ArticleThe journal of physical chemistry. B2014
Aligning experimental and theoretical anisotropic B-factors: water models, normal-mode analysis methods, and metrics.
Article in The journal of physical chemistry. B, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 4 papers.
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4 citing papers in PubMed.
- Explicit versus implicit consideration of binding partners in protein-protein complex to elucidate intrinsic dynamics.Biophysical reviews · 2022Review
- Predicting Protein Functional Motions: an Old Recipe with a New Twist.Biophysical journal · 2020Article
- Transferable aspherical atom model refinement of protein and DNA structures against ultrahigh-resolution X-ray data.Acta crystallographica. Section D, Structural biology · 2016Article
- Molecular dynamics simulation of triclinic lysozyme in a crystal lattice.Protein science : a publication of the Protein Society · 2016Article
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2 authors.
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Abstract
The strength of X-ray crystallography in providing the information for protein dynamics has been under appreciated. The anisotropic B-factors (ADPs) from high-resolution structures are invaluable in studying the relationship among structure, dynamics, and function. Here, starting from an in-depth evaluation of the metrics used for comparing the overlap between two ellipsoids, we applied normal-mode analysis (NMA) to predict the theoretical ADPs and then align them with experimental results. Adding an extra layer of explicitly treated water on protein surface significantly improved the energy minimization results and better reproduced the anisotropy of experimental ADPs. In comparing experimental and theoretical ADPs, we focused on the overlap in shape, the alignment of dominant directions, and the similarity in magnitude. The choices of water molecules, NMA methods, and the metrics for evaluating the overlap of ADPs determined final results. This study provides useful information for exploring the physical basis and the application potential of experimental ADPs.
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