Protein Secondary Structure

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Protein Secondary Structure

• Lecture 2/19/2003

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Three Dimensional Protein Structures
Confirmation Spatial arrangement of atoms that
depend on bonds and bond rotations. Proteins can
change conformation, however, most proteins have
a stable native conformation. The native
protein is folded through weak interactions a)
hydrophobic interaction b) Hydrogen bonds c)
Ionic bonds d) Van der Waals attractions
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A Denatured protein is unfolded, random dangling,
and often precipitated (cooking egg whites). The
Native conformation is dictated by its amino acid
sequence. ? primary structure is everything. A
one dimensional strand of DNA contains four
dimensional data height width depth
life span!!
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The Amide bond
Linus Pauling and Corey determined the structure
of the peptide bond by X-ray.
40 double bond character. The amide bond or
peptide bond C-N bond is 0.13A? shorter than C?-N
bond. The carbonyl bond is .02 A? longer then
those for ketones and aldehydes Resonance gives
85 kJmole-1 stability when bond is planar!!
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Peptide bonds are planar Resonance energy depends
on bond angle 180? is max angle ? cis or trans
peptide bond. Most peptide bonds are trans, 10
that follow proline may be cis Note differences
between bond angles and bond lengths comparing
cis and trans forms.
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Torsion angles
Rotation or dihedral angles C?-N ? phi C?-C
? psi When a peptide chain is fully extended
the angles are defined as 180? or -180?. At
180? one gets a staggered conformation. (all
trans) i.e. ethane
Note alternating CO pointing in opposite
directions.
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When viewed down the N to C terminus axis,
rotation to the right or clock wise increases the
angle of rotation. Must start with the fully
extended form which is defined as 180o or
-180o Note this picture and the one in the book
is not correct!! The Y angle should go the the
other direction
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Start with fully extended protein structure
Rotate counter clockwise start at 180o and
decrease angle
Rotate clockwise start at -180o and increase angle
This is Ca-carbonyl bond or psi angle, Y
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Ethane can exist as staggered or eclipsed
conformation
Staggered
eclipsed
There is a 12 kJmole-1 penalty in energy for an
eclipsed geometry Bulky amino acid side chains
have a much higher energy penalty. There are a
few favored geometries which the protein backbone
can fold
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If all ? ? angles are defined then the backbone
structure of a protein will be known!! These
angles allow a method to describe the proteins
structure and all backbone atoms can be placed in
a 3d grid with an x, y, z coordinate.
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Ramachandran plot
If you plot ? on the y axis and ? on the x axis,
you will plot all possible combinations of ?, ?.
This plot shows which angles are allowed or which
angles are sterically hindered for poly-l-alanine
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Secondary structure can be defined by f and y
angles
F Y ? helix rt handed -57 -47 ?
sheet -119 113 ?? ? sheet -139 135 310
helix -49 -26 collagen -51 153
Repeating local protein structure determined by
hydrogen bonding helices and pleated sheets.
12 proteins except for Gly and Pro
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Steric hindrance between the amide nitrogen and
the carbonyl
F -60o and Y 30o