proteins' DNA binding

proteins' DNA binding：DNA binding domain、DNA major groove、DNA repair.

proteins' DNA binding

• DNA binding domain
  • common DNA binding motifs
    • helix turn helix motifs
      • structure
        • one short turn links two α helixes
      • DNA interaction
        • 2 α helixes fix each other in right angle to form recognation helixes
          • one of the 2 α helixes fit and binds to DNA major groove
          • one of the 2 α helixes position the recognation helixes
      • domain organization
        • usually 2 helix turn helix motif in pairs
          • 3.4 nm in distance
            • equal to distance of one DNA turn
          • 2 recognizations strengthen the DNA-protein binding
      • role
        • essential for multicellular development in homeodomain
    • zinc finger motifs
      • structure
        • form 1: a zinc atom links an α-helical segment to a β-sheet segment
        • multiple zinc atoms may involved in one motif
      • DNA interaction
        • α-helical segment fit and binds to DNA major groove
      • domain organization
        • muliple zinc fingers cluster
          • β sheets space the α helixes for nearly 3.4nm
            • "hand"
          • strength of DNA-protein increased with fingers number
    • leucine zipper motifs
      • structure
        • 2 subunits
          • interaction beween their hydrophobic regions bond them together
          • the rest hydrophilic regions seperate to form a "Y" shape
      • DNA interaction
        • hydrophilic regions are α helixes, and both 2 helixes fit and binds to DNA major goove
      • feature
        • Different combinations bewteen 2 subunits provide good DNA recognation flexibility
• DNA major groove
  • structure
    • geomitry
      • helical groove
    • surface feature
      • accessible and bases uniqued nucleotides' hydrogen bonding donors & acceptors
  • function
    • media of DNA sequence-protein molecular recognation
• DNA repair
  • Direct repair
    • DNA ligase
      • repair "Nicks"
        • form phosphodiester bond between approximated 3'OH and 5' OPO32-
    • Alkyltransferase
      • deakylates
        • O4-alkylthymine
        • O6-methylguanine
      • Suicide inactivation
    • Photoreactivation
      • Photolyase (flavoprotein) repair UV leision using light as energy source
  • Excision repair
    • Methyl-directed Mismatch Repair (MMR)
      • mismatch targeting
      • require methylated DNA around to direct repair in e. coli
        • but not in human
      • excise by mut H
      • synthesize by DNApol III
    • Nucleotide Excision Repair (NER)
      • bulky leision targeting
      • excise and synthesized by DNApol I
    • Base Excision Repair (BER)
      • specific altered sites recognized by different glycosylases
      • exice by AP endonuclease
  • Strand break repair
    • Single-strand break repair
    • Double-strand break repair
      • Non-Homologous End Joining (NHEJ)
      • Homologous Recombination (HRR)
  • Ecoli SOS