EBI is an Outstation of the European Molecular Biology Laboratory. A web service for the analysis of macromolecular interactions and complexes MSD Protein Interfaces, Surfaces and Assemblies Glen van Ginkel PDB Depositions http://www.ebi.ac.uk/msd-srv/ prot_int/pistart.html
23
Embed
EBI is an Outstation of the European Molecular Biology Laboratory. A web service for the analysis of macromolecular interactions and complexes MSD Protein.
This document is posted to help you gain knowledge. Please leave a comment to let me know what you think about it! Share it to your friends and learn new things together.
Transcript
EBI is an Outstation of the European Molecular Biology Laboratory.
A web service for the analysis of macromolecular interactions and complexes
2. Accept everything which passes formal validation checks.
3. No experimental evidence for PQS is required.
4. If a depositor does not know or does not care (60-80% of instances for PQS), the curator is to decide.
5. The curator may use computing/modeling tools to assist the PQS annotation.
The wwPDB “rules” are:
www.wwpdb.org
5
Crystallography is special in that …
A) crystal is made of assemblies
6
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
7
Wealth of experimental data on PQS in PDB
Crystal = translated Unit CellsMore 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
PDB file (ASU)
• a single ASU• part of ASU
• several ASU• several parts of ASU
8
?no image or bad image
In (very) simple terms …
2
crystallisation
3
in crystal
? ?good image but no
associations
in vivo
1
9
PQS server @ EBI (Kim Henrick) Trends in Biochem. Sci. (1998) 23, 358 PITA server @ EBI (Hannes Ponstingl) J. Appl. Cryst. (2003) 36, 1116
A simple thing to do …
10
PQS server @ MSD-EBI (Kim Henrick) Trends in Biochem. Sci. (1998) 23, 358
http://pqs.ebi.ac.uk Method: progressive build-up by addition of monomeric chains that suit the selection criteria. The results are partly curated.
http://www.ebi.ac.uk/thornton-srv/databases/pita/ Method: recursive splitting of the largest complexes as allowed by crystal symmetry. Termination criteria is derived from the individual statistical scores of crystal contacts. The results are not curated.
PITA software @ Thornton group EBI (Hannes Ponstingl) J. Appl. Cryst. (2003) 36, 1116
Making assemblies from significant interfaces
11
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.)
Depends on the problem.
Stable macromolecular complexes, PQS: the interface should make a sound binding. Important properties:
• Sufficient free energy of binding• something else?
and properties that may be important for reaction pathway and dynamics:
What is a significant interface?
12
Jones, S. & Thornton, J.M. (1996) Principles of protein-protein interactions, Proc. Natl. Acad. Sci. USA, 93, 13-20.
10
20
30
40
50
60
20 40 60 80 1000Rank ordering bins
% o
f re
al i
nte
rfa
ces
Planar Nonplanar
rms of least-square plane
10
20
30
40
50
60
20 40 60 80 1000Rank ordering bins
% o
f re
al i
nte
rfa
ces
Low protrusion High protrusion
Protrusion index
10
20
30
40
50
60
20 40 60 80 1000Rank ordering bins
% o
f re
al i
nte
rfa
ces
Less hydrophobic More hydrophobic
Hydrophobicity
Low ASA High ASA
ASA
10
20
30
40
50
60
20 40 60 80 1000Rank ordering bins
% o
f re
al i
nte
rfa
ces
Real and superficial interfaces
13
“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.
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
“…the type of complexes need to be taken into account when characterizing interfaces between them.”
Jones, S. & Thornton, J.M., ibid.
Real and superficial interfaces
14
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:
ΔG diss0 =− ΔG int−TΔS0
Chemical stability of protein complexes
15
Solvation energy of protein complex
Solvation energies of dissociated subunits
Free energy of H-bond formation
Free energy of salt bridge formation
Number of H-bonds between dissociated subunits
Number of salt bridges between dissociated subunits
A1 A2 A3 A1A2A3
Dissociation into stable subunits with minimum
ΔG diss
Choice of dissociation subunits:
Protein affinity
Macromolecular Structure Database31.10.0716
Translational entropy
Rotational entropy
Sidechain entropy
Mass
Tensor of inertia
Solvent-accessible surface area
Symmetry number
Entropy of macromolecules in solutions
17
• crystal is represented as a periodic graph with monomeric chains as nodes and interfaces as edges
• each set of assemblies is identified by engaged interface types
• all assemblies may be enumerated by a backtracking scheme engaging all possible combinations of different interface types