Solution x-ray scattering and structure formation in protein dynamics

Abstract

We propose a computationally effective approach that builds on Landau mean-field theory in combination with modern nonequilibrium statistical mechanics to model and interpret protein dynamics and structure formation in small- to wide-angle x-ray scattering (S/WAXS) experiments. We develop the methodology by analyzing experimental data in the case of Engrailed homeodomain protein as an example. We demonstrate how to interpret S/WAXS data qualitatively with a good precision and over an extended temperature range. We explain experimental observations in terms of protein phase structure, and we make predictions for future experiments and for how to analyze data at different ambient temperature values. We conclude that the approach we propose has the potential to become a highly accurate, computationally effective, and predictive tool for analyzing S/WAXS data. For this, we compare our results with those obtained previously in an all-atom molecular dynamics simulation.

Atomistic molecular dynamics simulations of tubulin heterodimers explain the motion of a microtubule

“…Various model systems have been created by scientists to understand vital processes in cells. Biomembranes, proteins, peptides, ionic channels and nucleic acids are very popular to study by both experimental and simulation methods (Ayton et al 2007;Murugova et al 2020;Nakabeppu et al 2007;Subczynski and Pasenkiewicz-Gierula 2020;Kuhrova et al 2019;Ermilova et al 2017;Nasedkin et al 2017). Researchers have tried to relate various diseases to certain behaviors of proteins (Aguzzi and O'Connor 2010;Abriel et al 2013), to compositions of lipid bilayers (Ntarakas et al 2019;Ermilova 2019), to structures and behavior of nucleic acids (Maharana et al 2018;Roth et al 2011) etc.…”