1. Protein Interfaces, Surfaces and Assemblies
PISA
Protein Interfaces, Surfaces and Assemblies
Eugene Krissinel
CCP4 & EBI-MSD

2. PISA is a tool for the assessment of macromolecular interactions using data provided by protein crystallography.
Scope of tasks addressed by PISA:
identification and prediction of multimeric states
analysis of structure-function relationship
analysis and prediction of macromolecular interactions
analysis of macromolecular complexation and crystallisation
properties of macromolecular interfaces
search for interface/structure/assembly homologues
active site recognition and analysis
macromolecular surface analysis
other
Project started in 2004, supported by BBSRC research grant 721/B19544

3. PISA today Web-service hosted by EBI-MSD at
provides PISA analysis for all PDB entries and database searches
allows upload of PDB and mmCIF files for interactive PISA analysis
provides XML download of multimer data, which is used in server applications (BALBES) on molecular replacement
works on aminoacid, nucleic acid and ligand structures
more than 140,000 external queries served since the release
more than 1700 users
has a command-prompt stand-alone version

4. PISA basics
PISA is based on chemical thermodynamics:
for stable structures in the standard state.
DGdiss cannot be calculated exactly. PISA uses semiempirical models with parameters calibrated to available experimental data on multimeric states.
Precision of free energy estimates in PISA: ±5 kcal/mol
Success rate of PQS prediction: 80-90%

5. Last year activity – nucleic acids and ligands
Extension to include protein-DNA/RNA and ligand interactions
Derivation and calibration of interaction parameters
Database of ligand interactions (~6000 entries parameterized on atomic level)
Tools for database update and semi-automatic calculation of protein-ligand interactions
Core algorithm completely rewritten in order to:
implement changes needed to adopt protein-DNA/RNA and ligand interactions
optimize and speed-up the calculations

6. Last year activity – ligand control
Control over ligand processing:
Possibility to exclude certain ligands from processing
Choice of ligand processing modes:
Automatic
Fix all ligands
Free all ligands

7. Last year activity – adaptation for MSD&PDB
Interface and presentation improvements at request of PDB/MSD curation teams:
Consistent identification of symops in PISA pages
Adoption of symop nomenclature
Automatic generation of REMARK 350
Optimization of final assembly positions
Reporting on redundant assemblies (especially when ASU contains a fractional number of assemblies >1)
PISA is now employed by both MSD and as a mandatory processing tool for all depositions

8. Last year activity - PISA database
PISA database searches by
Multimeric state
Symmetry number
Space group
Homomeric type
Salt bridges
Disulphide bonds
List of ligands
List of keywords
Dissociation energy
Assembly ASA
Assembly BSA
Percent BSA

9. Last year activity - standalone PISA
Command-prompt, stand-alone PISA for inclusion into CCP4
Contains only data-processing part of “big” PISA, i.e. no database
For technical reasons, there are code differences from “big” PISA
Functionally identical to the corresponding parts of “big” PISA
Mimics web-page output of “big” PISA in plain text
Provides same XML output as “big” PISA
Works as a local server:
Maintains sessions
Data processing separated from data retrieval
Visualization using Rasmol

10. Standalone PISA example

11. Last year activity – tune-up and polishing
Last percent of improvement takes 99% of all efforts
Literally hundreds of small problems solved on everyday basis. Examples:
Inference of correct orthogonalisation codes
Choice of margins for identification of parallel monomeric units
Symmetry number calculations: superposition margins and unit enumeration order
Identification and proper treatment of overlapping symmetry mates with fractional occupancy
Unique labels for the download/visualisation data and wait pages to avoid caching on remote servers
Catching up with EBI systems update
PISA is roughly 60,000 C++ statements and small bugs are most probably still there
6 releases over year

12. Future plans
PISA is systematically underperforming on FABs. Possible reasons:
Neglect of electrostatic interactions
Neglect of entropy absorbance in flexible complexes
Both are very difficult problems to address
Last percent of improvement takes 99% of efforts

13. Future plans Analysis of “custom” assemblies
Allow for input without crystallographic data
Effectively inclusion of NMR entries as well
Detection of “custom” assemblies
Allow for report on specific assemblies otherwise missed as unstable
Automatic prediction of macromolecular interactions and assemblies by homologue search in PISA database
Assessment of crystal “quality”
Identification of fake PDB entries and depositions

14. Fake PDBs 2i07 2icc 2ice 2icf 2hr0 BSA 20% 51% 24% 10%
Interfaces per chain
9.56 7
6.12
8.33
3.5
Min. interfaces / chain 8 4 2
Connected crystal
Yes