Transcript Alpha Domain Structures, ppt file

CS882, Fall 2006
Lecture 3. α domain
structures
•Coiled-coil, knobs and hole packing
•Four-helix bundle
•Donut ring large structure
•Globin fold
•Ridges and grooves model
Packing together, they are stabler
 While isolated α helices often occur in proteins, they
are only marginally stable.
 They are stabilized by being packed together through
hydrophobic side chains.
 We will worry about membrane proteins later.
 Project: classify all alpha helix occurrences in the
PDB. In PDB, they tell you which amino acid belongs
to an alpha helix. However, you will need to decide
properly which structure an alpha helix belongs to.
Coiled coil
 In 1953, Francis Crick showed that the side chain interactions
are maximized if the two alpha helices are wound around each
other in a “coiled coil” arrangement.
 Such structures are the basis of some fibrous proteins, and
others. For fibers, sometimes many hundreds of amino acids to
make long flexible dimmer.
 Shorter coiled-coils are also used elsewhere.
Left handed supercoil
from two right-handed helices
The heptad repeat
 Number of residues per turn
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reduced from 3.6 to 3.5.
The pattern of side chain interaction
repeats every 7 residues, after 2
turns.
Such sequence is repetitive with
period 7.
One heptad repeat is labeled a-g.
Residue d is hydrophobic: often a
leucine. Residue a is also
hydrophobic
The side chains of e and g (often
charged a.a.) form ionic interactions
between 2 helices
Heptad structure and prediction?
 ‘d’ residue packs against
each other, ‘a’ residue packs
against each other.
 Heptad repeats provide
strong indications of alpha
helical coiled coil structures.
 They are found in many
proteins of diverse functions.
 Project: predicting such
structures? This not only
helps to predict secondary
but also double helices,
helping 3-D prediction.
Holding up two helices
 ‘a’ packs with ‘a’, and ‘d’
with ‘d’ (2 levels
squashed view)
 The e-g salt bridges
stabilize coiled coil
structures.
Just one side of helices,
From e’s to g’s.
Crick’s Knobs and hole model
 Alpha helices pack against each other according to knobs and hole
model:
 Side chain in the hydrophobic region of one alpha helix can contact
4 side chains from the other helix.
 The side chain of the residue at position d is directed into a hole at
the surface of the other helix, surrounded by 1 ‘d’, 2 ‘a’’s, 1 ‘e’, with
numbers n, n-3, n+4, n+1, resp.
 Two ‘d’s face each other (usually leucine, isoleucine)
knobs
Two
parallel
helices
holes
Superimpose
Four helix bundle
 Two alpha helices are not
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enough to build a domain.
The simplest and most frequent
alpha-helical domain is 4 alpha
helix bundle.
Green = hydrophobic residues,
packed inside hydrophobic core;
red = hydrophilic residues.
20o
This appears in many proteins
for oxygen transport, electron
carriers, storing iron atoms, coat
protein for some virus.
Project: predicting 4 helix
bundles? (Collect data first)
4 helix bundle
 Usually in 4 helix
bundle adjacent
helices are
antiparallel, such
as in Cytochrome
b562
 But other topology
is also possible, as
in Human growth
hormone: two pairs
of parallel helices,
joined in
antiparallel fasion.
Cytochrome b562
Human growth hormone
A pair of coiled coils packed with
knobs in holes model
 Rop protein has two
subunits.
 Each subunit is an
antiparallel coiled-coil in
which the hydrophobic side
chains are packed against
each other according to the
knobs and holes model.
 Two such subunits are
packed according to the
“ridges and grooves” model.
Rop protein
Large and complex ones
 Several enzymes are known
to have long polypeptide
chain of 300-400 a.a.
arranged in over 20 alpha
helices packed together in a
complex pattern to form a
globular domain.
 Bacterial muramidase:
 618 aa.
 450 aa at the N-terminal
side form a alpha-helical
domain
 27 alpha helices
 2 layered ring
 Diameter 30A
 Right handed super twist
The globin fold
Contains iron
 This fold has been found in many
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related proteins: myoglobin,
hemogobin, light capturing
assemblies in algae, …
Very different from 4 helix bundle,
The 8 helices are connected by
short loop regions, forming a
pocket for active site (this site for
myoglobin and hemoglobin binds
a heme group).
Length varies from 7 (C) to 28 (H)
in myoglobin. Adjacent helices
are not sequentially adjacent
(except for G and H which form
antiparallel pair).
Not from smaller motifs.
Globin fold: 8 alpha helices: A-H.
The white is heme group.
Ridges and grooves model
Groove
A helix.
Each aa
is represented
as one ball.
Treat that as
side chain.
In principle, the
ridges and grooves
are formed by side
chains that are
4 or 3 aa apart,
ridges fit into
grooves, when fold.
Ridges, every
3 amino acids,
counting from a
different angle
Ridges every 4
Amino acids
Grooves, between the ridges
How they fit: 250 and 500 angles
4-aa ridge fit 4-aa:
•Helix 2 flip over
•Superimpose on helix 1
•Turn 500, fit
ridges and grooves
3-aa ridge fit 4-aa ridge
•Helix 2 turn 450
•Superimpose on helix 1
•Turn helix 2 200, 4-3 fit.
Evolution: what affects protein fold?
 People studied 9 globin structures, trying to figure our what
positions are important for protein to be folded that way.
 They choose some “important” positions (functionally, or
structurally) trying to see what made the difference.
 They found essentially nothing (including size of amino acids,
matters, except there is a striking preferential conservation of
the hydrophobic character of the amino acids at the buried
positions.
 On the other hand, at the exposed positions, it actually does not
matter whether we have mutations from hydrophilic to
hydrophobic or vice versa, with one exception: the amino acid 6
in the beta chain in myoglobin (sickle cell disease)
 Project: do this study in a larger class of proteins, and more
carefully. (You can find protein class information at PDB, PFam,
SCOP websites.) Other structures, not just helix?