ArticleAdvances in bioinformatics2014
Secondary structure preferences of mn (2+) binding sites in bacterial proteins.
Article in Advances in bioinformatics, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 4 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
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.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
4 citing papers in PubMed, 10 citations in OpenAlex.
- Single nucleotide variants drive evolutionary phage-host arms race in anaerobic carbon dioxide-converting microbiome.Nature communications · 2026Article
- The core Cas1 protein of CRISPR-Cas I-B inCurrent research in microbial sciences · 2021Article
- Insights into the MnInternational journal of molecular sciences · 2020Article
- The influence of flanking secondary structures on amino Acid content and typical lengths of 3/10 helices.International journal of proteomics · 2014Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
1 author at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
3D structures of proteins with coordinated Mn(2+) ions from bacteria with low, average, and high genomic GC-content have been analyzed (149 PDB files were used). Major Mn(2+) binders are aspartic acid (6.82% of Asp residues), histidine (14.76% of His residues), and glutamic acid (3.51% of Glu residues). We found out that the motif of secondary structure "beta strand-major binder-random coil" is overrepresented around all the three major Mn(2+) binders. That motif may be followed by either alpha helix or beta strand. Beta strands near Mn(2+) binding residues should be stable because they are enriched by such beta formers as valine and isoleucine, as well as by specific combinations of hydrophobic and hydrophilic amino acid residues characteristic to beta sheet. In the group of proteins from GC-rich bacteria glutamic acid residues situated in alpha helices frequently coordinate Mn(2+) ions, probably, because of the decrease of Lys usage under the influence of mutational GC-pressure. On the other hand, the percentage of Mn(2+) sites with at least one amino acid in the "beta strand-major binder-random coil" motif of secondary structure (77.88%) does not depend on genomic GC-content.
Identifiers
What OpenQuestion holds
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.