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Eugene Krissinel Macromolecular Structure Database keb@ebi.ac.uk

Assessment of macromolecular interactions and identification of macromolecular assemblies in crystalline state (PISA software). Eugene Krissinel Macromolecular Structure Database keb@ebi.ac.uk. www.pdb.org. www.pdbj.org. www.ebi.ac.uk/msd. http://www.ebi.ac.uk/msd. Macromolecular Assemblies.

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Eugene Krissinel Macromolecular Structure Database keb@ebi.ac.uk

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  1. Assessment ofmacromolecular interactionsand identification ofmacromolecular assembliesin crystalline state(PISA software) Eugene KrissinelMacromolecular Structure Databasekeb@ebi.ac.uk

  2. www.pdb.org www.pdbj.org www.ebi.ac.uk/msd http://www.ebi.ac.uk/msd

  3. Macromolecular Assemblies Complexes of protein, DNA/RNA chains and ligands, stable in native environment The way the chains assemble represents the [Protein] Quaternary Structure (PQS) Macromolecular assemblies are often the Biological Units, performing a certain biochemical function Biological and biochemical significance of macromolecular assemblies is truly immense

  4. Biological Unit Example: Hemoglobin • Iron-containing oxygen-transport tetrameric protein complex • Oxygen gets bound to Fe+2 in heme ligand • Binding and release of ligands induces structural changes PDB code: 1a00

  5. Biological Units are Hard to Study Light / Neutron / X-ray / Small angle scatterings: mainly composition and multimeric state may be found. 3D shape may be guessed from mobility measurements. Electron microscopy: not a fantastic resolution and not applicable to all objects NMRis not good for big chains, even less so for protein assemblies. Very few quaternary structures have been identified experimentally.

  6. Asymmetric Unit vs. Biological Unit Crystal = translated Unit Cells More than 80% of macromolecular structures are solved by means of X-ray diffraction on crystals. It is reasonable to expect that Biological Units make construction blocks for the crystal. An X-ray diffraction experiment produces atomic coordinates of the Asymmetric Unit, which is stored as a PDB file. In general, neither Asymmetric Unit nor Unit Cell has any direct relation to Biological Unit. Biological Unit may be made of Unit Cell = all space symmetry group mates of ASU • a single ASU • part of ASU • several ASU • several ASU parts Biological Unit PDB file (ASU)

  7. Biological unit 1P30 Homotrimer! PDB entries and Biological Units PDB entry 1P30 A monomer?

  8. Biological Unit 2TBV 180-mer! PDB entries and Biological Units PDB entry 2TBV A trimer?

  9. 2 Biological Units in 1E94: A dodecamer and a hexamer! PDB entries and Biological Units PDB entry 1E94 ????????

  10. in vivo in crystal crystallisation 1 2 3 ? ? ? no image or bad image good image but no associations Protein Crystallography in Simple Words

  11. Significant interfaces? PQS server @ EBI(Kim Henrick) Trends in Biochem. Sci. (1998) 23, 358 PITA server @ EBI(Hannes Ponstingl) J. Appl. Cryst. (2003) 36, 1116

  12. Formation of N>2 -meric complexes is most probably a corporate process involving a set of interfaces. Therefore significance of an interface should not be detached from the context of protein complex Significant interfaces or artefacts? “No single parameter absolutely differentiates the interfaces from all other surface patches” Jones, S. & Thornton, J.M. (1996) Principles of protein-protein interactions, Proc. Natl. Acad. Sci. USA, 93, 13-20. “…the type of complexes need to be taken into account when characterizing interfaces between them.” Jones, S. & Thornton, J.M., ibid.

  13. Is there a Measure of Significance?

  14. Chemistry’s say It is not so much properties of individual interfaces but rather chemical stability of protein complex in general that really matters Protein chains will most likely associate into largest complexes that are still stable A protein complex is stable if its free Gibbs energy of dissociation is positive:

  15. Detection of Biological Units in Crystals Method Summary • Enumerate all possible assemblies in crystal, subject to crystal structure: space symmetry group, geometry and composition of the Asymmetric Unit (Graph Theory used) • Evaluate assemblies for chemical stability • Leave only stable assemblies in the list and range them by chances to be a Biological Unit : • Larger assemblies take preference • Single-assembly solutions take preference • Otherwise, assemblies with higher Gdiss take preference

  16. Classification of protein complexes Assembly classification on the benchmark set of 218 structures published in Ponstingl, H., Kabir, T. and Thornton, J. (2003) Automatic inference of protein quaternary structures from crystals. J. Appl. Cryst. 36, 1116-1122. 198+20 <=> 198homomers and 20 heteromers Fitted parameters: Classification error in Gdiss : ± 5 kcal/mol • Free energy of a H-bond : • Free energy of a salt bridge : • Constant entropy term : • Surface entropy factor : = 0.51 kcal/mol = 0.21 kcal/mol = 11.7 kcal/mol = 0.57·10-3 kcal/(mol*Å2)

  17. Classification error in :± 5 kcal/mol Classification of protein-DNA complexes Assembly classification on the benchmark set of 212 protein – DNA complexes published in Luscombe, N.M., Austin, S.E., Berman H.M. and Thornton, J.M. (2000) An overview of the structures of protein-DNA complexes. Genome Biol. 1, 1-37.

  18. Free energy of misclassifications

  19. Predicted: homohexamer Dissociates into 2 trimers 106 kcal/mol Biolgical unit: homotrimer Dissociates into 3 monomers 90 kcal/mol Misclassification of 1QEX BACTERIOPHAGE T4 GENE PRODUCT 9 (GP9), THE TRIGGER OF TAIL CONTRACTION AND THE LONG TAIL FIBERS CONNECTOR

  20. What is 1QEX? BACTERIOPHAGE T4 GENE PRODUCT 9 (GP9), THE TRIGGER OF TAIL CONTRACTION AND THE LONG TAIL FIBERS CONNECTOR Rossmann M.G., Mesyanzhinov V.V., Arisaka F and Leiman P.G. (2004) The bacteriophage T4 DNA injection machine. Curr. Opinion Struct. Biol. 14:171-180.

  21. 1S2E trimer Correct mainchain tracing Identified correctly Wrong mainchain tracing! 1QEX: nobody is perfect BACTERIOPHAGE T4 GENE PRODUCT 9 (GP9), THE TRIGGER OF TAIL CONTRACTION AND THE LONG TAIL FIBERS CONNECTOR 1QEX trimer 1QEX hexamer Identified wrongly

  22. Misclassification of 1D3U TATA-BINDING PROTEIN / TRANSCRIPTION FACTOR Predicted: octamer Dissociates into 2 tetramers 20 kcal/mol Functional unit: tetramer

  23. Predicted: dodecamer Dissociates into 2 hexamers 28 kcal/mol Misclassification of 1CRX CRE RECOMBINASE / DNA COMPLEX REACTION INTERMEDIATE Functional unit: trimer

  24. Synaptic complex 1CRX CRE RECOMBINASE / DNA COMPLEX REACTION INTERMEDIATE Guo F., Gopaul D.N. and van Duyne G.D. (1997) Structure of Cre recombinase complexed with DNA in a site-specific recombination synapse. Nature 389:40-46.

  25. Predicted: dimer Dissociates at 37 kcal/mol Apparent dimerization is an artefact due to the presence of Zn+2 ions added to the buffer to aid crystallization. Removal Zn from the file results in  3 kcal/mol Misclassification of 1TON TONIN Biological unit: monomer Fujinaga M., James M.N.G. (1997) Rat submaxillary gland serine protease, tonin structure solution and refinement at 1.8 Å resolution. J.Mol.Biol. 195:373-396.

  26. 50% 50% Reasons to be imperfect • Crystal packing may introduce interactions that are not engaged in native environment • Definition of Biological Unit is based on physiological function and may be to a certain degree subjective • Interaction artifacts are often due to the addition of binding agents in order to aid crystallization • Theoretical models of macromolecular complexation are simplified • Experimental data are of a limited accuracy • No explicit account for concentrations, temperature, pH and ionic strength

  27. Web-server PISA@MSD http://www.ebi.ac.uk/msd-srv/prot_int/pistart.html A new MSD-EBI tool for working with Protein Interfaces, Surfaces and Assemblies

  28. Web-server PISA@MSD

  29. Web-server PISA@MSD

  30. Conclusions • Chemical-thermodynamical models for protein complex stability allow one to recover biological units from protein crystallography data at 80-90% success rate • Considerable part of misclassifications is due to the difference of experimental and native environments and artificial interactions induced by crystal packing • Functional significance of protein interfaces cannot be reliably inferred only from their properties. Due to entropy contribution and entangled interactions, interface function is also subject to protein complex composition and geometry • Protein interface and assembly analysis software (PISA) is available for public use as a web-service from MSD@EBI. Acknowledgement. This work has been supported by research grant No. 721/B19544 from the Biotechnology and Biological Sciences Research Council (BBSRC) UK.

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