Peptide Bonds, Disulfide Bonds and Properties of Small Peptides

Abstract

The peptide bond links amino acids into head‐to‐tail polymers in proteins as peptides. Chemically, the peptide bond is an amide with restricted rotation about the carbon–nitrogen bond. This restricted rotation combined with free rotation around the alpha carbon of the linked amino acids define the three‐dimensional structure of all proteins. The structure of a peptide or protein can be further stabilised by introducing disulfide crosslinks, a chemical oxidation between two sulfhydryl groups of the amino acid cysteine stabilise specific conformations of peptides and proteins. Small peptides, which often function biologically as hormones or other signalling molecules can also be useful model systems for investigating protein structure and function. The introduction of disulfide bonds and a change in conformation between the cis and trans conformations of the proline peptide bond may be a barrier to the rapid formation of the proper protein structure. In the cell, enzymes are present to catalyse these processes.

Key Concepts:

  • The conformational flexibility around the alpha carbon of peptides connected by peptide bonds accommodates an enormous number of structures depending on the protein sequence.

  • Disulfides are chemical crosslinks between or within polypeptides that adds stability to the overall structure.

  • Conformational transitions involving proline residues in a protein can slow protein folding due to a slow conformational transition.

  • The enzymes protein disulfide isomerase and peptidyl proline isomerase function in the cell to catalyse slow chemical and configuration changes that retard protein folding.

Keywords: peptide structure and function; peptides; disulfides; proline isomerisation; protein disulfide isomerases

Figure 1.

The peptide bond. The double‐bond character of the C–N bond causes the atoms connected to it to lie in the same plane.

Figure 2.

Conformation around the α‐carbon. The dihedral angles, Φ and Ψ, specify the conformation of the peptide backbone. Rotation about these bonds allows the peptide to adopt the various helix, sheet and turn secondary structures found in folded proteins.

Figure 3.

The conformation of the peptide bond can have the two Cα atoms on the same side (cis) or on opposite sides (trans) of the peptide bond. Except for proline, the cis conformation is rarely found in proteins.

Figure 4.

Thermodynamic cycle linking the stability of a protein to the stability of the disulfide formation (Lin and Kim, ). N represents the native conformation of the protein and U represents the unfolded conformation. The increase in protein stability due to the presence of a disulfide bond (Kfold,SS/Kfold,SHSH) is equivalent to the increase in the stability (ease of oxidation) of the disulfide as the protein adopts its folded conformation (Kox,N/Kox,U).

Figure 5.

Reduction of the disulfides of ribonuclease A in the presence of a denaturant such as urea leads to the loss of all disulfides and its enzymatic activity. When the denaturant is removed by dialysis and an oxidant is provided to support disulfide formation, the protein refolds, forming disulfides with native pairings and regaining the enzymatic activity.

Figure 6.

PDI is organised in five domains. Adapted with permission from Edman et al..

Figure 7.

PDI catalyses both disulfide formation and isomerisation. In its disulfide state, PDI rapidly oxidises the substrate protein, forming substrate disulfides. Early in folding, disulfide formation is often incorrect because the wrong cysteine residues are connected or because the right cysteine residues are connected in the wrong temporal order. In its reduced state, PDI attacks incorrect disulfides and initiates their isomerisation. Multiple rounds of isomerisation may be required to finally arrive at the most stable arrangement of disulfides.

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Gilbert, Hiram F(Sep 2010) Peptide Bonds, Disulfide Bonds and Properties of Small Peptides. In: eLS. John Wiley & Sons Ltd, Chichester. http://www.els.net [doi: 10.1002/9780470015902.a0001328.pub2]