Interpreting solution X-ray scattering data using molecular simulations

JS Hub - Current opinion in structural biology, 2018 - Elsevier
Small-angle and wide-angle X-ray scattering in solution (SAXS, WAXS, SWAXS) is an
increasingly accurate method for obtaining information on biomolecular structures …

X-ray scattering studies of protein structural dynamics

SP Meisburger, WC Thomas, MB Watkins… - Chemical …, 2017 - ACS Publications
X-ray scattering is uniquely suited to the study of disordered systems and thus has the
potential to provide insight into dynamic processes where diffraction methods fail. In …

How accurate are accurate force-fields for B-DNA?

PD Dans, I Ivani, A Hospital, G Portella… - Nucleic Acids …, 2017 - academic.oup.com
Last generation of force-fields are raising expectations on the quality of molecular dynamics
(MD) simulations of DNA, as well as to the belief that theoretical models can substitute …

Long-timescale dynamics of the Drew–Dickerson dodecamer

PD Dans, L Danilāne, I Ivani, T Dršata… - Nucleic Acids …, 2016 - academic.oup.com
We present a systematic study of the long-timescale dynamics of the Drew–Dickerson
dodecamer (DDD: d (CGCGAATTGCGC) 2) a prototypical B-DNA duplex. Using our newly …

Polarizable force field for DNA based on the classical Drude oscillator: II. Microsecond molecular dynamics simulations of duplex DNA

JA Lemkul, AD MacKerell Jr - Journal of chemical theory and …, 2017 - ACS Publications
The structure and dynamics of DNA are governed by a sensitive balance between base
stacking and pairing, hydration, and interactions with ions. Force-field models that include …

SAXS studies of RNA: structures, dynamics, and interactions with partners

Y Chen, L Pollack - Wiley Interdisciplinary Reviews: RNA, 2016 - Wiley Online Library
Small‐angle X‐ray scattering, SAXS, is a powerful and easily employed experimental
technique that provides solution structures of macromolecules. The size and shape …

Reweighting of molecular simulations with explicit-solvent SAXS restraints elucidates ion-dependent RNA ensembles

M Bernetti, KB Hall, G Bussi - Nucleic acids research, 2021 - academic.oup.com
Small-angle X-ray scattering (SAXS) experiments are increasingly used to probe RNA
structure. A number of forward models that relate measured SAXS intensities and structural …

Theory and simulations for RNA folding in mixtures of monovalent and divalent cations

HT Nguyen, N Hori… - Proceedings of the …, 2019 - National Acad Sciences
RNA molecules cannot fold in the absence of counterions. Experiments are typically
performed in the presence of monovalent and divalent cations. How to treat the impact of a …

Simultaneous analysis of enzyme structure and activity by kinetic capillary electrophoresis–MS

GG Mironov, CM Clouthier, A Akbar, JW Keillor… - Nature chemical …, 2016 - nature.com
To enable the detection of protein conformational isomers, their enzymatic activity and their
inhibition in a single experiment, we developed a method based on kinetic capillary …

Counting the ions surrounding nucleic acids

DR Jacobson, OA Saleh - Nucleic acids research, 2017 - academic.oup.com
Nucleic acids are strongly negatively charged, and thus electrostatic interactions—screened
by ions in solution—play an important role in governing their ability to fold and participate in …