Secondary Protein - Structure

Introduction:
The secondary protein structure is the specific geometric shape caused by
intramolecular and intermolecular hydrogen bonding of amide groups. The geometry
assumed by the protein chain is directly related to molecular geometry concepts of
hybridization theory. Experimental evidence shows that the amide unit is a rigid planar
structure. This is derived from the planar triangle geometry of the carbonyl unit ( C =
O ). See the graphic on the left.
The geometry around the nitrogen is derived from an unusual situation with a planar
triangle geometry. Apparently, the double bond on oxygen can alternate to make a double
bond between carbon and nitrogen. Rotation around bonds C-C and N-C does take place.
The C=O and NH are always in a rigid plane. Notice that the carbonyl group and the
hydrogen on nitrogen are almost always trans to each other. The result is that chains of
amino acids as peptides with amide bonds reflect this geometry.
As a result of studying X-ray photographs and constructing molecular models, Linus
Pauling and Robert Cory, in 1951, proposed that the protein structures were either in the
form of an alpha helix or the beta pleated sheet.

Click for larger image

Alpha Helix:
In the alpha helix, the polypeptide chain is coiled tightly in the fashion of a spring. The
"backbone" of the peptide forms the inner part of the coil while the side chains extend
outward from the coil. The helix is stabilized by hydrogen bonds between the >N-H of
one amino acid and the >C=O on the 4th amino acid away from it.
One "turn" of the coil requires 3.6 amino acid units. The helix can be either right-handed
or left-handed in the sense of threads on a screw. The naturally occurring alpha helixes
found in proteins are all right-handed. Not all proteins have a helical structure, since
some do not have it at all and are random.
Alpha Helix :Main peptide in Chime is minus the hydrogens atoms. Also see "Different
Protein" to see all hydrogen atoms present in a 10 alanine peptide.
 Click for larger image

Structure of Silk:
The secondary structure of silk is an example of the beta pleated sheet. In this structure,
individual protein chains are aligned side-by-side with every other protein chain aligned
in an opposite direction. The protein chains are held together by intermolecular hydrogen
bonding, that is hydrogen bonding between amide groups of two separate chains. This
intermolecular hydrogen bonding in the beta-pleated sheet is in contrast to the
intramolecular hydrogen bonding in the alpha-helix.
The hydrogen on the amide of one protein chain is hydrogen bonded to the amide oxygen
of the neighboring protein chain. The pleated sheet effect arises form the fact that the
amide structure is planar while the "bends" occur at the carbon containing the side chain.
See the graphic on the left.
Fortunately, the "side" chain R groups in silk are not very bulky. The basic primary
structure of silk consists of a six amino acid unit that repeats itself. The sequence where
every other unit is glycine in silk is: -gly-ala-gly-ala-gly-ala-. Although glycine and
alanine make up 75-80% of the amino acids in silk, another 10-15% is serine and the
final 10 % contain bulky side chains such as in tyr, arg, val, asp, and glu.
These amino acids with bulky side chains disrupt the regular patterns set by the gly-ala-
ser. Different species of silkworms produce different portions of ordered and disordered
regions. The disordered regions provide a small amount of elasticity since the ordered
beta-pleated sheet is already fully extended and cannot stretch further without breaking.
The beta pleated sheet motif is found in many proteins along with the alpha helix
structure. The chains may run parallel (all N terminals on one end) or anti-parallel (N
terminal and C terminal ends alternate). See small graphic on left.