1. EMBL-EBI MSD database is structured around the fact that Proteins are “sticky”

2. EMBL-EBI A short biography of 1 protein whose very existence depends on being as sticky as possible

3. EMBL-EBI EMBL K02078 ttaacgcgta aattcaaaaa tctcaaattc cgacccaatc aacacacccg ataccccatg ccaataaaaa agtaacgaaa atcggcacta aaactgacaa ttttcgacac tgccgccccc ctacttccgc aaaccacacc cacctaaaag aaaatacaaa ataaaaacaa ttatatagag ataaacgcat aaaatttcac ctcaaaacat aaaatcggca cgaatcttgc tttataatac gcagttgtcg caacaaaaaa ccgatggtta aatacattgc atgatgccga tggcaagccc tgaggctttc ccctttcaat taggagtaat tttatgaata cccttcaaaa aggctttacc cttatcgagc tgatgattgt gatcgctatc gtcggcattt tggcggcagt cgcccttccc gcctaccaag actacaccgc ccgcgcgcaa gtttccgaag ccatcctttt ggccgaaggt caaaaatcag ccgtcaccga gtattacctg aatcacggca aatggccgga aaacaacact tctgccggcg tggcatcccc cccctccgac atcaaaggca aatatgttaa agaggttgaa gttaaaaacg gcgtcgttac cgccacaatg ctttcaagcg gcgtaaacaa tgaaatcaaa ggcaaaaaac tctccctgtg ggccaggcgt gaaaacggtt cggtaaaatg gttctgcgga cagccggtta cgcgcaccga cgacgacacc gttgccgacg ccaaagacgg caaagaaatc gacaccaagc acctgccgtc aacctgccgc gataaggcat ctgatgccaa atgaggcaaa ttaggcctta aattttaaat aaatcaagcg gtaagtgatt ttccacccgc ccggatcaac ccgggcggct tgtcttttaa gggtttgcaa ggcgggcggg gtcgtccgtt ccggtggaaa taatatatcg at

4. EMBL-EBI MNTLQKGFTL IELMIVIAIV GILAAVALPA YQDYTARAQV SEAILLAEGQ KSAVTEYYLN HGKWPENNTS AGVASPPSDI KGKYVKEVEV KNGVVTATML SSGVNNEIKG KKLSLWARRE NGSVKWFCGQ PVTRTDDDTV ADAKDGKEID TKHLPSTCRD NFDAK UniProt P02974

5. EMBL-EBI PDB 1AY2

6. MSD DATABASE pentamer

7. MSD DATABASE

8. negatively stained TEM images

9. Neisseria gonorrhoeae expressing pili and interacting with epithelial cells. The pili are polar flexible filaments of about 5.4 nm diameter and 2500 nm average length.

10. Type IV Pilin Structure and Assembly: X-Ray and EM Analyses of Vibrio cholerae Toxin-Coregulated Pilus and Pseudomonas aeruginosa PAK Pilin L. Craig, et al Molecular Cell, 11, 1139– 1150, 2003

11. EMBL-EBI Type IV pili are not merely passive sticky fibres but dynamic machines that participate in a surprising number of functions including:  Bacterial aggregation  Adhesion to host cells  Twitching motility  Pilus retraction  DNA transformation  In another bacterial species, motility.  Phage receptor in V. cholerae.

12. EMBL-EBI  EMBL  UniProt  PDB  Assembly (MSD)  Microscopy still not the full story - GENOME

13. EMBL-EBI Pilus gene organisation  Many copies of pilin gene throughout chromosome  Two are functional, pilE1 and pilE2  All other copies are silent  Antigenic variation occurs due to recombination (within mini-cassettes)

14. EMBL-EBI Antigenic variation in N. gonorrhoeae  A single cell can give rise to daughter cells expressing structurally and antigenically different pili  Gonococcus has the genetic capacity to make as many as a million different pilin variants  All able to bind to same host tissues and to cause the same disease symptoms

15. EMBL-EBI PDB Entries and X-Ray results 1.Crystal Structure 2.Molecular Structure (covalent) 3.Oligomeric Assembly What has all this got to do with MSD?

16. EMBL-EBI ChainsResiduesAtomsExp. ResultAssembly MSD Relational Database

17. EMBL-EBI KEY to MSD DataBase

18. EMBL-EBI Biological Context PDB  MSD Oxalate oxidase 1FI2 hexameric

19. EMBL-EBI PDB Xray coordinates  PDB entry the deposited coordinates usually consist of the contents of the asymmetric unit:  The contents of the ASU define a single copy of the macromolecule  The contents of the ASU consist of more than one copy of the macromolecule  The contents of the ASU require crystallographic symmetry operations to be applied to generate the complete macromolecule(s)  A combination of the above, including multiple copies and required symmetry transformations

20. EMBL-EBI benzene C6H6C6H6 Covalent bonded

21. EMBL-EBI Benzene crystallised in Space Group P6/m  6-fold rotation axis  Mirror plane

22. EMBL-EBI Benzene P6/m in the PDB ATOM C1 x1 y1 z1 occupancy 0.5 ATOM H1 x2 y2 z2 occupancy 0.5 Entire atomic contents:

23. EMBL-EBI  The stronger of the two is the hydrogen bond.  The weaker is the van der Waal's forces. Both interactions depend on the same fundamental cause, the charge on electrons, and how that results in attraction and repulsion at an atomic level. HELD TOGETHER BY WEAK FORCES

24. EMBL-EBI Quaternary Structure  Quaternary Structure is defined as that level of form in which units of tertiary structure aggregate to form homo- or hetero-multimers.  Consideration of the presence of a quaternary state is important in the understanding of a protein's biological function.

25. Crystal Structure

26. Oligomeric Assembly

27. EMBL-EBI Proteins don’t do this – pack by translationals

28. EMBL-EBI There are three main types of symmetry:  symmetry with respect to a plane (mirrors)  symmetry with respect to a line (rotations)  symmetry with respect to a point (inversions) Symmetry

29. EMBL-EBI  symmetry with respect to a line (rotations)  symmetry with respect to a plane (mirrors)  symmetry with respect to a point (inversions) Symmetry

30. EMBL-EBI 1, 2, 3, 4, 6 -fold rotational symmetry These are the only rotational symmetries that can exist in crystals; all others are disallowed. These five rotational axes are called the five Proper Axes Symmetries showing 5-, 7-, 8-, 9-, 10-, 11-, & 13- fold rotations are known for biological molecules – these are observed in the Asymmetric Unit. Rotational symmetry

31. 1g8h Applying 1 st 3-fold Rotation A A’ Residues of Chain A in interface

32. A A’ Residues of Chain A’ in interface

33. Applying 2 nd 3-fold Rotation A A’ A”

34. Also has a 2-fold rotation

35. Final Assembly is a Hexamer from 23 symmetry

36. EMBL-EBI If you add translations to rotation axes, you form what are call screw axes. For an nm screw axis, the rotational component is 360/n degrees, and the translations is m/n of the unit translation along the axis. In Biological Crystallography --> Polymers Helices are improper Screw axes – e.g. DNA Screw Axes

37. EMBL-EBI Also has a 2-fold rotation – infinite cylinder in crystal

38. Screw Axis

39. EMBL-EBI Screw Axes example tubulins

40. EMBL-EBI SYMMETRY Rules –BUT What about -

41. What happened to symmetry? 2:1 hetero-complex

42. The Ribosome – the champion Heterocomplex proteins tossed around the RNA

43. protein aggregates complicate the lives of people who study proteins in vitro

44. Protein Aggregation and Amyloid Diseases - Converting the protein from a soluble to a fibrillar structure