Secondary Structure

Protein Structure Tutorials

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Secondary Structure

Protein Structure Tutorials

Primary Structure
Secondary Structure
Tertiary Structure
Quaternary Structure

Secondary Structure: Alpha Helices and Beta Pleated Sheets

A protein's primary structure is the specific order of amino acids that have been linked together to form a polypeptide chain. But polypeptides do not simply stay straight as liniar sequences of amino acids. The fold back on themselves to create complex 3-dimensional shapes.

When examing different proteins, you will notice that there are two specifically recognizable shapes that are often repeated throughout a protein's 3-dimensional structure. One of these shapes looks like a curl and the other looks like rows or zig-zags.

The curls are called alpha helices and almost look like a spiral staircase or a spring. They exist when a protein's backbone curls up into a helical shape.

Click Here to display an alpha helix in the interactive display to the right.

The rows are called beta pleated sheets and almost look like a long line for a ride at an amusement park. They exist when a protein's backbone forms an extended zig-zag structure that passes back and forth.

Click Here to display a beta pleated sheet in the interactive display to the right.

The organization and frequency of these two structures in a protein's overall 3-dimensional shape is called the protein's secondary structure.

Secondary Structures in a Real Protein

One type of protein that clearly shows both an alpha helix and a beta pleated sheet is a zinc finger protein, which helps regulate DNA expression in a cell's nucleus. This relatively small protein is only 28 amino acids long but includes a four-turn alpha helix and a two strand beta pleated sheet.

Click Here to show a zinc finger protein in the interactive display to the right.

Visualizing Complex Protein Structures

Protein structures can become very visually overwhelming. This is especially true for large proteins, which can be thousands of amino acids long and include tens of thousands of atoms!

Because of this, proteins are often visually represented using different display formats and color schemes. Click on the buttons below to see the zinc finger protein in the interactive display to the far right shown in some of the most common display formats and color schemes.

Ball & Stick Format displays every single atom in a protein with a small sphere and represents the bonds between these atoms with thin sticks. In Ball & stick format
CPK Color Scheme colors every atom by its element type. Carbon atoms are gray, nitrogen atoms are blue, oxygen atoms are red and hydrogen atoms are white.

Each of the different display formats and color schemes used in protein visualization has advantages and disadvantages.

For example, spacefill format is an excellent way to represent the overall globular shape of a protein, but may make it difficult to see details at the very center of the protein. Cartoon format is an excellent way to see the overall path of a protein's backbone, but may not shown the details of each individual amino acid's R-group.

Hydrogen Bonds Help Support Secondary Structures

Alpha helices and beta sheets are supported and reinforced by hydrogen bonds. A hydrogen bond is a weak bond formed when a hydrogen atom is covalently bonded to an atom and interacts with another atom.

Hydrogen bonds often form between the backbone atoms of different amino acids in the two secondary structures of proteins. A hydrogen atom covalently bound to the nitrogen atom of one amino acid interactes with the oxygen atom of another amino acid.

Click on the links below to see hydrogen bonds represented as yellow cylinders in the two types of secondary structures.

Secondary Structures in Other Common Proteins

Click on the images below to view each of the three proteins discussed earlier in the interactive display to the right. Each protein will be colored with the Structure Color Scheme (alpha helices colored magenta and beta sheets colored yellow) to emphesize each protein's unique secondary structures.

Hemoglobin Proteins safely carry oxygen in the blood.

Insulin Proteins help regulate sugar in the bloodstream.

Green Fluorescent Proteins create bioluminescence in animals like jellyfish.

Move on to Tertiary Structure