Threedimensional structure of proteins

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Three-dimensional structure of proteins

• Three-dimensional structure of proteins is
  determined by it amino acid sequence.
• Function of the protein depends on its structure.
• Each protein has a unique or nearly unique
  structure.
• Non-covalent interactions are the most important
  forces stabilizing the three dimensional
  structure of the protein.
• There common structural patterns in vast protein
  architecture.

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Protein Conformation

• Spatial arrangement of atoms in the protein
  called conformation.
• Proteins can have several stable conformations,
  moving from one to the other should not involve
  breaking covalent bonds.
• Proteins in any of the functional, folded
  conformations are called, native

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Protein conformation is stabilized by weak
interactions

• Hydrogen bonds with water play a key role in the
  protein conformation and solubility.
• Polar and charged groups with in the core of the
  protein must have hydrogen bonding partners.
• Substitution of one amino acid for another can
  have destabilizing effect.

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Tertiary and Quaternary structures of proteins

• Three dimensional arrangement of all atoms in the
  protein is called tertiary structure.
• Three dimensional arrangement of two or more
  separate peptides in a complex is called
  quaternary structure.

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Proteins have common structural patterns.

• Supersecondary structures, motifs or folds, are
  particularly stable arrangements of several
  elements of the secondary structure.
  (helix-turn-helix)
• Large proteins (gt300 a.a) may fold into several
  stable globular units called domains
  (transcription factors).

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Rules for secondary structure.

• Hydrophobic side groups must be buried inside the
  folds, therefore, layers must be created (b-a-b
  a-a).
• a-helix and b-sheet, if occur together, are found
  in different structural layers.
• Adjacent polypeptide segments are stacked
  together.
• Connections between secondary structures do not
  form knots.
• The b-sheet is the most stable.

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Protein denaturation and folding

• Loss of secondary structure called denaturation.
• Denaturation can be accomplished by
• Heat
• pH
• Organic solvents Urea, GuHCl
• Removal of denaturing agents can lead to
  refolding of the secondary structure-renaturation.
  
• Renaturation-proof of the primary structure
  function relationship.

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