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Hot to cold

Hot to cold. Investigation of citrate synthase in thermophiles , mesophiles , and psychrophiles. Virginia Balke Delaware Technical & Community College. Class. Biotechnology II Protein unit Amino acids Protein structure Protein purification Bioinformatics in Biotechnology I BLAST

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Hot to cold

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  1. Hot to cold Investigation of citrate synthase in thermophiles, mesophiles, and psychrophiles Virginia Balke Delaware Technical & Community College

  2. Class • Biotechnology II • Protein unit • Amino acids • Protein structure • Protein purification • Bioinformatics in Biotechnology I • BLAST • Primer design

  3. Question • How does the structure of an enzyme vary among thermophiles, mesophiles, and psychrophiles? • Are the amino acids in the active site conserved? • Does the environment drive the evolution of the protein or does evolution of the protein permit living in the environment?

  4. Sequences – Citrate synthase • Psychromonasingrahamii • Flavobacteriumpsychrophilum • Psychrobacterarcticus • Pseudoalteromonashaloplanktis • Colwelliapsychrerythraea • Escherichia coli • Staphylococcus aureus • Bacillus cereus • Pseudomonas aeruginosa • Streptomycescoelicolor • Picrophilustorridus (Archaea) • Aquifexaeolicus • Thermotogamaritima • Thermusaquaticus • Geobacillusthermodinitrificans • All genomes are found in IMG

  5. MUSCLE – Multiple Sequence Alignment

  6. WebLogo Compare with Pfam HMM Logo

  7. Phylogram Investigate the outliers

  8. Cn3D Thermotogamaritima Escherichia coli

  9. Extensions • Add other species • Primary literature search • Reported structure differences • Codon usage • Compare other proteins common to all species • DNA gyrase, fumarase, enolase, translational elongation factors • 16S rRNA sequences • GC content

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