SrasV1, Ncbi, Merge, bibRecord, 002E37

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

Identifieur interne : 002E37 ( Ncbi/Merge ); précédent : 002E36; suivant : 002E38

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

Auteurs : Andrei Santos Siqueira [Brésil] ; Alex Ranieri Jerônimo Lima [Brésil] ; Rafael Conceição De Souza [Brésil] ; Alberdan Silva Santos [Brésil] ; João Lídio Da Silva Gonçalves Vianez Júnior [Brésil] ; Evonnildo Costa Gonçalves [Brésil]

Source :

Molecular biology reports [ 1573-4978 ] ; 2017.

RBID : pubmed:28756560

Descripteurs français

English descriptors

KwdEn :
- Amino Acid Sequence, Bacteria (metabolism), Bacterial Proteins (chemistry), Bacterial Proteins (genetics), Bacterial Proteins (metabolism), Carrier Proteins (chemistry), Carrier Proteins (genetics), Carrier Proteins (metabolism), Computer Simulation, Cyanobacteria (metabolism), Lectins (chemistry), Lectins (genetics), Lectins (metabolism), Membrane Proteins, Protein Binding, Protein Conformation, Protein Structural Elements.
MESH :
- chemical , chemistry : Bacterial Proteins, Carrier Proteins, Lectins.
- chemical , genetics : Bacterial Proteins, Carrier Proteins, Lectins.
- metabolism : Bacteria, Bacterial Proteins, Carrier Proteins, Cyanobacteria, Lectins.
- Amino Acid Sequence, Computer Simulation, Membrane Proteins, Protein Binding, Protein Conformation, Protein Structural Elements.

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.

DOI: 10.1007/s11033-017-4116-1
PubMed: 28756560

Links toward previous steps (curation, corpus...)

to stream PubMed, to step Corpus: 000A91
to stream PubMed, to step Curation: 000A91
to stream PubMed, to step Checkpoint: 000B07

Links to Exploration step

pubmed:28756560

Le document en format XML

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<term>Lectines ()</term>
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<term>Lectines (métabolisme)</term>
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<front><div type="abstract" xml:lang="en">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.</div>
</front>
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<Abstract><AbstractText>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.</AbstractText>
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In silico analysis of the cyanobacterial lectin scytovirin: new insights into binding properties.

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

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