Lecture9&10-SecStr

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Unformatted text preview: BIOC*2580
Lectures
9
&
10.
Protein
Secondary
Structure
 
 1
 
 Synopsis:
 The
 polypeptide
 backbone
 flexes
 by
 rotation
 about
 its
 single
 bonds.
 Two
 arrangements
 result
 in
 regular
 repetitive
 structure,
 alpha
 helix
 and
 beta
 sheet.
 
 The
 particular
 secondary
structure
present
is
dependent
on
the
local
amino
acid
sequence.
Amino
acid
can
be
 grouped
in
three
classes:
amino
acids
with
bulky
side
chains
prefer
to
form
beta
sheet;
a
second
 group
 of
 amino
 acids
 have
 side
 chains
 that
 disrupt
 secondary
 structure;
 the
 remaining
 amino
 acids
tend
to
form
alpha
helix.

 
 Reading:
Lehninger
p.
116‐125
(4th
ed
p.
118‐125).

 
 
 Secondary
structure 
is
the
occurrence
of 
regular
repetitive
patterns
such
as
helix 
over
 short
 sections
of
the
polypeptide
chain.

 
 Why
is
there
a
pattern?
 
 The
 polypeptide
 chain
 forms
 a
 backbone
 structure
 in
 proteins.
 
 On
 first
 inspection,
 this
 structure
 appears
 to
 be
 connected
 entirely
 by
 single
 C‐C
 or
 C‐N
 bonds.
 It
 should
therefore
be
as
 flexible
as
a
simple
 hydrocarbon
chain.
 
 Flexing
in
a
covalent
chain
structure
does
not
 occur
 by
 bending
 bonds,
 and
 and
 can
 be
 achieved
 while
 the
 normal
 tetrahedral
 or
 trigonal
 planar
 bond
 angles
 are
 maintained.
 Instead,
 different
 shapes
 are
 obtained
 by
 rotation
about
the
axis
of
single
bonds.
 
 A
 chain
 made
 only
 of
 single
 bonds
 is
 highly
 flexible.
 All
 polypeptides
 can
 adopt
 a
 form
 which
 is
 flexible,
 but
 is
 random
 and
 disordered
 in
 bond
 orientation.
 This
 is
 called
 the
 denatured
 state
 of
 the
 protein.
 Proteins
 become
 denatured
 at
 elevated
 temperature
 or
 in
 the
 presence
 of
 disruptive
 solvents.
 Because
 there
 is
 no
 orderly
 arrangement,
denatured
protein
is
non‐functional.
 
 Most
proteins
also
have
an
ordered
arrangement
called
the
 native
 state.
 The
 organization
 of
 the
 native
 state
 places
 amino
 acids
 in
 3‐dimensional
 space
 in
 the
 arrangement
 required
for
proper
function,
and
this
poses
the
question
of
 why
any
special
patterns
should
exist
at
all.
 
 
 Page
1
of
6
 BIOC*2580
Lectures
9
&
10.
Protein
Secondary
Structure
 
 2
 
 Orderly
 arrangements
 of
 the
 polypeptide
 backbone
 were
 first
 studied
 by
 examining
 fibrous
 proteins
called
keratins:
 
 alpha‐keratin
‐
protein
of
hair,
skin
and
wool;
 
 beta‐keratin
or
fibroin
‐
spider
and
silkmoth
silk.
 
 The
 keratins
 were
 studied
by
 X‐ray
 diffraction,
a
technique
 in
which
X‐rays
are
reflected
off
 a
 regular
 repetitive
 structure
 such
 as
 a
 crystal
 or
 fiber
 of
 protein.
 The
 reflected
 X‐rays
 form
 a
 characteristic
pattern
if
the
repetitive
spacing
in
the
sample
is
comparable
to
X‐ray
wavelengths.
 Since
 X‐rays
 have
 the
 same
 dimensions
 as
 atoms
 and
 bonds,
 repetitive
 features
 in
 molecular
 structure
can
be
detected.
If
the
X‐ray
wavelength
is
known,
the
 size
of
the
 repeating
pattern
 in
the
protein
can
be
calculated.
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 X‐ray
 diffraction
 is
 discussed
 in
 Lehninger
 Box
 4‐5
 p.
 132‐133
 (4th
 ed
 p.
 136‐137).
 However
 detailed
theory
of
X‐ray
diffraction
is
beyond
the
scope
of
this
course.
 
 Visible
light
can
also
be
diffracted
‐
for
example,
a
spectrum
of
colors
can
be
seen
reflected
from
 the
back
of
a
compact
disk.
The
music
is
recorded
on
the
CD
as
a
pattern
of
closely
spaced
dots,
 and
the
dots
are
spaced
at
a
similar
distance
to
light
wavelengths.
Since
different
wavelengths
 are
deflected
a
different
angles,
white
light
break
up
into
a
spectrum.

 X‐Ray
diffraction
gave
the
following
measurements
for
repeating
patterns:
 Major
pattern

 



Minor
pattern
 α ‐keratin
 
 
 5.4
Å
 
 
 
 1.5Å
 β ‐keratin
or
fibroin

 
 7.0
Å
 
 
 
 3.5Å
 
 The
angstrom
unit
(Å),
1
x
10‐10
metre,
is
a
measure
of
distance
commonly
used
for
atomic
 structures;
for
example
the
hydrogen
atom
and
the
C‐H
bond
are
about
1
Å
in
size.
 
 Page
2
of
6
 BIOC*2580
Lectures
9
&
10.
Protein
Secondary
Structure
 
 3
 
 The
 structural
 basis
 of
 these
 repeat
 distances
 were
 worked
 out
 by
 Linus
 Pauling.
 Pauling
 understood
the
importance
of
knowing
precise
atomic
radii,
bond
lengths
and
angles
and
used
 these
to
create
exact
scale
models
of
possible
structures.
 
 From
 bond
 length
 measurements,
 Pauling
 first
 worked
 out
 that
 the
 peptide
 bond
 behaves
 as
 a
 double
 bond,
 due
 to
 the
 contribution
 of
 the
 second
 resonance
 form
 of
 the
 amide.
 This
 would
 make
 the
 peptide
bond
 rigid
and
unable
to
rotate
freely,
and
it
 can
 only
 form
 distinct
 cis
 and
 trans
 geometric
 isomers.
 In
 a
 protein,
 peptide
 bonds
 are
 almost
 invariably
 trans
as
 shown
on
the
left.
Bond
rotation
is
 allowed
 only
 at
 the
 only
 the
 alpha‐carbon
 atoms
 in
 the
chain.
 
 Pauling's
evidence
was
a
comparison
 C‐N
and
double
C=N
bonds
with
 the
 peptide
bond
length
of
1.32
Å.

 
 Since
 bond
 length
 correlates
 with
 bond
 order,
 this
 suggested
 to
 Pauling
 that
 the
 peptide
 bond
 behaves
more
like
a
double
bond.

 
 (Lehninger
Fig
4‐2,
p.
116
(4th
ed
Fig
4‐2,
p.
118‐119)).
 
 At
first,
Pauling
treated
peptide
bonds
as
flexible
single
bonds,
but
the
peptide
chain
was
free
to
 adopt
 such
 a
 variety
 of
 structures
 that
 no
 single
 consistent
 pattern
 would
 emerge.
 When
 Pauling
 included
 rigid
 peptide
 bonds
 in
 his
 models,
 he
 found
 that
 it
 limited
 the
 number
 of
 possible
arrangements
so
that
now
only
certain
well‐defined
patterns
would
be
stable.
 
 Pauling's
models
were
based
on
the
idea
that
the
>C
=
N<
state
of
the
peptide
bond
maintains
a
 flat
trigonal
planar
structure
which
is
quite
 rigid.
In
the
peptide
backbone,
rigid
peptide
bonds
 are
linked
through
the
α‐carbon
atoms,
which
have
tetrahedral
shape.
Hence
at
each
α‐carbon,
 the
 backbone
 takes
 a
 109o
 bend.
 Pauling
 then
 found
 that
 his
 models
 could
 adopt
 two
 basic
 patterns.

Due
to
the
constraints
of
bond
angles
and
atom
size,
any
other
arrangement
would
 force
atoms
to
intrude
on
each
other’s
space:
 
 • a
 helical
state
in
which
the
bond
rotation
at
the
 α‐carbon
bonds
was
repeatedly
 in
the
same
direction.
 • an
 extended
state
in
which
the
bond
rotation
at
the
 α‐carbon
bonds
 alternated
 in
direction,
resulting
in
a
zig‐zag
structure
for
the
peptide
chain.
 
 It
is
also
possible
to
set
the
peptide
chain
in
a
non‐repetitive
arrangement
called
random
coil.
 
 Page
3
of
6
 BIOC*2580
Lectures
9
&
10.
Protein
Secondary
Structure
 
 4
 
 The
helical
form
models
could
be
built
with
varying
degrees
of
twist,
but
one
model
fit
the
 atomic
dimensions
especially
well:
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 Alpha
helix
 
 α ‐helix
 has
 3.6
 amino
 acids
 per
 turn
 of
 the
 helix.
 This
 places
 the
 C=O
 group
of
amino
acid
#1(red
O
atom
and
gray
C)
exactly
in
line
with
the
 H‐N
 group
 (blue
 N
 atom)
 of
 amino
 acid
 #5
 (and
 C=O
 #2
 with
 H‐N
 #6).
 The
alignment
and
spacing
is
ideal
for
a
hydrogen
bond
C=O:‐‐‐H‐N,
and
 hydrogen
 bonding
 makes
 this
 structure
 especially
 stable.
 The
 distance
 separating
 each
 turn
 of
 the
helix
was
5.4
Å,
which
matches
the
major
repeat
distance
in
alpha‐keratin,
hence
the
name
 alpha‐helix.
Since
5.4
Å
/
3.6
is
1.5
Å,
the
 α−helix
has
an
amino
acid
every
1.5
Å,
matching
the
 minor
periodic
repeat
of
α−keratin.
 
 The
α‐helix
was
also
found
to
be
exclusively
right
handed;
a
left
handed
arrangement
has
similar
 dimensions,
 but
 places
 the
 amino
 acid
 side
 chain
 R
 too
 close
 to
 the
 C=O
 group,
 making
 the
 structure
over‐crowded.
 The
right
handed
version
of
the
helix
places
side
chain
R
next
to
the
 much
smaller
N‐H,
for
a
better
fit.
 
 In
the
initial
X‐ray
studies
of
myoglobin,
the
same
periodic
repeats
as
the
 α‐keratin
helix
were
 recognized.
 
 The
 realization
 that
 myoglobin
 was
 largely
 α‐helix
 was
 a
 major
 step
 in
 solving
 its
 tertiary
structure,
the
first
globular
protein
to
have
its
full
3‐dimensional
structure
worked
out.

 
 
 Page
4
of
6
 BIOC*2580
Lectures
9
&
10.
Protein
Secondary
Structure
 
 
 5
 Pauling's
 extended
 state
 model
 matched
 the
 spacing
 of
 fibroin
 or
 beta
 keratin
 exactly
 (3.5
 Å
 and
 7.0Å).
 In
 the
 extended
 state,
 H‐bonding
 NH
 and
 CO
 groups
 point
 out
 to
 each
 side.
 By
 lining
 up
 extended
 strands
 side
 by
 side,
 H‐bonds
 bridge
 from
 strand
 to
 strand.
 H‐bonds
 may
 link
 extended
strands
 lined
 up
 in
 parallel
 (same
 direction)
 or
 antiparallel
 (opposite
 directions)
 orientations.
 
 
 
 Arrangements
 with
 multiple
 strands
 form
 a
 two
 dimensional
 structure
 called
 a
 beta
 sheet,
 so
 named
because
they
form
the
basis
of
beta
keratin
structure.
 
 The
alignment
of
H‐bonds
is
much
better
in
the
antiparallel
arrangement.

 
 When
the
beta
sheet
is
viewed
from
the
edge
(at
left)
instead
of
face‐on
(above),
a
striking
zig‐ zag
pattern
is
seen.
This
shows
how
the
beta
sheet
structure
gives
bulky
amino
acid
side
chains
 the
 maximum
 space
 and
 freedom
 of
 movement.
 Note
 also
 that
 odd‐numbered
 amino
 acids
 appear
on
one
side
of
the
sheet
and
even
numbered
on
the
opposite
side.
 
 Page
5
of
6
 BIOC*2580
Lectures
9
&
10.
Protein
Secondary
Structure
 
 6
 
 Different
amino
acids
prefer
particular
secondary
structures:
 
 The
 extended
 structure
 leaves
 the
 maximum
 space
 free
 for
 the
 amino
 acid
 side
 chains:
 as
 a
 result,
those
amino
acids
with
large
bulky
side
chains
prefer
to
form
beta
sheet
structures:
 
 Tyr,
Trp
(sometimes
Phe)
are
just
plain
large.

 Ile,
Val,
Thr
are
bulky
and
awkward
due
to
branched
β‐carbon.
 Cys
has
a
large
S
atom
on
β‐carbon.
 
 The
 β‐carbon
 atom
 is
 the
 first
 atom
 on
 the
 side
 chain,
 so
 bulky
 groups
 are
 crowded
 up
 the
 backbone.
 The
 presence
 of
 bulky
 groups
 on
 the
 second
 carbon,
 e.g
 in
 leucine,
 is
 less
 of
 a
 crowding
problem.

 
 The
main
criterion
for
alpha
helix
preference
is
that
the
amino
acid
side
chain
should
cover
and
 protect
the
backbone
H‐bonds
in
the
core
of
the
helix
from
disruption
by
the
surrounding
H2O.
 
 alpha‐helix
preference:
Ala,
Leu,
Met,
Phe,
Glu,
Gln,
His,
Lys,
Arg
 
 The
remaining
amino
acids
have
side
chains
that
disrupt
secondary
structure,
and
are
known
as
 secondary
structure
breakers:
 
 Gly,
Pro,
Asn,
Asp,
Ser
 
 In
the
case
of
 Gly,
the
side
chain
is
a
single
H
atom,
too
small
to
shield
backbone
H‐bonds
from
 disruption
by
the
surrounding
H2O.
 Proline
is
unique
because
its
side
chain
is
directly
linked
to
the
backbone
N,
and
obstructs
the
 space
where
the
H‐bond
would
otherwise
form.
 In
 the
 case
 of
 Asp,
 Asn
 and
 Ser,
 the
 side
 chain
 is
 at
 an
 ideal
 length
 to
 form
 H‐bonds
 with
 adjacent
backbone
N‐H
or
C=O
groups.

As
a
result
these
amino
acids
actually
disrupt
adjacent
H‐ bonds
instead
of
protecting
them.
 
 Clusters
of
breakers
give
rise
to
regions
known
as
loops
or
turns
which
mark
the
boundaries
of
 regular
secondary
structure,
and
serve
to
link
up
secondary
structure
segments.

 
 There
 are
 various
 schemes
 that
 give
 the
 amino
 acids
 numerical
 weights
 or
 rankings
 for
 their
 preferences,
and
several
computer
programs
can
predict
the
secondary
structure
from
the
given
 sequence
(Lehninger
Table
4‐1,
p.
119
(4th
ed
p.
125,
Fig
4‐10)).

Amino
acids
select
a
 secondary
 structure
 by
 consensus,
 not
 individually.
 If
 you
 have
 a
 few
 amino
 acids
 that
 prefer
 helix
 randomly
scattered
in
a
majority
of
beta
sheet
formers,
the
structure
adopted
is
entirely
 beta
 sheet.
 A
 section
 of
 polypeptide
 is
 likely
 to
 form
 alpha
 helix
 if
 it
 contains
 60%
 helix
 formers
 in
 runs
of
6
amino
acids
or
more,
and
no
more
than
20%
breakers.
A
section
of
polypeptide
is
likely
 to
form
beta
sheet
if
it
contains
60%
beta
sheet
formers
in
runs
of
5+
amino
acids,
and
no
more
 than
20%
breakers.
2
or
more
breakers
in
a
run
of
4
amino
acids
are
usually
necessary
to
initiate
 a
turn
or
loop.
 
 Page
6
of
6
 ...
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This note was uploaded on 09/21/2011 for the course BIOOC 2580 taught by Professor Douger during the Fall '10 term at University of Guelph.

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