PDBe Protein Interfaces, Surfaces and Assemblies A web service for the analysis of macromolecular interactions and complexes Gaurav Sahni, Ph.D.

Protein Quaternary Structures (PQS) Assembly of protein chains, stable in native environment PQS is often a Biological Unit, performing a certain physiological function 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. 2

1 2 4 3 PQS are difficult to calculate… If we know the sequence ... VNKERTFLAVKPDGVARGLVGEIIARYEKKGFVLVGLKQLVPTKDLAESHYAEHKERPFF then we can calculate ... If we know the sequence ... 1 50 - 90% Secondary Structure (CASP 5), depending on method 2 Nearly 0% Quaternary Structure. Docking of given number of given structures: 5 - 20% success (CAPRI 5) 4 10 - 90% Tertiary Structure (CASP 5), depending on method and target 3 The MSD group is part of the PDB, the Protein Data Bank who is composed of 3 sites: the RCSB in USA, the PDB-j in Japan and the ePDB/MSD in Europe. We collaborate closely with the RCSB who maintain the Protein Data Bank (PDB) in the USA. Structures deposited through the AutoDep tool are processed at the EBI and are then passed to the RCSB. PDB is the single repository of all publicly available macromolecular structures The Protein Data Bank started in 1971, the archive has now around 19,000 entries 3

But PQS are assigned to many PDB entries! Most of those are PROBABLE Quaternary Structures. Depositor’s say 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 is to decide. The curator may use computing/modeling tools to assist the PQS annotation. The wwPDB “rules” are: www.wwpdb.org

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

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

Unit Cell = all space symmetry group mates of ASU 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)

A simple thing to do …

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: Aminoacid composition Geometrical complementarity 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?

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:

Detection of Biological Units in Crystals: PISA Method Summary Build periodic graph of the crystal Enumerate all possibly 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

If you have to ask ... USE PDBePisa 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 !!

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

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

Details about the interface…

Summary Difficulties determining PQS Properties of protein contacts What is a protein quaternary structure (PQS)? Difficulties determining PQS Properties of protein contacts Which answers can PISA give?