ArticleMethods in enzymology2023
Refinement of multiconformer ensemble models from multi-temperature X-ray diffraction data.
Article in Methods in enzymology, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 17 papers.
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17 citing papers in PubMed.
- Understanding how enzymes work: the journey to ensemble-function studies.The FEBS journal · 2026Review
- Pinpointing Protein Crystal Structures over a Broad Temperature Range Using Hydrophobic Protection.ACS omega · 2026Article
- Some Like It Hot -Structural Changes in Extremophile Rubredoxin at 120 °C.Angewandte Chemie (International ed. in English) · 2026Article
- Towards patient-relevant structures: reviewing body-temperature biological macromolecules and their ligands for pharmaceutical applications.Acta crystallographica. Section D, Structural biology · 2026Review
- Bayesian multi-state multi-condition modeling of a protein structure based on X-ray crystallography data.bioRxiv : the preprint server for biology · 2025Article
- Ten rules for a structural bioinformatic analysis.PLoS computational biology · 2025Article
- Temperature-Resolved Crystallography Reveals Rigid-Body Dominance over Local Flexibility in B‑Factors.ACS omega · 2025Article
- Evolution of macromolecular crystallography beamlines at the Swiss Light Source and SwissFEL.Journal of synchrotron radiation · 2025Article
- Probing the modulation of enzyme kinetics by multi-temperature, time-resolved serial crystallography.Nature communications · 2025Article
- Cryo2RT: a high-throughput method for room-temperature macromolecular crystallography from cryo-cooled crystals.Acta crystallographica. Section D, Structural biology · 2024Article
- Identifying protein conformational states in the Protein Data Bank: Toward unlocking the potential of integrative dynamics studies.Structural dynamics (Melville, N.Y.) · 2024Article
- Functional protein dynamics in a crystal.Nature communications · 2024Article
- Functional Protein Dynamics in a Crystal.bioRxiv : the preprint server for biology · 2024Article
- Cell phenotypes can be predicted from propensities of protein conformations.Current opinion in structural biology · 2023Review
- Representing structures of the multiple conformational states of proteins.Current opinion in structural biology · 2023Review
- Protein conformational ensembles in function: roles and mechanisms.RSC chemical biology · 2023Review
- Temperature as a modulator of allosteric motions and crosstalk in mesophilic and thermophilic enzymes.Frontiers in molecular biosciences · 2023Review
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6 authors.
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Abstract
Conformational ensembles underlie all protein functions. Thus, acquiring atomic-level ensemble models that accurately represent conformational heterogeneity is vital to deepen our understanding of how proteins work. Modeling ensemble information from X-ray diffraction data has been challenging, as traditional cryo-crystallography restricts conformational variability while minimizing radiation damage. Recent advances have enabled the collection of high quality diffraction data at ambient temperatures, revealing innate conformational heterogeneity and temperature-driven changes. Here, we used diffraction datasets for Proteinase K collected at temperatures ranging from 313 to 363 K to provide a tutorial for the refinement of multiconformer ensemble models. Integrating automated sampling and refinement tools with manual adjustments, we obtained multiconformer models that describe alternative backbone and sidechain conformations, their relative occupancies, and interconnections between conformers. Our models revealed extensive and diverse conformational changes across temperature, including increased bound peptide ligand occupancies, different Ca
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