Structure-based screening of binding affinities via small-angle X-ray scattering

IUCrJ
Po-Chia ChenJanosch Hennig

Abstract

Protein-protein and protein-ligand interactions often involve conformational changes or structural rearrangements that can be quantified by solution small-angle X-ray scattering (SAXS). These scattering intensity measurements reveal structural details of the bound complex, the number of species involved and, additionally, the strength of interactions if carried out as a titration. Although a core part of structural biology workflows, SAXS-based titrations are not commonly used in drug discovery contexts. This is because prior knowledge of expected sample requirements, throughput and prediction accuracy is needed to develop reliable ligand screens. This study presents the use of the histidine-binding protein (26 kDa) and other periplasmic binding proteins to benchmark ligand screen performance. Sample concentrations and exposure times were varied across multiple screening trials at four beamlines to investigate the accuracy and precision of affinity prediction. The volatility ratio between titrated scattering curves and a common apo reference is found to most reliably capture the extent of structural and population changes. This obviates the need to explicitly model scattering intensities of bound complexes, which can be strongl...Continue Reading

References

Nov 1, 1995·Journal of Biomolecular NMR·F DelaglioA Bax
Dec 16, 2003·The Journal of Biological Chemistry·Ulrika MagnussonSherry L Mowbray
Jun 14, 2005·Proceedings of the National Academy of Sciences of the United States of America·Jie WangEvan R Kantrowitz
Oct 11, 2007·The Journal of Physical Chemistry. B·Jan LipfertSebastian Doniach
Feb 22, 2011·Nature Structural & Molecular Biology·James Wesley FairmanChris Godfrey Dealwis
Oct 12, 2012·Journal of the American Chemical Society·Nozomi AndoCatherine L Drennan
Mar 5, 2013·Journal of Biomolecular NMR·Jonathan J Helmus, Christopher P Jaroniec
Mar 19, 2013·Annual Review of Biophysics·Robert P Rambo, John A Tainer
Apr 27, 2013·Nature·Robert P Rambo, John A Tainer
Apr 30, 2013·Nature Methods·Greg L HuraJohn A Tainer
Aug 22, 2013·Progress in Nuclear Magnetic Resonance Spectroscopy·Mike P Williamson
Aug 27, 2013·Biophysical Journal·Dina Schneidman-DuhovnyAndrej Sali
Sep 17, 2013·The Journal of Biological Chemistry·Byron C H ChuHans J Vogel
Dec 25, 2013·Journal of Synchrotron Radiation·Yannick G SpillMichael Nilges
Mar 5, 2014·The FEBS Journal·Anne T Tuukkanen, Dmitri I Svergun
Jun 27, 2014·Nature Protocols·Soren SkouNozomi Ando
Oct 30, 2014·Nucleic Acids Research·Erica ValentiniDmitri I Svergun
Apr 1, 2012·Journal of Applied Crystallography·Maxim V PetoukhovDmitri I Svergun
Dec 17, 2014·Bioinformatics·Woonghee LeeJohn L Markley
Dec 30, 2014·Journal of Synchrotron Radiation·Alvin Samuel AcerboRichard Edward Gillilan
Jan 6, 2016·Biochimica Et Biophysica Acta·A R von GundlachA Rosenhahn
Apr 14, 2016·Wiley Interdisciplinary Reviews. RNA·Yujie Chen, Lois Pollack
Nov 20, 2016·Protein Science : a Publication of the Protein Society·Subrata PaulHans J Vogel
Nov 29, 2016·European Journal of Pharmaceutics and Biopharmaceutics : Official Journal of Arbeitsgemeinschaft Für Pharmazeutische Verfahrenstechnik E.V·Masakazu FukudaAkiko Koga
Aug 16, 2017·Journal of Applied Crystallography·D FrankeD I Svergun
Sep 7, 2017·Acta Crystallographica. Section D, Structural Biology·Jill TrewhellaAndrew E Whitten
Nov 11, 2017·IUCrJ·Enrico F SemeraroTheyencheri Narayanan
Dec 9, 2017·Advances in Experimental Medicine and Biology·Tiago N CordeiroPau Bernadó
Oct 12, 2018·Biophysics Reviews·Po-Chia Chen, Janosch Hennig

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Methods Mentioned

BETA
X-ray
NMR
size-exclusion
SAXScreen
chip

Software Mentioned

SAXScreen
nmrglue
matplotlib
SAXS
SAXS Merge
Zenodo

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