Utility of B-factors in protein science: interpreting rigidity, flexibility, and internal motion and engineering thermostability
Z Sun, Q Liu, G Qu, Y Feng, MT Reetz - Chemical reviews, 2019 - ACS Publications
The term B-factor, sometimes called the Debye–Waller factor, temperature factor, or atomic
displacement parameter, is used in protein crystallography to describe the attenuation of X …
displacement parameter, is used in protein crystallography to describe the attenuation of X …
Macromolecular room temperature crystallography
M Fischer - Quarterly Reviews of Biophysics, 2021 - cambridge.org
X-ray crystallography enables detailed structural studies of proteins to understand and
modulate their function. Conducting crystallographic experiments at cryogenic temperatures …
modulate their function. Conducting crystallographic experiments at cryogenic temperatures …
[PDF][PDF] New tools for the analysis and validation of cryo-EM maps and atomic models
PV Afonine, BP Klaholz, NW Moriarty… - … Section D: Structural …, 2018 - journals.iucr.org
Recent advances in the field of electron cryomicroscopy (cryo-EM) have resulted in a rapidly
increasing number of atomic models of biomacromolecules that have been solved using this …
increasing number of atomic models of biomacromolecules that have been solved using this …
EMRinger: side chain–directed model and map validation for 3D cryo-electron microscopy
Advances in high-resolution cryo-electron microscopy (cryo-EM) require the development of
validation metrics to independently assess map quality and model geometry. We report …
validation metrics to independently assess map quality and model geometry. We report …
Accessing protein conformational ensembles using room-temperature X-ray crystallography
JS Fraser, H Van Den Bedem… - Proceedings of the …, 2011 - National Acad Sciences
Modern protein crystal structures are based nearly exclusively on X-ray data collected at
cryogenic temperatures (generally 100 K). The cooling process is thought to introduce little …
cryogenic temperatures (generally 100 K). The cooling process is thought to introduce little …
A multi-crystal method for extracting obscured crystallographic states from conventionally uninterpretable electron density
In macromolecular crystallography, the rigorous detection of changed states (for example,
ligand binding) is difficult unless signal is strong. Ambiguous ('weak'or 'noisy') density is …
ligand binding) is difficult unless signal is strong. Ambiguous ('weak'or 'noisy') density is …
Hidden alternative structures of proline isomerase essential for catalysis
JS Fraser, MW Clarkson, SC Degnan, R Erion, D Kern… - Nature, 2009 - nature.com
A long-standing challenge is to understand at the atomic level how protein dynamics
contribute to enzyme catalysis. X-ray crystallography can provide snapshots of …
contribute to enzyme catalysis. X-ray crystallography can provide snapshots of …
Alternate states of proteins revealed by detailed energy landscape mapping
What conformations do protein molecules populate in solution? Crystallography provides a
high-resolution description of protein structure in the crystal environment, while NMR …
high-resolution description of protein structure in the crystal environment, while NMR …
Ligand binding remodels protein side-chain conformational heterogeneity
SA Wankowicz, SH de Oliveira, DW Hogan… - Elife, 2022 - elifesciences.org
While protein conformational heterogeneity plays an important role in many aspects of
biological function, including ligand binding, its impact has been difficult to quantify …
biological function, including ligand binding, its impact has been difficult to quantify …
Modelling dynamics in protein crystal structures by ensemble refinement
Single-structure models derived from X-ray data do not adequately account for the inherent,
functionally important dynamics of protein molecules. We generated ensembles of structures …
functionally important dynamics of protein molecules. We generated ensembles of structures …