Protein Lec 4

Protein Lec 4

1. Protein similar structure

   • 30%+ aa sequence identity equal, proteins have same 3D fold
   • Below 25% aa sequence similarity, only 10% aligned pairs have structural similarity
   • Twilight zone: 20-30% similar identity
   • Midnight zone: <20% similar identity
   • NOTE: structure is conserved more than sequence

2. Dali server

   • Searching for structural homologs

3. Homologous proteins: similar amino acid sequence

4. Paralogs: homologs which arose from gene duplication (may have different function)

5. Orthologs: homologous proteins found in different species (evolved from same gene in common ancestor - usually same function)

6. BLAST

   • search for homologs and examine amino acid alignment
   • program compares nucleotide / protein sequences to data bases and calculates structural similarity
   • Calculates an expect value (E-value) for each alignment
     • how many hits you can expect to see by chance when searching a database of a certain size
     • Lower E-value = significant alignment

7. Protein sequence alignment

   • Comparison of protein sequences is a powerful way to uncover evolutionary relationships, structural homologies and functional similarities
   • Identify residues that have been conserved during evolution, and which therefore must be structurally and functionally important
   • Highly conserved residues might contribute to the core fold of the protein (the structurally important parts) OR these regions may be involved with surface interacts with binding partners OR they contribute to catalytic function or folding
   • % identity
     • Add up * = A Total residues in protein = B A/B *100 = % identity
   • % conservation
     • Add all * and : = A total residues = B A/B * 100 = % conservation

8. Sequence LOGOs

   • visualise alignment
   • Protein or amino acid
   • At that 'point' what were the different outcomes