Principles of Protein Structure

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Principles of Protein Structure
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Different Levels of Protein Structure
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Common Secondary Structure Elements

• The Alpha Helix

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Properties of alpha helix

• 3.6 residues per turn, 13 atoms between H-bond
  donor and acceptor
• ?approx. -60º ? approx. -40º
• H- bond between CO of ith residue -NH of
  (i4)th residue
• First -NH and last CO groups at the ends of
  helices do not participate in H-bond
• Ends of helices are polar, and almost always at
  surfaces of proteins
• Always right- handed
• Macro- dipole

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Alpha Helix
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Helical wheel
Residues i, i4, i7 occur on one face of
helices, and hence show definite pattern of
hydrophobicity/ hydrophilicity
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Association of ??helices coiled coils
Introduction to Molecular Biophysics
These coiled coils have a heptad repeat abcdefg
with nonpolar residues at position a and d and
an electrostatic interaction between residues e
and g.
Isolated alpha helices are unstable in solution
but are very stable in coiled coil structures
because of the interactions between them
The chains in a coiled-coil have the polypeptide
chains aligned parallel and in exact axial
register. This maximizes coil formation
between chains.
The coiled coil is a protein motif that is often
used to control oligomerization.
They involve a number of alpha-helices wound
around each other in a highly organised manner,
similar to the strands of a rope.
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The Leucine Zipper Coiled Coil
Introduction to Molecular Biophysics
Initially identified as a structural motif in
proteins involved in eukaryotic transcription.
(Landschultz et al., Science 240 1759-1763
(1988).
Originally identified in the liver transcription
factor C/EBP which has a Leu at every seventh
position in a 28 residue segment.
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Association of ??helices coiled coils
The helices do not have to run in the same
direction for this type of interaction to occur,
although parallel conformation is more common.
Antiparallel conformation is very rare in trimers
and unknown in pentamers, but more common in
intramolecular dimers, where the two helices are
often connected by a short loop.
Chan et al., Cell 89, Pages 263-273.
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Basis for the helical dipole
In an alpha helix all of the peptide dipoles are
oriented along the same direction. Consequently,
the alpha helix has a net dipole moment.
Since the dipole moment of a peptide bond is 3.5
Debye units, the alpha helix has a net
macrodipole of n X 3.5 Debye units (where n
number of residues) This is equivalent to 0.5
0.7 unit charge at the end of the helix.
The amino terminus of an alpha helix is positive
and the carboxy terminus is negative.
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(No Transcript)
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• Structure of human TIM
• Two helix dipoles are seen to play important
  roles
• Stabilization of inhibitor 2-PG
• Modulation of pKa of active site His-95.

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Helical Propensities

• Ala -0.77
• Arg -0.68
• Lys -0.65
• Leu -0.62
• Met -0.50
• Trp -0.45
• Phe -0.41
• Ser -0.35
• Gln -0.33
• Glu -0.27
• Cys -0.23
• Ile -0.23
• Tyr -0.17
• Asp -0.15
• Val -0.14
• Thr -0.11
• Asn -0.07
• His -0.06
• Gly 0

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Common Secondary Structure Elements

• The Beta Sheet

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Secondary structure reverse turns
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Secondary StructurePhi Psi Angles Defined

• Rotational constraints emerge from interactions
  with bulky groups (ie. side chains).
• Phi Psi angles define the secondary structure
  adopted by a protein.

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The dihedral angles at Ca atom of every residue
provide polypeptides requisite conformational
diversity, whereby the polypeptide chain can fold
into a globular shape
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Ramachandran Plot
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Secondary Structure
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Beyond Secondary Structure

• Supersecondary structure (motifs) small,
  discrete, commonly observed aggregates of
  secondary structures
• b sheet
• helix-loop-helix
• bab
• Domains independent units of structure
• b barrel
• four-helix bundle
• Domains and motifs sometimes interchanged

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Common motifs
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Supersecondary structure Crossovers in
b-a-b-motifs
Left handed
Right handed
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EF Hand

• Consists of two perpendicular 10 to 12 residue
  alpha helices with a 12-residue loop region
  between
• Form a single calcium-binding site
  (helix-loop-helix).
• Calcium ions interact with residues contained
  within the loop region.
• Each of the 12 residues in the loop region is
  important for calcium coordination.
• In most EF-hand proteins the residue at position
  12 is a glutamate. The glutamate contributes both
  its side-chain oxygens for calcium coordination.

Calmodulin, recoverin Regulatory proteins
Calbindin, parvalbumin Structural proteins
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EF Fold
Found in Calcium binding proteins such as
Calmodulin
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Helix Turn Helix Motif

• Consists of two a helices and a short extended
  amino acid chain between them. 
• Carboxyl-terminal helix fits into the major
  groove of DNA.  
• This motif is found in DNA-binding proteins,
  including l repressor, tryptophan repressor,
  catabolite activator protein (CAP)

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Leucine Zipper
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Rossman Fold

• The beta-alpha-beta-alpha-beta subunit
• Often present in nucleotide-binding proteins

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What is a Protein Fold?

• Compact, globular folding arrangement of the
  polypeptide chain
• Chain folds to optimise packing of the
  hydrophobic residues in the interior core of the
  protein

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Common folds
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Tertiary structure examples All-a
Cytochrome Cfour-helix bundle
AlamethicinThe lone helix
Rophelix-turn-helix
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Tertiary structure examples All-b
b sandwich
b barrel
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Tertiary structure examples a/b
placental ribonucleaseinhibitor a/b horseshoe
triose phosphateisomerase a/b barrel
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Four helix bundle

• 24 amino acid peptide with a hydrophobic surface
• Assembles into 4 helix bundle through hydrophobic
  regions
• Maintains solubility of membrane proteins

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Oligonucleotide Binding (OB) fold
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TIM Barrel

• The eight-stranded a /b barrel (TIM barrel)
• The most common tertiary fold observed in high
  resolution protein crystal structures
• 10 of all known enzymes have this domain

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Zinc Finger Motif
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• Domains are independently folding structural
  units.

Often, but not necessarily, they are contiguous
on the peptide chain. Often domain boundaries
are also intron boundaries.
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• Domain swapping
• Parts of a peptide chain can reach into
  neighboring structural elements helices/strands
  in other domains or whole domains in other
  subunits.

Domain swapped diphteria toxin
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Transmembrane Motifs

• Helix bundlesLong stretches of apolar amino
  acidsFold into transmembrane alpha-helicesPosit
  ive-inside rule Cell surface receptors Ion
  channels Active and passive transporters
• Beta-barrelAnti-parallel sheets rolled into
  cylinder Outer membrane of Gram-negative
  bacteria Porins (passive, selective diffusion)

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Quaternary Structure

• Refers to the organization of subunits in a
  protein with multiple subunits
• Subunits may be identical or different
• Subunits have a defined stoichiometry and
  arrangement
• Subunits held together by weak, noncovalent
  interactions (hydrophobic, electrostatic)
• Associate to form dimers, trimers, tetramers etc.
  (oligomer)
• Typical Kd for two subunits 10-8 to 10-16M
  (tight association)
• Entropy loss due to association - unfavorable
• Entropy gain due to burying of hydrophobic groups
  - very favourable

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Structural and functional advantages of
quaternary structure

• Stability reduction of surface to volume ratio
• Genetic economy and efficiency
• Bringing catalytic sites together
• Cooperativity (allostery)

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Quaternary structure ofmultidomain proteins