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A web service for the analysis of macromolecular interactions and complexes

PDB e P rotein I nterfaces, S urfaces and A ssemblies http:// pdbe.org /PISA . A web service for the analysis of macromolecular interactions and complexes. Summary. What is a protein quaternary structure (PQS)? Problems in determining PQS Properties of protein contacts

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A web service for the analysis of macromolecular interactions and complexes

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  1. PDBeProtein Interfaces, Surfaces and Assemblies http://pdbe.org/PISA A web service for the analysis of macromolecular interactions and complexes

  2. Summary • What is a protein quaternary structure (PQS)? • Problems in determining PQS • Properties of protein contacts • What does PISA actually do?

  3. Protein Quaternary Structures (PQS) Assembly of protein chains, stable in native environment • PQS can often be a Biological Unit, performing a certain physiological function in that quaternary state. • PQS is a difficult subject for experimental studies • Neutron/X-ray scattering: mainly composition and multimeric state may be found. • Dynamic light scattering: 3D shape may be guessed from mobility measurements. • Electron microscopy: not a fantastic resolution and not applicable to all objects • NMR is not good for big chains, even less so for protein assemblies.

  4. If we know the sequence ... 1 VNKERTFLAVKPDGVARGLVGEIIARYEKKGFVLVGLKQLVPTKDLAESHYAEHKERPFF then we can calculate ... 2 50 - 90%Secondary Structure (CASP 5), depending on method 4 3 Nearly 0% Quaternary Structure. Docking of given number of given structures: 5 - 20% success (CAPRI 5) 10 - 90%Tertiary Structure (CASP 5), depending on method and target PQS are difficult to calculate…

  5. The wwPDB “rules” are: www.wwpdb.org Depositor’s say usually prevails. Accept everything which passes formal validation checks. No experimental evidence for PQS is required. If a depositor does not know or does not care (60-80% of instances for PQS), the curator decides. The curator use computing/modeling tools to assist the PQS annotation (PDBePISA). PQS are assigned to many PDB entries! Most of those are PROBABLEQuaternary Structures.

  6. Crystallography is special in that … A) crystal is made of assemblies

  7. Crystallography is special in that … B) there is no need to dock subunits – the docking is given by crystal structure Macromolecular interfaces should be viewed as an additional and important artifact of protein crystallography

  8. Wealth of experimental data on PQS in PDB 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 PQS make building blocks for the crystal. An X-ray diffraction experiment produces atomic coordinates of the Asymmetric Unit (ASU), which are stored as a PDB file. In general, neither ASU nor Unit Cell has any direct relation to PQS. The PQS may be made of Unit Cell = all space symmetry group mates of ASU • a single ASU • part of ASU • several ASU • several parts of ASU PDB file (ASU)

  9. A simple thing to do …

  10. What is a significant interface? Depends on the problem. • Protein functionality: the interface should be engaged in any sort of interaction, including transient short-living protein-ligand and protein-protein etc. associations. Obviously important properties: • Affinity (comes from area, hydrophobicity, electrostatics, H-bond density etc.) • and properties that may be important for reaction pathway and dynamics: • Amino Acid composition • Geometric complementarities • Overall shape, compactness • Charge distribution • etc. • Stable macromolecular complexes, PQS: the interface should make a sound binding. Important properties: • Sufficient free energy of binding • something else?

  11. Chemical stability of protein complexes • It is not 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 energy of dissociation is positive:

  12. Detection of Biological Units in Crystals: PISA MethodSummary • Build periodic graph of the crystal • Enumerate all possible stable assemblies • Evaluate assemblies for chemical stability • Leave only sets of 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

  13. Web-server PISA (pdbe.org/PISA) E. Krissinel and K. Henrick (2007). Inference of macromolecular assemblies from crystalline state. J. Mol. Biol. 372, 774--797.

  14. Web-server PISA http://www.pdbe.org/PISA/

  15. http://www.pdbe.org/PISA/

  16. http://www.pdbe.org/PISA/ Details about the interface…

  17. http://www.pdbe.org/PISA/

  18. http://www.pdbe.org/PISA/ Database Analysis Search for PDB entries that contain Protein and DNA AND where Protein Interacts with the DNA.

  19. http://www.pdbe.org/PISA/ Click to view Protein-DNA Complex Click to view details

  20. http://www.pdbe.org/PISA/ Search other entries that have similar interfaces.

  21. http://www.pdbe.org/PISA/

  22. If you have to ask ... • What quaternary structure can my crystal structure have? • What are the crystal contacts and interfaces in my structure? • What is the size of the crystal interfaces? • What are the energetics that keep my quaternary structure together? • Are there any other structures in the PDB that have similar interfaces? USE PDBePisa Upload your own PDB file for analysis !!

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