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Protein structure and evolution

Protein structure and evolution. Protein structure. Primary structure Secondary structure Tertiary structure Quaternary structure. Primary structure. Amino acid sequence, e.g., for tubeworm carbonic anhydrase

jael-glenn
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Protein structure and evolution

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  1. Protein structure and evolution

  2. Protein structure • Primary structure • Secondary structure • Tertiary structure • Quaternary structure

  3. Primary structure • Amino acid sequence, e.g., for tubeworm carbonic anhydrase • MAAWDYEANGPATWAKSFPLAAGKKQSPIDIDPASVSKKSTSALVASYNPAASNTLTNTGLSFQVSVDGTLSGGPLGNEYKAASFHFHWSKTSAEGSEHTVAGKAYAAEAHIVHYNAAKYASFQDAVKADDGLAVLATFIQPGATNAGVQKIIDLLPSVPTKGDTATIPGGFDVACLLPGDQSKYWYYPGSLTTPPCFESVTWIVYKDPIQLCENQLAALRKITGCNFRPTLGLCGRQVSSSF

  4. Secondary structure • Alpha helixes and beta sheets • Protein domain-level structure http://www.imb-jena.de/image_library/GENERAL/alpha_r_helix_1.gif http://cnx.org/content/m11614/latest/beta_sheet_cartoon.JPG

  5. Tertiary structure • 3D structure of a protein • Subunit-level structure http://www.biologie.uni-hamburg.de/b-online/fo42/1rus.gif

  6. Quaternary structure • How the subunits interact with eachother • ‘Holoenzyme’-level structure http://www.bact.wisc.edu/Microtextbook/images/book_4/chapter_2/2-30.jpg

  7. Protein evolution What diverges? What is conserved?

  8. What diverges? • Third nucleotide of codons • Silent substitutions • No alteration of primary, secondary, tertiary, quaternary structure

  9. What diverges? • Replacement of one amino acid by a chemically similar one • Alteration of primary structure • No, or minimal, alteration of secondary, tertiary, quaternary structure http://www.neb.com/nebecomm/tech_reference/images/amino.gif

  10. What diverges? • ‘Structural’ amino acids away from the active site http://opm.phar.umich.edu/phpthumb/phpThumb.php?src=../images/proteins/2iwv.gif&w=400

  11. What is conserved? • Active site residues Form I Form II Form I

  12. What is conserved? • Sites of covalent modification • E.g., histidine kinases http://www.uni-kl.de/FB-Biologie/AG-Hakenbeck/TGrebe/HPK/Table5.htm

  13. What is conserved? • Sites that interact with • Other subunits • Allosteric regulators http://www.photosynthesisresearch.org/images/Andersson%20rub2L.jpg

  14. Case study • Carboxysomal carbonic anhydrase

  15. Carbonic anhydrase • Catalyzes the following: • CO2 + H2O H2CO3 • Which in turn facilitates H2CO3  H+ + HCO3 - • 3 families (a, b, g) • Within each family: homologs • Apparent when comparing their amino acid sequences • BUT: each family arose independently http://www.scripps.edu/pub/goodsell/pdb/pdb49/pdb49_1.html

  16. …A fourth family of CA’s? HCO3- HCO3- HCO3- CA CO2 CO2 Ru bisco biomass

  17. Carboxysomal carbonic anhydrase • Carbonic anhydrase activity • But sequence-based methods… • No apparent homologs • Proposed a fourth class of CA’s (e-class) So et al., 2004

  18. Structure of CsoS3 was solved • Protein was • Overexpressed in E. coli • Purified • Crystallized • Structure determined via X-ray absorption

  19. Active site of carboxysomal carbonic anhydrase is same as b-CAs Sawaya, M. R. et al. J. Biol. Chem. 2006;281:7546-7555

  20. Structure based sequence alignment of CsoSCA and beta-carbonic anhydrase homologs Csome { Csome { Csome { Csome { Sawaya, M. R. et al. J. Biol. Chem. 2006;281:7546-7555

  21. Moral of the story Less conserved More conserved • Primary structure • Secondary structure • Tertiary structure

  22. Another moral of the story • Very, very distantly related proteins can reveal their relatedness by examining their structure • Moderately distantly-to-closely-related proteins can reveal their relatedness by examining their sequence

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