# Protein Secondary Structure The most common regular secondary structures are: - $\alpha$- helix - $\beta$-sheet - parallel vs antiparallel - $\alpha$-keratin - two right-handed “$\alpha$-helix”-like helices - heptapeptide repeat $(A-b-c-D-e-f-g)_n$ with residues A & D being nonpolar - no proline or glycine (would heavily influence structure) - collagen (triple helix) - three left handed helices (requires a lot of prolines and glycines) - Gly - X - Pro/Hyp - - Gly - Pro **Salt Bridges:** - https://en.wikipedia.org/wiki/Salt_bridge_%28protein_and_supramolecular%29 - The bonding energy of a salt bridge is significantly higher than that of a sole hydrogen bond - Salt bridges are a combination of two noncovalent interactions: hydrogen bonding & ionic bonding - Remember that hydrogen bonds are not a type of ionic bond/pairing - The difference in electronegativity between the Hydrogen and it’s bonded atom is so high that Hydrogen imitates having a partial charge ## Alpha Helices ![[Pasted image 20240226111933.png|400]] ![[Pasted image 20240226111829.png|400]] 3.6 residues per turn (not a perfect repeat) - when amino acids #### Stabilization & Disruption of Helices 1. Proline 2. Glycine 3. Bulky Aromatics 4. Electrostatics Steric Effects: - Proline has a significant impact on the polypeptide folding due to its bond to the alpha carbon amino group (too rigid) - Glycine is far too flexible due to its side chain only consisting of a hydrogen (too noodley) - Bulky aromatic residues (Tyrosine, Tryptophan, Phenylalanine) are more likely to collide and disrupt stability of helix Electrostatic Effects: - The position of residues relative to their neighbors can contribute to destabilization or stabilization depending on its properties - Two nearby negatively charged residues would repel eachother and disrupt the helix - When checking for electrostatic interaction, compare the charges of the a.a. 3-4 positions down (3.6 per turn) As a result of these factors, a single amino acid mutation can make significant changes to the formation of the $\alpha$-helix #### Coiled Coil Interactions A subset known as a **coiled coil** can form when multiple $\alpha$-helices wrap around eachother in a sort of “helical bundle”; can be tertiary (same protein) or quaternary (different protein) - Ex: keratin, myosin, collagen ![[Pasted image 20240226113016.png|300]] ## Beta Sheets ![[Pasted image 20240226113844.png|400]] A $\beta$-strand needs another $\beta$-strand to form a $\beta$-sheet (whereas $\alpha$-helices are “self-contained”). The carbonyl group of one stand and the NH groups on the adjacent strand connect to maximize H-bond formation - Typically, a $\beta$-sheet region is composed of 4-6 separate strands, each of which are 8-10 residues in length - Adjacent amino acids are related by a rotation of 180 degrees, causing side chains to emerge from opposite sides (alternating up and down) - Spider silk is an example of $\beta$-sheets stacked on top of eachother → a lot of Antiparallel $\beta$-Sheets - H-bonds are strongest at linear angles, causing parallel $\beta$-sheets to be relatively weaker ### Turns and Loops Some polypeptide sections are less regular (random coil) and allow for turns to occur at the ends of alpha helices and beta sheets - Turns are typically very short to minimize the amount of unfilled H-bonds (especially of the carbonyl & NH groups) - Typically composed of proline (assists in turning) or glycine (assists in flexibility) --- beta sheets and alpha helices don’t tend to interact with eachother ### Additional - beta sheets can form larger helical structures - Collagen is a left-handed helix, right-handed superhelix