Protein Functional Site Prediction

1. Protein Functional Site Prediction • The identification of protein regions responsible for stability and function is an especially important post-genomic problem • With the explosion of genomic data from recent sequencing efforts, protein functional site prediction from only sequence is an increasingly important bioinformatic endeavor.

2. What is a “Functional Site”? • Defining what constitutes a “functional site” is not trivial • Residues that include and cluster around known functionality are clear candidates for functional sites • We define a functional site as catalytic residues, binding sites, and regions that clustering around them.

3. Protein

4. Protein + Ligand

5. Functional Sites (FS)

6. Regions that Cluster Around FS

7. Phylogenetic motifs • PMs are short sequence fragments that conserve the overall familial phylogeny • Are they functional? • How do we detect them?

8. Phylogenetic motifs • PMs are short sequence fragments that conserve the overall familial phylogeny • Are they functional? • How do we detect them? • First we design a simple heuristic to find them • Then we see if the detected sites are functional

9. Scan for Similar Trees Whole Tree

10. Scan for Similar Trees Whole Tree

11. Scan for Similar Trees Whole Tree Windowed Tree

12. Scan for Similar Trees Whole Tree Windowed Tree Partition Metric Score: 6

13. Scan for Similar Trees Whole Tree Windowed Tree Partition Metric Score: 8

14. Scan for Similar Trees Whole Tree Windowed Tree Partition Metric Score: 4

15. Scan for Similar Trees Whole Tree Windowed Tree Partition Metric Score: 6

16. Scan for Similar Trees Whole Tree Windowed Tree Partition Metric Score: 8

17. Scan for Similar Trees Whole Tree Windowed Tree Partition Metric Score: 6

18. Scan for Similar Trees Whole Tree Windowed Tree Partition Metric Score: 6

19. Scan for Similar Trees Whole Tree Windowed Tree Partition Metric Score: 0

20. Scan for Similar Trees Whole Tree Windowed Tree Partition Metric Score: 6

21. Scan for Similar Trees Whole Tree Windowed Tree Partition Metric Score: 6

22. Scan for Similar Trees Whole Tree Windowed Tree Partition Metric Score: 8

23. Scan for Similar Trees Whole Tree Windowed Tree Partition Metric Score: 0

24. Scan for Similar Trees Whole Tree Windowed Tree Partition Metric Score: 6

25. Scan for Similar Trees Whole Tree Windowed Tree Partition Metric Score: 6

26. Scan for Similar Trees Whole Tree Windowed Tree Partition Metric Score: 6

27. Phylogenetic Motif Identification • Compare all windowed trees with whole tree and keep track of the partition metric scores • Normalize all partition metric scores by calculating z-scores • Call these normalized scores Phylogenetic Similarity Z-scores (PSZ) • Set a PSZ threshold for identifying windows that represent phylogenetic motifs

28. Set PSZ Threshold

29. Regions of PMs

30. Map PMs to the Structure

31. Map PMs to the Structure Set PSZ Threshold

32. Map PMs to the Structure Map Set PSZ Threshold

33. Map PMs to the Structure Map Set PSZ Threshold

34. PMs in Various Structures

35. PMs and Traditional Motifs

36. TIM Phylogenetic Similarity False Positive Expectation

37. TIM Phylogenetic Similarity False Positive Expectation

38. TIM Phylogenetic Similarity False Positive Expectation

39. TIM Phylogenetic Similarity False Positive Expectation

40. Cytochrome P450 Phylogenetic Similarity False Positive Expectation

41. Cytochrome P450 Phylogenetic Similarity False Positive Expectation

42. Enolase Phylogenetic Similarity False Positive Expectation

43. Glycerol Kinase Phylogenetic Similarity False Positive Expectation

44. Glycerol Kinase Phylogenetic Similarity False Positive Expectation

45. Myoglobin Phylogenetic Similarity False Positive Expectation

46. Myoglobin Phylogenetic Similarity False Positive Expectation

47. Evaluating alignments • For a given alignment compute the PMs • Determine the number of functional PMs • Those identifying more functional PMs will be classified as better alignments

48. Protein datasets

49. Running time

50. Functional PMs PAl=blue MUSCLE=red Both=green (a)=enolase, (b)ammonia channel, (c)=tri-isomerase, (d)=permease, (e)=cytochrome