1. Russell Group, Protein Evolution _________ ____ Rob Russell Cell Networks University of Heidelberg Interactions and Modules: the how and why of molecular interactions

2. Russell Group, Protein Evolution _________ ____ Proteins are modular Since the early 1970s it has been observed that protein structures are divided into discrete elements or domains that appear to fold, function and evolve independently.

3. Russell Group, Protein Evolution _________ ____ “Low sequence complexity” (Linker regions? Flexible? Junk? Domains on a sequence Signal peptide (secreted or membrane attached) Transmembrane segment (crosses the membrane) Tyrosine kinase (phosphorylates Tyr) Immunoglobulin domains (bind ligands?) SMART domain ‘bubblegram’ for human fibroblast growth factor (FGF) receptor 1 (type P11362 into web site: smart.embl.de)

4. Russell Group, Protein Evolution _________ ____ Finding domains in a sequence

5. Russell Group, Protein Evolution _________ ____ A library of protein domains for signaling Pawson & Nash, Science, 2003

6. Russell Group, Protein Evolution _________ ____ Domains assemble to form higher-order structures Pawson & Nash, Science, 2003

7. Russell Group, Protein Evolution _________ ____ How proteins interact

8. Russell Group, Protein Evolution _________ ____ Protein A homology (e.g.) Two-hybrid interaction Protein B Protein C Protein D Modelling interactions by homology X Can we use the C/D structure to predict an interaction between A & B?

9. Russell Group, Protein Evolution _________ ____ Family AFamily B ? Can structure help solve the specificity problem?

10. Russell Group, Protein Evolution _________ ____ Structure Asp Arg Asp Phe Interface pair potentials + - Side-chain to side-chain Side-chain to main-chain Alignments InterPreTS Interaction Prediction through Tertiary Structure Aloy & Russell, PNAS, 99, 5896, 2002. Aloy & Russell, Bioinformatics. 19, 161, 2003. 1tx4A PIVLRETVAYLQA-------HALTTE... YFE7_YEAST PLIISSIFSYMDKIYPDLPNDKVR-T... 1tx4B KLVIVGDGACGKTCLLIVNSKDQF--... RHO4_YEAST KIVVVGDGAVGKTCLLISYVQGTFPT... Score Significance (Do RHO4 & YFE7 interact?)

11. Russell Group, Protein Evolution _________ ____ How proteins interact

12. Russell Group, Protein Evolution _________ ____ Domain peptide interactions Recognition of ligands or targeting signals Post-translational modifications

13. Russell Group, Protein Evolution _________ ____ 3BP1_MOUSE/528-537 APTMPPPLPP PTN8_MOUSE/612-629 IPPPLPERTP SOS1_HUMAN/1149-1157 VPPPVPPRRR NCF1_HUMAN/359-390 SKPQPAVPPRPSA PEXE_YEAST/85-94 MPPTLPHRDW SH3-interacting motif PxxP “instance” “perpetrator” “motif” “victim” Peptides interacting with a common domain often show a common pattern or motif usually 3-8 aas. Linear motifs Puntervol et al, NAR, 2003; www.elm.org (Eukaryotic Linear Motif DB)

14. Russell Group, Protein Evolution _________ ____ Domains: large globular segments of the proteome that fold into discrete structures and belong in sequence families. Linear motifs: small, non-globular segments that do not adopt a regular structure, and aren’t homologous to each other in the way domains are. Motifs lie in the disordered part of the proteome. Linear motifs versus domains

15. Russell Group, Protein Evolution _________ ____ Intrinsically unstructured or disordered proteins or protein fragments

16. Russell Group, Protein Evolution _________ ____ Disorder predictors (IUPred, RONN, DisORPred, etc)

17. Russell Group, Protein Evolution _________ ____ Neduva & Russell, Curr. Opin. Biotech, 2006 Linear motif mediated interactions are everywhere Include motifs for: Targeting – e.g. KDEL Modifications – e.g. phosphorylation Signaling – e.g. SH3 About 200 are currently known, likely many more still to be discovered

18. Russell Group, Protein Evolution _________ ____ Finding peptides or linear motifs in a sequence Finding these modules much harder than for domains. Domains are long (>30 AA) and belong to sequence families that help detect new family members Linear motifs are typically < 8 amino acids long and have simple patterns e.g. PxxP will occur in most sequences randomly and these are not SH3 domains See: elm.eu.org