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Protein Secondary Structure (Alpha Helix (Five factors affect ability to…
Protein Secondary Structure
Alpha Helix
R-groups on outside
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
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
Alanine most common--most likely to form
B-pleated sheets
B sheets can have either same or opposite amino to carboxyl orientations
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