Transcript Extra slides (lecture Fri. 10/10)

Examples of two kinds of ‘b-turns’ in proteins
Text, Figure 6-14
Geometric details are
not so important for
our discussions. One
point to note however
is that Pro and Gly are
very common in turns.
Pro tends to break
typical a and b
secondary structure
elements (why?), and
its restricted geometry
can help force a bend.
Gly is the most flexible
and so can
accommodate angles
not allowed for other
amino acids.
Different amino acids prefer different types of
secondary structures (or turns)
Importance:
Text, Table 6-1
Table 6-1
• Important to take
into account if
you were
engineering
different amino
acids into a
protein
• Important for
predicting (2°)
structure from
sequence
Different classes of protein architecture
Basic
elements of
secondary
structure
‘Globular proteins’: combination
of 2° elements into a globular
shape, generally with a
hydrophobic core, typically
soluble, cytosolic, includes most
enzymes.
Fibrous or filamentous proteins:
extended repetition of 2°
elements, typically structural,
insoluble (e.g. keratin, collagen).
Transembrane: restricted
combination of 2 ° elements in the
lipid bilayer – bundles of ahelices or a b-barrel.
lipid bilayer
An example of a repetitive structure present in
fibrous proteins such as keratin: ‘coiled coils’
Looking down an a-helix: Almost repeats after 7
residues (7*100° = 700°, which is close to but just
short of 2 complete turns (720 °). Sometimes a
sequence pattern can be seen repeating about
every 7 residues (positions a and d being
hydrophobic, so that two helices line up side by
side). The twisting results from 700° being short
of two full turns.
Figure 6-15a
Similar (but shorter)
coiled-coils (or ‘leucine
zippers’) occur also in
globular proteins.
Another repetitive structure in fibrous proteins:
the collagen triple helix
• highly repetitive sequence (GXX)n, where X’s are
usually proline or hydroxyproline
Text, Figure 6-18
Figure 6-18
Fibrous proteins often
employ unusual amino
acids (and covalent
cross-links)
prolyl hydroxylase
proline
Figure 6-19
Vitamin C deficiency causes scurvy
hydroxyproline
required for collagen
synthesis
Fibrous proteins often
employ unusual amino
acids (and covalent
cross-links)
Text, Figure 6-19
unusual cross-linking of
multiple side chains used to
hold together multiple collagen
fibrils
Figure 6-19
Globular proteins: methods for determining
3D structures at atomic level detail
• X-ray crystallography
• the dominant method
• practically no size limit (e.g. whole ribosome,
whole viruses, etc.), as long as crystals can be
grown
• Multi-dimensional NMR
• useful for smaller structures
• no crystals required
• can give more dynamic information
• Electron microscopy
• newer instruments are making it possible to
approach atomic level detail for special cases
(e.g. icosahedral viruses)
Figure 6-19
An extreme oversimplification of protein Xray crystallography
pure
protein
an ‘electron
density map’,
showing the
distribution of
electron density
in 3-dimensions
(note that
electrons are
what scatter Xrays)
X-ray
diffraction
experiment
special computer
programs and
expertise
In X-ray crystallography, the level of detail
you can see is described by the ‘resolution’
Text, Figure 6-23
What the heck? This textbook figure is
seriously wrong about what you can see
at different levels of resolution.
Figure 6-23
NMR structure determination works under
different principles
• different types of experiments make it possible
to establish the secondary structure of different
parts of the protein, and to establish distances
between different amino acid residues
• knowing the distances between groups makes it
possible to infer 3D positions for the atoms
Figure 6-24
NMR can give
a more
dynamic
picture of a
protein,
although
uncertainty in
positions can
be hard to
discriminate
from dynamics
Globular protein structure arises from
combinations of 2° elements. Some
patterns are very common.
Text, Figure 6-28
Figure 6-28
Globular protein structures are sometimes
classified as all a, all b, or a/b
Text, Figure 6-29
Figure 6-29
Even within the same class, tremendous
variety is possible.
Two very different antiparallel beta structures are shown.
Note the differences in connectivity and overall shape.
Figure 6-30a
Larger proteins are generally arranged in
multiple ‘domains’.
A domain is typically described
as an ‘independently folding
unit’, which is sometimes hard
to define or establish.
The protein at the right has two
domains.
Distinct domains are usually formed by
contiguous regions of the primary
structure, like an N-terminal domain
and a C-terminal domain, but there are
exceptions in which the domains are
discontinuous. in which case the
backbone passes more than once
between domains.
Evolutionarily related proteins, whose
sequences have diverged very far in evolution,
may retain their common structure.
This has revealed a tremendous amount of information
about protein function, cell biology, and evolution in
general.
Text: “Thus, it appears that the essential structural and functional
elements of proteins, rather than their amino acid residues, are conserved
during evolution”.
Figure 6-32
Evolutionarily related proteins, whose
sequences have diverged very far in evolution,
may retain their common structure.
This has revealed a tremendous amount of information
about protein function, cell biology, and evolution in
general.
structure of the
structure of the
tubulin subunits
that assemble to
make the
eukaryotic
microtubule
bacterial ftsZ
protein, now
understood to be
part of a primitive
bacterial
cytoskeleton. Its
amino acid
sequence is so
divergent from
tubulin that no
similarity could
be detected until
the structures
were known.
Quaternary structure (4°):
Types of oligomers (‘oligo’ meaning “few”):
• homo-oligomeric (multiple copies of the same
subunit)
• e.g. a2, a3, a4, etc. (where a refers to the ‘subunit’
identity, not an a helix)
• hetero-oligomeric (different protein chains)
• e.g. ab, a2b2, a2bg, etc.
• sometimes the distinct subunits in a heterooligomer are actually similar (e.g. evolutionarily
related to each other), making them ‘almost’
homomeric. Hemoglobin (a2b2) is a well known
example.
Figure 6-33
Quaternary structure (4°):
Homo-oligomers (and pseudo homo-olgomers) are
nearly always arranged in a symmetric fashion so
that every subunit is in essentially the same
environment as the other identical ones. This
gives rise to two general situations:
• essentially linear (or sometimes
tubular) filaments or helices
• finite symmetric assemblies
a structural protein
from a large capsid
Figure 6-33
actin filament
hemoglobin
Illustration of
the types of
symmetry
possible for
protein
assemblies
1 subunit: monomer
2 subunits: dimer
3 subunits: trimer
4 subunits: tetramer
5 subunits: pentamer
6 subunits: hexamer
.
.
.
Figure 6-34
Cyclic symmetries
Text, Figure 6-34a
For larger n, tend to look like
a ring (or cycle) of subunits
Figure 6-34a
Dihedral symmetries
For n>2, tend to look like
double-ring structures
Figure 6-34b
Cubic symmetries
a model of the
carboxysome shell
Includes:
• some rare enzyme
complexes
• nearly all protein capsids
(i.e. viruses)
Figure 6-34c