About: Continuous flexibility analysis of SARS-CoV-2 Spike prefusion structures

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

Attributes	Values
type	Academic Article research paper schema:ScholarlyArticle
isDefinedBy	Covid-on-the-Web dataset
has title	Continuous flexibility analysis of SARS-CoV-2 Spike prefusion structures
Creator	Wrapp, Daniel Mclellan, Jason Carazo, Jose-Maria Chacon, Pablo Conesa, Pablo Fonseca-Reyna, Yunior Foster, Brent Herreros, David Losana, Patricia Marabini, Roberto Martínez, Marta Melero, Roberto Ramírez-Aportela, Erney Sanchez-Garcia, Ruben Tagare, Hemant Vilas, José-Luis Carlos, Oscar Del Caño, Laura Sorzano,
topic	covid:6b2211981f70055d82db58a2aac87db2016b32e4#this
Source	BioRxiv; Medline; PMC
abstract	With the help of novel processing workflows and algorithms, we have obtained a better understanding of the flexibility and conformational dynamics of the SARS-CoV-2 spike in the prefusion state. We have re-analyzed previous cryo-EM data combining 3D clustering approaches with ways to explore a continuous flexibility space based on 3D Principal Component Analysis. These advanced analyses revealed a concerted motion involving the receptor-binding domain (RBD), N-terminal domain (NTD), and subdomain 1 and 2 (SD1 & SD2) around the previously characterized 1-RBD-up state, which have been modeled as elastic deformations. We show that in this dataset there are not well-defined, stable, spike conformations, but virtually a continuum of states moving in a concerted fashion. We obtained an improved resolution ensemble map with minimum bias, from which we model by flexible fitting the extremes of the change along the direction of maximal variance. Moreover, a high-resolution structure of a recently described biochemically stabilized form of the spike is shown to greatly reduce the dynamics observed for the wild-type spike. Our results provide new detailed avenues to potentially restrain the spike dynamics for structure-based drug and vaccine design and at the same time give a warning of the potential image processing classification instability of these complicated datasets, having a direct impact on the interpretability of the results.
has issue date	2020-07-08(xsd:dateTime)
bibo:doi	10.1101/2020.07.08.191072
bibo:pmid	32676604
has license	cc-by-nc-nd
sha1sum (hex)	6b2211981f70055d82db58a2aac87db2016b32e4
schema:url	https://doi.org/10.1101/2020.07.08.191072
resource representing a document's title	Continuous flexibility analysis of SARS-CoV-2 Spike prefusion structures
has PubMed Central identifier	PMC7359526
has PubMed identifier	32676604
schema:publication	bioRxiv
resource representing a document's body	covid:6b2211981f70055d82db58a2aac87db2016b32e4#body_text
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