How anisotropic and isotropic atomic displacement parameters monitor protein covalent bonds rigidity: isotropic B-factors underestimate bond rigidity
Copyright policy )How anisotropic and isotropic atomic displacement parameters monitor protein covalent bonds rigidity: isotropic B-factors underestimate bond rigidity
AbstractUnder 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.
- University of Pavia Italy
- UNIVERSITA DEGLI STUDI DI PAVIA Italy
- University of Vienna Austria
- Universität Wien Austria
- Universität Wien Austria
Models, Molecular, Atomic displacement parameter, Crystallography, Short Communication, Molecular, B-factor, Proteins, 106041 Structural biology, 106041 Strukturbiologie, Crystallography, X-Ray, Hirshfeld rigidity test, CD-HIT, Covalent bond, Models, RESTRAINTS, X-Ray, Protein structure, Anisotropy, Atomic resolution
Models, Molecular, Atomic displacement parameter, Crystallography, Short Communication, Molecular, B-factor, Proteins, 106041 Structural biology, 106041 Strukturbiologie, Crystallography, X-Ray, Hirshfeld rigidity test, CD-HIT, Covalent bond, Models, RESTRAINTS, X-Ray, Protein structure, Anisotropy, Atomic resolution
citations This is an alternative to the "Influence" indicator, which also reflects the overall/total impact of an article in the research community at large, based on the underlying citation network (diachronically).3 popularity This indicator reflects the "current" impact/attention (the "hype") of an article in the research community at large, based on the underlying citation network.Top 10% influence This indicator reflects the overall/total impact of an article in the research community at large, based on the underlying citation network (diachronically).Average impulse This indicator reflects the initial momentum of an article directly after its publication, based on the underlying citation network.Average
Citations provided by BIP!Popularity provided by BIP!