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What is angle A?
ω - Omega
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What is angle B?
φ - Phi
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What is angle C?
Ψ - Psi
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What torsion angle does omega like?
~180 degrees
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Conformational propensity
Frequency in which a residue adopts a given conformation
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Does conformational propensity apply to main chain atoms?
Yes
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What does conformational propensity depend upon?
- Residue physiochemical properties
- Sequence context (flanking residues) [Lesser extent]
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Outline hou-Fasman method
Calculate single propensity for each residue type and secondary structure.
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Problems with the Chou-fasman model
- Based solely on physiochemical properties
- Does not account for sequence context
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Cho fasman formula
P[Secondary structure]= (%Residue[Secondary structure]/%All Residues[Secondary structure])
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GOR Method
- Select a residue for propensity examination
- Examine the eight residues to either side (17 residue total window)
- Use the Chou-fasman formula
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Glutamate has an α-helix propensity of 1.51. What does this mean?
Glu is in an α-helix ~50% more than not
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What direction do R-groups lean on α-helices?
Toward the N-terminus
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Why do branched residues dislike helices?
Their large R-groups cause steric clashes
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Which secondary structure favours large R-groups?
β-sheets
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Two types of helix cap (N and C)
- Glu (N) - Uses side chain for hydrogen bonding
- Ala (C) - Uses main chain NH3 for bidentate H-bonds (310)
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Why is helix capping important?
To satisfy hydrogen bonding on the ends of an α-helix.
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Residues preferring α-helices
- Glutamate (N-cap)
- Alanine (C-cap)
- Methionine
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Residues preferring sheets
- β-branched residues and TyrosineTyrosine, valine , isoleucine and threonine
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Residues preferring turns
- Proline, glycine and small polar charged residues
- Proline, glycine, aspartate, asparagine and serine
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Residues generally preferring nonspecific secondary structures over turns
- Leucine, phenylalanine and tryptophan
- Nonpolar
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Residues with no real preference
- Arginine
- Cysteine
- Glutamate
- Histidine
- Lysine
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Residue sequence preceding a helix
...-Pro-Gly-Pro-Gly-... (Helix whithin twelve residues)
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