Secondary/ tertiary structure of proteins

[Cheman]

Why does the secondary/ tertiary structure of a protein exist? Is it due to the fact that all the bonds in polypeptide are not straight as we tend to draw them? ie - bond angle, such as the 109.5 degrees for C-C, exist and also bonds are free to rotate unless hydrogen bonds are present. (as they are in polypeptides.)

Thanks in advance.

 

[quetzalcoatl9]

the so-called "weak forces" are responsible for giving a complex molecule it's conformation. note that there isn't necessarily one fixed conformation, but a probability based upon the total energy of the molecule. the lowest energy state is generally considered to be the true conformation, but this is not always true in living systems.

obviously the bond angle of a peptide bond (and rotation around it) will influence this, but the weak force interactions between the amino acid side chains is primarily responsible for giving the protein its conformation.

actually computing these conformations based upon the amino acid sequence is an incredibly difficult challenge, as you can probably imagine.

 

[Monique]

Sulfur bridges play an important role in protein folding, also weak forces such as ionic bonds, van der Waals forces, hydrogen bonds, burying of non-polar side chains etc.

 

[quasi426]

In order to understand why secondary structures occur such as two of the more ubiquitous secondary structures (alpha helix and the beta sheets) one must understand the hydrophobic effect. I can expand on this if someone requests but basically the hydrophobic sidechains tend to be buried in the core of the protein and the hydrophilic amino acid sidechains tend to be exposed on the surface-water interface. One then may say, "Well so what if the side chain is nonpolar/hydrophobic all amino acids are composed of a polar carboxyl and amino component." So nature has a way of satisfying all these polar groups with hydrogen bonds through secondary structures such as alpha helices and beta sheets.

 

[quasi426]

Why does the secondary/ tertiary structure of a protein exist? QUOTE]

The tertiary structures of a protein or the three dimensional shape a protein takes in solution is basically a thermodynamically driven process. There is one shape that the protein can assume where its Gibbs free energy will be the most negative. So just think of all the amino acid sidechains rotating and bending into a final conformation where the free energy is at a minimum. This process is directly dependent on the environment or the solution the protein! For example at very high temperatures the tertiary structure is different then it is in physiological conditions, it is generally "denatured" or not in its native state. This just means that it is not in the same fold it is in physiological conditions. Also remember that a proteins tertiary structure, like most biochemical phenamena, is not static. It is constantly "breathing" or moving due to side chain rotations etc.