Summary: Structural Bioinformatics

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  • 1 Protein structure introduction

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  • Nam 3 special amino acids.

    • Cysteine
      • can create disulfide bridge
      • post-translational modification
    • Proline
      • forms ring with backbone
      • different phi/psi angles
    • Glycine
      • no side chain
      • different phi/psi angles
  • What is the R value? (pdb-file)

    • One value per structure
    • Measures how well the simulated diffraction pattern matches the experimentally-observed diffraction pattern.
    • A totally random set of atoms will give an R-value of about 0.63, whereas a perfect fit would have a value of 0.
    • Typical values are about 0.20. 
  • What is the B-value/temperature factor?

    • one value per atom
    • measure for the amount of smearing of the electron density
    • Values under 10 create a model of the atom that is very sharp, indicating that the atom is not moving much and is in the same position in all of the molecules in the crystal. Values greater than 50 or so indicate that the atom is moving so much that it can barely be seen.
  • 2 Protein folding

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  • What determines secondary structure?

    • Planarity of the peptide bond
    • favourable hydrogen bonding patterns
    • steric hindrance
  • How to calculate a propensity?

    See equation.
  • What types of forces and effects would be relevant for structure?

    • Van der Waals
    • Electrostatics
    • Hydrogen bonding
    • Entropic effects
    • Hydrophobic effect
  • What is a hydrogen bond?

     A hydrogen bond (H-bond) is a type of attractive (dipole-dipole) interaction between an electronegative atom and a hydrogen atom bonded to another electronegative atom.
  • What are the largest contributors to the stability of a folded protein?

    The buried hydrophobic amino acids.
  • What is the equation for entropy?

    With kb = boltzman factor en omega = the number of microscopic conformations
  • Explain Anfinsen’s Theorem.

    • Primary structure determines tertiary structure.
    • Anfinsen proposed that the information determining the tertiary structure of a protein resides in the chemistry of its amino acid sequence.
    • It was demonstrated that, after cleavage of disulfide bonds and disruption of tertiary structure, many proteins could spontaneously refold to their native forms. 
    • This lead to general acceptance of the ‘thermodynamic hypothesis’.

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