Protein evolusion

这是一篇关于Protein evolusion的思维导图，主要内容有Terms describe evolusionary history、New functional protein、principle for bioinformatics。

Protein evolusion

• Terms describe evolusionary history
  • Homology
    • means common ancestor
    • subdivisions
      • orthologs
        • between species common ancestor (results by speciation)
        • usually same function
      • paralogs
        • in species common ancestor (results by gene duplication, but still same species)
        • usually novel functions
    • evidence for common ancestor
      • sequences similarity
        • genes
        • protein 1' structures
      • structural similarity
        • should be more similar than genes
        • because genes change faster(degeneracy coding)
          • some times structural similarity may compeletely lost
          • selfish structure/ peptide sequence?
  • Analogy
    • means convergent evolution
    • Structural
      • convergent structure, but no same function
        • shit?
        • Global structural analogues
        • some homologous and analougous are so vague and unable to determine
      • e.x. molecular mimicry between nucleic acid and proteins
        • 1. eEf R
        • 2. TATAbp
        • 3. restriction enzyme inhibitor
    • Functional
      • convergent function, but no similar structure
        • but specific local structure always similar
          • aminotransferase
            • asparate aminotransferase
            • D-aminoacids aminotransferase
          • proteinase catalytic triad
            • chymotrypsin
            • carboxypeptidase
• New functional protein
  • Amino acids Mutation
    • ex. serin protease
      • changing active site residues change the cleavage specificity
    • ex. NAD,NADP specific enzymes
  • Domain variation
    • duplication, addition, insersion of domains
    • Domains
      • Structural and functional independence protein region
    • e.x. transcription factors, aminoacyl tRNA synthase, signaling molecules
  • Moon light protein?
    • more roles for 1 protein
    • ex
      • Phosphoglucose isomerase
        • glycolysis
        • growth factor
      • Enolase
        • glycolysis
        • structural protein in eye lens
        • transcription factor
        • parasite defence protein
        • RNAase
• principle for bioinformatics
  • DNA sequence similarity
    • provide evidence for functional similarity
      • BLAST
  • Domains are more reliable units
    • exon reshuffling hypothesis
    • Domain analysis provides a more reliable guess
      • since you understand each domains' function, you know the whole
  • protein 3D conformation can be predicted by sequences
    • by calculation of conformation energies...
    • so structure comparation is a more valid/solid evidence for homologous
      • structures changes much harder than genes
    • and structure often provides guides for their intramolecular interactions
  • protein engineering
    • modify existing protein scalffold
      • ex. add active site on non-catalytic structure
    • creating new protein folds
      • try and fail on computer modeling
        • first create basic secondary structure parttern
          • Then modify ammino acids to improve it
    • domain reshuffling
      • change DNA binding domain's specificity and its arrached effector domain
        • zink finger: recognize 3 nt