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Using X-ray structures for bioinformatics
Robbie P. JoostenNetherlands Cancer Institute
Autumnschool 2013
Structures in bioinformatics
• Understand biology– Direct interpretation
– Data mining– Homology modeling
• Drug design• Molecular dynamics
Basic rule: Better structures → Better
results
Introduction
Right structure(s) for the job
1.Selection: find (a number of) PDB entries
2.Validation: check the quality of your selection
3.Optimisation: maximise the quality of your selection
Focus on X-ray structures
Introduction
X-ray structures have a history
1. Protein expression2. Crystallisation3. X-ray diffraction
experiment4. Model building and
refinement5. Deposition at the PDB
All these steps affect the final PDB
file
Selection
Protein expressionA ‘construct’ is made• Partial proteins– E.g. only extracellular domain of membrane protein
• Frankenstein proteins– Fusion proteins or chimeras
• Mutants are introduced – Some by accident!
• Poly-histidine tags added for purification
• Altered glycosylation state– Large sugars hamper crystallisation
History
CrystallisationThe protein stacks regularly to form a crystal• Protein still functional in the crystal
• Much solvent in the crystal (~40%)• Some residues can move– Disorder: missing loops/side chains– Alternate conformation
History
CrystallisationBeware of crystal packing• One copy of the protein can influence the next
History
CrystallisationChemicals are used for crystallisation• Buffers to stabilise the pH• Precipitants– Change solubility of the protein– Neutralise local charges– Bind water– High concentrations are used• Compounds compete with natural ligands
• Examples:– Polyethylene glycol (PEG)– Ammonium sulphate
History
CrystallisationBeware of the crystallisation conditions
History
CrystallisationBeware of the crystallisation conditions
History
X-ray diff ractionTypical experiment
History
X-ray source
Detector
X-ray diff raction• X-rays interact with electrons– Atoms with few electrons (H, Li) do not diffract well
• X-rays cause damage to the protein– Acidic groups (ASP en GLU) can be destroyed
– Disulphide bridges are broken– Hydrogens are stripped– Cooling crystals in liquid nitrogen helps• Glycerol added to the crystal!
History
X-ray diff raction• We are not using a microscope• We don’t measure everything we need
History
X-ray diffraction gives an indirect and incomplete measurement
ρ (𝑥 , 𝑦 , 𝑧 )= 1𝑉 ∑
h∑𝑘∑𝑙
𝐹h𝑘𝑙𝑒[− 2𝜋 𝑖 (h𝑥+𝑘𝑦+𝑙𝑧 )−𝛼]
MeasuredMissing: phase
Model building and refinement
Iterative process
History
Phases + calculated X-ray data
Electron density maps
Structure model
Measured X-ray diffraction
data
Initial phases
FT
FT
Model building
History
Two types of maps1. Regular electron density map (2mFo-
DFc)2. Difference map (mFo-DFc)
Model building and refinement
Fitting atoms to the ED map and trying to remove difference density peaks
HistoryModel building and refinement
• Requires skill and experience• Requires time and patience• Requires good software
Lack of any of these can be seen in the final PDB file
HistoryModel building and refinement
• Both coordinates and experimental X-ray data are deposited
• PDB standardises files and adds annotation
• Sometimes things go wrong
History
Deposition at the PDB
LINKs between alternate conformations
History
Deposition at the PDB
History
Deposition at the PDBUn-biological LINKs (in 1a1a)
LINK C ACE C 100 N PTH C 101
LINK C PTH C 101 N GLU C 102
LINK CF PTH C 101 OG SER A 188
LINK N DIP C 103 C GLU C 102
LINK C ACE D 100 N PTH D 101
LINK C PTH D 101 N GLU D 102
LINK N DIP D 103 C GLU D 102
Think of what happened to the
structure before you downloaded it
Use the experimental data• Resolution says very little about the structure
• (free) R-factor gives the overall fit of the structure to the experimental data
• For biological interpretation more detail is needed
Use the maps
Validation
X-ray specific validation
Which is the better structure of berenil bound to DNA?
Validation
X-ray specific validation
PDB id Resolution R
268d 2.0 0.160
1d63 2.0 0.183
Validation
X-ray specific validationThe real-space R-factor (RSR)• A per-residue score of how well the atoms fit the map
• Works like the R-factor (lower is better)
Maps can help distinguish the good and bad bits of a structure
Validation
X-ray specific validation
Poorly fitted side-chains
Evil peptides
ValidationThings you can find in maps
The wrong drug
ValidationThings you can find in maps
Sequence error K -> R• Accidental mutant• Also a missing sulfate
ValidationThings you can find in maps
Missing water Missing alternate conformation
ValidationThings you can find in maps
• Visualisation in Coot– http://www2.mrc-lmb.cam.ac.uk/personal/pemsley/coot/
• Get maps and real-space R values from the Electron Density Server– http://eds.bmc.uu.se/eds/index.html– Direct interface with Coot
• Get maps and updated models from PDB_REDO
Practical session
Validation
Checking maps
Maps show things you cannot see
otherwise
• Solved by a diverse group of scientists– People make errors & gain experience
• Since 1976– Structures are not updated
• Solved with the methods of their era– Methods improve over time
Structures in the PDB do not represent the best we can do
NOW
Optimisation
Structures in the PDB
• Take structure + experimental data• Use latest X-ray crystallography methods– Decision making: use case-specific methods
– Create new methods when needed
• Improve model quality– Fit with experimental data– Geometric quality
• Fix errorsPDB_REDO
OptimisationImprove structures in PDB
Step 1: prepare data• Clean-up structure and X-ray data• Data mining
Step 2: establish baseline• Fit with experimental data (R-factors)
• Geometric quality– Validation with WHAT_CHECK
Optimisation
PDB_REDO method
Step 3: re-refine structure (with Refmac)
• Improve fit with experimental data– Use restraints to improve geometric quality
• Improve description of protein dynamics– Concerted movement of groups of atoms (TLS)
– Anisotropic movement of individual atoms
Optimisation
PDB_REDO method
Step 4: rebuild structure • Delete nonsense waters• Flip peptide planes• Rebuild side-chains– Add missing ones– Optimise H-bonding
Step 5: validate structure • Geometry• Density map fit• Ligand interactions
Optimisation
PDB_REDO method
• www.cmbi.ru.nl/pdb_redo– > 72,000 structures (98%)– Detailed methods & reprints
• Directly in molecular graphics software– YASARA– CCP4mg– Coot (needs plugin)– PyMOL (needs plugin)
• Linked via PDBe & RCSB
Availability
PDB_REDO databank
Worse Same Better0%
25%
50%
75%
100%
8%12%
80%
Ramachandran plot
• Improved fit with the data• Better geometry
Worse Same Better0%
25%
50%
75%
100%
9%17%
74%
R-free
Worse Same Better0%
25%
50%
75%
100%
4%
22%
74%
Fine packing
Optimisation
Does it work? ( 1 2 , 0 0 0 s t r u c t u re s )
MolProbity validation ( 1 e o i )
PDB PDB_REDO
Optimisation
OptimisationElectrostatics calculations
• ‘Missing’ positive lysine atoms distort electrostatics calculations
• Adding missing atoms correctly describes C-terminus interaction with side chains
• Wrong peptide plane in peptide ligand
• Fixed by PDB_REDO• Better understanding of H-bonds in the interaction
Optimisation
Protein-ligand interaction
OptimisationProtein-protein interaction
• Packing interface with poor ionic interactions
• Rebuilt interface properly describes ionic dimerisation interactions
Optimised structures give a better view of
the biology of the protein
PDB_REDOersAmsterdam:• R Joosten• K Joosten• A Perrakis
Key contributors:Eleanor Dodson, Ian Tickle, Paul Emsley, Ethan Merritt, Elmar Krieger, Thomas Lütteke, Rachel Kramer Green, Sanchayita Sen
Nijmegen:• T te Beek• M Hekkelman• G Vriend
Cambridge:• G Murshudov• F Long