Lecture11-TertStr -...

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Unformatted text preview: BIOC*2580
Lecture
11:
Tertiary
structure
&
protein
folding
 
 1
 
 Synopsis:
 Proteins
 consist
 of
 polypeptide
 chains
 that
 fold
 up
 in
 a
 highly
 specific
 manner.
 The
 starting
 point
 for
 folding
 is
 the
 formation
 of
 secondary
 structure,
 which
 is
 a
 function
 of
 the
 amino
acid
sequence.
Interruptions
of
the
regular
secondary
structure
by
"breaker"
amino
acids
 create
 points
of
flexibility
in
the
backbone.
Folding
is
then
largely
determined
by
clustering
of
 nonpolar
 side
chains
to
form
the
core
of
a
globular
protein.
The
majority
of
proteins
fold
into
a
 few
distinct
patterns:
α‐helix
clusters,
antiparallel
β‐barrels,
parallel
α/β
barrels
and
parallel
α/β
 sandwiches.
 
 Reading:
Lehninger
p.
123‐138
(4th
ed
p.
125‐144).

 
 
 Fibrous
proteins
and
globular
proteins
 
 The
simplest
tertiary
structure
for
a
protein
to
adopt
is
a
single
uniform
secondary
structure:
 
 α ‐keratin
is
alpha
helix
(Lehninger
Fig.
4‐10
(4th
ed
Fig.
4‐11))
 
 fibroin
(β‐keratin)
is
antiparallel
β ‐sheet
(Lehninger
Fig.
4‐13
(4th
ed
Fig
4‐14))
 
 collagen
forms
a
unique
 triple
helical
structure,
the
 collagen
helix
(Lehninger
Fig.
4‐11,12

(4th
 ed
 Fig
 4‐12,13)).
 
 This
 is
 not
 considered
 a
 generic
 secondary
 structure,
 since
 collagen
 helix
 depends
on
a
specific
repeating
sequence
‐(Gly‐Pro‐Pro)n‐.
 Secondary
 structures
 by
 themselves
 are
 rigid,
 and
 give
 the
 protein
 an
 overall
 fibrous
 shape,
 whereas
most
proteins
are
globular.
 
 
 A
 globular
 shape
 is
 the
 result
 of
 folding
 the
 polypeptide
onto
itself
and
depends
on
the
following:
 
 1)
 Clearly
 defined
 interruptions
 in
 the
 secondary
 structure;
 clusters
 of
 secondary
 structure
 breaker
 amino
 acids
 Gly,
 Pro,
 Ser,
 Asn
 Asp
 interrupt
 rigid
 segments
 of
 secondary
 structure,
 creating
 more
 flexible
 turn
 or
 loop
 regions
 where
 the
 polypeptide
 can
fold
back
on
 itself.
Clusters
may
be
pairs
of
strong
 breakers
(Gly,
Pro)
or
runs
with
3
breakers
out
of
four.
 
 A
turn
is
a
break
of
2‐3
residues,
often
of
well
defined
 structure,
whereas
a
 loop
is
a
longer
 section
of
amino
 acids
with
less
regular
arrangements.
 
 
 
 
 Page
1
of
6
 BIOC*2580
Lecture
11:
Tertiary
structure
&
protein
folding
 
 2
 
 2)
 The
 folded
 protein
 brings
 together
 almost
 all
 the
 non‐polar
 amino
 acids
 in
 the
 core
 of
 the
 globular
 shape.
 The
 non‐polar
 or
 hydrophobic
 amino
 acids
 are
 thus
 grouped
 away
 from
 direct
 contact
 with
 H2O.
 By
 default
 the
 outer
 shell
 of
 a
 folded
 protein
 is
 largely
 made
 up
 of
 polar
 amino
 acids
 that
 interact
 well
 with
 the
 surrounding
 H2O.
 The
grouping
of
 non‐polar
amino
acids
together
by
 hydrophobic
interaction
accounts
for
about
50%
of
 the
 energy
 responsible
 for
 stabilizing
 the
 folded
 form.
The
figure
shows
a
cross
section
through
the
 protein
 myoglobin,
 with
 polar
 amino
 acids
 shown
 in
green
and
non‐polar
in
red.
 
 3)
 The
 ideal
 folded
 state
 interlocks
 like
 a
 jigsaw
 puzzle.
 The
 figure
 on
 the
 right
 shows
 two
 of
 the
 helices
 in
 myglobin;
 sidechains
on
theleft
helix
(red)
interlock
with
sidechains
on
the
 right
helix
(blue).
 
 This
arrangement
maximizes
the
number
of
close
atom
to
atom
 contacts.
 Atoms
 that
 are
 in
 perfect
 contact
 bind
 via
 a
 weak
 attractive
force
called
the
van
der
Waals
interaction.
 This
force
 becomes
strongly
repulsive
if
atoms
are
too
close
together,
and
 fades
to
zero
if
atoms
are
spaced
apart
by
more
than
two
atom
 diameters.

 
 Since
 the
 van
 der
 Waals
 interaction
 may
 be
 weak
 (0.1
 to
 1
 kJ
 compared
 with
 26
 kJ
 for
 a
 hydrogen
 bond
 or
 400
 kJ
 for
 a
 covalent
 bond),
 the
 overall
 effect
 is
 significant
 only
 if
 a
 large
 number
 of
 van
 der
 Waals
 contacts
 exist,
 i.e.
 atom
 to
 atom
 contacts
 at
 the
 ideal
 distance
 of
 separation.
 This
 can
 be
 true
 for
 a
 correctly
 folded
 protein,
 since
 a
 protein
 molecule
 contains
 thousands
of
atoms
in
contact.
 
 Improperly
folded
arrangements
don't
achieve
this
precise
fit
so
that
only
a
few
van
der
Waals
 contacts
are
made
at
ideal
distances.
When
atoms
are
too
far
apart,
there
is
no
interaction,
 when
too
close,
there
is
strong
repulsion.
 
 Other
stabilizing
interactions
include:
 
 1. Ion
pairs,
‐ve
charged
side
chains
paired
up
with
a
+ve
charged
neighbour.
 2. H‐bonds
between
donor
groups
such
as
Arg,
Lys,
His,
Asn,
Gln,
Ser,
Thr
Tyr
and
acceptor
 groups
such
as
Asp,
Glu,
Asn,
Gln,
His,
Ser
Thr,
Tyr.
 3. Disulfide
bonds,
which
form
between
pairs
of
Cys
side
chains
which
are
align
side
by
side
 the
folded
protein
(more
on
this
in
the
next
lecture).
 
 Page
2
of
6
 BIOC*2580
Lecture
11:
Tertiary
structure
&
protein
folding
 
 3
 
 Most
proteins
fold
in
a
limited
number
of
patterns
 
 Protein
 structures
 usually
 arise
 from
 simple
 combinations
 of
 secondary
 structures,
 sometimes
 known
as
supersecondary
structures,
e.g.
helix‐turn‐helix,
β‐hairpins,
βαβ
units.
 
 A
sequence
with
mostly
groups
of
 α− helix‐forming
AAs
will
fold
into
an
 α ‐helix
 bundle
 In
 schematic
 diagrams,
 cylinders
 often
 represent
 helices.
 Alpha
 helical
 segments
 in
 the
 polypeptide
are
interrupted
at
intervals
by
 breaker
amino
acids
forming
the
connecting
loops.
 Often
Pro
is
found
near
the
N‐terminal
of
a
helix
while
Gly
often
marks
the
C‐terminal
limit
of
 each
helix.
Inward
facing
amino
acids
are
mostly
non
polar,
and
interlock
jigsaw
puzzle
style
to
 hold
 the
 bundle
 together.
 Some
 ion
 pairs
 or
 H‐bond
 pairs
 may
 link
 adjacent
 helices
 along
 the
 outer
shell
of
the
protein.

 
 Since
the
a‐helix
has
3.6
amino
acid
per
turn,
or
about
7
amino
acids
for
2
turns,
arrangement
of
 polar
(P)
and
non
polar
(N)
in
the
sequence
in
a
pattern
similar
to
–PNNPPNP‐
 will
place
all
the
 nonpolar
side
chains
on
one
face
of
the
helix,
leading
to
the
folding
shown
above.
 
 Bundles
 of
 6‐10
 helices
 such
 as
 myoglobin
 (eight
 helices)
appear
more
complex
because
the
helices
 tend
to
splay
apart.
 Beta
sheet
preferring
amino
acids
are
 not
absent,
 but
 their
 distribution
 is
 rather
 scattered
 so
 their
 "vote"
 is
 not
 effective.
 Alpha
 helical
 amino
 acids
 are
 more
 clustered
 so
 their
 presence
 determines
 the
 secondary
 structure
 wherever
 they
 are
 present
in
a
local
majority.
 
 
 
 Page
3
of
6
 BIOC*2580
Lecture
11:
Tertiary
structure
&
protein
folding
 
 4
 
 A
sequence
with
mostly
groups
of
β ‐sheet‐forming
AAs
folds
into
antiparallel
β ‐ sheet
 
 extended
strands
 
 
 
 
 
 breakers
 
 
 Greek
key
 
 H‐bonds
 motif
 
 Extended
 or
 β ‐strands
 are
 represented
 by
 the
 arrow
 symbols
 in
 the
 figure.
 Two
 strands
 connected
by
a
turn
naturally
tend
to
form
a
 hairpin
structure.

A
hairpin
that
flops
over
gives
 rise
 to
 a
 four‐stranded
 unit
 called
 the
 Greek
 key
 (because
 it
 is
 said
 to
 resemble
 a
 decorative
 motif
in
ancient
Greek
pottery).

Since
the
strands
run
in
opposite
directions
in
these
cases,
they
 line
 up
 into
 an
 antiparallel
 β ‐sheet.
 
 Antiparallel
 is
 more
 stable
 than
 parallel
 due
 to
 the
 good
 alignment
of
H‐bonds
between
strands.
 
 Amino
 acids
 are
 frequently
 arranged
 to
 alternate
 nonpolar
 and
 polar
 side
 chains.
 Since
 a
 strand
 has
 a
 zig‐zag
 backbone,
 this
 places
all
nonpolar
amino
acids
on
one
side
of
the
sheet,
and
all
 polar
on
the
opposite
side.
 
 The
 sheet
 is
 sufficiently
 flexible
 that
 it
 can
 wrap
 around
 itself
 so
 that
 the
 nonpolar
 side
 chains
 face
 each
 other
 on
 the
 inside,
 leaving
 polar
amino
acids
on
the
outside.

An
open
fold
 is
 produced
 from
 a
 sheet
 of
 3‐5
 strands,
 but
 when
 there
 are
 6
 or
 more
 strands,
 the
 opposite
edges
can
connect
up
via
 H‐bonds
to
 produce
a
closed
antiparallel
beta
barrel.
 
 The
 structure
 shown
 is
 part
 of
 immunoglobulin
 or
 antibody
 protein.
 Yellow
 arrows
 are
 β‐strands,
 blue
 sections
 are
 turns
 and
 loops
 are
 white.
 Sometimes
 a
 loop
 may
 form
 a
 short
 helical
segment
(red)
that
is
peripheral
to
 the
 β‐sheet
 core.
 Lehninger:
 p.
 137
 (4th
 ed
p.
142).
 
 
 Page
4
of
6
 BIOC*2580
Lecture
11:
Tertiary
structure
&
protein
folding
 
 5
 
 Proteins
with
alternating
β ‐strand
and
α ‐helix
segments
 A
parallel
beta
sheet
(extended
strands
all
running
in
the
same
direction)
can't
form
from
one
 continuous
polypeptide
chain.
Instead,
when
a
polypeptide
consists
of
alternating
β‐strands
and
 α‐helix,
this
allows
the
polypeptide
to
run
in
one
direction
up
the
β‐strands,
and
then
back
down
 through
the
connecting
α‐helix.
 Proteins
 which
 alternate
 β‐strands
 and
 α‐helix
 can
 form
 multistranded
parallel
β‐sheets.
The
parallel
sheet
is
less
stable,
due
 to
the
angled
 H‐bonds,
and
is
usually
totally
nonpolar
so
the
sheet
is
 buried
and
 protected
from
contact
with
H2O.

If
the
helices
all
lie
on
 one
 side
 of
 the
 sheet,
 the
 sheet
 folds
 on
 itself
 to
 form
 a
 barrel,
 shown
in
schematic
 form
on
the
right.
If
helices
 lie
on
both
sides
of
 the
sheet,
this
results
in
a
sandwich
structure
(see
next
page).
 
 
 A
central
 β‐sheet
at
the
core
(yellow
strands)
wraps
around
to
form
 aclosed
 cylinder
 or
 barrel
 structure,
 forming
 a
 non
 polar
 core.
 This
 is
 surrounded
 by
 the
 connecting
α‐helices
(red),
for
example
in
the
protein
triose
phosphate
isomerase.

Lehninger
p.
 137
(4th
ed
p.
141,
Fig
4‐21).
 
 
 Page
5
of
6
 BIOC*2580
Lecture
11:
Tertiary
structure
&
protein
folding
 
 
 Parallel
α/β
sandwiches
form
when
the
connecting
α‐helices
are
 arranged
on
both
sides
of
a
central
parallel
β‐sheet.
The
β‐sheet
is
not
 flat,
and
is
usually
twisted,
but
does
not
wrap
around
to
form
a
cylinder
 like
a
barrel.
The
helices
cover
the
central
non‐polar
sheet
and
protect
it
 from
contact
with
H2O.
 Lactate
 dehydrogenase
 is
 an
 example
 of
 an
 parallel
 α/β
sandwich
(parallel
 β‐sheet
in
 yellow,
surrounding
 α‐helices
in
red).

 
 
 Domains
 Many
 proteins
 may
 appear
 more
 complex,
 because
 they
are
large
enough
to
have
several
 folding
units
or
 domains.
Each
domain
of
 about
10‐20
kDa
folds
up
as
 an
 independent
 entity,
 so
 a
 large
 polypeptide
 of
 50
 kDa
may
be
made
up
of
3
or
4
domains,
each
with
its
 own
folding
pattern.
 
 Lactate
 dehydrogenase
 folds
 as
 upper
 and
 lower
 domains.
In
this
example,
both
domains
happen
to
be
 alpha‐beta
 sandwiches,
 but
 in
 many
 proteins
 the
 different
domains
may
have
different
organizations.
 
 
 Page
6
of
6
 
 
 
 
 
 
 6
 ...
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