The Peptide Bond
Proteins consist of one or more strings of amino acids joined end-to-end to produce a polypeptide. The characteristics of each protein are due to the different amino acids that are combined to make the polpeptide(s). Each of the 20 or so common amino acids has a different side chain but the basic structure is common to all amino acids.
Amino acids have a central α-carbon atom, a carboxylate group (—COO⊖), and an amino group (—NH3⊕). The fourth group attached to the α-carbon is the side chain (The third group is —H). Side chains can be as simple as —H (= glycine), or —CH3 (= alanine). In the example shown on the right, the side chain is —CH2OH (= serine).
Proteins are synthesized by the translation machinery consisting of ribosomes , aminoacyl-tRNAs, and various translation factors. The template for synthesis is messenger RNA (mRNA) copied from the gene. Amino acids are strung together in a particular order specified by the mRNA codons.
The biosynthesis reaction is complex. It is coupled to hydrolysis of at least three ATP equivalents because the joining of two amino acids is thermodynamically unfavorable. The actual chain elongation reaction is catalyzed by the peptidyl transferase activity of the ribosome. The new bond that is created is called a peptide bond.
In the reaction shown above, the carboxylate group of the amino acid alanine is joined to the amino group of the amino acid serine to create a dipeptide with a peptide bond. Water is eliminated in this reaction. During protein synthesis the reaction continues as the mRNA is translated and long strings of several hundred amino acid residues are made.
The peptide bond has some interesting properties that play an important role in determining the three-dimensional structure of proteins. Look at the traditional depiction of the peptide bond in part (a) (top) of the figure on the left. It shows the actual peptide bond as a single bond and the bond between the carbon atom and the oxygen atom as a double bond. Note that the nitrogen atom has a pair of unshared electrons represented by the two red dots.
The middle structure shows that one electron from the nitrogen and carbon atoms can redistribute to form a double bond between C and N. This leaves an unshared pair of electrons on the oxygen atom. The actual bonding pattern is a mixture of these two resonance forms as shown in the bottom structure.
The partial double bond nature of the peptide bond has important consequences since it inhibits rotation around this bond. With a single bond there is free rotation so the groups on either side can adopt many different conformations. With a double bond there is very little rotation and the groups on either side are locked into the conformation that was formed when the bond is created.
The peptide bond has enough of a double bond characteristic to prevent rotation of the two newly joined amino acid residues. Thus, the O—C—N—H atoms around the peptide bond lie in a single plane shown in blue in the figure on the right.
What this means is the polypeptide chain is somewhat stiff and rigid. It can only adopt conformations that result from rotation around the other bonds in the chain. There are only two of these other bonds that can rotate. Looking at the central α2 carbon atom above, you can see that there can be rotation around the N—Cα bond and around the Cα—C bond.
The angle of rotation around the N—Cα bond is called Φ (phi) and the angle around the Cα—C bond is called Ψ (psi). For each pair of amino acid residues, these two angles are all that's needed to specify the three-dimensional shape of the polypeptide backbone of the protein.
Not all angles are possible as shown on the left. If the two negatively charged oxygen atoms are too close together they will repel one another. This clash is called steric hindrance and it further limits the number of possible conformations of the polypeptide chain.
A Ramachandran plot (also known as a Ramachandran map or a Ramachandran diagram), developed by Gopalasamudram Narayana Ramachandran, is a way to visualize dihedral angles φ against ψ of amino acid residues in protein structure. It shows the possible conformations of φ and ψ angles for a polypeptide.
Mathematically, the Ramachandran plot is the visualization of a function . The domain of this function is the torus. Hence, the conventional Ramachandran plot is a projection of the torus on the plane, resulting in a distorted view and the presence of discontinuities.
One would expect that larger side chains would result in more restrictions and consequently a smaller allowable region in the Ramachandran plot. In practice this does not appear to be the case; only the methylene group at the β position has an influence. Glycine has a hydrogen atom, with a smaller van der Waals radius, instead of a methyl group at the β position. Hence it is least restricted and this is apparent in the Ramachandran plot for Glycine for which the allowable area is considerably larger.
In contrast, the Ramachandran plot for proline shows only a very limited number of possible combinations of ψ and φ.
The Ramachandran plot was calculated just before the first protein structures at atomic resolution were determined. Forty years later there were tens of thousands of high-resolution protein structures determined by X-ray crystallography and deposited in the Protein Data Bank (PDB). From one thousand different protein chains, Ramachandran plots of over 200 000 amino acids were plotted, showing some significant differences, especially for glycine (Hovmöller et al 2002). The upper left region was found to be split into two; one to the left containing amino acids in beta sheets and one to the right containing the amino acids in random coil of this conformation.
- Web-based tool showing Ramachandran plot of any PDB entry
- Pymol with the DynoPlot extension
- VMD, distributed with dynamic Ramachandran plot plugin
- Swiss PDB Viewer
See also PDB for a list of similar software.
- G.N. Ramachandran, C. Ramakrishnan & V. Sasisekharan (1963): Stereochemistry of polypeptide chain configurations. In: J. Mol. Biol. vol. 7, p. 95-99. PMID 13990617
- S. Hovmöller, T. Zhou & T. Ohlson (2002) Conformations of amino acids in proteins. In: Acta Cryst. vol. D58, p. 768-776.