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 …

[PDF][PDF] Best practices for time-resolved serial synchrotron crystallography

EC Schulz, BA Yorke, AR Pearson… - … Section D: Structural …, 2022 - journals.iucr.org
With recent developments in X-ray sources, instrumentation and data-analysis tools, time-
resolved crystallographic experiments, which were originally the preserve of a few expert …

Defining a new nomenclature for the structures of active and inactive kinases

V Modi, RL Dunbrack Jr - Proceedings of the National …, 2019 - National Acad Sciences
Targeting protein kinases is an important strategy for intervention in cancer. Inhibitors are
directed at the active conformation or a variety of inactive conformations. While attempts …

Temporal and spatial resolution of distal protein motions that activate hydrogen tunneling in soybean lipoxygenase

JPT Zaragoza, AR Offenbacher, S Hu… - Proceedings of the …, 2023 - National Acad Sciences
The enzyme soybean lipoxygenase (SLO) provides a prototype for deep tunneling
mechanisms in hydrogen transfer catalysis. This work combines room temperature X-ray …

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 …

An expanded allosteric network in PTP1B by multitemperature crystallography, fragment screening, and covalent tethering

DA Keedy, ZB Hill, JT Biel, E Kang, TJ Rettenmaier… - Elife, 2018 - elifesciences.org
Allostery is an inherent feature of proteins, but it remains challenging to reveal the
mechanisms by which allosteric signals propagate. A clearer understanding of this intrinsic …

Mapping the conformational landscape of a dynamic enzyme by multitemperature and XFEL crystallography

DA Keedy, LR Kenner, M Warkentin, RA Woldeyes… - Elife, 2015 - elifesciences.org
Determining the interconverting conformations of dynamic proteins in atomic detail is a
major challenge for structural biology. Conformational heterogeneity in the active site of the …

Codon-specific Ramachandran plots show amino acid backbone conformation depends on identity of the translated codon

AA Rosenberg, A Marx, AM Bronstein - Nature communications, 2022 - nature.com
Synonymous codons translate into chemically identical amino acids. Once considered
inconsequential to the formation of the protein product, there is evidence to suggest that …

Rescue of conformational dynamics in enzyme catalysis by directed evolution

R Otten, L Liu, LR Kenner, MW Clarkson… - Nature …, 2018 - nature.com
Rational design and directed evolution have proved to be successful approaches to
increase catalytic efficiencies of both natural and artificial enzymes. Protein dynamics is …

Ensemble-function relationships to dissect mechanisms of enzyme catalysis

F Yabukarski, T Doukov, MM Pinney, JT Biel… - Science …, 2022 - science.org
Decades of structure-function studies have established our current extensive understanding
of enzymes. However, traditional structural models are snapshots of broader conformational …