References#
Overview articles#
These provide a good start learn the motivation and key methods behind MD-based SAS interpretation:
Predicting solution scattering patterns with explicit-solvent molecular simulations
Leonie Chatzimagas and Jochen S. Hub
Submitted to Meth. Enzymol., edited by John Tainer
arXiv, doi:10.48550/arXiv.2204.04961
Structure and ensemble refinement against SAXS data: combining MD simulations with Bayesian inference or with the maximum entropy principle
Leonie Chatzimagas and Jochen S. Hub
Submitted to Meth. Enzymol., edited by John Tainer
bioRxiv, doi:10.1101/2022.04.05.487171
SAXS/WAXS/SANS curve predictions from MD simulations#
Validating solution ensembles from molecular dynamics simulation by wide-angle X-ray scattering data
Po-chia Chen and Jochen S. Hub
Biophys. J., 107, 435-447 (2014) [www]
WAXSiS: a web server for the calculation of SAXS/WAXS curves based on explicit-solvent molecular dynamics
Christopher J. Knight and Jochen S. Hub
Nucleic Acids Res., 43, W225-W230 (2015) [www]
SAXS/WAXS/SANS-driven MD simulations#
Interpretation of solution X-ray scattering data by explicit-solvent molecular dynamics
Po-chia Chen and Jochen S. Hub
Biophys. J., 108, 2573–2584 (2015) [www]
Combined small-angle X-ray and neutron scattering restraints in molecular dynamics simulations
Po-chia Chen, Roman Shevchuk, Felix Strnad, Charlotte Lorenz, Lukas Karge, Ralph Gilles, Andreas Stadler, Janosch Hennig, Jochen S. Hub
J. Chem. Theory Comput. 15, 84687-4698 (2019) [www]
Bayesian refinement of protein structures and ensembles against SAXS data using molecular dynamics
Roman Shevchuk and Jochen S. Hub
PLoS Comp. Biol., 13, e1005800 (2017) [www]
SAXS-guided maximum-entropy ensemble refinement#
SAXS-restrained ensemble simulations of intrinsically disordered proteins with commitment to the principle of maximum entropy
Markus R. Hermann and Jochen S. Hub
J. Chem. Theory Comput., 15, 95103-5115 (2019) [www]
SAXS curves of detergent micelles: effects of asymmetry, shape fluctuations, disorder, and atomic details
Miloš T. Ivanović, Markus R. Hermann, Maciej Wójcik, Javier Pérez, Jochen S. Hub
J. Phys. Chem. Lett. 11, 945-951 (2020) [www]
Applications#
Interpretatinon of time-resolved SAXS/WAXS data#
Ultrafast anisotropic protein quake propagation after CO-photodissociation in myoglobin
Levin U.L. Brinkmann and Jochen S. Hub
Proc. Natl. Acad. Sci. USA, 113, 10565–10570 (2016) [www]
Anisotropic time-resolved solution X-ray scattering patterns from explicit-solvent molecular dynamics
Levin U.L. Brinkmann and Jochen S. Hub
J. Chem. Phys. 143, 104108 (2015) [www]
Protein-detergent and soft-matter complexes#
Structural properties of protein-detergent complexes from SAXS and MD simulations
Po-chia Chen and Jochen S. Hub
J. Phys. Chem. Lett. 6, 5116–5121 (2015) [www]
Temperature-dependent atomic models of detergent micelles refined against small-angle X-ray scattering data
Milos T. Ivanovic, Linda Bruetzel, Jan Lipfert, and Jochen S. Hub
Angew. Chem. Int. Ed. 57, 5635-5639 (2018) [www]
Merging in-solution X-ray and neutron scattering data allows fine structural analysis of membrane-protein detergent complexes
Gaetan Dias Mirandela, et al.
J. Phys. Chem. Lett. 9, 3910-3914 (2018) [www]
Effect of the ion cloud on SAXS curves and on the apparent radius of gyration#
Quantifying the influence of the ion cloud on SAXS profiles of charged proteins
Milos T. Ivanovic, Linda K. Bruetzel, Roman Shevchuk, Jan Lipfert, and Jochen S. Hub
PCCP 20, 26351-26361 (2018) [www]
Intrinsically disordered proteins#
Disentangling polydispersity in the PCNA-p15PAF complex, a disordered, transient and multivalent macromolecular assembly
Tiago Cordeiro, Po-chia Chen, Alfredo De Biasio, Nathalie Sibille, Francisco Blanco, Jochen S. Hub, Ramon Crehuet, Pau Bernado
Nucleic Acids Res. 45, 1501-2015 (2017) [www]