How exactly does the primary structure of a protein influence its secondary structure?
Would the exact order of amino acids matter in this case?
Most of the backbones (except proline) of amino acids are the same, so I don't think the order of the amino acids would make a difference in secondary structure...
- 6 months agoFavorite Answer
Secondary structure is created by hydrogen bonding. The location of these interactions is determined by where the amino acids are located in the string of amino acids that make up a proteins primary structure. Thus changing the amino acid order will change hydrogen bonding because it will change the proximity of hydrogen donors and acceptors to each other.
I apologize: the location of the amino acids do play a role, but the side chains do not function as the main contributors to hydrogen bonding. The alpha helixes and beta sheets are created by the hydrogen from the amino group and the oxygen from the carboxyl group. However, the types of side chains present DOES cause changes in secondary structure. Negatively charged side chains causes repulsion preventing alpha helixes and beta sheets from forming. So, if you were to have an abundance of glutamate amino acids in a row, the repulsion of the negatively charged side chains would prevent formation of hydrogen bonds at that particular region. Also, the placement of amino acid side chains plays a role in secondary structure. Changing the placement of positivity and negatively charged side chains also cause destabilization, decreasing the formation of hydrogen bonds. So, a change in amino acid sequence will change the formation of hydrogen bonds because of repulsion and attractive forces between different R groups of the amino acids.
- Anonymous6 months ago
The primary structure of proteins determines secondary and tertiary structure. Even though an entire amino acid is electrically neutral, there are some parts that are slightly more positive and other parts that are more negative. Adjacent amino acids may attract or repulse one another based on those charges and the arrangements of their atoms. If the parts of two adjacent amino acids that are close to each other attract each other, it would result in a different shape than if they repulse one another.
- 6 months ago
Secondary structure is formed mainly as a result of hydrogen bonding between the carboxyl group of one amino acid and the amino group of another amino acid, forming alpha helices and beta-pleated sheets. There are other types of folds, but they aren't that common.
"Different amino-acid sequences have different propensities for forming α-helical structure. Methionine, alanine, leucine, glutamate, and lysine uncharged ("MALEK" in the amino-acid 1-letter codes) all have especially high helix-forming propensities, whereas proline and glycine have poor helix-forming propensities. Proline either breaks or kinks a helix, both because it cannot donate an amide hydrogen bond (having no amide hydrogen), and also because its sidechain interferes sterically with the backbone of the preceding turn – inside a helix, this forces a bend of about 30° in the helix's axis. However, proline is often seen as the first residue of a helix, it is presumed due to its structural rigidity. At the other extreme, glycine also tends to disrupt helices because its high conformational flexibility makes it entropically expensive to adopt the relatively constrained α-helical structure."
According to wikipedia, the propensity for alpha helices to form is dependent on the sequence of amino acids, as some have more free energy on their residues than others (less free energy = higher likelihood to form an alpha helix). I assume this is similar in regard to beta-pleated sheets, but you can look that up yourself if you are interested :)
In general, secondary structure is dependent on primary structure because some sequences and individual amino acids have a higher propensity to form alpha helices and beta-pleated sheets, which can be measured by the amount of free energy available on the residues of those specific amino acids.Source(s): https://en.wikipedia.org/wiki/Alpha_helix