1. Alpha/Beta structures Barrels, sheets and horseshoes

2. Common features Parallel  strands are arranged in barrels or sheets Individual  strands are connected by  helices  motif is a building unit

3. TIM barrel First observed in enzyme Triosephosphate Isomerase

4. The core of TIM barrel Core is tightly packed with hydrophobic amino acids Three layers of sidechains

5. Residue distribution in TIM barrel

6. Unusual exception Methylmalonyl- Coenzyme A mutase has small hydrophilic residues in the inside of barrel Coenzyme A (green) binds in the barrel

7. TIM barrel as a domain TIM barrel is always associated with enzymatic function Pyruvate kinase

8. Location of active site in TIM barrels

9. Double barrels Phosphoribosyl anthranilate (PRA) isomerase and Indoglycerol phosphate (IGP) synthase in E.coli (enzyme catalysing two reactions in the tryptophan biosynthesis)

10. Barrel 1 Barrel 2 Some other microorganisms have two separate single-barrel proteins Some microorganisms have triple barrel homologous protein, where the third barrel catalyzes still another reaction in Trp synthesis pathway

11. TIM barrels: example of enzyme evolution There is evidence that new enzymes can evolve by changing the active site of TIM barrel

12. Both enzymes are TIM barrels with 26% sequence identity

13. ordinary horseshoe  -horseshoe fold  horseshoe Present in many proteins with completely unrelated functions

14. Number of  repeats can vary considerably

15. Hydrophobic core of  horseshoe In between  strands and helices, NOT in the middle of horseshoe Many leucines in conserved positions  horseshoe proteins are called also LRR (leuine rich repeats) proteins

16. Leucine-rich motif in the horseshoe a- aliphatic amino acid X- any amino acid The motif is strong enough to be used in structure prediction

17.  open twisted sheet Parallel or mixed  -sheet with  helices on both sides Number of  -strands vary from 4 to 10 Called also Rossman fold Lactate dehydrogenase

18. Topology In TIM barrels and horseshoe proteins the topology is fixed In open sheets topology can vary a lot TIM Open  sheet

19. Location of active site in  open twisted sheet

20. Sandwiches.... mmmm

21. Protein structure sandwiches Layered molecules, where each layer represents either  or  structure Represents one of “A” levels in CATH classification Most common:  double sandwich  triple sandwich  double sandwich Open  sheets can be considered.....  sandwiches

22. What’s that? TATA box binding protein (TBP) is a... sandwich That’s right,  double

23. End of story? No other  proteins? There is a good deal of other  proteins However, most of them have folds with very few representatives, so they will be not discussed here