PROTEIN STRUCTURE

• Proteins


  First, of primary importance (Greek)
• There are ~10 million proteins in nature
• Proteins make up > ½ dry weight of most organisms
• Peptides


  MW ≤ 10000 Da
• Variety of protein functions

  • Structural
  • Transport
  • Protective
  • Regulatory
  • Catalytic
  • Motion
  • Storage
  • Source of energy
• In nature, form follows function
• Protein folding


  1. Newly synthesized polypeptide

  2. Fold into specific 3-D arrangement (conformation)

  3. Posttranslational modifications may add/remove chemical groups
• Configuration


  Geometric relationship between a given set of atoms; interconversion requires breaking covalent bonds

  
• Conformation


  Spatial relationship of every atom in a molecule; interconversion via rotation about single bonds
• Protein classification by gross characteristics

  • Soluble (extracted using aqueous solution) vs. integral membrane proteins
  • Globular (axial ratios not over 3) vs. fibrous (axial ratios ≥10)
  • Lipoproteins, glycoproteins, metalloproteins

  
• Proteins


  • Constructed using modular principles
  • Synthesis employs AAs joined by peptide bond
  • Folding embodied in four orders of protein structure
• Primary structure


  Linear sequence of AAs in polypeptide chain, held by peptide bonds and position of -S-S- bonds

  
• Abnormal AA sequence changes in primary structure can cause defective proteins and genetic diseases
• Peptide bond


  Most important covalent bond, formed by condensation, determines primary structure

  
• Peptide bond


  • Generally trans, polar, can form hydrogen bonds, resistant to hydrolysis

  
• Types of bonds in proteins

  • Covalent peptide bonds (~400 kJ/mol)
  • Covalent disulfide bonds (~214 kJ/mol)
  • Hydrogen bonds (4.2-25 kJ/mol)
  • Hydrophobic interactions (<4.2 kJ/mol)
  • Ion bonds (<21 kJ/mol)

  
• Secondary structure


  Regular arrangements of AAs (3-30) based on H-bonding
• α-helix


  • Right-handed, extensive H-bonding, 3.6 AAs per turn, 0.54 nm pitch
  • Disrupted by Pro, Gly, charged/bulky AAs
• β-structures


  • All peptide bonds involved in H-bonding, composed of extended β-strands (parallel or antiparallel)

  
• β-bends


  • Reverse direction of polypeptide chain, 4 AAs (Pro, Gly), stabilized by H- and ionic bonds

  
• Nonrepetitive secondary structures


  • Less regular, simple structures like loops and coils
• Supersecondary structures (motifs)


  Combination of secondary structure elements connected by non-repetitive elements
• Supersecondary structures


  • α-α corner
  • Twisted β-sheet
• Tertiary structure


  Overall 3D arrangement of all atoms in a protein
• Domain


  Basic unit of structure and function in a polypeptide chain, built from combinations of supersecondary elements

  
• Interactions stabilizing tertiary structure

  • Disulfide bonds
  • Hydrophobic interactions
  • Hydrogen bonds
  • Ionic interactions

  
• Disulfide bonds


  Covalent linkage between -SH groups of cysteine residues, stabilize 3D shape and prevent denaturation

  
• Disulfide bond formation


  Not specific, catalyzed by protein sulfhydryl-oxidase and protein disulfide isomerases

  
• Dietary riboflavin deficiency can lead to improper folding of disulfide-containing proteins
• Quaternary structure


  Arrangement of polypeptide chains (subunits) into a single protein, can have 2 to hundreds of subunits

  
• Quaternary structures


  • HIV protease
• Disulfide bonds


  Covalent bonds formed between two sulfur atoms in cysteine residues of proteins

  
• Dietary riboflavin deficiency


  Increased incidence of improper folding of disulfide-containing proteins
• Protein quaternary structure


  The arrangement of polypeptide chains (subunits) into a single protein (a multisubunit protein) consisting of two or more polypeptide chains that may be structurally identical or totally unrelated (oligomer, multimer)

  
• Multimeric proteins can have from two to hundreds of subunits
• Quaternary structure results from interactions between the subunits of multisubunit (multimeric) proteins or large protein assemblies
• Some multimeric proteins


  • Have a repeated unit consisting of a single subunit or a group of subunits referred to as a protomer
  • Protomers are usually characterized by rotational or helical symmetry
• Subunits


  • Held together by noncovalent interactions (and possibly also by disulfide bonds)
  • May either function independently of each other, or may work cooperatively
• Protein folding


  1. Stepwise

  2. Modular

  3. Thermodynamically favoured

  4. Auxiliary proteins assist folding

  5. Chaperones participate in the folding of over half of all mammalian proteins

  6. Folding is a dynamic process
• Proline-cis,trans-isomerases (cyclophilins)


  • Catalyze isomerization of proline from trans to cis configuration common in β turns
  • Also participate in the folding of proteins expressed by viral invaders, consequently, they are pursued as targets for the development of drugs – e.g. Cyclosporine and Alisporivir for the treatment of HIV, hepatitis C etc.