protein folding

这是一篇关于protein folding的思维导图，主要内容有primary structure、secondary structure、teritary structure、Globular and fibrous proteins等。

protein folding

• primary structure
  • characteristic
    • linear sequence of protein
    • 2 types of amino acid: N-; C-
    • includes disulphide bridges -S-S-
  • example
    • 1
      • cysteine's residues can get rid of a water and form a disulphide bridge.
    • 2
      • insulin have 2 chains
        • chainA 21residues
        • chainB 30residues
  • non-colavent interactions
    • hydrogen bonds
      • 氢键
    • electrostatistic attraction
      • 静电力
    • van der waals interactions
      • 范德华相互作用
    • hydrophobic interaction
      • 疏水相互作用
        • 疏水氨基酸位于蛋白质内部，亲水位于外部
  • sequence determines structure
    • amyloid fibrils
    • oligomers
    • amorphous aggregates
    • partially folded states
    • native state
    • folding intermediates
  • peptides are planar
    • what cause?
      • C==N peptide bond
      • other can turn around
    • how is the planar?
      • colavent bonds hold primary structure together
      • angles determine the conformation of peptide backbone and ‘fold’of the protein
    • geometry of torsion angles
      • phi ψ
        • C-N
      • psi φ
        • CooH-C
  • ramachandran plot 拉氏构象图
    • Ramachandran plot（拉氏图）是由G. N. Ramachandran等人[1]于1963年开发的，用来描述蛋白质结构中氨基酸残基二面角ψ和φ是否在合理区域的一种可视化方法。同时也可以反映出该蛋白质的构象是否合理
      • 深蓝色为完全允许，浅蓝色允许 白色不允许
    • effects
      • distinct torsion angles
      • folding patterns --conformation
• secondary structure
  • polypeptide's main chain atoms' local spatial arrangement
    • α螺旋
      • 描述
        • 节距
          • 3.6amino acid ----360°旋转 ；pitch=0.54nm
        • 顺时针螺旋
          • right hand helix: turns clockwise from N- to C-
        • 氨基酸间距
          • a amino acid occupies 0.15nm
        • r集团特征
          • R group outside the helix
        • H键在N和C，还有隔几个的氢键
          • H bonds between N-H and C=O stablize the structure
          • hydrogen bond between: intramolecular COi-NHi+4
      • sequence affect a helix stability
        • not all polypeptide sequences adopt helical tructure
        • ala leu benefits a helix formation because of hydrophobic
        • pro gly are helix breaker because Ca-N is impossible to rotate; tiny R group supports other conformations
    • β折叠
      • definition and structure
        • extended strands of amino acids
        • hydrogen bonds form between the strands
          • intermolecular
          • 在分子内的氢键连接
      • Rgroups ——directional
      • types
        • paralell
          • R groups alternate side to side
          • do not meet every secandary amino acid between chains
          • 2aa = 0，7nm
        • anti-parallel
          • r group alternate side to side
          • meet every amino acid between chains
      • zig-zag pattern parallel/anti-parallel—— NH-Cα-CO
      • multiple βsheets are placed between βsheets
      • H bonds can stablize the structure
  • amino acids exists prefrences in forming structure
• teritary structure
  • characteristic
    • 3-D structure
    • protein shape
    • a and beta sheets combind together
    • amino acids far apart in the protein sequence
  • motifs
    • folding patterns containing 1 or more elements of secondary structure
      • beita arfa-beta loop
    • domains
      • part of a polypeptide chain
        • calcium binding domains
      • fold into a distinct shape often has a specific functional role
• Globular and fibrous proteins
  • Fibrous 纤维状
    • Role – support, shape,
    • protecKon
    • Long strands or sheets
    • Single type of repeaKng
    • secondary structure
    • e.g. collagen
  • Globular 球状
    • Role – catalysis,
      • regulaKon
    • Compact shape
    • Several types of
    • secondary structure
    • e.g. carbonic anhydrase
• Collagen （胶原蛋白）
  • • Triple helical arrangement of collagen
    • chains
  • • Contain Gly – X – Y repeaKng
    • sequence
  • • Hydrogen bonds stablise
    • interacKons between chains
  • • Collagen fibrils formed from
    • collagen molecules
    • covalently cross-linked
• Folding of water soluble proteins e.g. Myoglobin （肌红蛋白）
  • polypeptide chains fold
  • hydrophobic side chains are buried
  • polar and charged side chains are on surface
• Folding of membrane proteins e.g. porins
  • often show inside-out distribution of amino acids
• Quaternary structure （四级结构）
  • molecular machines
  • up to 60(ribosome 55protein and 3RNA)
  • dimer. trimer, tetramer
  • number and arrangement of subunits
  • multiprotein complexes