| Chem 431 |
Biochemistry |
Fall 2001 |
| Lecture Notes:: 17 September |
© R. Paselk 2001 |
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3D Structure of Proteins II
Secondary Structure, cont.
Alpha helix:
(Figure 6.8, pg 129 of your text) [overhead 2.31 S, 5.15 P] The
most frequent secondary structure is the right-handed a-helix.
- In this cylinder-like structure the amino acid residues curl
around in a spring structure.
- There is a rise/residue (movement along the axis) of 0.15
nm and a pitch (rise/turn) of 0.54 nm.
- There are 3.6 residues per turn and 13 atoms/H-bonded "ring"
- this makes it a 3.613 helix.
- Very importantly, the H-bonds are nearly linear and therefore
of near maximum strength. The side chains of the helix stick
out from the sides.
- The stability of the helix is determined in part by the side
chains. Thus glycine allows too much rotational freedom to favor
this structure, while very large or like charged side chains
can also destabilize it.
- As you might expect a proline residue stops a helix abruptly
since proline' s angles are not accommodated in the helix.
{You can look at an a-helix and
explore its properties by going to the Protein
G page at CMU, then click on helix in the top window. The
right window allows you to select a variety of views and to focus
on different aspects of the helix. Note that all of the visualization
tools seen in the exercise
operate with these images.}
Beta Strand: (Figure 6.9-.11,
pg 130, 131 of your text) [overhead 5.19 P] The next secondary
structural element is the b-strand,
which is seen in the supersecondary structures called parallel
and anti-parallel beta sheets [overheads 7.16 & 17 V&V].
- The beta strand is in a sense an abstract structure, since,
unlike the a-helix, a b-strand
does not exist alone, there is always another strand to make
a sheet.
- In the older literature b-sheets
are considered secondary structures, but they are more consistently
considered super secoundary with the current nomenclature.
- Beta strands are nearly fully extended, thus they have very
little extensibility (stretch).
- Beta strands are stabilized by hydrogen bonding to adjacent
b-strands. Thus they are stabilized
by inter-strand H-bonds whereas a-helices
are stabilized by intra-strand H-bonds.
Collagen strand: This is a specialized structure occurring
in only a particular family of fibrous proteins. It does not
occur in globular proteins that I am aware of. We will ook at
the collegen triple helix with super secondary structures below.
Non-repetitive secondary elements: Proteins can also
have non-repetitive secondary structures which consist of a few
residues in a turn or loop. Among these are:
- Type I turns: Fig. 6.12, left, p 170 [overhead 7.22, V&V]
four amino acid residues in a 180° turn, usually H-bonded
between the carbonyl O of the first residue and the amide N of
the fourth. Proline is often the second residue. [overhead, 7-22
V&V] {Go to the Protein
G page at CMU, then click on Type I turn in the top window.
Try looking at the beta-hairpin loops as well. What's the difference?}
- Type II turns: Fig. 6.12, right, p 170 [overhead 7.22, V&V]
four amino acid residues in a 180° turn, usually H-bonded
between the carbonyl O of the first residue and the amide N of
the fourth. Glycine is most frequently the third residue and
proline is often the second residue. [overhead, 7-22 V&V]
- b-bulge: Fig 6.13, p 171. One
strand has one extra, non-intrachain H-bonding, aa residue. Not
that a bulge changes the direction of the structure, but only
slightly instead of the radical change seen with a turn.
- A partial turn of a 310 helix. Short sections
of this helix often occur at the ends of a-helices
as transitional elements.
-
Tertiary Structures
The Tertiary structure describes the overall folding
of a single covalent structure.
- Lysozyme
model (on-line Chime model at CMU) [overhead, model]
- Myoglobin [overhead]
As the number of known protein structures increased additional
patterns became obvious within the tertiary level of structure:
Motifs & Domains.
Super Secondary structures (Motifs)
- Let's briefly look at the two classical structures based
on the beta-strand:
- Anti-parallel b-pleated sheet
(b-meander): strong, linear H-bonds
spaced adjacent, then R grp, then single, then R grp, then adjacent
etc. (Fig 6.11 b, p 169) [overhead 7-17 V&V, 5.19 P]
- Parallel b-sheet: evenly spaced,
but slanted H-bonds (less stable), (Fig 6.11 a, p 169)
[overhead 5.19 P]
- bab unit: alternate pattern of
beta-strands and alpha-helices
Let's next look at some other, more common motifs found in
globular proteins (Fig 6.28, p 145 of your text):
- Hairpin - b-strand-short loop-b-strand {see CMU Protein
G reference above}
- aa motif - two successive alpha-helices
with slightly inclined axis to give better contact between side
chains
- Beta barrel (Fig 6.27, p 145) [overhead 7-19, V&V; 6.15
c, MvH]
Review/Enhancement: X-ray Difraction determination of protein
structure.
- Review x-ray diffraction learned in Chem 109
- Note the each crystal point now becomes many points, each
with its own "reflecting" plane.
- Rotation to determine relative locations in three space results
in thousands of reflections
- Need to add heavy metals to act as "beacons" to
locate positions in absolute space, and need to do a couple of
times isomorphically (without altering the proteins structure
- isomorphic replacements).
- Finally use fourier transforms to convert angles and intensities
of reflections to 3-D map of protein.
-
- Last modified 17 September 2001
Pathway Diagrams
