Lectures 5 and 6

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Lectures 5 and 6
Peptides levels of protein structure -seconda
ry structure ?-helices, ?-sheets
super-secondary structures (?-barrels,
coiled-coils etc.) ?- and ?-turns
etc. -tertiary and quaternary structure.
-protein folding. -post-translational
modification.
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Figure 6.27 summary of the levels of protein
structure
peptide bond H-bond interactions within
backbone side chains interactions side chains
interactions (electrostatic, H-bonds and van
der Waals)
The folded protein structure is stabilized by a
variety of weak chemical interactions, and, in
some cases, covalent (disulfide) bonds between
cysteine residues
Disulfide bonds
R CH2SSCH2R
Cys Cys
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Protein structure overview
Structural element Description primary
structure amino acid sequence of protein
secondary structure helices, sheets,
turns/loops super-secondary structure associatio
n of secondary structures domain self-containe
d structural unit tertiary structure folded
structure of whole protein includes
disulfide bonds quaternary structure assembled
complex (oligomer) homo-oligomeric (1
protein type) hetero-oligomeric (gt1
type)
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Planar character of a peptide bond
Figure 5.12 - partial double bond character
prevents the peptide bond from rotating
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Figure 6.2 rotation about the alpha carbon
- with the lack of rotation around the peptide
bond the point of flexibility along the backbone
of the protein arises at the ? - carbon.
?-carbon
? (phi) and ? (psi) are the angles of rotation
around the ?-carbon bonds
conformation of backbone (and type of secondary
structure assumed) can be described by ? and ?.
bonds allowing for rotation along the protein
backbone
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A steric conformation that is not allowed
provides a reference point for ? and ?
Figure 6.9
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Ramachandran plot
Psi (?)
no steric clashes
Phi (F)
- Phi (F) and Psi (?) indicate rotation around
the alpha carbon for each amino acid residue in
the polypeptide this rotation allows the
polypeptide to assume its various
conformations. - some conformations of the
polypeptide backbone result in steric clashes
between atoms and are disallowed. - glycine has
no side chain and is therefore conformationally
highly flexible (it is often found in turns).
permitted if atoms are more closely spaced
note you do not have to know material on this
slide for exams.
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Protein secondary structure helices
-rod-like, usually right-handed (although
left-handed helices exist) ? helix by far the
most common.
-mostly maintained by intra-chain H-bonds between
gtCO group of each peptide residue and the gtN-H
group of the 4th amino acid away atoms in H
bonds all lie in straight line.
- ? helices are about 10 residues on average.
H-bonding in ? helix
- R groups in ? helices lie towards the outside
and are sometimes staggered to minimize steric
hindrance.
- helices can form bundles, coiled coils, etc.
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Protein secondary structure ? helices
F, y determine secondary structures
Main chain Ca
F -57o Y -47o
Ribbon
In addition to hydrogen bonding between atoms of
the back-bone, the stability of the ? helix is
influenced by R group interactions i.e.
charge-charge, van der Waals (hydrophobic) and
steric interactions (e.g. small residues such as
Ala but not Gly are more common than bulky
residues such as Tyr or Asn).
Amide plane
a-carbon i4
Hydrogen bond i, i4
a-carbon i
Side chains R outside the helix
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Helical Wheel
- a tool to visualize the position of amino acids
around an ? helix - allows for quick
visualization of whether a side of a helix posses
specific chemical properties - example shown is
a helix that forms a Leucine Zipper
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Most amino acids like to be in an ?
helix. notable exceptions GLYCINE small side
chain generates
a wide array of ? and
? values. PROLINE special structure-makes

peptide chain rigid.
No Hydrogen On this N to H-Bond
O
C-O
N
H
- thus, proline residues often serve as ?-helix
breakers. - both residues are often found at the
boundaries of ? helices and in turns.
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Proteins with ? helices
Major structural component in many proteins, some
globular proteins contain mostly ? helices,
connected by turns (i.e., hemoglobin 70 ?
helices)
Some interesting ? helices - small DNA binding
helices - membrane spanning helices -
amphipathic helices - coiled coils
(super-secondary structures).
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DNA Binding - an ?? helix fits perfectly into the
major groove of double stranded DNA. - many DNA
binding proteins use particular ?? helices to
recognize a specific DNA sequence and bind to it
via H-bonds.
dsDNA
Membrane spanning - contains hydrophobic amino
acids in the central region to allow the protein
to cross a bi-layer membrane.
Hydrophilic Hydrophobic
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Amphipathic Helices Amphipathic hydrophilic
hydrophobic - these helices posses hydrophilic
amino acids on one side and hydrophobic residues
on the other. - these ? helices in some cases
can be used to associate a protein to a membrane.
Hydrophobic
Hydrophilic
hydrophilic head group
aliphatic carbon chain
lipid bilayer
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Protein structure ? sheets
- the basic unit of a ? sheet is called a ? strand
N
O
C
- repeating unit like the ? helix
- ? sheets can form various higher-level
structures, super-secondary structures such as
silk fibroin and ? barrels
parallel
twisted
anti-parallel
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Protein secondary structure ? sheet
Cter
Nter
Antiparallel F-139o y135o
Parallel F-119o y113o
F-57o y-47o
a Carbon
Carbon (C0)
a Carbon
Cter
Nter
? helix ? sheet (antiparallel)
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The ? sheets or ?-pleated sheets

• - strands of amino acids held together in sheets
  by INTER-STRAND H-Bonding
• - bonding between backbone gtCO and gtN-H on
  different strands
• strands of the b sheets tends to be twisted and
  inclined, especially in a b barrel
• - the R-groups lie perpendicular to the sheets
  stick out on either face of the sheet

• Note ? sheets cannot be transmembrane unless
  they are part of a ?-barrel structure

differential arrangement of R-groups with
different properties can produce variable polarity
R
R
R
R
R
R
R
R
R
R
R
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? sheets and DNA
- an ? helix is of appropriate size to fit in the
major groove of DNA - ? sheets fit very well
into the minor groove of DNA double helices - ?
sheets can also used in DNA binding but are
generally less commonly used
? helix
? sheet
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• Certain super-secondary structures can produce
  fibrous proteins- elongated or filamentous
  proteins that play key structural roles in animal
  tissues (e.g. skin, connective tissues etc.),
  often outside the cell.
• Examples
• -?-keratin- monomer is ? helix subunits form
  strong, stretchy and flexible intermediate
  filaments of which hair, nails and parts of skin
  are composed.
• collagen- (the most abundant vertebrate protein)-
  monomer is an unusual left-hand helix the
  remarkably strong and somewhat elastic fibres
  form the bone matrix, the basic structure of
  tendons and important elements of skin.
• silk fibroin- ?-sheet-based structural unit of
  which spider webs and silk (produced by
  silkworms) are constructed.

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?-keratin the individual molecules are long ?
helices in which every fourth amino acid residue
is hydrophobic thus, each helix has a stripe
of hydrophobicity along one side. -Pairs of these
helices wind about each other in left-hand
fashion to produce coiled-coiled dimers that are
stabilized by interactions between the
hydrophobic residues. -These dimers then
associate to form higher-order structures (see
next slide)
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Proposed structure for ?-keratin intermediate
filaments
protein monomer of filament ?-keratin
-assembly of intermediate filaments pairs of
coiled-coils form protofilaments, which in turn
associate in pairs to form protofibrils- flexible
and very strong cables-like structures. -?-keratin
contains large amounts of cysteine and filaments
are stabilized by disulfide bond cross-linking in
certain tissues (e.g. nails, but less prominent
in hair).
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• Silk Fibroin an example of a super-secondary
  structure involving ? sheets.
• -composed of layers of ? sheets containing
  repeats of sequence consisting almost entirely of
  Gly, Ala and Ser (facilitates stacking).
• layered ? sheets provide toughness flexibility.

Figure 6.12
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Collagen fibres An example of a super-secondary
structure based on an unusual helical molecule
Basic subunit tropocollagen-a triple helix
consisting of three left-hand helices (with 3.3
residues per turn) coiled around each other in
right-hand direction -abundance of Gly-X-Y (X
is usually Pro and Y is Pro or hydroxy-Pro)
repeat ensures stability of helix. -subunits are
packed together in staggered fashion to form
collagen fibres that undergo extensive
cross-linking (reinforces their strength).
triple coiled-coil
Fig. 6.13
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Protein structure turns/loops
beta-sheet
alpha-helix
- there are various types of turns, differing in
the number of residues and H-bonding pattern
- loops are typically longer (they are often
called coils) most loops do not usually have a
regular, or repeating, structure but, parallel
strands in ? sheets are often joined by longer
loops that sometimes contain ? helices.
loop (usually exposed on the surface of proteins)
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? turns
Figure 6.18
There are two classes of ? turns - type I - type
II Note the position of R2 and R3 in both
cases Type I turns have the R groups on the same
side. Type II turns have the R groups on
opposite sides. note residue 3 is usually
glycine Note H-bonding between backbones of
residue 1 4
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? turns
Proline
A 3 amino acid turn utilizing proline at the
turn. H-bonding with CO of residue 1 and N-H of
residue 3
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Two types of ?-sheet structures note that the
strands in the parallel structure are connected
by longer loops (these may contain ?-helical
segments).
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Protein tertiary structure
- Globular proteins key roles in most chemical
(especially enzymes) and many structural
functions in the cell they possess compact
tertiary structures generated by the folding and
packing of secondary structure elements,
super-secondary structure elements, and
domains. - tertiary folding is usually stabilized
by a variety of non-covalent interactions (but
only R group interactions are at play). -
H-bonding - ionic interactions - van der Waals
forces - hydrophobic interactions - can be
stabilized by covalent bonds di-sulphide
linkages (bonds)
-Cys
-S
-Cys
-S
-Cys
oxidizing agent
-Cys
Cystine
CystEine
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Figure 5.1 Tertiary structure of Myoglobin
a-helix
Heme ligand
a-amino-acid side chain
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Protein domains
- many globular proteins consist of several
compact, locally folded and stable regions called
domains i.e. modular units. - domains tend
to have 40 up to 200-350 amino acids - fewer
than 50 difficult to fold stably - more than 300
difficult to fold correctly - a single domain is
typically made of a single stretch of primary
sequence however, there are many exceptions.
Hydrophilic
domain 1
domain 2
Hydrophobic Core
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For example the Src protein consists of four
different domains
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Figure 6.16 Examples of some globular proteins
- viewing proteins as secondary structure models
parallel beta-barrel - alpha/beta sequence
beta-sandwich
helix bundles
twisted beta-sheet
anti-parallel beta-sheet