* Secondary structure -- protein folding brought by linking carbonyl and amide groups of the backbone together by means of hydrogen bonds
Types: alpha-helices, beta-sheets, turns and loops
Linus Pauling -- predicted right-handed alpha-helix and planar peptide groups
Why do alpha helices form?
- Solved by Linus Pauling, to neutralize the main-chain atom charges (NH and C=O) making hydrophobic cores possible through hydrogen bonding
- Formed by phi (X) and psi (Y) angles of -60 and -50 degrees (bottom left quadrant of Ramachandran plot)
Alpha-helix measurements
- 3.6 residues per turn (H-bond froms between n and residue n+4)
- 5.4A patch, so one full turn is 5.4A tall
- Therefore, each additional residue gives a rise of 1.5A per residue (5.4A/3.6residues)
- Mostly right-handed, thumb points in the direction of translation (N-termini to C-termini), finger curls in the helix curling direction
end of helices (N+) usually found on the surface of the proteins
side-chains in alpha-helices are outside and points downward looking like a christmas tree
**bad Proline, produces steric, no H in NH bond to donate, so interferes with H-bond pattern
solvents (h2O) also causes bends
preference for (aliphatic): ala, leu, glu, met
against (hydroxyl): pro, gly, ser, tyr
Locations
* surface helices: amphipathic (high hydrophobic moment, 50% hydrophobic 50% hydrophilic
* membrane helices: hydrophobic (low hydrophobic moment, all hydrophobic)
* soluble helices: hydrophilic (low hydrophobic moment, all hydrophilic)
helical wheel to help determine hydrophobic moment (50-50 hydrophobic, hydrophilic)
Non-common helices / variations:
- pi helix (n+5)(4.3-16) (short and stuby, more residues per turn)
- 3-10 helix (n+3) (3 residues = 10 atoms per turn)
groove - the through, bottom, A long narrow furrow or channel.
ridge - the one pointing up, A long narrow elevation on the ocean floor.
http://www.cryst.bbk.ac.uk/PPS2/course/section9/9_helhel.html
- i+4n ridge (more common) than i+3n (slightly more slanted) ridge
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