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Deciphering protein post-translational modifications using chemical biology tools

Nature Reviews Chemistry volume 4, pages 674–695 (2020)Cite this article

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Abstract

Proteins carry out a wide variety of catalytic, regulatory, signalling and structural functions in living systems. Following their assembly on ribosomes and throughout their lifetimes, most eukaryotic proteins are modified by post-translational modifications; small functional groups and complex biomolecules are conjugated to amino acid side chains or termini, and the protein backbone is cleaved, spliced or cyclized, to name just a few examples. These modifications modulate protein activity, structure, location and interactions, and, thereby, control many core biological processes. Aberrant post-translational modifications are markers of cellular stress or malfunction and are implicated in several diseases. Therefore, gaining an understanding of which proteins are modified, at which sites and the resulting biological consequences is an important but complex challenge requiring interdisciplinary approaches. One of the key challenges is accessing precisely modified proteins to assign functional consequences to specific modifications. Chemical biologists have developed a versatile set of tools for accessing specifically modified proteins by applying robust chemistries to biological molecules and developing strategies for synthesizing and ligating proteins. This Review provides an overview of these tools, with selected recent examples of how they have been applied to decipher the roles of a variety of protein post-translational modifications. Relative advantages and disadvantages of each of the techniques are discussed, highlighting examples where they are used in combination and have the potential to address new frontiers in understanding complex biological processes.

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Fig. 1: Protein post-translational modifications diversify the proteome.
Fig. 2: Genetic-code expansion.
Fig. 3: SPPS, protein ligation and intein splicing.
Fig. 4: Site-specifically modified proteins accessed via chemical synthesis and amide-forming ligations.
Fig. 5: Site-specifically modified proteins accessed via protein semi-synthesis and trans-splicing.
Fig. 6: Enzymatic protein modifications and ligations.
Fig. 7: Mimics and stable analogues of PTMs.

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Acknowledgements

A.C.C. is supported by a UQ Development Fellowship (project 613982) and an Early Career Researcher Grant (project 616535) from the University of Queensland. J. Rosengren and O. Gajsek are gratefully acknowledged for helpful discussions and feedback.

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    Anne C. Conibear

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Glossary

Proteome

All the proteins present in a cell, tissue or organism at a given time.

Post-translational modifications

(PTMs). Covalent modifications to a protein after its assembly on the ribosome.

Proteoforms

Modified and/or processed forms of a protein arising from a single gene.

PTM sites

Specific amino acid residues bearing one or more post-translational modifications (PTMs).

Canonical amino acids

The 20 standard amino acids encoded in the genetic code and incorporated into proteins by endogenous protein biosynthesis processes.

Aminoacyl-tRNA synthetase

(aa-tRNA synthetase). Enzyme that loads an amino acid onto tRNA bearing the respective anticodon for that amino acid.

Bioorthogonal handle

Functional group that is not found in biological systems, allowing chemical reactions to be carried out in complex mixtures of biomolecules without affecting native processes.

Directed evolution

Selection of a protein or nucleic acid with a desired trait by iterative cycles of genetic diversification, library screening and replication of functional variants.

Histone

One of several proteins that associate with DNA in eukaryotic nuclei and help to package it into chromatin.

Glycoproteins

Proteins that have one or more oligosaccharide chains covalently attached to an amino acid side chain.

Depsipeptides

Peptides that contain an ester linkage in place of one of the backbone amide bonds.

Epigenetic regulation

Control of gene expression and activity that is heritable and does not involve changes in the DNA sequence.

Amyloidogenic protein

A protein that produces or tends to produce fibrillar aggregates.

Consensus sequence

A representative protein or nucleic acid sequence comprising the most frequently occurring residues at each position, calculated by aligning multiple sequences.

Nucleosomes

The basic structural units of eukaryotic chromatin, comprising a segment of DNA wrapped around eight histones.

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Conibear, A.C. Deciphering protein post-translational modifications using chemical biology tools. Nat Rev Chem 4, 674–695 (2020). https://doi.org/10.1038/s41570-020-00223-8

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