About: In silico investigations of possible routes of assembly of ORF 3a from SARS-CoV

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An Entity of Type : schema:ScholarlyArticle, within Data Space : wasabi.inria.fr associated with source document(s)

Attributes	Values
type	Academic Article research paper schema:ScholarlyArticle
isDefinedBy	Covid-on-the-Web dataset
has title	In silico investigations of possible routes of assembly of ORF 3a from SARS-CoV
Creator	Hsu, Hao-Jen Fischer, Wolfgang
Source	Medline; PMC
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. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1007/s00894-011-1092-6) contains supplementary material, which is available to authorized users.
has issue date	2011-05-04(xsd:dateTime)
bibo:doi	10.1007/s00894-011-1092-6
bibo:pmid	21541740
has license	no-cc
sha1sum (hex)	039b533e7611877bbac1bb21650fa324fdfccb8c
schema:url	https://doi.org/10.1007/s00894-011-1092-6
resource representing a document's title	In silico investigations of possible routes of assembly of ORF 3a from SARS-CoV
has PubMed Central identifier	PMC7087964
has PubMed identifier	21541740
schema:publication	J Mol Model
resource representing a document's body	covid:039b533e7611877bbac1bb21650fa324fdfccb8c#body_text
is schema:about of	named entity 'events' named entity 'expressed' named entity 'protocol' named entity 'simulations' named entity 'membrane protein' named entity 'VIRUS' named entity 'BIOINFORMATICS' named entity 'ROLE' named entity 'WATER MOLECULES' named entity 'XENOPUS OOCYTES' named entity 'APPROACHES' named entity 'SECOND' named entity 'LOOPS' named entity 'ORF' named entity 'CHANNELS' named entity 'EVENTS' named entity 'INCLUDE' named entity 'PERFORMED' named entity 'IDENTIFIED' named entity 'COMPLETE' named entity 'PROTOCOL' named entity 'BUNDLE' named entity 'SIMULTANEOUSLY' named entity 'MOLECULAR DYNAMICS SIMULATIONS' named entity 'OCCASIONAL' named entity 'STRUCTURAL MODELS' named entity 'COMPUTATIONAL' named entity 'FORMS' named entity 'PROTEIN ' named entity 'SUGGEST' named entity 'EQUILIBRATION' named entity 'COMPARED' named entity 'INDIVIDUAL' named entity 'STUDY' named entity 'ENVIRONMENT' named entity 'SARS-COV' named entity 'ROUTES' named entity 'TRAPPED' named entity 'BASED' named entity 'SEVERE ACUTE RESPIRATORY SYNDROME' named entity 'CROSSING' named entity 'EXPRESSED' named entity 'ASSEMBLY' named entity 'SHORT' named entity 'TMD' named entity 'TOPOLOGY' named entity 'TRANSMEMBRANE' named entity 'MEMBRANE PROTEIN' named entity 'POSSIBLE' named entity 'INVESTIGATIONS' named entity 'A LIPID' named entity 'ORF' named entity 'ASSEMBLY' named entity 'GENERATE' named entity 'INVESTIGATED' named entity 'MONOMERS' named entity 'CORONA' named entity 'MODELS' named entity 'ASSESS' named entity 'EXPERIMENTS' named entity 'LACKING' named entity 'APPROACH' named entity 'LUMEN' named entity 'A 274' named entity 'HUMAN' named entity 'IN SILICO' named entity 'LIKELY' named entity 'PORE' named entity 'AMINO ACID' named entity 'METHODS' named entity 'PROPOSED' named entity 'RESULTS' named entity 'STABILITY' covid:arg/039b533e7611877bbac1bb21650fa324fdfccb8c named entity 'channels' named entity 'human' named entity 'assess' named entity 'simultaneously' named entity 'acid' named entity 'assembled'

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