Evidence map›Paper›PMID 33327448›Full record

ArticleInternational journal of molecular sciences2020

Conformation of the Intermediates in the Reaction Catalyzed by Protoporphyrinogen Oxidase: An In Silico Analysis.

Abigail L Barker, Hamlin Barnes, Franck E Dayan

Open access · goldAbstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in International journal of molecular sciences, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 2 papers.

0numbers the graph read from it
0cells of the map it votes in
2citing papers in PubMed
0.4field-weighted citation impact, top 39% of its field
1 · What the graph read from it

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.

2 · The registry

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.

3 · Its place in the literature

Who cites it

2 citing papers in PubMed, 7 citations in OpenAlex.

  1. The Physical Chemistry and Chemical Physics (PCCP) Section of theInternational journal of molecular sciences · 2021
    Article
  2. Advances in the Chemistry of Porphyrins and Related Macrocycles.International journal of molecular sciences · 2021
    Article
4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

3 authors at 1 institution in 1 country.

Abigail L BarkerAgricultural Biology Department, Colorado State University, Fort Collins, CO 80523, USA.ORCID 0000-0003-2806-4148
Hamlin BarnesAgricultural Biology Department, Colorado State University, Fort Collins, CO 80523, USA.
Franck E DayanAgricultural Biology Department, Colorado State University, Fort Collins, CO 80523, USA.ORCID 0000-0001-6964-2499
Colorado State University · US

Funding

No grant is acknowledged in the PubMed record.

6 · The paper itself

Abstract

Protoporphyrinogen oxidase (PPO) is a critical enzyme across life as the last common step in the synthesis of many metalloporphyrins. The reaction mechanism of PPO was assessed in silico and the unstructured loop near the binding pocket was investigated. The substrate, intermediates, and product were docked in the catalytic domain of PPO using a modified Autodock method, introducing flexibility in the macrocycles. Sixteen PPO protein sequences across phyla were aligned and analyzed with Phyre2 and ProteinPredict to study the unstructured loop from residue 204-210 in the

Indexed as

CatalysisComputer SimulationProtoporphyrinogen OxidaseProtoporphyrinsTetrapyrrolesProtoporphyrinogen OxidaseProtoporphyrinsTetrapyrrolesdocking of tetrapyrrole macrocyclesLennard-Jones forcesreaction mechanism

Identifiers

PMID33327448
PMCPMC7764921
OpenAlexW3111122862

What OpenQuestion holds

Textmetadata
LicenceCC BY
Read underepoch 390

Registered trials

None linked

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.