SAXS studies on mixtures, assemblies, flexible systems€¦ · EMBL Hamburg SAXS studies on...
Transcript of SAXS studies on mixtures, assemblies, flexible systems€¦ · EMBL Hamburg SAXS studies on...
![Page 1: SAXS studies on mixtures, assemblies, flexible systems€¦ · EMBL Hamburg SAXS studies on mixtures, assemblies, flexible systems . I(s) s INTRO I Lecture 1: Introduction Lecture](https://reader030.fdocuments.net/reader030/viewer/2022041101/5eda213cb3745412b570d17d/html5/thumbnails/1.jpg)
Melissa GräwertEMBL Hamburg
SAXS studies on mixtures, assemblies, flexible systems
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I(s)
s
INTRO I
Lecture 1: Introduction
Lecture 2: Instrumentation
Lecture 3: sample preparation
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I(s)
s
Shape
determination
Missing
fragments
Structure
validation
Rigid body
modelling
INTRO I
Lecture 4: ab initio modelling
Lecture 5: advanced modelling
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I(s)
s
Shape
determination
Oligomeric mixtures
Flexible systems
Missing
fragments
Structure
validation
Rigid body
modelling
INTRO I
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Introduction:
* What mixtures are we talking about
* When can SEC-SAXS help?
CHROMIXS
* How do these influence the SAXS data
Case studies:* Oligomeric equilibrium
- Insulin, Sanofi OLIGOMER
* Flexible systems
*Higher molecular weight species
- mAB, Roche
*Ensemble approach
EOM
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What mixtures are we talking about
- Sample impurities: often unknown
IMPURITIES
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Batch mode or SEC-SAXS mode
SEC-SAXS/MALLS
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monomer
mixture
Graewert & Svergun (2020)
Biochem (Lond) 42(1), 36-42
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Graewert & Svergun (2020)
Biochem (Lond) 42(1), 36-42
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Graewert & Svergun (2020)
Biochem (Lond) 42(1), 36-42
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Graewert & Svergun (2020)
Biochem (Lond) 42(1), 36-42
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SEC-SAXS data processing
with CHROMIXS
CHROMIXS
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CHROMIXS
Load data directory
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Data from SASBDB : SASDFN8
CHROMIXS
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Removal of pre-peak
separationNo background drift
Strong signal
CHROMIXS
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Removal of pre-peak
separationNo background drift
Strong signal
Take all frames if possible
CHROMIXS
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Sample Automatic Selection
CHROMIXS
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CHROMIXS
Buffer Automatic Selection
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Process Selection
CHROMIXS
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CHROMIXS
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CHROMIXS
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CHROMIXS
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~ 423 kD
Expected: 479 kD
CHROMIXS
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Selection Eraser
CHROMIXS
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Sample Manual Selection
CHROMIXS
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Buffer Manual Selection
CHROMIXS
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Process Selection
CHROMIXS
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CHROMIXS
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CHROMIXS
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Estimate RG
CHROMIXS
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CHROMIXS
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Batch mode or SEC-SAXS mode
NOT ALWAYS
SEC-SAXS
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Why not to perform SEC-SAXS(+MALLS)?
- Some practical examples
column interactions
SEC-SAXS
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AB
- Nice peak
- Removal from unbound substance
- Return to background
- Good data!
SEC-SAXS
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A
B
SEC-SAXS
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Why not to perform SEC-SAXS(+MALLS)?
- Some practical examples
Separation/
Column interactionsRadiation damage
SEC-SAXS
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SEC-SAXS
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Why not to perform SEC-SAXS(+MALLS)?
- Some practical examples
separation limits
SEC-SAXS
Dilution effect
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Why not to perform SEC-SAXS(+MALLS)?
- There are some limits!
“Hmmm, I don’t know
which peak it is?”
SEC-SAXS
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Why not to perform SEC-SAXS(+MALLS)?
- There are some limits!
1. Trip: 2. Trip:
SEC-SAXS
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When performing SEC-SAXS(+MALLS)?
Remember
“ideal sample”
Pre-analysis of sample is very important
not quite pure sample
SEC-SAXS is analytical! Not
preparative!
radiation damage can be a issue
Measure batch sample as well, add
scavengers
Sample stability, low affinity complexes
Sample can be altered with column
interaction
SEC-SAXS
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What mixtures are we talking about
- Impurities in protein dilution: contaminations
- Oligomeric mixtures
- Assemblies (low affinity)
- Flexible systems
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How do mixtures scatter?
monomer
In monodisperse systems (non-interacting):
random orientation (tumbling in solution)
size, shape and internal structure
Mixtures
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How do mixtures scatter?
mixture
monomer
For equilibrium and non-equilibrium
mixtures,
- scattering intensities of each species
Ik(s)
- volume fractions
Mixtures
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How do mixtures scatter? And what if our system is
flexible? Conformational polydispersity (eg.
IDPs)
• <Almost> infinite range of conformations
• Cannot really identify all possible vk and
Ik(s)
• Requires a more indirect approach
Mixtures
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Introduction:
* What mixtures are we talking about
* How do these influence the SAXS data
Case studies:* Oligomeric equilibrium
(Insulin, Sanofi)
* Flexible systems
*Higher molecular weight species
(mAB, Roche)
*Ensemble approach
(characterization of a cancer drug
target)
(vaccine development)
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1. Analysis of oligomeric species
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MONOMER
biologically active,
circulating form
highly physicochemically
unstable
exogenous insulins
to ensure sufficient shelf life
formulated as compact
oligomers
(mainly hexamers/
crystalline state)
1. Analysis of oligomeric species
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?MONOMER
biologically active,
circulating form knowing the quaternary structure of
insulin and insulin analogues
under pharmaceutical formulation
conditions is important for improving
the physical and chemical stability of
the drug product as well as for fine-
tuning the absorption
kinetics upon subcutaneous injection
1. Analysis of oligomeric species
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?MONOMER
biologically active,
circulating form
Lantus®
Toujeo® shift in isoel. point
Apidra®
1. Analysis of oligomeric species
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Comparison: insulin glulisine in Apidra® insulin glargine in Lantus®
• Similar I(0) = similar in size
MW estimates ~ hexamer
• Negative curvature at low s
Repulsion more pronounced
for insulin glargine
Nagel et al. 2019 Biophys. Chem. 253:106226
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Comparison: insulin glulisine in Apidra® insulin glargine in Lantus®
• Similar I(0) = similar in size
MW estimates ~ hexamer
• Negative curvature at low s
Repulsion more pronounced
for insulin glargine
prevent further association
and undesired aggregation
• Faster decay of Apidra curve
larger species present in
formulation
Nagel et al. 2019 Biophys. Chem. 253:106226
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Insulin glulisine in Apidra® primarily consists of hexamers with a significant
fraction of monomers and dodecamers which partially dissociate into monomers
upon dilution with placebo
-fits with dodecamers
- fits without dodecamers3.49 mg/ml
1.74 mg/ml
0.87 mg/ml
Nagel et al. 2019 Biophys. Chem. 253:106226
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Insulin glargine in Lantus® and Toujeo® show strong repulsive interactions under
formulation conditions and strong attractive interactive upon dilution
No clear conc.
dependent
dissociation
Toujeo® at c=1/3
correlates with
Lantus®
Nagel et al. 2019 Biophys. Chem. 253:106226
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In the formulation conditions of Lantus® and Toujeo® (insulin
glargine), the drug substance seems to be in a more stable hexamer-dimer
equilibrium with only trace amounts of dodecamers.
Nagel et al. 2019 Biophys. Chem. 253:106226
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Highlights
In marketed formulations, the two insulin analogues glulisine
and glargine do not consist of pure hexamers.
Insulin glulisine (Apidra) is predominantly present as
hexamers with significant fractions of monomers and
dodecamers under formulation conditions.
Dilution studies, to characterize the association/dissociation
properties and to mimic the subcutaneous scenario upon
injection to some extent, reveal a dissociation of the hexamers
and dodecamers into monomers for insulin glulisine.
The insulin glargine in Lantus® and Toujeo® demonstrates a
hexamer-dimer equilibrium, which is maintained upon dilution
with water.
SAXS powerful tool for such an investigation!
1. Analysis of oligomeric species
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OLIGOMER
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OLIGOMER
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OLIGOMER
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OLIGOMER
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OLIGOMER
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OLIGOMER
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OLIGOMER
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OLIGOMER
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OLIGOMER
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OLIGOMER
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OLIGOMER
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OLIGOMER
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Fit curve
OLIGOMER
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OLIGOMER
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Looking at flexible systems
- Kratky plot (I(s)*s2 vs s)
This plot provides a sensitive means of monitoring the degree of
compactness
Globular particle : bell-shaped curve
Gaussian chain : plateau at large s-values
!!! but beware: a plateau does not imply a Gaussian chain
Myelin
BSA
Apoferritin
Journal of Molecular Biology,
06 Feb 2020, 432(9):3078-3092
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Looking at flexible systems
- Kratky plot (I(s)*s2 vs s)
This plot provides a sensitive means of monitoring the degree of
compactness
Characterize proteins
Screen for changes
Mathiasen et al. 2016
FEBS J. Aug;283(16):3134-54.
Flexible Systems
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bell-shaped curve with a peak position at s
= √3, typical for globular particles
plateau, as expected for extended and
possibly flexible proteins
Dimensionless Kratky plots
Characterization of mAb dimers reveals predominant dimer forms
common in therapeutic mAbs. (Plath et al. 2016; Mabs)
Dimer 1
Dimer 2
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Characterization of mAb dimers reveals predominant dimer forms
common in therapeutic mAbs. (Plath et al. 2016; Mabs)
- SAXS data supports TEM
analyses and shape parameters
from light scattering and AUC
- first study that extensively
describes compact mAb species
of dimer2
- The impact of these different
dimer species on safety and
efficacy is of great interest for
future pharmaceutical
development of therapeutic
antibodies
Summary:
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Introduction:
* What mixtures are we talking about
* How do these influence the SAXS data
Case studies:* Oligomeric equilibrium
(Insulin, Sanofi)
* Flexible systems
*Higher molecular weight species
(mAB, Roche)
*Ensemble approach
(characterization of a cancer drug
target)
(vaccine development)
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Dmitri SvergunPau Bernado
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Ensemble approach
1) Pool of random structures
are generated (~10.000) and
there scattering profiles are calculated
2) Ensemble of sub structures
are selected from this pool
3) Compare distribution of
structural parameters from group
of substructures compared to
those of complete pool
Graewert & Svergun (2020)
Biochem (Lond) 42(1), 36-42
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Journal of Molecular Biology,
06 Feb 2020, 432(9):3078-3092
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Assessing overall flexibility
Polykretis et al. 2019
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• X-chromosome-linked inhibitor of apoptosis
protein(XIAP)
• 497-residue cytoplasmic zinc-binding protein
• expressed in most human tissues
• three zinc-binding baculovirus IAP repeat (BIR)
domains
• a ubiquitin-associated(UBA) domain
• a C-terminal, zinc-binding Really Interesting New
Gene (RING) domain
• XIAP = potent inhibitor of apoptosis (blocking
the proteolytic activity of caspases
• is overexpressed in tumours (potentiates cell
survival and resistance to chemotherapeutics)
• XIAP has become an important target for the
development of cancer treatments
Assessing overall flexibility
Polykretis et al. 2019
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Assessing overall flexibility Ab initio modelling:
disc-like flat conformation
SEC-SAXS:
Homomeric dimer
Rg 38 Å
P(r):
almost Gausian
compact
Dmax
130 Å
Polykretis et al. 2019
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Assessing overall flexibility
HADDOCK calculations(40 000 models)
X-tal structures of single domains
N-terminus and the inter-domain linkers make up more
than20% of the overall sequence
preserve the BIR1and RING homodimers (C2 symmetry)
experimental restraints
SAXS: Rg=38Å
EPR-DEER: Cys202–Cys202 = 38.6Å
Cys351–Cys351 >70Å
Polykretis et al. 2019
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Assessing overall flexibility
Crysol:
Selection of HADDOCK
models
Polykretis et al. 2019
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Assessing overall flexibility
EOM:
Improved fit,
selection of elongated
compact structures
Polykretis et al. 2019
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Assessing overall flexibility
• X-chromosome-linked inhibitor of apoptosis
protein(XIAP)
• first structural model of the full-length XIAP dimer
• integrated approach: nuclear magnetic
resonance, small-angle X-ray scattering and
electron paramagnetic resonance data
• XIAP adopts a compact and relatively rigid
conformation, implying that the spatial
arrangement of its domains must be taken into
account when studying the interactions with its
physiological partners and in developing effective
inhibitors (not simplistic beads-on-a-string
approach)
Polykretis et al. 2019
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Yang et al. 2019
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C3d-opsonised antigen complex
Co-ligation of the B cell antigen receptor
with complement receptor 2 on B-cells
significantly lowers the threshold required
for B cell activation
fusions of antigens with C3d polymers have
shown great potential in vaccine design
unique complement activating
characteristics Staphylococcus aureus
immunomodulator Sbi to develop “pro-
vaccines.”
spontaneously coats antigens with C3
degradation products in a natural way
Yang et al. 2019
Antigen
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26/05/202091
Sbi-III Sbi-IV Ag85bN’ C’
1 71 142 170 457
Ag85b
Sbi-IVSbi-III
1 2 3 4 5 6
C3D
Dmax
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Introduction:
* What mixtures are we talking about
* How do these influence the SAXS data
Case studies:* Oligomeric equilibrium
(Insulin, Sanofi)
* Flexible systems
*Higher molecular weight species
(mAB, Roche)
*Ensemble approach
(characterization of a cancer drug
target)
(vaccine development)
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> seq
KVTCLVCRKGDNDEFLLLCDGCDRGCHIYCHRPKMEAVPEGD
WFCTVCLAQQV
EGEFTQKPGFPKRGQKRKSGYSLNFSEGDGRRRRVLLRGRE
SPAAGPRYSEEGLSPSKRRRLSMRNHQHSGSV
LTFCEIILMEMESHDAAWPFLEPVNPRLVSGYRRIIKNPMDFST
MRERLLRGGYTSSEEFAADALLVFDNCQTFNED
DSEVGKAGHIMRRFFESRWEEFY
?
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26/05/202097
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26/05/2020100
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26/05/2020101
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Tallant et al, Structure 23(1):80-92 (2015)
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Introduction:
* What mixtures are we talking about
* When can SEC-SAXS help?
CHROMIXS
* How do these influence the SAXS data
Case studies:* Oligomeric equilibrium
- Insulin, Sanofi OLIGOMER
* Flexible systems
*Higher molecular weight species
- mAB, Roche
*Ensemble approach
EOM
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Thank you: to everybody who contributed to all these
programs
Thank you: to our Users with exciting biological questions
(here: Sanofi, Banci Lab (Florence), Roche, van Elsen Lab
(Bath))
Thank you: for your attention!