Branden and Tooze (BT), Introduction to Protein Structure, Chapter 2.
A tutorial on the secondary structure of proteins using CHIME plugin for Netscape (Netscape Navigator 3.01 only) is available from U. Mass.; click here (U. Mass)
The secondary structure of proteins can also be examined by visiting the website at Carnegie Mellon University (click here)
A most comprehensive chapter on the protein secondary structure containing numerous 3D-images can be examined at this site set up by K. D. Berndt of Karolinska Institute of Sweden (click here)
Secondary Structure- The secondary structure of globular protein refers to the regular, recurring, and localized structure of the backbone atoms in the polypeptide chain. There are three common types: helix, b-sheet, and b-turn. Within each type, there are several distinct forms, which are specified by their characteristic (f, y) values and H-bonding patterns.
Helix. This is the most abundant type of secondary structure, characterized by a spiral conformation of the polypeptide backbone. We shall apply the PDB data to examine three forms of helices. In particular, we shall first look at two distinct forms of helix, the right-handed a-helix and the 3.010-helix, found in hemoglobin. Hemoglobin is a tetrameric protein consisting of two a-subunits and two b-subunits. The a-subunit has 141 amino acid residues, and b-subunit has 146. The polypeptide chain of the b-subunit has 8 helical segments, A through H. The a-subunit, however, has 7, lacking the D helix. With the exception of C helix, all helical segments in hemoglobin are right-handed a-helices. We can now use RasMol program, a molecular modeling graphics, to examine the 3D-structure of the A-helix (residues 3 (Ser) to 18 (Gly)) in the a-chain of human hemoglobin (1hba.pdb) .
a-Helix. After you click on (1hba.pdb), the 3D-structure of a2b2-hemoglobin shows up in the display (or main) window. In addition, you should see an icon called 'RasMol Command Line' at the bottom of the screen. Open it, and you can arrange and see both the display and command-line windows simultaneously. The command-line window can accept commands that you type. Now you type sequentially the following command lines:
restrict 3-18a and mainchain You can zoom in the 3D-image of the
A-helix with the mouse's left button while holding down the shift
key. You can carry out the translational motion of the image along the
X- or Y-axis with the mouses's right button. By holding down the shift
key while pressing the mouse's right button, you can rotate the image around
the Z-axis. You can also rotate the image on the screen by pressing the
mouse's left button and then move the mouse around. Now, you can take a
close look at the right-handed a-helix.
3.010
Helix.
The C-helix in the a- or b-subunit
of hemoglobin is a 3.010 helix. You can use the following command
lines to generate the 3D-image of the backbone of C-helix from the a-subunit
of hemoglobin
(1hba.pdb):
restrict 36-42a and mainchain
Now, you can examine closely the structural
features as well as the H-bonding pattern associated with the 3.010
helix.
Kinked helix. If a proline residue is present
in the interior of an a-helix, the basic structure
of
a-helix is modified. Specifically, the helical
axis is kinked by ~25o from the linear conformation. Furthermore,
the total number of H-bonds in the helical segment is reduced by 2. You
can examine the 3D-image of a kinked helix containing 22 residues by clicking
first the membrane protein mellitin (2mlt.pdb)
followed by typing the script in the Command-Line Window as given below:
restrict ((2-13a) and mainchain), pro14a, ((15-23a) and
mainchain)
A kinked helix should appear on the
main window. You can now take a close look at the steric effect of proline's
cyclic side chain (colored cyan) on the neighboring residues in the helical
structure.
b-Sheet.
This is the second element of protein secondary structure. Two or more
polypeptide segments within a protein can pair up by H-bonds to form b-sheets.
Unlike a-helix, adjacent segments (or strands)
linked by H-bonds can come from distant sequence of the chain. The (f,
y)-angles are (-119o, +113o) for pure parallel
and (-139o, +135o) for pure antiparallel b-sheets.
In either case the (f,y)-space is larger than
that of the a-helix. The b-sheet
is thus a more extended structure.
define s1 (lys41.CB, pro42.CB, val43.CB, asn44.CB, thr45.CB,
phe46.CB, val47.CB, his48.CB)
Using a similar approch, 3D-images of parallel b-sheets
in globular proteins can also be generated. A three-strand parallel b-sheet
obtained with flavodoxin (5nll.pdb)
is
shown in the demo-page.
Now you can use these 3D-images to examine the structural
features of b-sheets in proteins. In these images
, all beta-carbons are colored black.
b-turn. This is the third element of protein secondary structure.
There are three basic types of ideal b-turn.
Type 1 is the most common one with (f2, Y2) and (f3, Y3)
being (-60, -30) and (-90, 0), respectively. You can examine the 3-D structure by clicking
Type I turn. Type II is very similar to Type I, except that the central amide plane flips by 180o
and that the third residue must be glycine. The values of
(f2,Y2) and (f3,Y3)
for Type II b-turn are (-60, 120) and (80,0). You can
examine this structure by clincking Type II turn.
Type III turn is simply a single turn of 3.010 helix with repeated
(f,Y) of (-60, -30). It can be seen by clicking Type III turn
center val10a.N
wireframe 80
hbonds 10
background white
First, align the A-helix of hemoglobin
molecule, an a-helix, along the X-axis and see
how many H-bonds are present in this helical segment composed of 16 residues.
Furthermore, the H-bonding pattern (C=Oi....H-Ni+4)
should be recognized.
Next, align the A-helix along the
Y-axis and look at the directions of carbonyl C=O groups. The N- and C-termini
are Ser and Gly, respectively. If you click on any atom at one end of the
helical segment, RasMol will report back to you the name of the atom. In
addition, the residue in which the atom belongs will also appear on the
Command-Line Window. Hence, you will be able to identify the N- or C-terminus
of the A-helix. Now, you should be able to find out whether the C=O bond
in an a-helix is pointing at the N- or C-terminus of the
sequence.
Finally, align the A-helix along the
Z-axis with the N-terminus facing you. Here, you have a top view by looking
down the helical axis. With this view, you will note that Ca
atoms of all residues in an a-helical segment
are located at the square corners of the 'helical wheel' .
center thr39a.N
wireframe 80
hbonds 10
background white
center pro14a.Ca
wireframe 60
hbonds
select pro14a and sidechain
color cyan
background white
Ribonuclease has two b-sheets.
One comprises three strands, which are antiparallel. We can examine a section
of the 3-D imagine of the antiparallel b-sheet
of ribonuclease by clicking first the PDB file (5rsa.pdb)
and then type the following command lines:
define s2 (met79.CB, ser80.CB, ile81.CB, thr82.CB, asp83.CB,
cys84.CB, arg85.CB, glu86.CB, thr87.CB)
restrict ((41-48) and mainchain),s1, ((79-87) and mainchain),s2
wireframe 80
hbonds 20
color hbonds cyan
center thr82.N
background [230, 230, 230]
select (s1, s2)
color black