ArticleProtein science : a publication of the Protein Society2018
Determination of chemical identity and occupancy from experimental density maps.
Article in Protein science : a publication of the Protein Society, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 7 papers.
What it found
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Who cites it
7 citing papers in PubMed, 12 citations in OpenAlex.
- Recognizing lysine-cysteine crosslinks in proteins.Protein science : a publication of the Protein Society · 2021Article
- Local and global analysis of macromolecular atomic displacement parameters.Acta crystallographica. Section D, Structural biology · 2020Article
- Opportunities and challenges for assigning cofactors in cryo-EM density maps of chlorophyll-containing proteins.Communications biology · 2020Review
- Crystallographic identification of spontaneous oxidation intermediates and products of protein sulfhydryl groups.Protein science : a publication of the Protein Society · 2019Article
- Catalytic mechanism of DNA polymerases-Two metal ions or three?Protein science : a publication of the Protein Society · 2019Review
- Crystallographic evidence for two-metal-ion catalysis in human pol η.Protein science : a publication of the Protein Society · 2019Article
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Authors and funding
1 author at 1 institution in 1 country.
Funding
Abstract
Three basic electronic properties of molecules, electron density (ED), charge density (CD), and electrostatic potentials (ESP), are dependent on both atomic mobility and occupancy of components in the molecules. Small protein subunits may bind large macromolecular complexes with a reduced occupancy or an increased atomic mobility or both due to affinity-based functional regulation, and so may substrates, products, cofactors, ions or solvent molecule to the active sites of enzymes. A quantitative theory is presented in this study that describes the dependence of atomic functions on atomic B-factor in Fourier transforms of the corresponding maps. An application of this theory is described to an experimental ED map at 1.73-Å resolution, and to an experimental CD map at 2.2-Å resolution. All the three density functions are linearly proportional to occupancy when the structure factor F(000) term of Fourier transforms of experimental density maps is included. Upon application of this theory to both experimental CD and ESP maps recently reported for photosystem II-light harvesting complex II supercomplex at 3.2-Å resolution, the occupancy of two extrinsic protein subunits PsbQ and PsbP is determined to be 20.4 ± 0.2%, and the negative mean ESP value of vitreous ice displaced by the supercomplex on electron scattering path is estimated to be 3% of the mean ESP value of protein α-helices.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.