ArticleJournal of molecular modeling2012
In silico investigations of possible routes of assembly of ORF 3a from SARS-CoV.
Article in Journal of molecular modeling, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 13 papers.
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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
13 citing papers in PubMed, 26 citations in OpenAlex.
- Article
- Viral channel forming proteins--How to assemble and depolarize lipid membranes in silico.Biochimica et biophysica acta · 2016Review
- Membrane protein assembly: two cytoplasmic phosphorylated serine sites of Vpu from HIV-1 affect oligomerization.Scientific reports · 2016Article
- Targeting the Channel Activity of Viroporins.Advances in protein chemistry and structural biology · 2016Review
- Genotype-specific differences in structural features of hepatitis C virus (HCV) p7 membrane protein.Biochimica et biophysica acta · 2015Article
- Structure based computational assessment of channel properties of assembled ORF-8a from SARS-CoV.Proteins · 2015Article
- Modeling the structure of SARS 3a transmembrane protein using a minimum unfavorable contact approach.Journal of chemical sciences (Bangalore, India) · 2015Article
- Computational Docking Study of p7 Ion Channel from HCV Genotype 3 and Genotype 4 and Its Interaction with Natural Compounds.PloS one · 2015Article
- Atomistic detailed mechanism and weak cation-conducting activity of HIV-1 Vpu revealed by free energy calculations.PloS one · 2014Article
- Article
- Assembling an ion channel: ORF 3a from SARS-CoV.Biopolymers · 2013Article
- Computational modeling of the p7 monomer from HCV and its interaction with small molecule drugs.SpringerPlus · 2013Article
- Mechanism of function of viral channel proteins and implications for drug development.International review of cell and molecular biology · 2012Review
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
2 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
ORF 3a of human severe acute respiratory syndrome corona virus (SARS-CoV) has been identified as a 274 amino acid membrane protein. When expressed in Xenopus oocytes the protein forms channels. Based on bioinformatics approaches the topology has been identified to include three transmembrane domains (TMDs). Since structural models from experiments are still lacking, computational methods can be challenged to generate such models. In this study, a 'sequential approach' for the assembly is proposed in which the individual TMDs are assembled one by one. This protocol is compared with a concerted protocol in which all TMDs are assembled simultaneously. The role of the loops between the TMDs during assembly of the monomers into a bundle is investigated. Molecular dynamics simulations for 20 ns are performed as a short equilibration to assess the bundle stability in a lipid environment. The results suggest that bundles are likely with the second TMD facing the putative pore. All the putative bundles show water molecules trapped within the lumen of the pore with only occasional events of complete crossing.
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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.