An important characteristic of protein structure is its rigid ness and planarity of its 3 dimensional structure. A particular 3-D conformation which arises from a certain arrangement of amino acids, gives rise to function. The hydrogen of the substituted amino group is always TRANS to the carbonyl oxygen.
There is no freedom of rotation about the carbonyl carbon and the nitrogen atom of the peptide unit, because of its double bond character, and hence the peptide group is planar.
Polypeptide chains can fold into repeated structures called Alpha Helices, and ß-Sheets
Alpha Helix
The alpha helix is a rod like structure, which has its main polypeptide chain on the inner part of the rod, and the side chains extend outwards, in a helical array, i.e. less steric clash as the side chains are widely separated. All the CO and NH groups in the main chain are hydrogen bonded, and as a consequence stabilize the alpha helix.
So basically, as seen from the above picture the alpha helix is like a narrow looking tube, with its polypeptide chain coiled up tightly, almost like a telephone wire. Hydrogen bonding is at its maximum, and runs straight down the tube - like structure and locks the conformation in place.
Also another important characteristic of the alpha helix is that each residue is related to the next one by translation by 1.5Å, and a rotation of about 100º, which gives 3.6 amino acid residues per turn of the helix.
ß - Pleated Sheets
The alpha helix and the beta sheets were both discovered by Pauling and Corey. The names come from the fact that alpha being the first periodic structural motif discovered, and beta the second. The structure is:
ß - pleated sheet
In beta pleated sheets the polypeptide backbone is stretched and not tightly coiled like in the helical structure, as seen in the structure above. Also beta sheets are stabilized by hydrogen bonds which are formed by NH and CO groups on different strands that line up side by side to give a 2-D like structure. One can get parallel beta sheets, i.e.
where ß - strands run in the same direction, and antiparallel beta sheets, i.e.
where ß - strands run in opposite directions.
One can also get ß - Turns or also know as reverse turns, which are just are polypeptide chains that reverse direction, and they are often connected by ß - antiparallel strands.
Next topic is Protein Architecture, where primary, secondary, and tertiary structures will be discussed.