Secondary Structure of Proteins
The term secondary structure refers to the locally coiled regions of the
helical structure. The secondary structure and various helices which are characteristic of it marks the start of what the protein requires to remain stable and perform its desired function.
In 1950 Linus Pauling and some of his fellow collaborators systematically began to analyze the various conformations of proteins and came up with four principles that the helical structure would have to adhere to in
inorder for the protein molecule to ramain stable.
Principles of Protein Structure
Bond lengths and bond angles should be distorted as little
as possible.
Atoms should not approach each other any more than there Van
will allow them.
Amide groups must remain planar and in trans figuration.
Noncovalent bonding is necessary for the stability of
polypeptide folding.
The two primary secondary conformations that were determined were that of the alpha helix and
beta sheet.
Alpha helix
The alpha helix
conformation is one of the most prevalent conformations that can be found in polypeptide chains of all kinds. There are many factors which account for this such as the stability which arises from the tight atom packing and the geometry of the hydrogen atoms in the helix.
Alpha helices are characterized by hydrogen bonds which are found within the polypeptide chain and its circular staircase shape whihc winds in a right handed stair-shape fashion. The alpha helix has:
3.6 residues/turn
Rise 0.15
13 atoms in H-bonded Ring
Beta Sheet
The beta sheet which is the other largely found conformation amongst many proteins which exhibit secondary structure involves the further folding of the polypeptide chain. This occurs by acutually strecthing the polypeptide chain and laying it side by side. By doing so hydrogen bonds are able to actually form between individual chains which are adjacent to one another. This provides for a greater amount of stability for the protein. Hydrogen bonds not only form between carboxyl groups, but between different stands of the polypeptide. Beta sheets often run in opposite directions to give parallel and antiparallel sheets.
Antiparallel Sheets
2.0 residues/turn
Rise 0.34
Parallel Sheets
2.0 residues/turn
0.32 Rise
3(10) and Pie Helices
3(10) helice and pie helices are two other helice conformations that were proposed. The 3(10) helice may be found in some proteins but is less common than that of the alpha helix and beta sheet. The pie helix, though sterically possible has not been observed . This may be to the fact that it contains a whole down the middle which is too big for van der Waals interactions to occur and to small to admit stabilizing water molecules.
Interesting Links
Explanation of Amino Acids, Polypeptide Chain, and Secondary Structure
Links to RNA Protein Structures and Structural Biology Websites
Explanaiton of All Four Helices
Main Page -- Delta G
