Protein Tertiary Structure

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Protein Tertiary Structure
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Protein Tertiary Structure

• Packing
• helix-helix packing
• sheet-sheet packing
• helix-sheet packing
• Protein Structural Classes
• All Alpha
• All Beta
• Alpha and Beta

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Helix Helix Packing
The Ridge-Groove model
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Pairs of helices
W angle between the 2 axes
D distance between the two axes
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Two types of ridges in helices
Ridge 4n
Ridge 3n
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Ridge groove model for helix-helix packing
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Example Helix B and G in myoglobin
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Example Helix B and G in myoglobin
Backbone Sidechain
Backbone only
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Sheet-Sheet Packing

• Parallel sheets tend to be covered by helices on
  both sides
• Anti-parallel sheets tend to have one side
  covered by a sheet sandwich-type structure.
  Two types of packing aligned, or orthogonal

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Aligned sheet-sheet packing
Approx. 20 degrees between the directions of the
sheets
Sidechains are well packed
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Orthogonal Sheet-Sheet Packing
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Helix-Sheet Packing

• Because the periodicities of helices and strands
  are different, there is not regular packing
  patterns.
• Helices tend to be on both sides of parallel beta
  sheets.

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Protein Architectures

• All a proteins
• All b proteins
• Alpha and beta proteins
• - a/b proteins (alternating a and b)
• - a b proteins

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All-Alpha topologies

• The lone helix
• The helix-turn-helix motif

Glucagon (hormone involved Is regulating sugar
metabolism) PDB code 1GCN
ROP RNA-binding Protein PDB code 1ROP
The 2 helices are twisted
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All-Alpha topologies (2)
The four helix bundle
hydrophobic
hydrophilic
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Four helix bundle topologies
Rop dimer PDB 1ROP
Myohemerythrin PDB code 2mhr
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All Beta Topology
Beta sandwiches
Fatty acid binding protein PDB code 1IFB
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The Greek Key Topology
Folds including the Greek key topology include 5
to 13 strands.
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The Greek Key Topology
Gamma crystallin. PDB code 2GCR
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The Jellyroll Topology
A Greek key with an extra swirl
PDB code 2STV (coat protein of a virus)
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The Beta Propellor
Seven-plated propellor Each plate is a
four-stranded anti-parallel sheet PDB code 1ERJ
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The Beta Helix
PDB code 1EZG
Antifreeze protein from Tenebrio Molitor (beetle)
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The Rossman Fold
Alternate beta / alpha motif Always right handed
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The Horseshoe
PDB code 2BNH
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The alpha/beta barrel
In a succession of alpha/beta motifs, if the
first strand Hydrogen bonds to the last, then
the structure resemble a Barrel. PDB code 1TIM
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Summary

• Stacking of helices is best described using the
  ridge-groove model.
• Anti-parallel sheets tend to have one side
  covered by a sheet sandwich-type structure.
  Two types of packing aligned, or orthogonal.
• Helices tend to be on both sides of parallel beta
  sheets.
• There are three main classes of proteins all
  Alpha, all Beta and Alpha Beta. Sometimes, the
  latter is divided in two, considering the
  alternating alpha/beta proteins as defining their
  own class.
• Bundles are common alpha-proteins
• Common beta folds include the greek key, the
  jellyroll, and sandwiches. More unusual beta
  structures include the beta propeller and the
  beta helix
• The Rossman fold (alternating alpha/beta) is a
  common motif in proteins. It is found in the
  horseshoe, as well as in the TIM fold.