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

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Presentation on theme: "EMBL-EBI MSD database is structured around the fact that Proteins are “sticky”"— Presentation transcript:

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  Pili are thin, protein tubes  The pilus has a shaft composed pilin.  At the end of the shaft is the adhesive tip structure having a shape corresponding to that of specific glycoprotein or glycolipid receptors on a host cell  Because both the bacteria and the host cells have a negative charge, pili may enable the bacteria to bind to host cells without initially having to get close enough to be pushed away by electrostatic repulsion.  Once attached to the host cell, the pili can depolymerize and enable adhesions in the bacterial cell wall to make more intimate contact.

12 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.

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

14 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)

15 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

16 EMBL-EBI One of the body's innate defences is the ability to physically remove bacteria from the body by:  constant shedding of surface epithelial cells  coughing, sneezing, vomiting, and diarrhoea  removal by bodily fluids such as saliva, blood, mucous, and urine. PILI are the pathogen’s answer to Mankind's physical defence systems

17 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?

18 EMBL-EBI ChainsResiduesAtomsExp. ResultAssembly MSD Relational Database

19 EMBL-EBI KEY to MSD DataBase

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

21 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

22 A crystal is a periodic arrangement of a motif in a lattice. The motif can be a single atom, a small molecule, a protein or any combination thereof. Often the motif, also referred to as to the 'asymmetric unit', is subjected to a number of symmetry operations yielding differently oriented copies.

23 EMBL-EBI benzene C6H6C6H6 Covalent bonded

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

25 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:

26 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

27 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.

28 Crystal Structure

29 Oligomeric Assembly

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

31 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

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

33 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

34 1g8h Applying 1 st 3-fold Rotation A A’ Residues of Chain A in interface

35 A A’ Residues of Chain A’ in interface

36 Applying 2 nd 3-fold Rotation A A’ A”

37 Also has a 2-fold rotation

38 Final Assembly is a Hexamer from 23 symmetry

39 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

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

41 Screw Axis

42 EMBL-EBI Screw Axes example tubulins

43 EMBL-EBI SYMMETRY Rules –BUT What about -

44 What happened to symmetry? 2:1 hetero-complex

45 The Ribosome – the champion Heterocomplex proteins tossed around the RNA

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

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

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