Macromolecular Structure Database group

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http//www.ebi.ac.uk/msd-srv/prot_int/pistart.html
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What PISA is about
Crystal translated Unit Cell
More than 80 of protein structures are solved by
means of X-ray diffraction on crystals. An X-ray
diffraction experiment produces atomic
coordinates of the crystals Asymmetric Unit
(ASU). In general, neither ASU nor Unit Cell has
any relation to Biological Units, or stable
protein complexes which act as units in
physiological processes. PISA attempts to recover
Biological Units from the protein crystallography
data.
Unit Cell all space symmetry group mates of ASU
PDB file
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Crystal interfaces
Stability of protein complexes depends on
properties of protein-protein interfaces, such as

• free energy of formation DGint
• solvation energy gain DGS
• interface area
• hydrogen bonds and salt bridges across the
  interface
• hydrophobic specificity

PISA calculates crystal contacts and their
physical-chemical properties
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Interface assessment
A crystal may be viewed as a packing of
assemblies with biologically insignificant
contacts between them. Protein assembly is a
packing of monomeric units with biologically
relevant interfaces between them. PISA is a tool
to assess crystal interfaces for biological
significance.
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Properties of assemblies
Protein assemblies may exist in certain
conditions and dissociate in other. Sometimes
aggregation properties are the key to biological
function. PISA calculates properties of protein
assemblies, such as free energy of dissociation
DGdiss, and predicts a probable dissociation
pattern.
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PISA workflow summary
1. Calculate properties of all structures 2. Calcu
late all crystal contacts and their
properties 3. Find all assemblies which are
possible in given crystal 4. Evaluate all
assemblies for chemical stability and leave only
potentially stable ones 5. Range assemblies by
chances to be a biological unit
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Enumerating assemblies in crystal

• crystal is represented as a periodic graph with
  monomeric chains as vertices 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

Example crystal with 3 interface types
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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

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Protein affinity
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Entropy of dissociation
Murray C.W. and Verdonik M.L. (2002) J.
Comput.-Aided Mol. Design 16, 741-753.
Mass of i-th subunit
k-th principal moment of inertia of i-th subunit
Fitted parameter
Fitted parameter
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Benchmark results
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.
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 0.5710-3 kcal/(molÅ2)
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What is beyond the benchmark set?
Classification results obtained for 366 recent
depositions into PDB in reference to manual
classification in MSD-EBI
32145 ltgt 321 homomers and 45 heteromers
Classification error in ?Gdiss 5 kcal/mol
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Is it ever going to be 100?
Nobody should be that naive, because

• theoretical models for protein affinity and
  entropy change upon protein complexation are
  primitive
• coordinate (experimental) data is of a limited
  accuracy
• there is no feasible way to take conformations in
  crystal into account
• experimental data on multimeric states is very
  limited and not always reliable - calibration of
  parameters is difficult
• protein assemblies may exist in some environments
  and dissociate in other - a definite answer is
  simply not there

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Web-server PISA
http//www.ebi.ac.uk/msd-srv/prot_int/pistart.html
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