Protein Secondary Structure

Alpha Helix

R-groups on outside

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each turn includes 3.6 residues

Forms more readily than other possible conformations

Due to optimal use of H bonds. H bonds between hydrogen attached to electronegative nitrogen of peptide linkage and electronegative carboxyl oxygen atom of the fourth amino acid on the amino-terminal side of that peptide bond.

Every peptide bond, except those, close to the ends of the helix, participate in such bonding

RIght handed most common

B-pleated sheets

Five factors affect ability to form

intrinsic propensity of amino acids to form alpha helices

interactions between r-groups, particularily those spaced 3-4 residues apart

Bulkiness of adjacent groups

Occurrence of Pro and Gly Residues

Pro introduces kink due to ring structure

Gly has better things to do

Interactions between amino acid residues at ends of the helical segment

B sheets can have either same or opposite amino to carboxyl orientations

Alanine most common--most likely to form

B-Turns

connect two adjacent segments of an antiparallel beta-sheet

Pro and Gly are most common

H-bonds between 1st and 4th residues

Ramachandran plots

Left handed alpha helix top right

Right handed alpha helix bottom left

Parallel and antiparallel b sheets top left