Direct shape determination of intermediates in evolving macromolecular solutions from small-angle scattering data

IUCrJ
Petr V Konarev, Dmitri I Svergun

Abstract

Many important biological processes like amyloid formation, viral assembly etc. can be monitored in vitro. Small-angle X-ray scattering (SAXS) is one of the most effective techniques to structurally characterize these processes in solution. For monodisperse systems and some oligomeric mixtures, low-resolution shapes can be determined ab initio from the SAXS data, but for evolving systems, such analysis is hampered by the presence of multiple species and no direct reconstruction procedures are available. The authors consider a frequently occurring case where the scattering from the initial and final states of the process are known but there exists a major (unknown) intermediate component. A method is presented to directly reconstruct the low-resolution shape of this transient component together with its volume fractions from multiple scattering patterns recorded from an evolving system. The method is implemented in the computer program DAMMIX freely available to academic users and its effectiveness is illustrated in several synthetic and experimental examples.

References

Jul 19, 2005·Biochimica Et Biophysica Acta·R AramayoN Boisset
Aug 29, 2006·Journal of Molecular Biology·Xiaofeng ZhangWinfried Meining
Apr 7, 2007·Journal of the American Chemical Society·Pau BernadóDmitri I Svergun
May 3, 2007·PLoS Biology·Bente VestergaardDmitri I Svergun
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Feb 5, 2015·Biophysical Journal·Sonia CovaceuszachAntonino Cattaneo
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Aug 16, 2017·Journal of Applied Crystallography·D FrankeD I Svergun
Oct 13, 2017·Journal of Applied Crystallography·Jesse Bennett HopkinsSoren Skou

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Citations

Jan 30, 2020·ELife·Lior OnnDebra Toiber
Dec 26, 2018·Journal of Biomolecular Structure & Dynamics·Mikhail V KovalchukVladimir I Timofeev
Apr 10, 2021·Journal of Applied Crystallography·Karen Manalastas-CantosDaniel Franke
Aug 28, 2021·Molecules : a Journal of Synthetic Chemistry and Natural Product Chemistry·Martin A SchroerPeter Kopcansky
Nov 13, 2021·Protein Science : a Publication of the Protein Society·Petr V KonarevDmitri I Svergun

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Methods Mentioned

BETA
X-ray
nuclear
electron microscopy
size-exclusion chromatography
SANS

Software Mentioned

MIXTURE
DAMMIN
DAMMIX
SAS
GASBORMX
COSMICS
DAMMIF
SUPCOMB
CRYSOL
OLIGOMER

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