Modelling dynamics in protein crystal structures by ensemble refinement

By Tom Burnley, Pavel V. Afonine, Paul D. Adams, P. Gros. 2012

255 citations recorded by the source corpus.

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 by time-averaged refinement, where local molecular vibrations were sampled by molecular-dynamics (MD) simulation whilst global disorder was partitioned into an underlying overall translation–libration–screw (TLS) model. Modeling of 20 protein datasets at 1.1–3.1 Å resolution reduced cross-validated Rfree values by 0.3–4.9%, indicating that ensemble models fit the X-ray data better than single structures. The ensembles revealed that, while most proteins display a well-ordered core, some proteins exhibit a ‘molten core’ likely supporting functionally important dynamics in ligand binding, enzyme activity and protomer assembly. Order–disorder changes in HIV protease indicate a mechanism of entropy compensation for ordering the catalytic residues upon ligand binding by disordering specific core residues. Thus, ensemble refinement extracts dynamical details from the X-ray data that allow a more comprehensive understanding of structure–dynamics–function relationships. DOI: http://dx.doi.org/10.7554/eLife.00311.001

Subfields: Materials Chemistry, Molecular Biology

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Citations in the corpus

Macromolecular structure determination using X-rays, neutrons and electrons: recent developments in Phenix (2019, methodology): “(ii) Ensemble refinement (phenix.ensemble_refinement) combines crystallographic refinement with molecular dynamics to produce ensemble models fitted to diffraction data (Burnley et al., 2012).”
Flexible torsion-angle noncrystallographic symmetry restraints for improved macromolecular structure refinement (2014, result): “This observation is consistent with previous reports (Smart et al., 2012), and is also supported by the variation in TLS (translation, libration, screw-rotation) models observed for NCS-related chains in some cases (Burnley et al., 2012).”
Advances in methods for atomic resolution macromolecular structure determination (2020, background): “…can use experimental X-ray diffraction data to create models of alternative conformations or entire conformational ensembles is now available 132–136 , allowing crystallographers to maximize the amount of structural and biophysical information that can be accessed from data collected at…”
Meeting Review: Diffuse X-Ray Scattering to Model Protein Motions (2014, unknown): “…Elsevier Ltd All rights rese argued that diffuse scattering should be used to test TLS models, and Mark Wilson (Wilson, 2013) has noted that diffuse scattering could be used to develop and validate more detailed contact network (van den Bedem et al., 2013) or ensemble models (Burnley et al., 2012).”
Bringing diffuse X-ray scattering into focus (2017, methodology): “improve ensemble models derived from time-averaged refinement using the scheme by Gros and colleagues [43].”
Computational protein structure refinement: Almost there, yet still so far to go (2017, background): “, alternate conformations for flexible loops.(81) Computational refinement methods could in principle deliver such ensembles and comparisons could be made against crystallographic B-factors or NMRderived ensembles.”
Reprogramming homing endonuclease specificity through computational design and directed evolution (2013, background): “For example, libraries with full randomization of positions 18, 33, 59 and 68 yielded no high-surviving variants for position (cid:4) 4C, but a library with a motif lysine ﬁxed at position 33 (and randomization of the other three positions, as well as position 31) showed 46% survival after two…”