Ramon Tabtiang Brent Cezairliyan Robert Grant Jesse Cochrane Robert Sauer

1. Consolidating critical binding determinants by non cyclic rearrangement of protein secondary structure Ramon Tabtiang Brent Cezairliyan Robert Grant Jesse Cochrane Robert Sauer

2. Overview • Background and Basic Terminology • Cyclic Permutation and Domain swapping • Measures Used • Future Work • Future Research Questions

3. Background • Dimer • Homo-Dimer • Protein Structure • Primary, Secondary (α helix, β strands/sheet), Tertiary, Quaternary Types • Domain • Folding • Arc Repressor

4. Cyclic Permutation

5. Domain Swapping

6. Inference from previous experiments • Protein fold is a complementary packing system and not precisely manner in which elements should be connected. • Structural permutations should be allowed. • But there was no initial success

7. Permutation

8. Results • Initial Chain: arm-β-αA-αB-linker-arm-β-αA-αB • Final Chain: arm-β-linker- β -αA-αB-linker-αA-αB

11. Results • Arc fold was maintained after non cyclic rearrangement. • Addition of linkers had no effect on thermodynamic stability • Arc-L1-Arc protein refolded in sub-millisecond time. • Bonded with operator DNA with nanomolar affinity.

12. Applications • Sequence similarity of two proteins • Addition tool for protein engineering alongside directed mutagenesis, protein fusions, sequence identification, randomization. • Success will depend on fold of protein, topology and appropriate linkers.

13. Databases • Protein Data Bank(PDB) • Swiss-Prot: Probabilistic approach • SCOP and CATH: Organized hierarchically into different classes and fold types

14. Structure comparison strategies • RMSD • DALI • CE • Gene Ontology (GO) • Structural Classification of Proteins (SCOP) • Detecting Permuted Proteins • Bipartite graph matching application

15. Detecting Permuted Proteins • Large scale study to search for permuted proteins in the Protein Data Bank • 3,336 protein structures taken from the PDBSELECT90 data set • The difference in their lengths was no more than 75 residues. • The two proteins shared approximately the same secondary structure content.

17. Bipartite graph matching application • Find the shortest distance F(i) from the source node s to every other node I using the Bellman-Ford algorithm. • Assign a new weight w’(i, j) to each edge that does not originate from the source nodes as follows, w’(i, j) =w(i, j) + [F(i)−F(j)] • Update Fall as F’all=Fall−Fd. • Reverse the direction of the edges along the shortest path from s to d . • If Fall > Fd and a path exists between s and d then go back to step 1

18. Challenges • Global similarity vs Local similarity • Alignment methods • Small structural fluctuations

19. References • Rapid motif-based prediction of circular permutations in multi-domain proteins-January Weiner ,Geraint Thomas and Erich Bornberg-Bauer • Topology independent protein structural alignment -Joe Dundas, TA Binkowski, BhaskarDasGupta and JieLiang (UIC) • Non-sequential alignments in protein structure comparison: rare exceptions or protein feature? - AlexejAbyzov, (Northeastern University) • Learn about PDB (http://www.youtube.com/watch?feature=player_embedded&v=arO8EgsKvo8&list=PLGVe6BxyFHNXxqzpzmP8ZV1bbn3N2YrmI)

20. Thank You