The Future of Structural Biology Disorder? or Dynamics? 10 Å.
Transcript of The Future of Structural Biology Disorder? or Dynamics? 10 Å.
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The Future of Structural Biology
Disorder? or Dynamics?
10 Å
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What is the structure of “disorder” ?
a grand challenge for structural biology in the 21st century
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R. Neutze et al., Nature 406, pp. 752-757 (2000)
Promise of Single-molecule Imaging
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lysozyme: thermal motion
RMS displacement from B factors
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The Future of Structural Biology
Problem:
XFELs cannot solve the
“resolution problem”
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Muybridge’s galloping horse (1878)
Real space reciprocal
“Time-resolved” diffraction
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Muybridge’s galloping horse (1878)
Real space reciprocal
Average electron density
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Supporting a model with data
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What can we do now?
1) Make the molecule sit still
2) Preserve sample integrity
3) Model the average structure
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Make the molecule sit still
1) 20 years of biochemistry
2) How long to find this in a random search?
3) Biophysical assays for rigidity?
4) What about function?
5) What if function and “disorder” are the same thing?
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Plastic deformation
= poor
diffraction
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Elastic deformation
= non-
isomorphism
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RH 84.2% vs 71.9% Riso = 44.5%RMSD = 0.18 Å
Non-isomorphism in lysozyme
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Dear James
The story of the two forms of lysozyme crystals goes back to about 1964 when it was found that the diffraction patterns from different crystals could be placed in one of two classes depending on their intensities. This discovery was a big set back at the time and I can remember a lecture title being changed from the 'The structure of lysozyme' to 'The structure of lysozyme two steps forward and one step back'. Thereafter the crystals were screened based on intensities of the (11,11,l) rows to distinguish them (e.g. 11,11,4 > 11,11,5 in one form and vice versa in another). Data were collected only for those that fulfilled the Type II criteria. (These reflections were easy to measure on the linear diffractometer because crystals were mounted to rotate about the diagonal axis). As I recall both Type I and Type II could be found in the same crystallisation batch . Although sometimes the external morphology allowed recognition this was not infallible.
The structure was based on Type II crystals. Later a graduate student Helen Handoll examined Type I. The work, which was in the early days and before refinement programmes, seemed to suggest that the differences lay in the arrangement of water or chloride molecules (Lysozyme was crystallised from NaCl). But the work was never written up. Keith Wilson at one stage was following this up as lysozyme was being used to test data collection strategies but I do not know the outcome.
An account of this is given in International Table Volume F (Rossmann and Arnold edited 2001) p760.
Tony North was much involved in sorting this out and if you wanted more info he would be the person to contact. I hope this is helpful. Do let me know if you need more.
Best wishes
Louise
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average structure: 1-sigma contour
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Ringer: systematic map sampling
Lang et al. (2010) Protein Sci. 19, 1420-31. Fraser, et al. (2009) Nature 462, 669-73.
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-1
0
1
2
3
4
5
0 30 60 90 120 150 180 210 240 270 300 330 360
2Fo-Fc1 sigmameanvacuum
ele
ctr
on
de
nsi
ty (
e- /Å3)
χ1 angle (degrees)
Ringer: systematic map samplingRinger: systematic map sampling
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Independent estimates of F000
PDB Method F000 diff
3DKEMatthews et. al. (2008) 121700
+6.7%END map estimate 130500
2NVHMatthews et. al. (2006) 92800
+3.0%END map estimate 95656
1AHOCerutti et. al. (2010) 23177
-5.0%END map estimate 22020
Lang et al. (2014) PNAS USA 111, 237-242.
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"error bar" for electron density
-0.1
0
0.1
0.2
0.3
0.4
0.5
0.6
0.7
0.8
0.9
1
1.1
0 0.2 0.4 0.6 0.8 1
2Fo-Fc
sigma(2Fo-Fc)
0
0.1
0.2
0.3
0.4
0 5 10 15 20
Fobs
Fcalc
stru
ctur
e f
acto
r (e
- /ce
ll)
spot index fractional coordinate
elec
tron
den
sity
(e- /Å
3)
Lang et al. (2014) PNAS USA 111, 237-242.
error bars for electron density
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"error bar" for electron density
-0.1
0
0.1
0.2
0.3
0.4
0.5
0.6
0.7
0.8
0.9
1
1.1
0 0.2 0.4 0.6 0.8 1
2Fo-Fc
sigma(2Fo-Fc)
fractional coordinate
elec
tron
den
sity
(e- /Å
3)
Refinement
Against
Perturbed
Input
Data
Lang et al. (2014) PNAS USA 111, 237-242.
error bars for electron density
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1 “sigma” is not a good criterion
0
5
10
15
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0 0.2 0.4 0.6 0.8 1 1.2
RAPID SigFRAPID |Fo-Fc|mean1 "sigma"
Electron Number Density (e-/Å3)
norm
aliz
ed c
ount
s
Lang et al. (2014) PNAS USA 111, 237-242.
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Molecular Dynamics Simulation
1aho Scorpion toxin
0.96 Å resolution64 residuesSolvent: H20 + acetate
Cerutti et al. (2010).J. Phys. Chem. B 114, 12811-12824.
using realcrystal’s lattice
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30 conformers from 24,000
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Electron density from 24,000 conformers
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How many conformers are there?
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Answer: 40
How many conformers are there?
Rcryst = 0.0506 Rfree = 0.0556vs Fsim
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How many conformers are there?
Answer: 8
Rcryst = 0.0297Rfree = 0.0293vs Fsim
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How many conformers are there?
Rcryst = 0.0441Rfree = 0.0516vs Fsim
Answer: 2-14
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Rcryst = 0.1546Rfree = 0.1749vs Fobs
1aho:Rcryst = 0.1630Rfree = n/d
How many conformers are there?
Answer: 1-7
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How many conformers are there?
All differencefeaturesare in the solvent!
real data
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-0.5
0
0.5
1
1.5
2
2.5
3
0 10 20 30 40
residual
protein
bulk solvent
sim water
1 sigma
x along line y=z=0 (Å)
Ele
ctro
n n
um
ber
den
sity
(e
- /Å3)
How rough is the solvent?
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How “rough” is the solvent?
Rcryst = 0.0309Rfree = 0.0678vs Fsim
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The Future of Structural Biology
• will be noisy
• Averaging destroys resolution
• Multi-crystal data – isomorphism
• structures of the future must be 4D
• There is “life” below 1 σ