Integrative, dynamic structural biology at atomic resolution—it's about time

H Van Den Bedem, JS Fraser - Nature methods, 2015 - nature.com
Biomolecules adopt a dynamic ensemble of conformations, each with the potential to
interact with binding partners or perform the chemical reactions required for a multitude of …

Rigidity theory for biomolecules: concepts, software, and applications

SMA Hermans, C Pfleger, C Nutschel… - Wiley …, 2017 - Wiley Online Library
The mechanical heterogeneity of biomolecular structures is intimately linked to their diverse
biological functions. Applying rigidity theory to biomolecules identifies this heterogeneous …

Exposing hidden alternative backbone conformations in X-ray crystallography using qFit

DA Keedy, JS Fraser… - PLoS computational …, 2015 - journals.plos.org
Proteins must move between different conformations of their native ensemble to perform
their functions. Crystal structures obtained from high-resolution X-ray diffraction data reflect …

[图书][B] Modeling structure and dynamics of protein complexes with SAXS profiles

D Schneidman-Duhovny, M Hammel - 2018 - Springer
Small-angle X-ray scattering (SAXS) is an increasingly common and useful technique for
structural characterization of molecules in solution. A SAXS experiment determines the …

Developments in solution-state NMR yield broader and deeper views of the dynamic ensembles of nucleic acids

B Liu, H Shi, HM Al-Hashimi - Current opinion in structural biology, 2021 - Elsevier
Nucleic acids do not fold into a single conformation, and dynamic ensembles are needed to
describe their propensities to cycle between different conformations when performing …

Shortening the HIV-1 TAR RNA bulge by a single nucleotide preserves motional modes over a broad range of time scales

DK Merriman, Y Xue, S Yang, IJ Kimsey, A Shakya… - Biochemistry, 2016 - ACS Publications
Helix–junction–helix (HJH) motifs are flexible building blocks of RNA architecture that help
define the orientation and dynamics of helical domains. They are also frequently involved in …

Protein-RNA complexes and efficient automatic docking: expanding RosettaDock possibilities

A Guilhot-Gaudeffroy, C Froidevaux, J Azé, J Bernauer - PloS one, 2014 - journals.plos.org
Protein-RNA complexes provide a wide range of essential functions in the cell. Their atomic
experimental structure solving, despite essential to the understanding of these functions, is …

Geometric analysis characterizes molecular rigidity in generic and non-generic protein configurations

D Budday, S Leyendecker, H van den Bedem - Journal of the Mechanics …, 2015 - Elsevier
Proteins operate and interact with partners by dynamically exchanging between functional
substates of a conformational ensemble on a rugged free energy landscape. Understanding …

Role of conformational heterogeneity in ligand recognition by viral RNA molecules

L Levintov, H Vashisth - Physical Chemistry Chemical Physics, 2021 - pubs.rsc.org
Ribonucleic acid (RNA) molecules are known to undergo conformational changes in
response to various environmental stimuli including temperature, pH, and ligands. In …

GARN: Sampling RNA 3D structure space with game theory and knowledge-based scoring strategies

M Boudard, J Bernauer, D Barth, J Cohen, A Denise - PloS one, 2015 - journals.plos.org
Cellular processes involve large numbers of RNA molecules. The functions of these RNA
molecules and their binding to molecular machines are highly dependent on their 3D …