantly more than central residues, indicating that the reaction induces a structural transition far from the reaction site. Arrhenius analysis demonstrates a nearly threefold decrease in the activation energy of conformational diffusion upon reaction (8.0 kBT to 3.4 kBT), which occurs across the entire peptide, independently of residue position. This novel approach to EPR spectral analysis provides insight into the positional extent of disorder and the nature of the energy landscape of a highly reactive, intrinsically disordered library peptide before and after conjugation.