About: In silico analysis of the cyanobacterial lectin scytovirin: new insights into binding properties

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About: In silico analysis of the cyanobacterial lectin scytovirin: new insights into binding properties Goto Sponge NotDistinct Permalink

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 analysis of the cyanobacterial lectin scytovirin: new insights into binding properties
Creator	Santos, Silva Alberdan, · Conceição De Souza, Rafael Evonnildo, · Gonçalves, Costa Gonçalves, Silva Júnior, Vianez Lima, Jerônimo Lídio Da, João Ranieri, Alex Santos Siqueira, Andrei
Source	Medline; PMC
abstract	Scytovirin is a lectin isolated from the cyanobacterium Scytonema varium that has shown activity against HIV, SARS coronavirus and Zaire Ebola virus. Its 95 amino acids are divided into two structural domains (SD), the first spanning amino acids 1–48 (SD1) and the second 49–95 (SD2). Interestingly, the domains are nearly identical but differ in their affinities for carbohydrates. With the aim of enhancing understanding of the binding properties of scytovirin, we performed molecular dynamics (MD) simulations of scytovirin complexed with Man4. We set up three systems: (i) Man4 bound to both domains (SD1 + SD2) using the full-length protein; (ii) Man4 bound to an incomplete protein, containing only SD1 and (iii) Man4 bound to an incomplete protein containing only SD2. Contrary to other reports, binding free energy results suggest that Man4 can bind simultaneously to SD1 and SD2 binding regions, but SD1 individually has the best values of energy and the best affinity for Man4. Decomposition of the binding free energy showed that the residues that interact with Man4 were different in the three systems, suggesting that the binding mechanism of Man4 varies between full-length protein, SD1 and SD2. The results presented here may help to formulate strategies to use scytovirin and promote mutagenesis studies to improve the antiviral activity of scytovirin.
has issue date	2017-07-29(xsd:dateTime)
bibo:doi	10.1007/s11033-017-4116-1
bibo:pmid	28756560
has license	no-cc
sha1sum (hex)	b9f90c37d0dca4e2f389333472a5dff18a39f64f
schema:url	https://doi.org/10.1007/s11033-017-4116-1
resource representing a document's title	In silico analysis of the cyanobacterial lectin scytovirin: new insights into binding properties
has PubMed Central identifier	PMC7088960
has PubMed identifier	28756560
schema:publication	Mol Biol Rep
resource representing a document's body	covid:b9f90c37d0dca4e2f389333472a5dff18a39f64f#body_text
is schema:about of	named entity 'lectin' named entity 'LECTIN' named entity 'STUDIES' named entity 'BINDING' named entity 'ANTIVIRAL ACTIVITY' named entity 'NEW' named entity 'IN SILICO ANALYSIS' named entity 'PROMOTE' named entity 'MUTAGENESIS' named entity 'INSIGHTS' named entity 'PROPERTIES' named entity 'antiviral activity' named entity 'scytovirin' named entity 'cyanobacterial' named entity 'disulfide' named entity 'protein' named entity 'conformation' named entity 'antiviral activity' named entity 'interact' named entity 'NMR studies' named entity 'Scytonema varium' named entity 'hydrogen atoms' named entity 'PDB2PQR' named entity 'cyanobacteria' named entity 'electrostatic force' named entity 'structural domains' named entity 'biologically active' named entity 'scytovirin' named entity 'molecular docking' named entity 'hydrogen bonds' named entity 'force field' named entity 'proteolytic' named entity 'Scytonema varium' named entity 'mammalian cells' named entity 'PDB' named entity 'scytovirin' named entity 'root mean square deviation' named entity 'cyanobacteria' named entity 'ligation' named entity 'RMSD' named entity '1, 2' named entity 'molecular dynamics' named entity 'virus' named entity 'scytovirin' named entity 'protein' named entity 'HIV' named entity 'protein' named entity 'protein' named entity 'interact' named entity 'protein' named entity 'conjugate gradients' named entity 'scytovirin' named entity 'thermostat' named entity 'carbohydrates' named entity 'step 13' named entity 'scytovirin' named entity 'lectin' named entity 'deglycosylation' named entity 'protein' named entity 'carbohydrates' named entity 'protonation' named entity 'Carbohydrate' named entity 'mannose' named entity 'cyanobacteria' named entity 'viral diseases' named entity 'Ewald method' named entity 'steepest descent' named entity 'soybean' named entity 'binding mechanism' named entity 'scytovirin' named entity 'Particle Mesh'

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