ArticleScientific reports2016
Conformational Dynamics, Ligand Binding and Effects of Mutations in NirE an S-Adenosyl-L-Methionine Dependent Methyltransferase.
Article in Scientific reports, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 19 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
19 citing papers in PubMed, 39 citations in OpenAlex.
- Identifying potential binding sites for complex formation between Tyrosyl-DNA phosphodiesterase 1 and poly [ADP-ribose] polymerase 1.Physical chemistry chemical physics : PCCP · 2026Article
- ALG3 as a PanCancer Oncogene: Bioinformatics Analysis and Identification of Small-Molecule Inhibitors.Anti-cancer agents in medicinal chemistry · 2026Article
- Computational studies on the functional and structural impact of pathogenic mutations in enzymes.Protein science : a publication of the Protein Society · 2025Review
- CryoEM and crystal structure analyses reveal the indirect role played by Trp89 in glutamate dehydrogenase enzymatic reactions.The FEBS journal · 2025Article
- Design and immunogenic evaluation of multi-epitope vaccines for colorectal cancer: insights from molecular dynamics andFrontiers in oncology · 2025Article
- H-NOX Influences Biofilm Formation, Central Metabolism, and Quorum Sensing inJournal of proteome research · 2024Article
- Mut-Map: Comprehensive Computational Pipeline for Structural Mapping and Analysis of Cancer-Associated Mutations.Briefings in bioinformatics · 2024Article
- Article
- Unveiling the Multifaceted Capabilities of EndophyticPharmaceuticals (Basel, Switzerland) · 2024Article
- Article
- Deciphering Molecular Aspects of PotentialMetabolites · 2023Article
- In Silico Discovery of Potential Inhibitors Targeting the RNA Binding Loop of ADAR2 and 5-HT2CR from Traditional Chinese Natural Compounds.International journal of molecular sciences · 2023Article
- Integration of Chemoinformatics and Multi-Omics Analysis Defines ECT2 as a Potential Target for Cancer Drug Therapy.Biology · 2023Article
- Cheminformatics-Based Study Identifies Potential Ebola VP40 Inhibitors.International journal of molecular sciences · 2023Article
- Molecular and Biological Investigation of Isolated Marine Fungal Metabolites as Anticancer Agents: A Multi-Target Approach.Metabolites · 2023Article
- Insilico drug repurposing using FDA approved drugs against Membrane protein of SARS-CoV-2.Journal of pharmaceutical sciences · 2021Article
- Investigating molecular interactions between oxidized neuroglobin and cytochrome c.Scientific reports · 2018Article
- Effects of Mutations on Structure-Function Relationships of Matrix Metalloproteinase-1.International journal of molecular sciences · 2016Article
- Characterization of molecular interactions between Escherichia coli RNA polymerase and topoisomerase I by molecular simulations.FEBS letters · 2016Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
6 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Heme d1, a vital tetrapyrrol involved in the denitrification processes is synthesized from its precursor molecule precorrin-2 in a chemical reaction catalysed by an S-adenosyl-L-methionine (SAM) dependent Methyltransferase (NirE). The NirE enzyme catalyses the transfer of a methyl group from the SAM to uroporphyrinogen III and serves as a novel potential drug target for the pharmaceutical industry. An important insight into the structure-activity relationships of NirE has been revealed by elucidating its crystal structure, but there is still no understanding about how conformational flexibility influences structure, cofactor and substrate binding by the enzyme as well as the structural effects of mutations of residues involved in binding and catalysis. In order to provide this missing but very important information we performed a comprehensive atomistic molecular dynamics study which revealed that i) the binding of the substrate contributes to the stabilization of the structure of the full complex; ii) conformational changes influence the orientation of the pyrrole rings in the substrate, iii) more open conformation of enzyme active site to accommodate the substrate as an outcome of conformational motions; and iv) the mutations of binding and active site residues lead to sensitive structural changes which influence binding and catalysis.
Indexed as
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.