Gp120
From Proteopedia
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Despite abundant efforts in HIV research the HI-virus remains one of the most serious infectious health threats for human worldwide. Infection involves the entry of the virus into CD4 carrying cells and is mediated by the recognition of the <scene name='Journal:JBSD:41/Cv/2'>cellular CD4 surface protein</scene> (<span style="color:yellow;background-color:black;font-weight:bold;">colored in yellow</span>) by <scene name='Journal:JBSD:41/Cv/3'>gp120 of the viral envelope</scene> (<span style="color:lime;background-color:black;font-weight:bold;">colored in green</span>). The CD4-binding site of gp120 contains <scene name='Journal:JBSD:41/Cv/4'>two crucial loops</scene>, termed the <font color='blue'><b>‘CD4-binding loop’ (in blue)</b></font> and the <span style="color:salmon;background-color:black;font-weight:bold;">‘outer domain exit (ODE) loop’ (colored in salmon)</span>, respectively. Importantly, <scene name='Journal:JBSD:41/Cv/6'>this functional site</scene> is a key target site for gp120-ligands to interfere with the gp120-CD4 interaction and thereby hampering infection. <span style="color:white;background-color:black;font-weight:bold;">Carbons of the important residues are colored in white</span>, <font color='blue'><b>nitrogens in blue</b></font>, and <font color='red'><b>oxygens in red</b></font>. Therapeutic ligands include for instance soluble CD4 and its variants. | Despite abundant efforts in HIV research the HI-virus remains one of the most serious infectious health threats for human worldwide. Infection involves the entry of the virus into CD4 carrying cells and is mediated by the recognition of the <scene name='Journal:JBSD:41/Cv/2'>cellular CD4 surface protein</scene> (<span style="color:yellow;background-color:black;font-weight:bold;">colored in yellow</span>) by <scene name='Journal:JBSD:41/Cv/3'>gp120 of the viral envelope</scene> (<span style="color:lime;background-color:black;font-weight:bold;">colored in green</span>). The CD4-binding site of gp120 contains <scene name='Journal:JBSD:41/Cv/4'>two crucial loops</scene>, termed the <font color='blue'><b>‘CD4-binding loop’ (in blue)</b></font> and the <span style="color:salmon;background-color:black;font-weight:bold;">‘outer domain exit (ODE) loop’ (colored in salmon)</span>, respectively. Importantly, <scene name='Journal:JBSD:41/Cv/6'>this functional site</scene> is a key target site for gp120-ligands to interfere with the gp120-CD4 interaction and thereby hampering infection. <span style="color:white;background-color:black;font-weight:bold;">Carbons of the important residues are colored in white</span>, <font color='blue'><b>nitrogens in blue</b></font>, and <font color='red'><b>oxygens in red</b></font>. Therapeutic ligands include for instance soluble CD4 and its variants. | ||
For the development of more potent gp120-ligands targeting the CD4-binding site we investigated two gp120-proteins from two clinical HIV isolates that exhibit a decreased affinity for soluble CD4. Each variant exhibits a set of simultaneous mutations in the CD4-binding loop and the ODE-loop. The <scene name='Journal:JBSD:41/Cv/7'>mutant gp120(3-2)</scene> exhibits three mutations in the CD4-binding loop (P369A, I371L, T373M) and two mutations in the ODE-loop (G471E, D474N). The <scene name='Journal:JBSD:41/Cv/8'>gp120(2-1)</scene> protein contains three simultaneous mutations: V372E, T373M in the CD4-binding loop, and D474N in the ODE-loop. <font color='magenta'><b>Carbons of the mutated residues are colored in white</b></font>, <font color='blue'><b>nitrogens in blue</b></font>, <font color='red'><b>oxygens in red</b></font>, and <span style="color:yellow;background-color:black;font-weight:bold;">sulfur in yellow</span>. To understand the phenomenon of reduced CD4-binding on a structural level the two gp120 variants were modeled, each with its specific set of mutations, and simulated using molecular dynamics. The results show that the mutant glutamates of both variants play a key role for reduced CD4 binding by affecting the conformation of the CD4-binding and ODE-loop. This knowledge should be helpful to predict the resistance of novel gp120 mutants or to design gp120-ligands with improved binding properties. | For the development of more potent gp120-ligands targeting the CD4-binding site we investigated two gp120-proteins from two clinical HIV isolates that exhibit a decreased affinity for soluble CD4. Each variant exhibits a set of simultaneous mutations in the CD4-binding loop and the ODE-loop. The <scene name='Journal:JBSD:41/Cv/7'>mutant gp120(3-2)</scene> exhibits three mutations in the CD4-binding loop (P369A, I371L, T373M) and two mutations in the ODE-loop (G471E, D474N). The <scene name='Journal:JBSD:41/Cv/8'>gp120(2-1)</scene> protein contains three simultaneous mutations: V372E, T373M in the CD4-binding loop, and D474N in the ODE-loop. <font color='magenta'><b>Carbons of the mutated residues are colored in white</b></font>, <font color='blue'><b>nitrogens in blue</b></font>, <font color='red'><b>oxygens in red</b></font>, and <span style="color:yellow;background-color:black;font-weight:bold;">sulfur in yellow</span>. To understand the phenomenon of reduced CD4-binding on a structural level the two gp120 variants were modeled, each with its specific set of mutations, and simulated using molecular dynamics. The results show that the mutant glutamates of both variants play a key role for reduced CD4 binding by affecting the conformation of the CD4-binding and ODE-loop. This knowledge should be helpful to predict the resistance of novel gp120 mutants or to design gp120-ligands with improved binding properties. | ||
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+ | ==3D structures of Gp120== | ||
+ | [[Gp120 3D structures]] | ||
</StructureSection> | </StructureSection> | ||
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*Gp120 binary complex | *Gp120 binary complex | ||
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**[[4jb9]], [[4lsp]], [[4lsq]], [[4lsr]], [[4lsu]], [[5te6]], [[5fcu]], [[5f9w]], [[5f9o]], [[5f96]], [[5cd5]], [[4xvt]] - Gp120 Clade A/E + antibody <br /> | **[[4jb9]], [[4lsp]], [[4lsq]], [[4lsr]], [[4lsu]], [[5te6]], [[5fcu]], [[5f9w]], [[5f9o]], [[5f96]], [[5cd5]], [[4xvt]] - Gp120 Clade A/E + antibody <br /> | ||
**[[4yc2]], [[4ybl]], [[4s1s]], [[4s1r]], [[4s1q]] - Gp120 Clade A/E (mutant) + antibody <br /> | **[[4yc2]], [[4ybl]], [[4s1s]], [[4s1r]], [[4s1q]] - Gp120 Clade A/E (mutant) + antibody <br /> | ||
- | **[[ | + | **[[4i3r]], [[4i3s]], [[5kzc]], [[5if0]], [[5ies]], [[4jpv]] - Gp120 outer domain + antibody<br /> |
**[[5t33]] - Gp120 RHPA + antibody <br /> | **[[5t33]] - Gp120 RHPA + antibody <br /> | ||
**[[3u2s]] - Gp120 V1V2 region + antibody PG9<br /> | **[[3u2s]] - Gp120 V1V2 region + antibody PG9<br /> | ||
+ | **[[3se8]], [[3se9]], [[3hi1]], [[3rjq]], [[4jkp]], [[4jm2]], [[4lss]], [[4lsv]], [[4ywg]], [[4xvs]], [[3ngb]], [[4ye4]], [[4rwy]], [[4jan]], [[4lst]], [[5te7]], [[5f6j]], [[5te4]], [[6bf4]], [[5wb9]], [[5w6d]], [[5ukr]], [[5uem]], [[5igx]], [[4dvr]] - Gp120 + antibody<br /> | ||
+ | **[[3idx]], [[3idy]], [[2ny7]]. [[4jdt]], [[5fyl]], [[5fec]], [[6bck]] - Gp120 core (mutant) + antibody <br /> | ||
+ | **[[4rz8]], [[5f4l]], [[5f4p]], [[5f4r]] - Gp120 core + CD4 mimic <br /> | ||
+ | **[[4dku]], [[4dkv]] - Gp120 core (mutant) + CD4 mimetic<br /> | ||
+ | **[[4jzw]], [[4jzz]], [[4k0a]], [[4ka2]] - Gp120 core + CD4 mimetic miniprotein<br /> | ||
+ | **[[4jpj]], [[4rx4]] - Gp120 Clade A + antibody <br /> | ||
**[[3tgs]], [[4dko]], [[4dkp]], [[4dkq]], [[4dkr]] - Gp120 core + piperidine derivative<br /> | **[[3tgs]], [[4dko]], [[4dkp]], [[4dkq]], [[4dkr]] - Gp120 core + piperidine derivative<br /> | ||
**[[5u6e]] - Gp120 core + pyrrole derivative<br /> | **[[5u6e]] - Gp120 core + pyrrole derivative<br /> | ||
+ | **[[4dvx]], [[4dvw]], [[4dvv]], [[4dvt]], [[4dvs]] - Gp120 core (mutant) + piperazine derivative<br /> | ||
*Gp120 ternary complex | *Gp120 ternary complex | ||
+ | **[[5kjr]] - Gp120 Clade A/E + M48U1 peptide + antibody<br /> | ||
+ | **[[4rfo]], [[4rfn]] - Gp120 Clade A/E (mutant) + M48U1 peptide + antibody<br /> | ||
+ | **[[4h8w]] - Gp120 Clade A/E + CD4 + antibody<br /> | ||
**[[3jwd]], [[3jwo]], [[2i5y]], [[2i60]] - Gp120 core + hCD4 N terminal + antibody <br /> | **[[3jwd]], [[3jwo]], [[2i5y]], [[2i60]] - Gp120 core + hCD4 N terminal + antibody <br /> | ||
**[[2nxy]], [[2nxz]], [[2ny0]], [[2ny1]], [[2ny2]], [[2ny3]], [[2ny4]], [[2ny5]], [[2ny6]], [[1gc1]], [[1g9m]], [[1g9n]], [[1rzj]], [[1rzk]], [[1yyl]], [[1yym]], [[2b4c]] - Gp120 core (mutant) + hCD4 N terminal + antibody <br /> | **[[2nxy]], [[2nxz]], [[2ny0]], [[2ny1]], [[2ny2]], [[2ny3]], [[2ny4]], [[2ny5]], [[2ny6]], [[1gc1]], [[1g9m]], [[1g9n]], [[1rzj]], [[1rzk]], [[1yyl]], [[1yym]], [[2b4c]] - Gp120 core (mutant) + hCD4 N terminal + antibody <br /> | ||
**[[5a8h]], [[5a7x]], [[4rqs]], [[4r4h]], [[4r2g]], [[4p9h]] - Gp120 core + hCD4 D1-D2 domain + antibody<br /> | **[[5a8h]], [[5a7x]], [[4rqs]], [[4r4h]], [[4r2g]], [[4p9h]] - Gp120 core + hCD4 D1-D2 domain + antibody<br /> | ||
**[[4laj]] - Gp120 core + CD4 mimetic miniprotein + antibody<br /> | **[[4laj]] - Gp120 core + CD4 mimetic miniprotein + antibody<br /> | ||
+ | **[[5w4l]], [[5uwe]] - Gp120 core (mutant) + CD4 mimetic peptide + antibody<br /> | ||
**[[4r4f]], [[4r4n]] - Gp120 core + M48U1 peptide + antibody<br /> | **[[4r4f]], [[4r4n]] - Gp120 core + M48U1 peptide + antibody<br /> | ||
- | **[[ | + | **[[5v8l]], [[5v8m]], [[5uty]], [[5utf]], [[5um8]], [[5jsa]], [[5js9]], [[5i8h]], [[5d9q]], [[5cjx]], [[5c7k]], [[6ccb]], [[6mft]], [[6mdt]], [[6mco]], [[6d2p]], [[6ck9]], [[6ch9]], [[6ch8]], [[6ch7]] - Gp120 core + Gp41 + antibody<br /> |
- | **[[ | + | **[[5fyk]], [[5fyj]], [[4nco]], [[6nnj]], [[6nnf]], [[6nm6]] - Gp120 core (mutant) + Gp41 + antibody<br /> |
- | **[[ | + | **[[6cde]], [[6cdi]], [[6orn]], [[6oro]], [[6orp]], [[6orq]], [[6okp]], [[6nqd]], [[6nc3]], [[6nc2]], [[6mn7]], [[6e5p]], [[6cuf]], [[6cue]], [[6chb]], [[5u1f]], [[5thr]], [[4cc8]], [[3j70]] - Gp120 core + Gp41 + antibody – Cryo EM<br /> |
- | + | **[[3j5m]] - Gp120 core (mutant) + Gp41 + antibody – Cryo EM<br /> | |
- | **[[ | + | |
*Gp120 from HIV-2 binary complex | *Gp120 from HIV-2 binary complex | ||
- | **[[5fec]] - Gp120 core (mutant) + CD4<br /> | + | **[[5fec]], [[5cay]] - Gp120 core (mutant) + CD4<br /> |
*Gp120 from SIV | *Gp120 from SIV | ||
- | **[[2bf1]], [[3fus]] - Gp120 core | + | **[[2bf1]], [[3fus]] - Gp120 core<br /> |
+ | **[[3jcc]], [[3jcb]] - Gp120 core + CD4 + antibody – Cryo EM<br /> | ||
}} | }} | ||
Revision as of 07:42, 17 July 2019
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3D structures of Gp120
Updated on 17-July-2019
References
- ↑ Poignard P, Saphire EO, Parren PW, Burton DR. gp120: Biologic aspects of structural features. Annu Rev Immunol. 2001;19:253-74. PMID:11244037 doi:http://dx.doi.org/10.1146/annurev.immunol.19.1.253
- ↑ Kassler K, Sticht H. Molecular mechanism of HIV-1 gp120 mutations that reduce CD4 binding affinity. J Biomol Struct Dyn. 2013 Jan 9. PMID:23297802 doi:10.1080/07391102.2012.746946