Biology subjects

Keedy, D. A.

Publications and source records attributed to Keedy, D. A..

3 recordsLinked to original sources

bioRxiv2018

Model selection for biological crystallography

Structural biologists have fit increasingly complex model types to protein X-ray crystallographic data, motivated by higher-resolving crystals, greater computational power, and a growing appreciation for protein dynamics. Once fit, a more complex model will generally fit the experimental data better, but it also provides greater capacity to overfit to experimental noise. While refinement progress is normally monitored for a given model type with a fixed number of parameters, comparatively little attention has been paid to the selection among distinct model types where the number of parameters can vary. Using metrics derived in the statistical field of model comparison, we develop a framework for statistically rigorous inference of model complexity. From analysis of simulated data, we find that the resulting information criteria are less likely to prefer an erroneously complex model type and are less sensitive to noise, compared to the crystallographic cross-validation criterion Rfree. Moreover, these information criteria suggest caution in using complex model types and for inferring protein conformational heterogeneity from experimental scattering data.

biophysics↗

bioRxiv2018

qFit-ligand reveals widespread conformational heterogeneity of drug-like molecules in X-ray electron density maps

Proteins and ligands sample a conformational ensemble that governs molecular recognition, activity, and dissociation. In structure-based drug design, access to this conformational ensemble is critical to understand the balance between entropy and enthalpy in lead optimization. However, ligand conformational heterogeneity is currently severely underreported in crystal structures in the Protein Data Bank, owing in part to a lack of automated and unbiased procedures to model an ensemble of protein-ligand states into X-ray data. Here, we designed a computational method, qFit-ligand, to automatically resolve conformationally averaged ligand heterogeneity in crystal structures, and applied it to a large set of protein receptor-ligand complexes. We found that up to 29 % of a dataset of protein crystal structures bound with drug-like molecules present evidence of unmodeled, averaged, relatively isoenergetic conformations in ligand-receptor interactions. In many retrospective cases, these alternate conformations were adventitiously exploited to guide compound design, resulting in improved potency or selectivity. Combining qFit-ligand with high-throughput screening or multi-temperature crystallography could therefore augment the structure-based drug design toolbox.

biophysics↗

bioRxiv2017

New routes for PTP1B allosteric inhibition by multitemperature crystallography, fragment screening and covalent tethering

Allostery is an inherent feature of proteins and provides alternative routes to regulating function. Small-molecule allosteric inhibitors are often desirable; however, it remains challenging to identify surface sites in proteins which can bind small molecules and modulate function. We identified new allosteric sites in protein tyrosine phosphatase 1B (PTP1B) by combining multiple-temperature X-ray crystallography experiments and structure determination from hundreds of individual small-molecule fragment soaks. New modeling approaches reveal \"hidden\" low-occupancy conformational states for protein and ligands. Our results converge on a new allosteric site that is conformationally coupled to the active-site WPD loop, a hotspot for fragment binding, not conserved in the closest homolog, and distinct from other recently reported allosteric sites in PTP1B. Targeting this site with covalently tethered molecules allosterically inhibits enzyme activity. Overall, this work demonstrates how the ensemble nature of macromolecular structure revealed by multitemperature crystallography can be exploited for developing allosteric modulators.

biophysics↗