ultrascan-somo (us-somo): an integrated hydrodynamic and …saxs/download/... · 2017-10-17 ·...
TRANSCRIPT
![Page 1: UltraScan-SOMO (US-SOMO): An Integrated Hydrodynamic and …saxs/download/... · 2017-10-17 · Savelyev, Alexey - US-SOMO– SLAC Workshop– 28-30 Mar 2016 US-SOMO Website: somo.uthscsa.edu](https://reader033.vdocuments.mx/reader033/viewer/2022050100/5f3f6d289f052e09a82b72a2/html5/thumbnails/1.jpg)
Savelyev, Alexey - US-SOMO– SLAC Workshop– 28-30 Mar 2016
Alexey Savelyev
Workshop on SAXS and Diffraction Studies, SLAC National Acceleration Laboratory
28-30 March 2016
UltraScan-SOMO (US-SOMO): An Integrated Hydrodynamic and Small Angle Scattering
Data Analysis Software Suite
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Savelyev, Alexey - US-SOMO– SLAC Workshop– 28-30 Mar 2016
Outline
SAXS/WAXS data application to validation of computational models of DNA
Overview of US-SOMO Hydrodynamic and SAS capabilities
HPLC-SAXS module analysis tools
Tutorial
N S=DMAX (qMAX −q MIN) /π
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Savelyev, Alexey - US-SOMO– SLAC Workshop– 28-30 Mar 2016
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Savelyev, Alexey - US-SOMO– SLAC Workshop– 28-30 Mar 2016
WAXS example 1: fingerprints for DNA conformation
Tiede et al., PNAS 103, 3534, 2006Tiede et al., JACS 127, 16, 2005
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Savelyev, Alexey - US-SOMO– SLAC Workshop– 28-30 Mar 2016
WAXS example 2: differentiate btw NMR and X-ray structures
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Savelyev, Alexey - US-SOMO– SLAC Workshop– 28-30 Mar 2016
SAXS/WAXS example 3: differentiate btw. different all-atom computational DNA models
32-128 CPUs
New fully polarizable all-atom model for DNA based on Drude oscillator formalism
Savelyev & MacKerell, J Comp Chem, 35, 1219, 2014
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Savelyev, Alexey - US-SOMO– SLAC Workshop– 28-30 Mar 2016
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Savelyev, Alexey - US-SOMO– SLAC Workshop– 28-30 Mar 2016
Savelyev & MacKerell, J Phys Chem Lett, 6, 212, 2015
● Look at the q up to ~2.5 Å^-1
● Process entire MD trajectory (thousands of frames)
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Savelyev, Alexey - US-SOMO– SLAC Workshop– 28-30 Mar 2016
SAXS/WAXS example 3: differentiate btw. different all-atom computational DNA models
Savelyev & MacKerell, J Phys Chem Lett, 6, 212, 2015
Savelyev & MacKerell, J Comp Chem, 35, 1219, 2014Savelyev & MacKerell, J Phys Chem B, 118, 6742, 2014
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Savelyev, Alexey - US-SOMO– SLAC Workshop– 28-30 Mar 2016
Savelyev & MacKerell, J Phys Chem Lett, 6, 212, 2015
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Savelyev, Alexey - US-SOMO– SLAC Workshop– 28-30 Mar 2016
Savelyev & MacKerell, J Phys Chem Lett, 6, 212, 2015
MD simulations predict differential impact of Li+, Na+, K+ and Rb+ ions on DNA conformational properties
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Savelyev, Alexey - US-SOMO– SLAC Workshop– 28-30 Mar 2016
Savelyev, A, in preparation
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Savelyev, Alexey - US-SOMO– SLAC Workshop– 28-30 Mar 2016
Savelyev, A, in preparation
Tiede et al, JACS, 127, 16, 2005
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Savelyev, Alexey - US-SOMO– SLAC Workshop– 28-30 Mar 2016
Hydrated cations modulate minor groove via water-mediated hydrogen bonds with DNA strands
Savelyev & MacKerell, J Chem Theory Comput, 11, 4473, 2015
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Savelyev, Alexey - US-SOMO– SLAC Workshop– 28-30 Mar 2016
SAXS experiments on DNA in various ionic buffers are planned at NIST
Savelyev & MacKerell, J Chem Theory Comput, 11, 4473, 2015
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Savelyev, Alexey - US-SOMO– SLAC Workshop– 28-30 Mar 2016
New developments in the UltraScan SOlution MOdeler (US-SOMO)
Software Suite
E. H. Brookesa
J. Pérezb
P. Vachettec
A. Savelyeva
M. Roccod
aDept. of Biochemistry, U. of Texas Health Science Center at San Antonio, San Antonio, TX
bBeamline SWING, Synchrotron SOLEIL, Gif-sur-Yvette, Francec2BC, UMR 9198, Orsay, FrancedBiopolimeri e Proteomica, IRCCS AOU San Martino-IST, Genova, Italy
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Savelyev, Alexey - US-SOMO– SLAC Workshop– 28-30 Mar 2016
US-SOMO: Hydrodynamic calculationsMattia Rocco
Biopolimeri e Proteomica, IRCCS AOU San Martino-IST,
Istituto Nazionale per la Ricerca sul Cancro,
Genova, Italy
Olwyn ByronUniversity of Glasgow
Hydrodynamic tensor equation by matrix inversion or boundary element method or Zeno method (non rotational)
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Savelyev, Alexey - US-SOMO– SLAC Workshop– 28-30 Mar 2016
US-SOMO: GenApp Web-portal
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Savelyev, Alexey - US-SOMO– SLAC Workshop– 28-30 Mar 2016
US-SOMO SAS
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Savelyev, Alexey - US-SOMO– SLAC Workshop– 28-30 Mar 2016
US-SOMO SAS
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Savelyev, Alexey - US-SOMO– SLAC Workshop– 28-30 Mar 2016
US-SOMO: P(r) structural histogram
● Compute P(r)● Select distance range● Display residues colored by contribution
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Savelyev, Alexey - US-SOMO– SLAC Workshop– 28-30 Mar 2016
US-SOMO: SAS data treatment
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Savelyev, Alexey - US-SOMO– SLAC Workshop– 28-30 Mar 2016
Discrete MD
● Explores conformational space● Faster than standard MD● Discretizes the potential function● 20,000 * 50 fs = 1 ns● Implicit solvent● Anderson thermostat
Ding F, Dokholyan NV. Emergence of protein fold families through rational design. Public Library of Science, Comput Biol. (2006) 2(7):e85
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Savelyev, Alexey - US-SOMO– SLAC Workshop– 28-30 Mar 2016
US-SOMO● Bead model generation from atomic structures● Hydrodynamic parameter calculation● SAS
● Multiple Debye for I(q) from (explicitly hydrated) atomic structures or bead models
● Full, Quick (FoXS), S.H., and external interface to CRYSOL/N, FoXS● Customizable excluded volumes, scattering factors● Supports common 4 term Gaussian scattering factors and 5 term
● Waasmaier,. D. and Kirfel, A, New analytical scattering-factor functions for free atoms and ions, Acta Cryst. (1995). A51, 416-431
● CUDA Full Debye● S.H. Intel MIC Debye (Initial testing 10k Scatters < 500ms)
● Rg, Rc, Rt● P(r)● Best fit, NNLS fitting● Buffer subtraction tool● Batch & cluster computations● DMD on cluster for expanding conformation space● HPLC-SAXS tools
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Savelyev, Alexey - US-SOMO– SLAC Workshop– 28-30 Mar 2016
US-SOMO
● Website: somo.uthscsa.edu● GUI based: Windows, OSX, Linux, source code (GPL).● Brookes et al, UltraScan Solution Modeler: Integrated Hydrodynamic Parameter
and Small Angle Scattering Computation and Fitting Tools, ACM XSEDE 2012● “The overarching goal of our software is to provide an extensible
general framework for generating collections of candidate structures from an initial structure or structures, modeling candidate structures under various experimental methods and conditions, and subsequently globally fitting and screening candidate structure's models against sets of experimental data”
● Brookes E, Demeler B, Rosano C, Rocco M. The implementation of SOMO (SOlution MOdeller) in the UltraScan analytical ultracentrifugation data analysis suite: enhanced capabilities allow the reliable hydrodynamic modeling of virtually any kind of biomacromolecule. Eur Biophys J. 2010 Feb;39(3):423-35.
● Brookes E, Demeler B, Rocco M. Developments in the US-SOMO bead modeling suite: new features in the direct residue-to-bead method, improved grid routines, and influence of accessible surface area screening. Macromol Biosci. 2010 Jul 7;10(7):746-53.
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Savelyev, Alexey - US-SOMO– SLAC Workshop– 28-30 Mar 2016
HPLC-SAXS
N S=DMAX (qMAX −q MIN) /π
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Savelyev, Alexey - US-SOMO– SLAC Workshop– 28-30 Mar 2016
Typically Gaussian shaped profiles since diffusion is
the primary physical process responsible for band broadening during
separation
If not Gaussian, it could be: Interaction with the column matrix Superposition of multiple peaks Interaction between co-eluting species Weak self associations
SEC
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Savelyev, Alexey - US-SOMO– SLAC Workshop– 28-30 Mar 2016
Online SEC-SAXS
Separate immediately before measuring
Individual peaks are more likely to be monodisperse
First use paper, available to users who could self-manage FPLC
ID-18 BioCat / APS
Mathew, E., Mirza, A., & Menhart, N. 2004. Liquid-chromatography-coupled SAXS for accurate sizing of aggregating proteins. J. Synchrotron Rad. 11, 314-318.
First setup with user HPLC support
SWING/SOLEIL
David, G. & Pérez, J. 2009. Combined sampler robot and high-performance liquid chromatography: a fully automated system for biological small-angle X-ray scattering experiments at the Synchrotron SOLEIL SWING beamline. J. Appl. Cryst. 42, 892-900
Now available as primary method of analysis at multiple beamlines
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Savelyev, Alexey - US-SOMO– SLAC Workshop– 28-30 Mar 2016
Set of I(q), each a specific time or frame, Aldolase
q (linear)
Inte
nsity
(lo
g)
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Savelyev, Alexey - US-SOMO– SLAC Workshop– 28-30 Mar 2016
Set of I(t), each a specific q, Aldolase
time or frame (linear)
Inte
nsity
(lin
ear
)
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Savelyev, Alexey - US-SOMO– SLAC Workshop– 28-30 Mar 2016
US-SOMO / HPLC-SAXS / Aldolase / Test I(q) global
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Savelyev, Alexey - US-SOMO– SLAC Workshop– 28-30 Mar 2016
Gaussian Decomposition Procedure
Optionally use SVD to create a Truncated SVD set and/or determine expected number of Gaussians (eq. species)
Fit 1 typical I(t) with Gaussians or skewed Gaussians (EMG, GMG, EMG+GMG currently supported)
Globally fit Gaussians to all I(t)
Global fit applies physical constraints
Common centers
Common width
Common skew (for skewed Gaussians)
Fit uses all available data and considers physical constraints
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Savelyev, Alexey - US-SOMO– SLAC Workshop– 28-30 Mar 2016
US-SOMO / HPLC-SAXS / Aldolase / SVD analysis
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Savelyev, Alexey - US-SOMO– SLAC Workshop– 28-30 Mar 2016
Set of I(t), each a specific q
time or frame (linear)
Inte
nsity
(lin
ear
)
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Savelyev, Alexey - US-SOMO– SLAC Workshop– 28-30 Mar 2016
US-SOMO / HPLC-SAXS / Aldolase / Why common distortion?
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Savelyev, Alexey - US-SOMO– SLAC Workshop– 28-30 Mar 2016
Gaussian functions with distortions
Exponentially modified Gaussian (EMG):
Half-Gaussian modified Gaussian (GMG):
EMG+GMG:
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Savelyev, Alexey - US-SOMO– SLAC Workshop– 28-30 Mar 2016
US-SOMO / HPLC-SAXS / Aldolase / Final global EMG+GMG fitting
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Savelyev, Alexey - US-SOMO– SLAC Workshop– 28-30 Mar 2016
US-SOMO / HPLC-SAXS / Gaussian fitting
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Savelyev, Alexey - US-SOMO– SLAC Workshop– 28-30 Mar 2016
US-SOMO / HPLC-SAXS / Aldolase / Test I(q) 4th peak
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Savelyev, Alexey - US-SOMO– SLAC Workshop– 28-30 Mar 2016
US-SOMO / HPLC-SAXS / Aldolase / Test I(q) 3rd peak
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Savelyev, Alexey - US-SOMO– SLAC Workshop– 28-30 Mar 2016
US-SOMO / HPLC-SAXS / Aldolase / Test I(q) 2nd peak
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Savelyev, Alexey - US-SOMO– SLAC Workshop– 28-30 Mar 2016
US-SOMO / HPLC-SAXS / Aldolase / Test I(q) 1st peak
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Savelyev, Alexey - US-SOMO– SLAC Workshop– 28-30 Mar 2016
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Savelyev, Alexey - US-SOMO– SLAC Workshop– 28-30 Mar 2016
US-SOMO / HPLC-SAXS / AldolaseFrame #90: decomposition
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Savelyev, Alexey - US-SOMO– SLAC Workshop– 28-30 Mar 2016
Physically based capillary fouling removal
Better to not have foulingIf you do, this may help
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Savelyev, Alexey - US-SOMO– SLAC Workshop– 28-30 Mar 2016
Physically based capillary fouling removal
Integral Baseline Correction
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Savelyev, Alexey - US-SOMO– SLAC Workshop– 28-30 Mar 2016
Physically based capillary fouling removal
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Savelyev, Alexey - US-SOMO– SLAC Workshop– 28-30 Mar 2016
Effect of capillary fouling removal
Original data(frames 50-110)
Baseline correctedData(frames 50-110)
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Savelyev, Alexey - US-SOMO– SLAC Workshop– 28-30 Mar 2016
Effect of capillary fouling removal: scaling
Original data(q < 0.2 A-1)scaling to MAX value in the range of [45-65]
BL-corrected data(q < 0.2 A-1)scaling to MAX value in the range of [45-65]
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Savelyev, Alexey - US-SOMO– SLAC Workshop– 28-30 Mar 2016
Takeaways
Use SEC-SAXS for biological macromolecules
If you have true baseline separation, excellent, you should probably be ok simply taking the peak data, but global Gaussian decomposition will use all of the data
If you do not have true baseline separation, be very careful and you should use these techniques
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Savelyev, Alexey - US-SOMO– SLAC Workshop– 28-30 Mar 2016
US-SOMO / HPLC-SAXS / 3D View
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Savelyev, Alexey - US-SOMO– SLAC Workshop– 28-30 Mar 2016
US-SOMO / HPLC-SAXS / Concentration curve
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Savelyev, Alexey - US-SOMO– SLAC Workshop– 28-30 Mar 2016
US-SOMO / HPLC-SAXS / Concentration curve
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Savelyev, Alexey - US-SOMO– SLAC Workshop– 28-30 Mar 2016
Parameters to convert UV or RI signals to concentrationDetector calibration constants
Simultaneously fit Gaussians to concentration curveEach Gaussian is the curve of a specific species, so each Gaussian could conceivable have its own extinction coefficient and psv
c concentration (mg/cm3)Re is the diffusion length of the electron (cm)
Z is avg number of electrons per atom, A is avg # of nucleonsmn is the mass of a nucleon (g)
v2 is psv (cm3/g)
ρe is solvent e density (e/A3)
MW Computations
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Savelyev, Alexey - US-SOMO– SLAC Workshop– 28-30 Mar 2016
Entered per I(q) curve (either Gaussian derived or general I(q))
c concentration (mg/ml) can be computed from UV or RI curves
v2 psv (ml/g)
Entered in “Gaussian” options
Re the diffusion length of the electron (cm)Z/A avg number of electrons per avg # of nucleonsmn the mass of a nucleon (g)
Entered in “SAS curve options”
ρe solvent e density (e/A3)
MW Computations
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Savelyev, Alexey - US-SOMO– SLAC Workshop– 28-30 Mar 2016
US-SOMO / HPLC-SAXS / Make I(q)
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Savelyev, Alexey - US-SOMO– SLAC Workshop– 28-30 Mar 2016
US-SOMO / HPLC-SAXS / BSA q 0.0073
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Savelyev, Alexey - US-SOMO– SLAC Workshop– 28-30 Mar 2016
US-SOMO / HPLC-SAXS / BSA
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Savelyev, Alexey - US-SOMO– SLAC Workshop– 28-30 Mar 2016
US-SOMO / HPLC-SAXS / BSA
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Savelyev, Alexey - US-SOMO– SLAC Workshop– 28-30 Mar 2016
Make I(t)Make I(t)Selecttypicalcurve
Set baseline parameters
Apply b.l.params toall curves
Selecttypicalcurve
Setup initialGaussians
GaussFit
GlobalGauss
Fit
Opt.apply to
conc.curve
CollectHPLC-SAXSdata
Make I(q)Set of I(q)
curvesfor each
Gaussian peak
US-SOMO: HPLC-SAXSBrookes E., Perez J, Cardinali B, Profumo A., Vachette P & Rocco M. (2013) Fibrinogen
species as resolved by HPLC-SAXS data processing within the UltraScan Solution Modeler (US-SOMO) enhanced SAS module. J. Appl. Cryst. 46, 1823-1833