Protein Structure: Unusual Covalent Bonds

Abstract

Proteins are linear polypeptides made out of a small set of amino acids. The chemical diversity of the building blocks is limited, but a protein's covalent structure can be amended in vivo so that unusual linkages are introduced and new functionalities are conveyed. These covalent modifications may occur during translation or after the protein is fully synthesised; they may be spontaneous or enzymatic and transient or long lived. They are generally consequential to cellular function and integrity of the organism. The broad array of modification includes common and frequent substitutions such as phosphorylation and rarer alterations such as formylglycine formation. A survey of long‐lived modifications is presented from a physicochemical perspective with attention to biological relevance.

Key Concepts:

  • Covalent bonds other than found in the standard set of amino acids expand the chemical properties of proteins.

  • Unusual bonds are found in protein‐derived prosthetic groups.

  • Unusual covalent bonds play functional roles.

  • Some unusual covalent bonds are irreversibly formed and are markers of aging.

  • Many unusual bonds are reversibly formed and participate in regulatory mechanisms.

  • Unusual bonds are often difficult to detect and identify, especially in vivo.

  • Technological advances have improved the ability to detect modifications in entire proteomes.

Keywords: protein chemistry; post‐translational modification; cotranslational modification; prosthetic groups

Figure 1.

Some of the structures are mentioned in the text. Most hydrogen atoms are omitted for clarity. The unusual bonds and additions to the standard amino acids are marked in red, without mechanistic connotation (i.e. origin of atoms). Dotted lines indicate bonds to the rest of the protein structure. Comments are provided as needed and referred to by a number. Widespread modifications: (a) Cysteine modifications. (1) The disulfide group (dicysteine) is chiral and preferred torsion angle about the S–S bond is ∼±90°. (b) Phosphorylation. (c) Methylation. (d) Glycosylation and its modified substrates. (2) The linkage is a β‐N‐glycosidic bond and the sugar is N‐acetylglucosamine. (3) The linkage is an α‐O‐glycosidic bond and sugar is mannose. (4) The linkage is an α‐C‐glycosidic bond to tryptophan indole C2 and sugar is mannose. Additional displacements: (e) Nucleotidylation. (f) Lipid attachment. (5) 2‐[3‐Carboxyamido‐3‐(trimethylammonio)propyl]histidine: this modification of histidine occurs in a complex, multienzymatic post‐translational process. ADP‐ribosylation of diphthamide takes place at the imidazole ɛ‐nitrogen.

Figure 2.

Some of the structures are mentioned in the text. Most hydrogen atoms are omitted for clarity. The unusual bond and additions to the standard amino acids are marked in red, without mechanistic connotation (i.e. origin of atoms). Dotted lines indicate bonds to the rest of the protein structure. Comments are provided as needed and referred to by a number. Additional displacements: (a) Glypiation. (1) The R group is trimannoside, glucosamine and inositol phospholipids, linked in that order. (b) Acetylation. (c) Sulfation. Additional oxidoreductions: (d) (2) There are two possible products, with R or S stereochemistry at the sulphur. (3) Singly iodinated rings can also occur. Coupling provides thyroid hormone precursors such as pictured to the right. Condensations and rearrangements: (e) Protein–protein conjugation via isopeptide bond formation. (4) This linkage is found in ubiquitination and sumoylation and results from the coupling of a C‐terminal glycine and a lysine ɛ‐NH2. (5) This linkage results from the coupling of a glutamine and a lysine ɛ‐NH2. (f) Backbone alteration via isopeptide bond formation. (g) Cyclisation. (6) The cyclisation occurs at the N‐terminal position of the polypeptide chain. (h) Carbamylation.

Figure 3.

Prosthetic groups formed by attachment of a nonproteinic molecule. Most hydrogen atoms are omitted for clarity. The groups are shown in red. Dotted lines indicate bonds to the rest of the protein structure. Comments are provided as needed and referred to by a number. (1) The linkage is an amide bond between lipoic acid and a lysine ɛ‐NH2. (2) Covalent attachment is through the formation of thioether bonds. In the haem b cofactor, the substituents at positions 2 and 4 are vinyl groups. (3) The R group is d‐ribitol adenine dinucleotide in the case of FAD. The oxidised form of the isoalloxazine ring is shown in linkage to the 8α‐methyl group (His, Tyr and Cys). Linkage to the C6 atom of the flavin isoalloxazine ring also occurs (Cys and flavine mononucleotide). (4) Bilins found in the cyanobacterial and red algae phycobilisome are phycocyanin (shown) and phycoerythrin. (5) The linkage is to a lysine ɛ‐NH2 and results in an imine or Schiff base.

Figure 4.

Prosthetic groups formed by reaction of protein residues and additional modifications. (1) This group is formed at an N‐terminal serine. (2) p‐Hydroxybenzylideneimidazolidinone. This group is derived from a Ser‐Tyr‐Gly triad. The α‐carbons of the original amino acids are labelled. (3) 4‐Methylideneimidazole‐5‐one (MIO). This group is derived from an Ala‐Ser‐Gly triad. The α‐carbons of the original amino acids are labelled. (4) Desmosine: one of the crosslinks in elastin. Four lysines, three of which are first oxidised to the aldehyde stage, react to form the heterocycle. (5) The methionine is N‐terminal. (6) This ligation is catalysed by a vitamin K‐dependent γ‐glutamyl carboxylase acting on Glu.

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Lecomte, Juliette TJ, and Falzone, Christopher J(Feb 2013) Protein Structure: Unusual Covalent Bonds. In: eLS. John Wiley & Sons Ltd, Chichester. http://www.els.net [doi: 10.1002/9780470015902.a0003015.pub2]