ArticleJournal of molecular modeling2013
Investigation by MD simulation of the key residues related to substrate-binding and heme-release in human ferrochelatase.
Article in Journal of molecular modeling, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 5 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
5 citing papers in PubMed, 10 citations in OpenAlex.
- Impact of Phosphorylation at Various Sites on the Active Pocket of Human Ferrochelatase: Insights from Molecular Dynamics Simulations.International journal of molecular sciences · 2024Article
- Structural aspects of enzymes involved in prokaryotic Gram-positive heme biosynthesis.Computational and structural biotechnology journal · 2023Review
- Ferrochelatase: Mapping the Intersection of Iron and Porphyrin Metabolism in the Mitochondria.Frontiers in cell and developmental biology · 2022Review
- Insight into the function of active site residues in the catalytic mechanism of human ferrochelatase.The Biochemical journal · 2021Article
- Ferrochelatase π-helix: Implications from examining the role of the conserved π-helix glutamates in porphyrin metalation and product release.Archives of biochemistry and biophysics · 2018Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
4 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Molecular dynamics (MD) simulations of three models based on the crystal structure of the E343K variant of human ferrochelatase were performed in this study. The "open" and "closed" conformations of the enzyme obtained by simulations are in agreement with the corresponding crystal structures. The snapshots and the structure analysis indicate that alterations of the hydrogen bonds and the positions of E347 and E351 lead to a conformational change in the π-helix. The hydrogen bonded form of residue R164 could be regarded as a signal indicating alteration of the active site conformation. When R164 forms a hydrogen bond with D95, the active site is closed, and when a hydrogen bond is formed with E171, the active site is open. Interestingly, the protoporphyrin with Fe(2+) is observed to move noticeably out of the enzyme while the protoporphyrin lacking Fe(2+) remains almost fixed. Alterations of the hydrogen bonds between the propionate of the heme and R115, K118 and S303 trigger movement of the heme out of the active site. Residues E347 and E351, which are located on the π-helix and form an acidic path leading to a salt bridge interaction with the propionate of the heme, accelerate the release process.
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.