ArticleAmino acids2021
How anisotropic and isotropic atomic displacement parameters monitor protein covalent bonds rigidity: isotropic B-factors underestimate bond rigidity.
Article in Amino acids, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 2 papers.
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2 citing papers in PubMed, 3 citations in OpenAlex.
- ATLAS: protein flexibility description from atomistic molecular dynamics simulations.Nucleic acids research · 2024Article
- Uses and Abuses of the Atomic Displacement Parameters in Structural Biology.Methods in molecular biology (Clifton, N.J.) · 2022Article
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1 author at 1 institution in 2 countries.
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Abstract
Under the assumption that covalent bonds are rigid, it is possible to compare the estimations of rigidity based on anisotropic and isotropic B-factors. This is done by computing the difference of the mean-square displacements (Delta-u) of atoms A and Z along the covalent bond A-Z, which must be close to zero for a rigid bond. The analysis of a high-quality set of protein structures, refined at a resolution better than (or equal to) 0.8 Angstroms, showed that Delta-u is significantly close to zero when anisotropic B-factors are used, with an average 60% Delta-u reduction. This reduction is larger for larger B-factors and this suggests that care should be taken in data-mining procedures that involve isotropic B-factors, especially at lower resolution, when anisotropic B-factors cannot be determined and when the average B-factor increases.
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