Introduction to Protein Informatics Bioe144, Fall 2009 Lecture 1, part 2 Kimmen Sjölander

1. Introduction to Protein InformaticsBioe144, Fall 2009Lecture 1, part 2Kimmen Sjölander

2. Estimating phylogenetic trees using molecular data: nucleic acid data are best for close relationships (such as here), but amino acid data are best for distant relationships

3. What is homology? • Homology -> same form • Homology between two genes means “related by evolution, has a common ancestor”

4. Sequence similarity and evolutionary relationship • If two proteins have significant sequence similarity, they are related by evolution • It is not generally correct to say that two proteins are 50% homologous • However, 50% identity supports an assertion of homology • The converse is not true: two proteins can have undetectable sequence similarity but still be related by evolution • Questions: • What level of sequence similarity is significant? • If two sequences have undetectable sequence similarity, how can we determine if they are related?

5. Protein family distributions follows a power law

6. Antimicrobial Protein 1 Common horse chestnut Structural analysis reveals the common ancestry of plant and insect defensins 1BK8 1MYN Drosomycin, Antifungal protein Fruit Fly Only 22% Pairwise Identity (in the Twilight Zone) but structural and functional analyses support a common ancestry

7. Fundamental mechanisms underlying evolution of gene families Creighton, Proteins

8. Canonical example of gene family evolution and subsequent (tissue and temporal) subfunctionalization Creighton, Proteins

9. Proteins are composed of modular structural domains which are found in different domain architectures Leucine-Rich Repeat (LRR) Toll-Interleukin Receptor (TIR) domain Plant and animal innate immune systems are composed of molecules having a common evolutionary origin

10. G-protein-coupled receptors (GPCRs) This family displays both divergent and parallel evolution

11. Convergent evolutionFunctional similarity (and identical active sites)but structural dissimilarity supports an assertion that they do not share a common ancestor Subtilisin structure (1SBT A): One beta sheet surrounded by helices (primarily helical) Trypsin structure (3TGI E): Two beta barrels with two tiny helices (primarily beta)

12. Structure analysis suggests convergent evolution of these peptidases

13. G-protein-coupled receptors (GPCRs) This family displays both divergent and parallel evolution

14. Convergent evolutionFunctional similarity (and identical active sites)but structural dissimilarity supports an assertion that they do not share a common ancestor Subtilisin structure (1SBT A): One beta sheet surrounded by helices (primarily helical) Trypsin structure (3TGI E): Two beta barrels with two tiny helices (primarily beta)

15. Structure analysis suggests convergent evolution of these peptidases

16. 1BK8 Antimicrobial Protein 1 (Ah-Amp1) Common horse chestnut Proteins can diverge structurally and functionally from a common ancestor 1AGT Agitoxin 2 Egyptian Scorpion (K+ channel inhibitor) Drosomycin, Antifungal protein Fruit Fly 1CN2 Toxin 2 Mexican scorpion (Na+ channel inhibitor) 1AYJ Antifungal protein 1 (RS-AFP1) Radish

17. Sequence and structural divergence are related “The relation between the divergence of sequence and structure in proteins”, Chothia and Lesk. EMBO Journal 1986

18. Alignment accuracy drops with evolutionary divergence

19. Most alignment methods perform poorly when sequences are evolutionarily distant

22. Gene duplication produces protein superfamilies including paralogs with divergent functions

23. Percolation of annotation errors Domain shuffling Neofunctionalization stemming from gene duplication Homology-based functional annotations are fraught with systematic error Two key statistics: Up to 25% of sequences may be mis-annotated* Fewer than 3% of sequences have experimental support for their annotated function *Brenner, SE "Errors in Genome Annotation" Trends Genet. 1999 Brown & Sjölander, "Functional Classification using Phylogenomic Inference." PLoS Computational Biology, 2006 Gilks et al, “Modeling the percolation of annotation errors in a database of protein sequences” Bioinformatics 2002 Galperin and Koonin "Sources of Systematic Error in Functional Annotation of Genomes" In Silico Biology. 1998

24. Definitions • Divergent evolution: related from a common ancestor • Homolog: related by divergent evolution • Ortholog: related by speciation from a common ancestor • Paralog: related by duplication from a common ancestor • Xenolog: acquired by HGT (horizontal gene transfer) • Parallel evolution: within a family of divergently related genes, two (or more) genes can acquire similar functional specificities • Example: GPCRs (e.g., serotonin and dopamine receptors) • Convergent evolution: no common ancestor, but the two genes have acquired a similar function • Example, chymotrypsin and subtilisin • Some relationships are uncertain • Example: TIM barrel proteins

25. Homologs: orthologs and paralogs Ancestral gene Homologs: genes that have descended from a common ancestral gene. Gene 1 Gene2 Paralogs: the last evolutionary event separating the genes was duplication. D Orthologs: the last evolutionary event separating the genes was speciation. S Courtesy of Nir Yosef

26. Orthology prediction using trees S Super-orthologs Orthology: the MRCA must correspond to a speciation event. (By this definition, the Yeast sequence is orthologous to all sequences in this example.) Super-orthology is more restrictive than orthology: all nodes on a path between two leaves must correspond to a speciation event. (Zmasek & Eddy, 2002) D H1 C1 M1 R1 F1 W1 H2 C2 M2 R2 F2 W2 Yeast Human, Chimp, Mouse, Rat, Fly, Worm

27. Why is orthology important? Reconstructing the Tree of Life PPI prediction (using interlog analysis) Phylogenomic inference of protein function Phylogenetic profile construction Prediction of biological pathways and network alignment

28. Ortholog prediction accuracy Assessed vs TreeFam-A manually curated orthologs Dataset: 100 (non-homologous) human sequences from TreeFam-A, filtered to remove homologs. PHOG-O: Standard orthology definition PHOG-S: Super-orthologs (Zmasek & Eddy) PHOG-T: thresholded PHOGs PHOG-T(M); optimized for mouse PHOG-T(Z): optimized for zebrafish PHOG-T(F): optimized for fruit fly

29. Proteins interact with other molecules(bioinformatics methods exist to predict these interactions) Yeast network, taken from “Form follows function: the architecture of complex networks” Molecular Systems Biology 2:42, 2006

30. Example bioinformatics analysis of inorganic pyrophosphatase

31. Fasta format sequence of human inorganic pyrophosphatase 2, mitochondrial >sp|Q9H2U2|IPYR2_HUMAN Inorganic pyrophosphatase 2, mitochondrial MSALLRLLRTGAPAAACLRLGTSAGTGSRRAMALYHTEERGQPCSQNYRLFFKNVTGHYI SPFHDIPLKVNSKEENGIPMKKARNDEYENLFNMIVEIPRWTNAKMEIATKEPMNPIKQY VKDGKLRYVANIFPYKGYIWNYGTLPQTWEDPHEKDKSTNCFGDNDPIDVCEIGSKILSC GEVIHVKILGILALIDEGETDWKLIAINANDPEASKFHDIDDVKKFKPGYLEATLNWFRL YKVPDGKPENQFAFNGEFKNKAFALEVIKSTHQCWKALLMKKCNGGAINCTNVQISDSPF RCTQEEARSLVESVSSSPNKESNEEEQVWHFLGK

32. http://blast.ncbi.nlm.nih.gov/Blast.cgi

36. Top BLAST matches, ordered by E-value Note that because we searched SwissProt, we are missing many homologs (e.g., chimp)

37. Mouse match

38. Yeast match

39. Plasmodium falciparum match

40. Oryza sativa (rice) match

41. Helicobacter pylori match

42. Chimp ortholog (from a separate BLAST search against the Chimp genome)

43. Iterated homology search followed by phylogenetic analysis shows universal conservation of this gene family bpg032120

44. Key terms and concepts • Divergent vs convergent evolution • Parallel evolution • Homology • Adaptation • Phylogenetic distribution • Tree of Life • Horizontal gene transfer • Speciation • Gene duplication • Selection • Twilight Zone • Domain fusion and fission events • Domain architecture • Gene loss & expansion Evolution conserves form & function, but also generates novel forms and functions. Similarity in sequence is evidence of evolutionary pressure to conserve structure and/or function