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Understanding Protein Secondary Structure

This document discusses protein secondary structure and the factors that determine a protein's native conformation. It addresses the following key points: 1) Proteins can exist in different conformations but have a stable native structure determined by their amino acid sequence. This native structure is stabilized by weak interactions like hydrogen bonds and hydrophobic interactions. 2) The backbone of a protein is defined by phi (φ) and psi (ψ) torsion angles, which describe the rotation of atoms around peptide bonds. Restrictions on these angles due to steric hindrance result in common secondary structure motifs like alpha helices and beta sheets. 3) The Ramachandran plot maps possible phi and psi combinations, showing allowed

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Raju Gangadharan
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104 views13 pages

Understanding Protein Secondary Structure

This document discusses protein secondary structure and the factors that determine a protein's native conformation. It addresses the following key points: 1) Proteins can exist in different conformations but have a stable native structure determined by their amino acid sequence. This native structure is stabilized by weak interactions like hydrogen bonds and hydrophobic interactions. 2) The backbone of a protein is defined by phi (φ) and psi (ψ) torsion angles, which describe the rotation of atoms around peptide bonds. Restrictions on these angles due to steric hindrance result in common secondary structure motifs like alpha helices and beta sheets. 3) The Ramachandran plot maps possible phi and psi combinations, showing allowed

Uploaded by

Raju Gangadharan
Copyright
© Attribution Non-Commercial (BY-NC)
We take content rights seriously. If you suspect this is your content, claim it here.
Available Formats
Download as PPT, PDF, TXT or read online on Scribd

Protein Secondary Structure

Lecture 2/19/2003
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

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!!
The Amide bond
Linus Pauling and Corey determined the structure of the peptide
bond by X-ray.
C
O
N C
O
N
H
-
+
40% double bond character. The amide bond or peptide bond
C-N bond is 0.13A shorter than C
o-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!!
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.
Torsion angles
Rotation or dihedral angles

C
o-N
| phi
C
o-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 C=O pointing in opposite directions.
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 180
o
or -180
o

Note: this picture and the one in the book
is not correct!! The + angle should go
the the other direction

Rotate
clockwise start
at -180
o
and
increase angle
Rotate counter
clockwise start at +180
o

and decrease angle
This is Co-carbonyl bond or psi angle, +
Start with fully extended
protein structure
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
If all C + 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.
Ramachandran plot
If you plot on the y axis and C on the x axis, you
will plot all possible combinations of C, .
This plot shows which angles are allowed or which angles are
sterically hindered for poly-l-alanine
Secondary structure can be defined by | and
angles
u +

o helix rt handed -57 -47

| sheet -119 113

+| | sheet -139 135

3
10
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
Steric hindrance between the amide
nitrogen and the carbonyl
u = -60
o
and + = 30
o

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