Transcript Secondary structure of proteins - Home

The most important secondary structural elements of
proteins are:
A. α-Helix
B. Pleated-sheet structures
C. β Turns
•The most common secondary structures are
 the α-helix, the β-conformation, and turns.
α helix
The right-handed α-helix (αR) is one of the most
common secondary structures.
•The peptide chain is wound like a screw. Each turn
of the screw covers approximately 3.6 amino acid
residues.
•The pitch of the screw (i. e., the smallest distance
between two equivalent points) is 0.54 nm.
•α-Helices are stabilized by almost linear hydrogen
bonds between the NH and CO groups of residues,
which are four positions apart from each another in
the sequence
•Alpha helices are most commonly made up of
hydrophobic amino acids .
•The mirror image of the αR helix, the left handed αhelix (αL), is rarely found in nature,
PITCH
α helix
The CO group of one amino acid is hydrogen bonded
to the NH group of the amino acid four residues
away
Amino acids that can not be found in an
α-helix
 Proline: the nitrogen atom In prolineis part of rigid
ring and the rotation around N-αC bond is not
possible . In addition , the nitrogen atom of a
proline residue in peptide linkage has no
substitutent hydrogen to form hydrogen bond
with other residues . So it inserts a kink in the
chain, which interferes with the smooth, helical
structure.
 A .A residue with charged R-groups : if there large
numbers of charged a.a. (e.g. glu, asp, his, lys, or
arg) they disrupt the helix by forming ionic bonds,
or by electrostatically repelling or attracting each
other
3-Amino acids with bulky side chains: such as trp, or
a.a., such as val or ile, that branch at the β-carbon
(the first carbon in the R-group, next to the αcarbon) can interfere with formation of the α-helix
if they are present in large numbers and close to
each others.
Examples of α-helix
Alpha helices are found in almost all proteins to various
extents.
•Some proteins are entirely α –helix eg
α -keratin fibrous protein in hair.
•Other proteins have different amount of α -helix e.g.
hemoglobin has 80% α -helix
•Some proteins have no α -helices eg β–keratin in silk
α keratin
α-keratins is an example of a protein constructed almost
exclusively of α-helices .
•They are fibrous protein , insoluble and resistant to
stretching .They form tough fibers and found in hair , nails
,wool, claws, hooves, and much of the outer layer of skin
and are also constituents of intermediate filaments of the
cytoskeleton in certain cells .
•α-keratin is rich in cysteine which provides covalent
disulphide cross-links between adjacent polypeptide chains .
The -keratin helix is a right-handed α-helix .
•Two strands of -keratin, oriented in parallel
(with their amino termini at the same end), are wrapped
about each other to form a supertwisted coiled coil.
•The helical path of the supertwists is left-handed, opposite
in sense to the α-helix.
•The surfaces where the two helices touch are made up of
hydrophobic amino acid residues, their R groups meshed
together in a regular interlocking pattern.
This permits a close packing of the polypeptide chains
within the left-handed supertwist.
•So , α-keratin is rich in the hydrophobic residues Ala, Val,
Leu, Ile, Met, and Phe.
β-pleated sheet
The backbone of the polypeptide chain is extended into a
zigzag rather than helical structure
•The zigzag polypeptide chains can be arranged side by
side to form a structure resembling a series of pleats
•hydrogen bonds are formed between adjacent
segments of polypeptide chain.
•The individual segments that form a sheet are usually
nearby on the polypeptide chain, but can also be quite
distant from
each other in the linear sequence of the polypeptide;
they may even be segments in different polypeptide
chains.
The R groups of adjacent amino acids protrude
from the zigzag structure in opposite directions, creating
the alternating pattern
•The adjacent polypeptide chains in a sheet can be either
parallel or antiparallel(having the same or opposite aminoto-carboxyl orientations, respectively).
•When two or more sheets are layered close together within
a protein, the R groups of the amino acid residues on the
touching surfaces must be relatively small.
The pleated sheet:
•Holds proteins in a
parallel arrangement
with hydrogen bonds.
•Has R groups that
extend above and below
the sheet.
•Is typical of fibrous
proteins such as silk.
PARALLEL
ANTIPARALLEL
Limitations to the kinds of amino acids
that can occur in the β-structure
 R-groups of the amino acid residues on the
contact surfaces must be relatively small .
• If the R-groups are bulky or have like charges
, the pleated sheets can not exist because of
R-group interaction .
• Structural units comprising from 2-5 parallel
or anti parallel β-sheets are especially
common .
Example of β-pleated sheet structure
β-keratins contain 100% β-pleated sheet.
• Silk fibroin , a member of a class of β-keratins,
consist almost entirely of antiparallel β-sheets
• Fibroin and other β-keratins are rich in amino acids
having relatively small R-groups , particularly glycin
and alanine .
Differences between α-helix and βpleated sheets
 α-helix are rods while β-sheets are pleated sheets .
• Unlike α-helix , β-sheets are composed of two or more peptide
chains or a segments of fully extended polypeptide chain .
• A polypeptide chain in the β-sheets is almost fully extended
rather than being tightly coiled as in the α-helix
• The axial distance between adjacent a.a in β-sheets is 3.5A while
it is 1.5A in α-helix .
• β-sheet is stabilized by hydrogen bonds between NH and CO
groups in different polypeptide chains whereas in the α-helix
the hydrogen bonds between NH and CO groups in the same
polypeptide chain .
β Turns
 β Turns are often found at sites where the peptide
chain changes direction.
 β-Bends reverse the direction of a polypeptide chain,
helping it to form a compact, globular shape.
 They are usually found on the surface of protein
molecules
 These are sections in which four amino acid residues
are arranged in such a way that the course of the
chain reverses by about 180°into the opposite
direction.
 β-Bends are generally composed of four
amino acids, one of which may be proline the
amino acid that causes a “kink” in the
polypeptide chain. Glycine, the amino acid
with the smallest R-group, is also frequently
found in β-bends
 are stabilized by hydrogen bonds between
residues 1 and 4.
 β Turns are often located between the
individual strands of antiparallel pleated
sheets, or between strands of pleated sheets
and α helices
•The peptide groups of the central two residues
in β turns do not participate in any hydrogen
bonding.
•Gly and Pro residues often occur in β turns, the
former because it is small and flexible, the latter
because peptide bonds involving the imino
nitrogen of proline readily assume the cis
configuration.