Biology 2960 Computer Laboratory

Peptide Bonds and Protein Structure
This computer laboratory exercise is designed to strengthen your understanding of protein structure. In the first part of this exercise, you will go through two brief tutorials; (a) peptide bonds and (b) protein structure. In the second part of this exercise, you will examine a three protein examples that may contain secondary structures using FirstGlance, a simplified Jmol viewer.

Peptide Bonds

Peptides are a linear complex of amino acids. The amino acids are joined together to form simple peptides and eventually long (50-2000 amino acids) polypeptide chains (proteins). The figure to the right demonstrates a condensation reaction (dehydration synthesis, loss of water) showing the formation of a covalent peptide bond between two amino acids.
In the figure to the left, the amino acids are shown in a generalized form, so the R-groups are only given as R1 and R2. Like amino acids, peptides have an amino and a carboxyl end or terminal. The peptide bond lies in a plane with the α-carbons causing the R-groups of the amino acids to project from the plane of the peptide toward different coordinates in space. This planar characteristic of the peptide bond allows for two possible conformations in respect to the α-carbons, trans and cis conformations. When the two α-carbons are on opposite sides of the peptide bond, the R-groups are said to be in trans conformation. In contrast, when the two α-carbons are the same side of the peptide bond, the R-groups are said to be in cis conformation. The trans conformation is highly favored due to steric hinderance encountered in the the cis conformation.
In contrast to the peptide bond, rotations are permitted at the bonds between the amino group and the carbonyl group with the α-carbon. The angle of rotation between the amino group and the α-carbon is known as the φ angle of rotation. The angle of rotation between the carbonyl group and the α-carbon is known as the ψ angle of rotation.
Lastly, a protein can be covalently linked ("cross-linked") to another protein further down on the same polypeptide chain or onto another polypeptide chain through the oxidation of two cysteine residues. These linkages are called disulfide bonds.

These constraints of the peptide structure participate in the folding of proteins and the formation of secondary protein structures such as α-helices and β-strands/sheets.

Protein Structure

There are four levels of protein structure:
Primary structure refers to the sequence of amino acid residues in the polypeptide chain written left-to-right from the N-terminus to the C-terminus.

Secondary structures are ordered structures formed by internal hydrogen bonding between amino acid residues. The common secondary structures are the α-helix, the β-strand, and various loops and turns. More information is given below about secondary structures.

Tertiary structure of a polypeptide is the three-dimensional conformation forming distinct, independently folded regions called domains. The domain in the figure below is the "heme binding pocket" for the β-subunit of hemoglobin.

Quaternary structure only applies to proteins that are composed of more than one polypeptide chain. Each of the polypeptides is called a subunit.

Secondary Structure

Proteins are composed of amino acids joined together in peptide chains. Because of space constraints, these two bonds have limited ranges in which they allow rotation. The most common forms of protein secondary structure are the α-helix and the β-pleated sheet (or β-sheet).


In theory, an α-helix can be either right- or left-handed. The α-helices found in proteins are almost always right-handed. In an ideal α-helix, the pitch (advance within one complete rotation) is 0.54 nm, the rise (advance per amino acid) is 0.15 nm, and the number of amino acid residues required for one complete turn is 3.6.
Within an α-helix, each carbonyl oxygen (residue n) of the polypeptide backbone is hydrogen-bonded to the backbone amide hydrogen of the fourth residue further toward the C-terminus (residue n + 4). The hydrogen bonds that stabilize the helix are nearly parallel to the long axis of the helix.

A single intrahelical hydrogen bond would not provide appreciable structural stability but the cumulative effect of many hydrogen bonds within an α-helix stabilizes this conformation. Hydrogen bonds between amino acid residues are especially stable in the hydrophobic interior of a protein where water molecules are occluded and therefore cannot compete for hydrogen bonding.

The side chains of the amino acids in an α-helix point outward from the cylinder of the helix. The stability of an α-helix is affected by the identity of the side chains. Some amino acid residues are found in conformations more often than others. For example, alanine has a small, uncharged side chain and fits well into the α-helical conformation. Alanine residues are prevalent in the α-helices of all classes of proteins. In contrast, tyrosine and asparagine with their bulky side chains are less common in α-helices. Glycine, whose side chain is a single hydrogen atom, destabilizes α-helical structures since rotation around its α-carbon is so unconstrained. For this reason, many helices begin or end with glycine residues. Proline is the least common residue in an α-helix because its rigid cyclic side chain disrupts the right-handed helical conformation. In addition, proline it lacks a hydrogen atom on its amide nitrogen and cannot fully participate in intrahelical hydrogen bonding. For these reasons, proline residues are found more often at the ends of α-helices than in the interior.

Proteins vary in their α-helical content. In some, most of the residues are in helices. Other proteins contain very little structure. The average content of helices in proteins that have been estimated at 26%. The length of a helix in a protein can range from about 4 or 5 residues to more than 40, but the average is about 12.


When two adjacent β-strands line up they can from bridges of hydrogen bonds. This creates a very stable structure known as a β-sheet. Single β-strands are rarely found in proteins because the structure is not that much more stable than a random coil. There are two ways the β-strands can position themselves to form a β-sheet. They can be in either parallel or anti-parallel orientation. The orientation of the β-strands effect the pattern of hydrogen bonding and the general structure and functionality of the β-sheet. In the example shown to the right, three parallel β-strands line up edge to edge to form a highly stable sheet with multiple hydrogen bond (shown in yellow).

    Anti-parallel β-sheets
    In the anti-parallel sheet, the backbone carbonyl oxygens and the backbone amide protons are lined up perfectly so they form straight hydrogen bonds. The carbonyl oxygen and the amide hydrogen (proton) are placed directly opposite from its hydrogen bonding partner. The side chains point out perpendicular to the plane of the sheet. The anti-parallel conformation is more stable and more common conformation.

    Parallel β-sheets
    When the strands are in the parallel orientation, the carbonyl oxygen and the amide protons are staggered, and the hydrogen bonds are skewed (angled with respect to the plane of the sheet). As in anti-parallel β-sheets, the side chains of parallel β-sheets point out from the plane of the sheet.


Natural Sciences Learning Center
Washington University - Biology Department
Copyright © 2011 Wilhelm S. Cruz
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