I'm asked to tell which of the following peptide segments is most likely to be part of a stable Alpha Helix at physiological pH? Only 1 can be chosen
1. gly-gly-gly-ala-gly
2. gly-arg-lys-his-gly
3. pro-leu-thr-pro-trp
4. lys-lys-ala-arg-ser
5. glu-leu-ala-lys-phe
6. glu-glu-glu-glu-glu
7. tyr-trp-phe-val-lie
tyr-trp-phe-val-lie
Tyr-Trp-Phe-Val-iLe is wrong because of the big bulky tyr,trp, and phe.
Anything with Gly is wrong because gly is too flexible which causes it to form other helicies.
(This is the feedback given from Sapling)
To determine which of the peptide segments is most likely to be part of a stable alpha helix at physiological pH, we need to consider the properties of amino acids and the factors that promote alpha helix formation.
The key factors that contribute to the stability of an alpha helix are:
1. Presence of small or neutral amino acids: Amino acids that are small or have neutral side chains, such as glycine (Gly), alanine (Ala), leucine (Leu), or valine (Val), tend to favor alpha helix formation.
2. Lack of bulky or charged amino acids: Amino acids with bulky or charged side chains, such as arginine (Arg), lysine (Lys), histidine (His), or glutamic acid (Glu), disrupt the helical structure due to their size or charge.
3. Regular repeating patterns: Residues that show a repeating pattern in the sequence, such as proline (Pro), which introduces a kink in the structure due to its rigid structure, or tryptophan (Trp), which is known to destabilize helices, are less likely to form stable alpha helices.
Now let's evaluate each option:
1. gly-gly-gly-ala-gly: This sequence has a small amino acid (glycine) at the N-terminus and a small amino acid (alanine) in the middle, which are favorable for alpha helix formation. However, the presence of glycine at the C-terminus can disrupt the helical structure. Overall, this segment may have some helical propensity, but it might not be the most stable.
2. gly-arg-lys-his-gly: This sequence contains two positively charged amino acids (arginine and lysine) and one histidine, which has a bulky aromatic side chain. These characteristics are generally unfavorable for alpha helix formation. Therefore, this segment is less likely to form a stable alpha helix.
3. pro-leu-thr-pro-trp: This sequence contains two prolines, which introduce a kink in the helical structure, and a tryptophan, which destabilizes helices. Therefore, this segment is unlikely to form a stable alpha helix.
4. lys-lys-ala-arg-ser: This sequence contains two positively charged amino acids (lysine and arginine), which are unfavorable for alpha helix formation. Additionally, it has a serine, which is a small amino acid and may favor alpha helix formation. However, the presence of charged amino acids outweighs this factor, making this segment less likely to be part of a stable alpha helix.
5. glu-leu-ala-lys-phe: This sequence has two small amino acids (leucine and alanine) and one charged amino acid (lysine). While charged amino acids are generally unfavorable, the positive charge of lysine could potentially interact with the negatively charged glutamic acid in the surrounding environment. This interaction might help stabilize the helical structure. Therefore, this segment has a higher probability of forming a stable alpha helix compared to the previous segments we evaluated.
6. glu-glu-glu-glu-glu: This sequence contains only charged amino acids (glutamic acid). The presence of multiple charged amino acids with the same charge is very unfavorable for alpha helix formation. Therefore, this segment is unlikely to form a stable alpha helix.
7. tyr-trp-phe-val-lie: This sequence contains aromatic amino acids (tyrosine, tryptophan, and phenylalanine) and a small amino acid (valine), which are generally unfavorable for alpha helix formation. Additionally, it has an isoleucine, which is a nonpolar amino acid and generally promotes alpha helix formation. However, the presence of aromatic amino acids and lack of small and neutral amino acids outweigh the positive influence of isoleucine, making this segment less likely to form a stable alpha helix.
Based on the analysis above, option 5 (glu-leu-ala-lys-phe) is the most likely to be part of a stable alpha helix at physiological pH.