About: Structural insights into type I and type II of nsp4 porcine reproductive and respiratory syndrome virus (nsp4 PRRSV) by molecular dynamics simulations

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About: Structural insights into type I and type II of nsp4 porcine reproductive and respiratory syndrome virus (nsp4 PRRSV) by molecular dynamics simulations Goto Sponge NotDistinct Permalink

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

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type	Academic Article research paper schema:ScholarlyArticle
isDefinedBy	Covid-on-the-Web dataset
has title	Structural insights into type I and type II of nsp4 porcine reproductive and respiratory syndrome virus (nsp4 PRRSV) by molecular dynamics simulations
Creator	Aeksiri, Niran Jantafong, Tippawan
Source	Elsevier; Medline; PMC
abstract	Porcine reproductive and respiratory virus (PRRSV) causes major economic concerns for the swine industry worldwide. We have performed molecular dynamics simulations (MD) and principle component analysis (PCA) to investigate the role of the catalytic triad and conformational dynamics of type I and type II of nsp4 PRRSV. The results showed that the RMSF of residues 136–142 near the active site of all models was highly flexible. Moreover, we identified the effect of single structural mutations of the catalytic triad. The percentage of residue with a 0.1 nm RMSF value and PCA results revealed that the mutations affected domain I and II suggesting the wild types were more stable than the mutants. At the catalytic triad, the distances between H39 and S118 were very flexible while the distances between H39 and D64 were very stable. H39, D64 and S118 showed high occupancy percentage of the hydrogen bond interaction with many residues that are conserved in PRRSVAS, PRRSVES, LDVC, LDVP and EAV. Moreover, S118 of wild-type protein formed H-bonds with T134 and G135 but these interactions were lost in PRRSVAV (S118A) and PRRSVES (S117A) indicating that the substitution of important H-bond interaction in PRRSVAS (S118A) and PRRSVES (S117A) affected the flexibility around the catalytic triad, conformation and proteolytic activity. Overall, our study may provide the structural basic of the catalytic triad and be useful for testing the protein activity in future experiments.
has issue date	2017-03-24(xsd:dateTime)
bibo:doi	10.1016/j.jmgm.2017.03.015
bibo:pmid	28411461
has license	no-cc
sha1sum (hex)	405a2c2f0fd4e5b8bf8692a9728df332f9b89625
schema:url	https://doi.org/10.1016/j.jmgm.2017.03.015
resource representing a document's title	Structural insights into type I and type II of nsp4 porcine reproductive and respiratory syndrome virus (nsp4 PRRSV) by molecular dynamics simulations
has PubMed Central identifier	PMC7110526
has PubMed identifier	28411461
schema:publication	J Mol Graph Model
resource representing a document's body	covid:405a2c2f0fd4e5b8bf8692a9728df332f9b89625#body_text
is schema:about of	named entity 'TYPE I' named entity 'NSP4' named entity 'catalytic triad' named entity 'The' named entity 'domain' named entity 'type I' named entity 'type II' named entity 'INSIGHTS' named entity 'PCA' named entity 'MODELS' named entity 'TYPE I' named entity 'HIGHLY' named entity 'INDUSTRY' named entity 'PERFORMED' named entity 'RESPIRATORY VIRUS' named entity 'TO INVESTIGATE' named entity 'HYDROGEN BOND' named entity 'AFFECTED' named entity 'MUTATIONS' named entity '136' named entity 'PRINCIPLE COMPONENT' named entity 'MOLECULAR DYNAMICS SIMULATIONS' named entity 'D64' named entity 'STABLE' named entity 'CONCERNS' named entity 'PROVIDE' named entity 'TYPE II' named entity 'OCCUPANCY' named entity 'IDENTIFIED' named entity 'PROTEIN ' named entity 'OUR' named entity 'PROTEOLYTIC ACTIVITY' named entity 'WORLDWIDE' named entity 'RESIDUE' named entity 'ROLE' named entity 'WILD' named entity 'FLEXIBILITY' named entity 'INTERACTION' named entity 'SWINE' named entity 'CAUSES' named entity 'INTERACTIONS' named entity 'SINGLE' named entity 'VALUE' named entity 'TYPE II' named entity 'NSP4' named entity 'FORMED' named entity 'RMSF' named entity 'STUDY' named entity 'SITE OF' named entity 'HIGH' named entity 'TYPES' named entity 'H39' named entity 'MAJOR' named entity 'T134' named entity 'MOLECULAR DYNAMICS SIMULATIONS' named entity 'DOMAIN' named entity 'DISTANCES' named entity 'PROTEIN ACTIVITY' named entity 'PERCENTAGE' named entity 'PRRSV' named entity 'ECONOMIC' named entity 'EFFECT' named entity 'RESULTS' named entity 'STRUCTURAL' named entity 'INDICATING' named entity 'WILD-TYPE' named entity 'ACTIVE SITE' named entity 'PORCINE REPRODUCTIVE AND RESPIRATORY SYNDROME VIRUS' named entity 'NEAR' named entity 'DYNAMICS' named entity 'REPRODUCTIVE' named entity 'THESE' named entity 'USEFUL' named entity 'BUT' named entity 'ANALYSIS' named entity 'EXPERIMENTS' named entity 'PORCINE' named entity 'SUBSTITUTION' named entity 'BASIC' named entity 'TESTING'

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