In silico analysis of the cyanobacterial lectin scytovirin: new insights into binding properties.
Identifieur interne : 000E18 ( Main/Exploration ); précédent : 000E17; suivant : 000E19In 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.
Descripteurs français
- KwdFr :
- Bactéries (métabolisme), Conformation des protéines, Cyanobactéries (métabolisme), Lectines (), Lectines (génétique), Lectines (métabolisme), Liaison aux protéines, Protéines bactériennes (), Protéines bactériennes (génétique), Protéines bactériennes (métabolisme), Protéines de transport (), Protéines de transport (génétique), Protéines de transport (métabolisme), Protéines membranaires, Simulation numérique, Séquence d'acides aminés, Éléments structuraux des protéines.
- MESH :
- génétique : Lectines, Protéines bactériennes, Protéines de transport.
- métabolisme : Bactéries, Cyanobactéries, Lectines, Protéines bactériennes, Protéines de transport.
- Conformation des protéines, Lectines, Liaison aux protéines, Protéines bactériennes, Protéines de transport, Protéines membranaires, Simulation numérique, Séquence d'acides aminés, Éléments structuraux des protéines.
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
Affiliations:
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Instituto de Ciências Biológicas, Universidade Federal do Pará, Belem, Pará, Brazil. andrei.siqueira@icb.ufpa.br.</nlm:affiliation><country xml:lang="fr">Brésil</country><wicri:regionArea>Laboratório de Tecnologia Biomolecular - Instituto de Ciências Biológicas, Universidade Federal do Pará, Belem, Pará</wicri:regionArea><placeName><region type="state">Pará</region></placeName></affiliation></author><author><name sortKey="Lima, Alex Ranieri Jeronimo" sort="Lima, Alex Ranieri Jeronimo" uniqKey="Lima A" first="Alex Ranieri Jerônimo" last="Lima">Alex Ranieri Jerônimo Lima</name><affiliation wicri:level="2"><nlm:affiliation>Laboratório de Tecnologia Biomolecular - Instituto de Ciências Biológicas, Universidade Federal do Pará, Belem, Pará, Brazil.</nlm:affiliation><country xml:lang="fr">Brésil</country><wicri:regionArea>Laboratório de Tecnologia Biomolecular - Instituto de Ciências Biológicas, Universidade Federal do Pará, Belem, Pará</wicri:regionArea><placeName><region type="state">Pará</region></placeName></affiliation></author><author><name sortKey="De Souza, Rafael Conceicao" sort="De Souza, Rafael Conceicao" uniqKey="De Souza R" first="Rafael Conceição" last="De Souza">Rafael Conceição De Souza</name><affiliation wicri:level="2"><nlm:affiliation>Laboratórios de Investigação Sistemática em Biotecnologia e Biodiversidade Molecular - Instituto de Ciências Exatas e Naturais, Universidade Federal do Pará, Belem, Pará, Brazil.</nlm:affiliation><country xml:lang="fr">Brésil</country><wicri:regionArea>Laboratórios de Investigação Sistemática em Biotecnologia e Biodiversidade Molecular - Instituto de Ciências Exatas e Naturais, Universidade Federal do Pará, Belem, Pará</wicri:regionArea><placeName><region type="state">Pará</region></placeName></affiliation></author><author><name sortKey="Santos, Alberdan Silva" sort="Santos, Alberdan Silva" uniqKey="Santos A" first="Alberdan Silva" last="Santos">Alberdan Silva Santos</name><affiliation wicri:level="2"><nlm:affiliation>Laboratórios de Investigação Sistemática em Biotecnologia e Biodiversidade Molecular - Instituto de Ciências Exatas e Naturais, Universidade Federal do Pará, Belem, Pará, Brazil.</nlm:affiliation><country xml:lang="fr">Brésil</country><wicri:regionArea>Laboratórios de Investigação Sistemática em Biotecnologia e Biodiversidade Molecular - Instituto de Ciências Exatas e Naturais, Universidade Federal do Pará, Belem, Pará</wicri:regionArea><placeName><region type="state">Pará</region></placeName></affiliation></author><author><name sortKey="Vianez Junior, Joao Lidio Da Silva Goncalves" sort="Vianez Junior, Joao Lidio Da Silva Goncalves" uniqKey="Vianez Junior J" first="João Lídio Da Silva Gonçalves" last="Vianez Júnior">João Lídio Da Silva Gonçalves Vianez Júnior</name><affiliation wicri:level="2"><nlm:affiliation>Centro de Inovações Tecnológicas - Instituto Evandro Chagas, Ananindeua, Pará, Brazil.</nlm:affiliation><country xml:lang="fr">Brésil</country><wicri:regionArea>Centro de Inovações Tecnológicas - Instituto Evandro Chagas, Ananindeua, Pará</wicri:regionArea><placeName><region type="state">Pará</region></placeName></affiliation></author><author><name sortKey="Goncalves, Evonnildo Costa" sort="Goncalves, Evonnildo Costa" uniqKey="Goncalves E" first="Evonnildo Costa" last="Gonçalves">Evonnildo Costa Gonçalves</name><affiliation wicri:level="2"><nlm:affiliation>Laboratório de Tecnologia Biomolecular - Instituto de Ciências Biológicas, Universidade Federal do Pará, Belem, Pará, Brazil.</nlm:affiliation><country xml:lang="fr">Brésil</country><wicri:regionArea>Laboratório de Tecnologia Biomolecular - Instituto de Ciências Biológicas, Universidade Federal do Pará, Belem, Pará</wicri:regionArea><placeName><region type="state">Pará</region></placeName></affiliation></author></analytic><series><title level="j">Molecular biology reports</title><idno type="eISSN">1573-4978</idno><imprint><date when="2017" type="published">2017</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>Amino Acid Sequence</term><term>Bacteria (metabolism)</term><term>Bacterial Proteins (chemistry)</term><term>Bacterial Proteins (genetics)</term><term>Bacterial Proteins (metabolism)</term><term>Carrier Proteins (chemistry)</term><term>Carrier Proteins (genetics)</term><term>Carrier Proteins (metabolism)</term><term>Computer Simulation</term><term>Cyanobacteria (metabolism)</term><term>Lectins (chemistry)</term><term>Lectins (genetics)</term><term>Lectins (metabolism)</term><term>Membrane Proteins</term><term>Protein Binding</term><term>Protein Conformation</term><term>Protein Structural Elements</term></keywords><keywords scheme="KwdFr" xml:lang="fr"><term>Bactéries (métabolisme)</term><term>Conformation des protéines</term><term>Cyanobactéries (métabolisme)</term><term>Lectines ()</term><term>Lectines (génétique)</term><term>Lectines (métabolisme)</term><term>Liaison aux protéines</term><term>Protéines bactériennes ()</term><term>Protéines bactériennes (génétique)</term><term>Protéines bactériennes (métabolisme)</term><term>Protéines de transport ()</term><term>Protéines de transport (génétique)</term><term>Protéines de transport (métabolisme)</term><term>Protéines membranaires</term><term>Simulation numérique</term><term>Séquence d'acides aminés</term><term>Éléments structuraux des protéines</term></keywords><keywords scheme="MESH" type="chemical" qualifier="chemistry" xml:lang="en"><term>Bacterial Proteins</term><term>Carrier Proteins</term><term>Lectins</term></keywords><keywords scheme="MESH" type="chemical" qualifier="genetics" xml:lang="en"><term>Bacterial Proteins</term><term>Carrier Proteins</term><term>Lectins</term></keywords><keywords scheme="MESH" qualifier="génétique" xml:lang="fr"><term>Lectines</term><term>Protéines bactériennes</term><term>Protéines de transport</term></keywords><keywords scheme="MESH" qualifier="metabolism" xml:lang="en"><term>Bacteria</term><term>Bacterial Proteins</term><term>Carrier Proteins</term><term>Cyanobacteria</term><term>Lectins</term></keywords><keywords scheme="MESH" qualifier="métabolisme" xml:lang="fr"><term>Bactéries</term><term>Cyanobactéries</term><term>Lectines</term><term>Protéines bactériennes</term><term>Protéines de transport</term></keywords><keywords scheme="MESH" xml:lang="en"><term>Amino Acid Sequence</term><term>Computer Simulation</term><term>Membrane Proteins</term><term>Protein Binding</term><term>Protein Conformation</term><term>Protein Structural Elements</term></keywords><keywords scheme="MESH" xml:lang="fr"><term>Conformation des protéines</term><term>Lectines</term><term>Liaison aux protéines</term><term>Protéines bactériennes</term><term>Protéines de transport</term><term>Protéines membranaires</term><term>Simulation numérique</term><term>Séquence d'acides aminés</term><term>Éléments structuraux des protéines</term></keywords></textClass></profileDesc></teiHeader><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></TEI><affiliations><list><country><li>Brésil</li></country><region><li>Pará</li></region></list><tree><country name="Brésil"><region name="Pará"><name sortKey="Siqueira, Andrei Santos" sort="Siqueira, Andrei Santos" uniqKey="Siqueira A" first="Andrei Santos" last="Siqueira">Andrei Santos Siqueira</name></region><name sortKey="De Souza, Rafael Conceicao" sort="De Souza, Rafael Conceicao" uniqKey="De Souza R" first="Rafael Conceição" last="De Souza">Rafael Conceição De Souza</name><name sortKey="Goncalves, Evonnildo Costa" sort="Goncalves, Evonnildo Costa" uniqKey="Goncalves E" first="Evonnildo Costa" last="Gonçalves">Evonnildo Costa Gonçalves</name><name sortKey="Lima, Alex Ranieri Jeronimo" sort="Lima, Alex Ranieri Jeronimo" uniqKey="Lima A" first="Alex Ranieri Jerônimo" last="Lima">Alex Ranieri Jerônimo Lima</name><name sortKey="Santos, Alberdan Silva" sort="Santos, Alberdan Silva" uniqKey="Santos A" first="Alberdan Silva" last="Santos">Alberdan Silva Santos</name><name sortKey="Vianez Junior, Joao Lidio Da Silva Goncalves" sort="Vianez Junior, Joao Lidio Da Silva Goncalves" uniqKey="Vianez Junior J" first="João Lídio Da Silva Gonçalves" last="Vianez Júnior">João Lídio Da Silva Gonçalves Vianez Júnior</name></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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