MBM 3

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MBM 3

• Protein structure and function, B

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Learning Goals for MBM 3

• Understand the importance of the hydrophobic
  effect.
• Understand quaternary structure
• Be aware of how the structure of a protein
  determines its function
• Some examples of protein modification

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Protein structure a recap

• Primary
• covalent linkage
• peptide bonds and disulphide bridges.
• Secondary
• Small structural elements a-helices, b-sheets
  and b-turns
• Tertiary
• Defines the overall fold of the protein
• Inextricably linked to function

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Quaternary structure

• Not for all proteins
• Those where the active protein has more than 1
  component/sub-unit
• Describes the orientation or the subunits and
  their interactions
• Controls the activity and regulation of the
  protein allostery (its good to talk)

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Protein Structure and Stability a digression

• Why do proteins adopt unique, stable
  configurations?
• What drives protein folding?
• covalent linkage
• hydrogen bonds
• ionic interactions

?
?
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Protein folding - the hydrophobic effect

• Aliphatic and aromatic amino acids are
  hydrophobic
• Polar and charged amino acids are hydrophilic
• So protein folding should bury hydrophobic
  residues and expose hydrophilic ones to water
• Water has more freedom (greater entropy)
• No exposed hydrophobic regions to restrict its
  mobility

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Consequences of protein folding

• Hydrophobic protein core
• Charge-covered surface.
• Act as buffering groups
• Overall charge on protein can be used to separate
  them (electrophoresis)

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core

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Quaternary structure

• Not for all proteins
• Those where the active protein has more than 1
  component/sub-unit
• Describes the orientation or the subunits and
  their interactions
• Controls the activity and regulation of the
  protein allostery (its good to talk)

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Haemoglobin the classic example

• 4 subunits i.e. tetrameric protein
• 2 alpha subunits
• 2 beta subunits
• 2 delta subunits in foetal haemoglobin
• One haem group per subunit

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Haem and the Globin Structure

• Haem contains iron atom which enables interaction
  with the protein and with oxygen
• Globin fold 8 a-helices in a compact tertiary
  structure

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Haemoglobin quaternary structure
allosteric interactions
active, oxygen transporter
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Haemoglobin what does allostery mean?
FAST Overall Reaction (lungs)
O2
O2
O2
O2
O2
O2
O2
O2
O2
O2
Similarly FAST reverse reaction (working tissues)
globin with low affinity for oxygen
globin with high affinity for oxygen
O2
globin with bound oxygen
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Haemoglobin vs. Myoglobin

• Tetrameric
• Four globin molecules
• Allosteric interactions
• Oxygen binding and de-binding achieved over a
  narrow range of oxygen levels
• Good for organisms that breathe a lot e.g. humans

• Monomeric
• 1 copy of a globin fold
• No allostery
• Oxygen binding occurs at a much higher oxygen
  concentration than oxygen release.
• Good for organisms that hold a breath for ages
  e.g. diving mammals

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Protein modifications theres more to proteins
than 20 amino acids

• Reversible or irreversible
• Activate proteins or modify activity
• Direct proteins to a cellular compartment
• Enable proteinprotein or proteinligand
  interactions
• Cause protein degradation

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Protein ModificationsAmino acid level
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Collagen modifications and stability. 1)
Vitamin C dependent reactions

• Hydroxylation of proline
• (vitamin C activated enzyme)

CH
OH
proline
4-hydroxyproline
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Collagen triple-helical structure enabled by
triple-peptide repeat

• Several hundred repeats of Gly-X-Y (XPro,
  Yhydroxy-Pro)
• Three peptide chains, each with this repeat
• Intertwined, like strands of rope
• NOT a-helical. Unusual polyproline helix or
  collagen helix due to the regular Gly-X-Y
  pattern

30 nm
1.5 nm
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Collagen modifications and stability. 2)
Modification of lysine and cross-links

• Lysine (basic) converted to an aldehyde
• Cross-linking of modified lysine residues ( )
• Glycosylation (addition of sugar residues ) of
  lysine residues.

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Collagen multiple fibres form a high strength
cable

• Glycosylation of the ends of fibres
• Cross-links between modified lysine and histidine
  residues at ends of fibres
• Directional strength
• Parallel bundles in tendons
• Multi-oriented bundles in skin

gt 100 nm
gt 10 nm
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Protein homologysequence, structure and function

• Proteins that are gt25 identical in sequence will
  share a homologous 3D-structure
• Common function/mechanism
• Trypsin and chymotrypsin
• 40 identical at the amino acid level
• Same 3D structure (mostly b-sheet)
• Loops provide the specificity of the enzymes

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Trypsin a study of a protein in action

• Digestive protease

peptides
trypsin
protein to be digested (substrate)
amino acids
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Trypsin common catalytic triad mechanism
aspartate stabilises histidine histidine
stabilises serine serine highly reactive
nucleophile
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Summary

• Protein folding is directed by interactions with
  solvent water
• Many proteins are part of larger assemblies and
  have allosteric interactions
• Protein function is dependent on protein
  structure
• Protein modifications may control activity