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1.
J Biochem ; 176(3): 205-215, 2024 Sep 03.
Artículo en Inglés | MEDLINE | ID: mdl-38740386

RESUMEN

The viral infectivity factor (Vif) of human immunodeficiency virus 1 forms a complex with host proteins, designated as Vif-CBFß-ELOB-ELOC-CUL5 (VßBCC), initiating the ubiquitination and subsequent proteasomal degradation of the human antiviral protein APOBEC3G (A3G), thereby negating its antiviral function. Whilst recent cryo-electron microscopy (cryo-EM) studies have implicated RNA molecules in the Vif-A3G interaction that leads to A3G ubiquitination, our findings indicated that the VßBCC complex can also directly impede A3G-mediated DNA deamination, bypassing the proteasomal degradation pathway. Employing the Systematic Evolution of Ligands by EXponential enrichment (SELEX) method, we have identified RNA aptamers with high affinity for the VßBCC complex. These aptamers not only bind to the VßBCC complex but also reinstate A3G's DNA deamination activity by inhibiting the complex's function. Moreover, we delineated the sequences and secondary structures of these aptamers, providing insights into the mechanistic aspects of A3G inhibition by the VßBCC complex. Analysis using selected aptamers will enhance our understanding of the inhibition of A3G by the VßBCC complex, offering potential avenues for therapeutic intervention.


Asunto(s)
Aptámeros de Nucleótidos , Productos del Gen vif del Virus de la Inmunodeficiencia Humana , Aptámeros de Nucleótidos/química , Aptámeros de Nucleótidos/metabolismo , Humanos , Productos del Gen vif del Virus de la Inmunodeficiencia Humana/metabolismo , Productos del Gen vif del Virus de la Inmunodeficiencia Humana/química , Desaminasa APOBEC-3G/metabolismo , Desaminasa APOBEC-3G/genética , Desaminasa APOBEC-3G/química , Subunidad beta del Factor de Unión al Sitio Principal/metabolismo , Subunidad beta del Factor de Unión al Sitio Principal/química , Técnica SELEX de Producción de Aptámeros , VIH-1/metabolismo , Proteínas Cullin
2.
Nat Commun ; 14(1): 4037, 2023 07 07.
Artículo en Inglés | MEDLINE | ID: mdl-37419875

RESUMEN

Great effort has been devoted to discovering the basis of A3G-Vif interaction, the key event of HIV's counteraction mechanism to evade antiviral innate immune response. Here we show reconstitution of the A3G-Vif complex and subsequent A3G ubiquitination in vitro and report the cryo-EM structure of the A3G-Vif complex at 2.8 Å resolution using solubility-enhanced variants of A3G and Vif. We present an atomic model of the A3G-Vif interface, which assembles via known amino acid determinants. This assembly is not achieved by protein-protein interaction alone, but also involves RNA. The cryo-EM structure and in vitro ubiquitination assays identify an adenine/guanine base preference for the interaction and a unique Vif-ribose contact. This establishes the biological significance of an RNA ligand. Further assessment of interactions between A3G, Vif, and RNA ligands show that the A3G-Vif assembly and subsequent ubiquitination can be controlled by amino acid mutations at the interface or by polynucleotide modification, suggesting that a specific chemical moiety would be a promising pharmacophore to inhibit the A3G-Vif interaction.


Asunto(s)
VIH-1 , Productos del Gen vif del Virus de la Inmunodeficiencia Humana , Productos del Gen vif del Virus de la Inmunodeficiencia Humana/genética , Productos del Gen vif del Virus de la Inmunodeficiencia Humana/metabolismo , VIH-1/fisiología , ARN/metabolismo , Antivirales/farmacología , Antivirales/metabolismo , Aminoácidos/metabolismo , Desaminasa APOBEC-3G/química , Citidina Desaminasa/genética
3.
Nature ; 615(7953): 728-733, 2023 03.
Artículo en Inglés | MEDLINE | ID: mdl-36754086

RESUMEN

The APOBEC3 (A3) proteins are host antiviral cellular proteins that hypermutate the viral genome of diverse viral families. In retroviruses, this process requires A3 packaging into viral particles1-4. The lentiviruses encode a protein, Vif, that antagonizes A3 family members by targeting them for degradation. Diversification of A3 allows host escape from Vif whereas adaptations in Vif enable cross-species transmission of primate lentiviruses. How this 'molecular arms race' plays out at the structural level is unknown. Here, we report the cryogenic electron microscopy structure of human APOBEC3G (A3G) bound to HIV-1 Vif, and the hijacked cellular proteins that promote ubiquitin-mediated proteolysis. A small surface explains the molecular arms race, including a cross-species transmission event that led to the birth of HIV-1. Unexpectedly, we find that RNA is a molecular glue for the Vif-A3G interaction, enabling Vif to repress A3G by ubiquitin-dependent and -independent mechanisms. Our results suggest a model in which Vif antagonizes A3G by intercepting it in its most dangerous form for the virus-when bound to RNA and on the pathway to packaging-to prevent viral restriction. By engaging essential surfaces required for restriction, Vif exploits a vulnerability in A3G, suggesting a general mechanism by which RNA binding helps to position key residues necessary for viral antagonism of a host antiviral gene.


Asunto(s)
Desaminasa APOBEC-3G , VIH-1 , Proteolisis , Productos del Gen vif del Virus de la Inmunodeficiencia Humana , Animales , Humanos , Desaminasa APOBEC-3G/antagonistas & inhibidores , Desaminasa APOBEC-3G/química , Desaminasa APOBEC-3G/metabolismo , Desaminasa APOBEC-3G/ultraestructura , VIH-1/metabolismo , VIH-1/patogenicidad , ARN/química , ARN/metabolismo , Ubiquitina/metabolismo , Productos del Gen vif del Virus de la Inmunodeficiencia Humana/química , Productos del Gen vif del Virus de la Inmunodeficiencia Humana/metabolismo , Productos del Gen vif del Virus de la Inmunodeficiencia Humana/ultraestructura , Microscopía por Crioelectrón , Empaquetamiento del Genoma Viral , Primates/virología
4.
Nat Commun ; 13(1): 7117, 2022 11 19.
Artículo en Inglés | MEDLINE | ID: mdl-36402773

RESUMEN

APOBEC3 proteins (A3s) are enzymes that catalyze the deamination of cytidine to uridine in single-stranded DNA (ssDNA) substrates, thus playing a key role in innate antiviral immunity. However, the APOBEC3 family has also been linked to many mutational signatures in cancer cells, which has led to an intense interest to develop inhibitors of A3's catalytic activity as therapeutics as well as tools to study A3's biochemistry, structure, and cellular function. Recent studies have shown that ssDNA containing 2'-deoxy-zebularine (dZ-ssDNA) is an inhibitor of A3s such as A3A, A3B, and A3G, although the atomic determinants of this activity have remained unknown. To fill this knowledge gap, we determined a 1.5 Å resolution structure of a dZ-ssDNA inhibitor bound to active A3G. The crystal structure revealed that the activated dZ-H2O mimics the transition state by coordinating the active site Zn2+ and engaging in additional stabilizing interactions, such as the one with the catalytic residue E259. Therefore, this structure allowed us to capture a snapshot of the A3's transition state and suggests that developing transition-state mimicking inhibitors may provide a new opportunity to design more targeted molecules for A3s in the future.


Asunto(s)
Citidina Desaminasa , Oligonucleótidos , Desaminasa APOBEC-3G/química , Citidina Desaminasa/genética , ADN de Cadena Simple , Dominio Catalítico
5.
Mol Cell Proteomics ; 20: 100132, 2021.
Artículo en Inglés | MEDLINE | ID: mdl-34389466

RESUMEN

Structural analysis of host-pathogen protein complexes remains challenging, largely due to their structural heterogeneity. Here, we describe a pipeline for the structural characterization of these complexes using integrative structure modeling based on chemical cross-links and residue-protein contacts inferred from mutagenesis studies. We used this approach on the HIV-1 Vif protein bound to restriction factor APOBEC3G (A3G), the Cullin-5 E3 ring ligase (CRL5), and the cellular transcription factor Core Binding Factor Beta (CBFß) to determine the structure of the (A3G-Vif-CRL5-CBFß) complex. Using the MS-cleavable DSSO cross-linker to obtain a set of 132 cross-links within this reconstituted complex along with the atomic structures of the subunits and mutagenesis data, we computed an integrative structure model of the heptameric A3G-Vif-CRL5-CBFß complex. The structure, which was validated using a series of tests, reveals that A3G is bound to Vif mostly through its N-terminal domain. Moreover, the model ensemble quantifies the dynamic heterogeneity of the A3G C-terminal domain and Cul5 positions. Finally, the model was used to rationalize previous structural, mutagenesis and functional data not used for modeling, including information related to the A3G-bound and unbound structures as well as mapping functional mutations to the A3G-Vif interface. The experimental and computational approach described here is generally applicable to other challenging host-pathogen protein complexes.


Asunto(s)
Desaminasa APOBEC-3G/química , Subunidad beta del Factor de Unión al Sitio Principal/química , Proteínas Cullin/química , Ubiquitina-Proteína Ligasas/química , Productos del Gen vif del Virus de la Inmunodeficiencia Humana/química , Espectrometría de Masas , Modelos Moleculares
6.
J Mol Biol ; 432(23): 6042-6060, 2020 11 20.
Artículo en Inglés | MEDLINE | ID: mdl-33098858

RESUMEN

APOBEC3G (A3G) is a single-stranded DNA (ssDNA) cytosine deaminase that can restrict HIV-1 infection by mutating the viral genome. A3G consists of a non-catalytic N-terminal domain (NTD) and a catalytic C-terminal domain (CTD) connected by a short linker. While the CTD catalyzes cytosine deamination, the NTD is believed to provide additional affinity for ssDNA. Structures of both A3G domains have been solved individually; however, a full-length A3G structure has been challenging. Recently, crystal structures of full-length rhesus macaque A3G variants were solved which suggested dimerization mechanisms and RNA binding surfaces, whereas the dimerization appeared to compromise catalytic activity. We determined the crystal structure of a soluble variant of human A3G (sA3G) at 2.5 Å and from these data generated a model structure of wild-type A3G. This model demonstrated that the NTD was rotated 90° relative to the CTD along the major axis of the molecule, an orientation that forms a positively charged channel connected to the CTD catalytic site, consisting of NTD loop-1 and CTD loop-3. Structure-based mutations, in vitro deamination and DNA binding assays, and HIV-1 restriction assays identify R24, located in the NTD loop-1, as essential to a critical interaction with ssDNA. Furthermore, sA3G was shown to bind a deoxy-cytidine dinucleotide near the catalytic Zn2+, yet not in the catalytic position, where the interactions between deoxy-cytidines and CTD loop-1 and loop-7 residues were different from those formed with substrate. These new interactions suggest a mechanism explaining why A3G exhibits a 3' to 5' directional preference in processive deamination.


Asunto(s)
Desaminasa APOBEC-3G/ultraestructura , ADN de Cadena Simple/química , Proteínas de Unión al ADN/ultraestructura , Conformación Proteica , Desaminasa APOBEC-3G/química , Desaminasa APOBEC-3G/genética , Animales , Dominio Catalítico/genética , Cristalografía por Rayos X , ADN de Cadena Simple/genética , Proteínas de Unión al ADN/genética , Humanos , Macaca mulatta/genética , Mutación/genética , Unión Proteica/genética , Dominios Proteicos/genética , Zinc/química
7.
PLoS Pathog ; 16(9): e1008812, 2020 09.
Artículo en Inglés | MEDLINE | ID: mdl-32913367

RESUMEN

The APOBEC3 deaminases are potent inhibitors of virus replication and barriers to cross-species transmission. For simian immunodeficiency virus (SIV) to transmit to a new primate host, as happened multiple times to seed the ongoing HIV-1 epidemic, the viral infectivity factor (Vif) must be capable of neutralizing the APOBEC3 enzymes of the new host. Although much is known about current interactions of HIV-1 Vif and human APOBEC3s, the evolutionary changes in SIV Vif required for transmission from chimpanzees to gorillas and ultimately to humans are poorly understood. Here, we demonstrate that gorilla APOBEC3G is a factor with the potential to hamper SIV transmission from chimpanzees to gorillas. Gain-of-function experiments using SIVcpzPtt Vif revealed that this barrier could be overcome by a single Vif acidic amino acid substitution (M16E). Moreover, degradation of gorilla APOBEC3F is induced by Vif through a mechanism that is distinct from that of human APOBEC3F. Thus, our findings identify virus adaptations in gorillas that preceded and may have facilitated transmission to humans.


Asunto(s)
Desaminasa APOBEC-3G/metabolismo , Evolución Molecular , Productos del Gen vif/metabolismo , Interacciones Huésped-Patógeno , Síndrome de Inmunodeficiencia Adquirida del Simio/transmisión , Virus de la Inmunodeficiencia de los Simios/aislamiento & purificación , Replicación Viral , Desaminasa APOBEC-3G/química , Desaminasa APOBEC-3G/genética , Secuencia de Aminoácidos , Animales , Productos del Gen vif/química , Productos del Gen vif/genética , Gorilla gorilla , Humanos , Pan troglodytes , Filogenia , Conformación Proteica , Homología de Secuencia , Síndrome de Inmunodeficiencia Adquirida del Simio/virología
8.
J Virol ; 94(21)2020 10 14.
Artículo en Inglés | MEDLINE | ID: mdl-32847850

RESUMEN

Human immunodeficiency virus type 1 (HIV-1) Vif recruits a cellular ubiquitin ligase complex to degrade antiviral APOBEC3 enzymes (APOBEC3C-H) and PP2A phosphatase regulators (PPP2R5A to PPP2R5E). While APOBEC3 antagonism is the canonical function of HIV-1 Vif, this viral accessory protein is also known to trigger G2/M cell cycle arrest. Vif initiates G2/M arrest by degrading multiple PPP2R5 family members, an activity prevalent among diverse HIV-1 and simian immunodeficiency virus (SIV) isolates. Here, computational protein-protein docking was used to delineate a Vif/CBF-ß/PPP2R5 complex in which Vif is predicted to bind the same PPP2R5 surface as physiologic phosphatase targets. This model was tested using targeted mutagenesis of amino acid residues within or adjacent to the putative interface to show loss or retention, respectively, of Vif-induced PPP2R5 degradation activity. Additionally, expression of a peptide that mimics cellular targets of PPP2R5s robustly inhibited Vif-mediated degradation of PPP2R5A but not APOBEC3G. Moreover, live-cell imaging studies examining Vif-mediated degradation of PPP2R5A and APOBEC3G within the same cell revealed that PPP2R5A degradation kinetics are comparable to those of APOBEC3G with a half-life of roughly 6 h postinfection, demonstrating that Vif can concurrently mediate the degradation of distinct cellular substrates. Finally, experiments with a panel of patient-derived Vif isolates indicated that PPP2R5A degradation activity is common in patient-derived isolates. Taken together, these results support a model in which PPP2R5 degradation and global changes in the cellular phosphoproteome are likely to be advantageous for viral pathogenesis.IMPORTANCE A critical function of HIV-1 Vif is to counteract the family of APOBEC3 innate immune proteins. It is also widely accepted that Vif induces G2/M cell cycle arrest in several different cell types. Recently, it has been shown that Vif degrades multiple PPP2R5 phosphoregulators to induce the G2/M arrest phenotype. Here, computational approaches are used to test a structural model of the Vif/PPP2R5 complex. In addition, imaging studies are used to show that Vif degrades these PPP2R5 substrates in roughly the same time frame as APOBEC3 degradation and that this activity is prevalent in patient-derived Vif isolates. These studies are important by further defining PPP2R5 proteins as a bona fide substrate of HIV-1 Vif.


Asunto(s)
Desaminasa APOBEC-3G/química , VIH-1/genética , Proteína Fosfatasa 2/química , Productos del Gen vif del Virus de la Inmunodeficiencia Humana/química , Desaminasa APOBEC-3G/genética , Desaminasa APOBEC-3G/metabolismo , Secuencia de Aminoácidos , Sustitución de Aminoácidos , Sitios de Unión , Expresión Génica , Regulación de la Expresión Génica , Vectores Genéticos/química , Vectores Genéticos/metabolismo , Células HEK293 , Infecciones por VIH/virología , VIH-1/aislamiento & purificación , VIH-1/metabolismo , Células HeLa , Interacciones Huésped-Patógeno/genética , Humanos , Cinética , Modelos Moleculares , Mutación , Unión Proteica , Dominios y Motivos de Interacción de Proteínas , Proteína Fosfatasa 2/genética , Proteína Fosfatasa 2/metabolismo , Estructura Secundaria de Proteína , Proteolisis , Proteínas Recombinantes/química , Proteínas Recombinantes/genética , Proteínas Recombinantes/metabolismo , Transducción de Señal , Especificidad por Sustrato , Productos del Gen vif del Virus de la Inmunodeficiencia Humana/genética , Productos del Gen vif del Virus de la Inmunodeficiencia Humana/metabolismo
9.
Nat Commun ; 11(1): 632, 2020 01 31.
Artículo en Inglés | MEDLINE | ID: mdl-32005813

RESUMEN

APOBEC3G, a member of the double-domain cytidine deaminase (CD) APOBEC, binds RNA to package into virions and restrict HIV-1 through deamination-dependent or deamination-independent inhibition. Mainly due to lack of a full-length double-domain APOBEC structure, it is unknown how CD1/CD2 domains connect and how dimerization/multimerization is linked to RNA binding and virion packaging for HIV-1 restriction. We report rhesus macaque A3G structures that show different inter-domain packing through a short linker and refolding of CD2. The A3G dimer structure has a hydrophobic dimer-interface matching with that of the previously reported CD1 structure. A3G dimerization generates a surface with intensified positive electrostatic potentials (PEP) for RNA binding and dimer stabilization. Unexpectedly, mutating the PEP surface and the hydrophobic interface of A3G does not abolish virion packaging and HIV-1 restriction. The data support a model in which only one RNA-binding mode is critical for virion packaging and restriction of HIV-1 by A3G.


Asunto(s)
Desaminasa APOBEC-3G/química , Infecciones por VIH/enzimología , VIH-1/fisiología , Desaminasa APOBEC-3G/genética , Desaminasa APOBEC-3G/metabolismo , Animales , Dimerización , Infecciones por VIH/virología , VIH-1/genética , Interacciones Huésped-Patógeno , Humanos , Macaca mulatta , Dominios Proteicos , ARN Viral/genética , ARN Viral/metabolismo , Ensamble de Virus , Replicación Viral
10.
J Phys Chem B ; 124(2): 366-372, 2020 01 16.
Artículo en Inglés | MEDLINE | ID: mdl-31867969

RESUMEN

The importance of cell surfaces in the self-assembly of proteins is widely accepted. One biologically significant event is the assembly of amyloidogenic proteins into aggregates, which leads to neurodegenerative disorders like Alzheimer's and Parkinson's diseases. The interaction of amyloidogenic proteins with cellular membranes appears to dramatically facilitate the aggregation process. Recent findings indicate that, in the presence of surfaces, aggregation occurs at physiologically low concentrations, suggesting that interaction with surfaces plays a critical role in the disease-prone aggregation process. However, the molecular mechanisms behind the on-surface aggregation process remain unclear. Here, we provide a theoretical model that offers a molecular explanation. According to this model, monomers transiently immobilized to surfaces increase the local monomer protein concentration and thus work as nuclei to dramatically accelerate the entire aggregation process. This physical-chemical theory was verified by experimental studies, using mica surfaces, to examine the aggregation kinetics of amyloidogenic α-synuclein protein and non-amyloidogenic cytosine deaminase APOBEC3G.


Asunto(s)
Desaminasa APOBEC-3G/metabolismo , Proteínas Amiloidogénicas/metabolismo , Multimerización de Proteína , alfa-Sinucleína/metabolismo , Desaminasa APOBEC-3G/química , Silicatos de Aluminio/química , Proteínas Amiloidogénicas/química , Membrana Celular/metabolismo , Cinética , Microscopía de Fuerza Atómica , alfa-Sinucleína/química
11.
Elife ; 82019 12 18.
Artículo en Inglés | MEDLINE | ID: mdl-31850845

RESUMEN

APOBEC3G (A3G), an enzyme expressed in primates with the potential to inhibit human immunodeficiency virus type 1 (HIV-1) infectivity, is a single-stranded DNA (ssDNA) deoxycytidine deaminase with two domains, a catalytically active, weakly ssDNA binding C-terminal domain (CTD) and a catalytically inactive, strongly ssDNA binding N-terminal domain (NTD). Using optical tweezers, we measure A3G binding a single, long ssDNA substrate under various applied forces to characterize the binding interaction. A3G binds ssDNA in multiple steps and in two distinct conformations, distinguished by degree of ssDNA contraction. A3G stabilizes formation of ssDNA loops, an ability inhibited by A3G oligomerization. Our data suggests A3G securely binds ssDNA through the NTD, while the CTD samples and potentially deaminates the substrate. Oligomerization of A3G stabilizes ssDNA binding but inhibits the CTD's search function. These processes explain A3G's ability to efficiently deaminate numerous sites across a 10,000 base viral genome during the reverse transcription process.


Asunto(s)
Desaminasa APOBEC-3G/metabolismo , ADN de Cadena Simple/metabolismo , Factores Inmunológicos/metabolismo , Desaminasa APOBEC-3G/química , Factores Inmunológicos/química , Unión Proteica , Conformación Proteica , Dominios Proteicos
12.
Nucleic Acids Res ; 47(14): 7676-7689, 2019 08 22.
Artículo en Inglés | MEDLINE | ID: mdl-31424549

RESUMEN

The potent antiretroviral protein APOBEC3G (A3G) specifically targets and deaminates deoxycytidine nucleotides, generating deoxyuridine, in single stranded DNA (ssDNA) intermediates produced during HIV replication. A non-catalytic domain in A3G binds strongly to RNA, an interaction crucial for recruitment of A3G to the virion; yet, A3G displays no deamination activity for cytidines in viral RNA. Here, we report NMR and molecular dynamics (MD) simulation analysis for interactions between A3Gctd and multiple substrate or non-substrate DNA and RNA, in combination with deamination assays. NMR ssDNA-binding experiments revealed that the interaction with residues in helix1 and loop1 (T201-L220) distinguishes the binding mode of substrate ssDNA from non-substrate. Using 2'-deoxy-2'-fluorine substituted cytidines, we show that a 2'-endo sugar conformation of the target deoxycytidine is favored for substrate binding and deamination. Trajectories of the MD simulation indicate that a ribose 2'-hydroxyl group destabilizes the π-π stacking of the target cytosine and H257, resulting in dislocation of the target cytosine base from the catalytic position. Interestingly, APOBEC3A, which can deaminate ribocytidines, retains the ribocytidine in the catalytic position throughout the MD simulation. Our results indicate that A3Gctd catalytic selectivity against RNA is dictated by both the sugar conformation and 2'-hydroxyl group.


Asunto(s)
Desaminasa APOBEC-3G/metabolismo , ADN de Cadena Simple/metabolismo , ADN/metabolismo , Espectroscopía de Resonancia Magnética/métodos , Simulación de Dinámica Molecular , ARN/metabolismo , Desaminasa APOBEC-3G/química , Desaminasa APOBEC-3G/genética , Biocatálisis , Citidina/química , Citidina/metabolismo , ADN/química , ADN/genética , ADN de Cadena Simple/química , ADN de Cadena Simple/genética , Desaminación , VIH-1/genética , VIH-1/metabolismo , Humanos , Unión Proteica , ARN/química , ARN/genética , ARN Viral/química , ARN Viral/genética , ARN Viral/metabolismo , Especificidad por Sustrato , Virión/genética , Virión/metabolismo
13.
Artículo en Inglés | MEDLINE | ID: mdl-31165049

RESUMEN

APOBEC3G (A3G) is a cellular protein that inhibits HIV-1 infection through virion incorporation. The interaction of the A3G N-terminal domain (NTD) with RNA is essential for A3G incorporation in the HIV-1 virion. The interaction between A3G-NTD and RNA is not completely understood. The A3G-NTD is also recognized by HIV-1 Viral infectivity factor (Vif) and A3G-Vif binding leads to A3G degradation. Therefore, the A3G-Vif interaction is a target for the development of antiviral therapies that block HIV-1 replication. However, targeting the A3G-Vif interactions could disrupt the A3G-RNA interactions that are required for A3G's antiviral activity. To better understand A3G-RNA binding, we generated in silico docking models to simulate the RNA-binding propensity of A3G-NTD. We simulated the A3G-NTD residues with high RNA-binding propensity, experimentally validated our prediction by testing A3G-NTD mutations, and identified structural determinants of A3G-RNA binding. In addition, we found a novel amino acid residue, I26 responsible for RNA interaction. The new structural insights provided here will facilitate the design of pharmaceuticals that inhibit A3G-Vif interactions without negatively impacting A3G-RNA interactions.


Asunto(s)
Desaminasa APOBEC-3G/química , Desaminasa APOBEC-3G/metabolismo , VIH-1/inmunología , ARN Viral/metabolismo , Desaminasa APOBEC-3G/genética , Análisis Mutacional de ADN , Infecciones por VIH/inmunología , Infecciones por VIH/virología , Simulación del Acoplamiento Molecular , Unión Proteica
14.
Chem Asian J ; 14(13): 2235-2241, 2019 Jul 01.
Artículo en Inglés | MEDLINE | ID: mdl-31116511

RESUMEN

Human APOBEC3G (A3G) inhibits the replication of human immunodeficiency virus-1 by deaminating cytidine at the 3'-end in the target motif 5'-CCC-3' in viral cDNA during reverse transcription. It in vitro deaminates two consecutive cytidines in a 3'->5' order. Although a crystal structure of the A3G catalytic domain (A3G-CD2) with DNA was reported, it is unknown why residues involved in enzymatic reaction are distributed widely. Here, we introduced an iodine atom into the C-5 position of cytidine (dC6 I ) in DNA 5'-ATTC4 C5 C6 I A7 ATT-3' (TCCC6 I ). It switches the deamination sequence preference from CCC to TCC, although small dC6 I deamination was observed. Solution structures of A3G-CD2 in complexes with products DNA TCUC6 I and TCUU6 I indicate that the substrate DNA binds A3G-CD2 in TCC and CCC modes. The dC6 deamination correlates with the 4th base type. The CCC mode favours dC6 deamination, while the TCC mode results in dC5 deamination. These studies present an extensive basis to design inhibitors to impede viral evolvability.


Asunto(s)
Desaminasa APOBEC-3G/metabolismo , Citidina/metabolismo , ADN/metabolismo , Desaminasa APOBEC-3G/química , Secuencia de Bases , Dominio Catalítico , Citidina/química , ADN/química , Desaminación , Humanos , Modelos Moleculares , Unión Proteica , Conformación Proteica , Espectroscopía de Protones por Resonancia Magnética
15.
Virology ; 527: 21-31, 2019 01 15.
Artículo en Inglés | MEDLINE | ID: mdl-30448640

RESUMEN

The APOBEC3 enzyme family are host restriction factors that induce mutagenesis of HIV-1 proviral genomes through the deamination of cytosine to form uracil in nascent single-stranded (-)DNA. HIV-1 suppresses APOBEC3 activity through the HIV-1 protein Vif that induces APOBEC3 degradation. Here we compared two common polymorphisms of APOBEC3F. We found that although both polymorphisms have HIV-1 restriction activity, APOBEC3F 108 A/231V can restrict HIV-1 ΔVif up to 4-fold more than APOBEC3F 108 S/231I and is partially protected from Vif-mediated degradation. This resulted from higher levels of steady state expression of APOBEC3F 108 A/231 V. Individuals are commonly heterozygous for the APOBEC3F polymorphisms and these polymorphisms formed in cells, independent of RNA, hetero-oligomers between each other and with APOBEC3G. Hetero-oligomerization with APOBEC3F 108 A/231V resulted in partial stabilization of APOBEC3F 108 S/231I and APOBEC3G in the presence of Vif. These data demonstrate functional outcomes of APOBEC3 polymorphisms and hetero-oligomerization that affect HIV-1 restriction.


Asunto(s)
Citosina Desaminasa/genética , Infecciones por VIH/genética , VIH-1/genética , Polimorfismo Genético , Replicación Viral , Desaminasa APOBEC-3G/química , Desaminasa APOBEC-3G/genética , Citosina Desaminasa/química , ADN Viral/genética , Células HEK293 , VIH-1/fisiología , Heterocigoto , Humanos , Mutación , Multimerización de Proteína , Estabilidad Proteica , Virión/metabolismo , Productos del Gen vif del Virus de la Inmunodeficiencia Humana/genética , Productos del Gen vif del Virus de la Inmunodeficiencia Humana/metabolismo
16.
Sci Rep ; 8(1): 17953, 2018 12 18.
Artículo en Inglés | MEDLINE | ID: mdl-30560880

RESUMEN

APOBEC3G (A3G) belongs to the family of cytosine deaminases that play an important role in the innate immune response. Similar to other, two-domain members of the APOBEC family, A3G is prone to concentration-dependent oligomerization, which is an integral for its function in the cell. It is shown that oligomerization of A3G is related to the packing mechanism into virus particle and, is critical for the so-called roadblock model during reverse transcription of proviral ssDNA. The role of oligomerization for deaminase activity of A3G is widely discussed in the literature; however, its relevance to deaminase activity for different oligomeric forms of A3G remains unclear. Here, using Atomic Force Microscopy, we directly visualized A3G-ssDNA complexes, determined their yield and stoichiometry and in parallel, using PCR assay, measured the deaminase activity of these complexes. Our data demonstrate a direct correlation between the total yield of A3G-ssDNA complexes and their total deaminase activity. Using these data, we calculated the relative deaminase activity for each individual oligomeric state of A3G in the complex. Our results show not only similar deaminase activity for monomer, dimer and tetramer of A3G in the complex, but indicate that larger oligomers of A3G retain their deaminase activity.


Asunto(s)
Desaminasa APOBEC-3G/química , Desaminasa APOBEC-3G/metabolismo , Multimerización de Proteína , Desaminasa APOBEC-3G/genética , Activación Enzimática , Humanos , Microscopía de Fuerza Atómica/métodos , Unión Proteica
17.
J Mol Biol ; 430(24): 4891-4907, 2018 12 07.
Artículo en Inglés | MEDLINE | ID: mdl-30414963

RESUMEN

Human APOBEC3H is a single-stranded (ss)DNA deoxycytidine deaminase that inhibits replication of retroelements and HIV-1 in CD4+ T cells. When aberrantly expressed in lung or breast tissue, APOBEC3H can contribute to cancer mutagenesis. These different activities are carried out by different haplotypes of APOBEC3H. Here we studied APOBEC3H haplotype II, which is able to restrict HIV-1 replication and retroelements. We determined how the dimerization mechanism, which is mediated by a double-stranded RNA molecule, influenced interactions with and activity on ssDNA. The data demonstrate that the cellular RNA bound by APOBEC3H does not completely inhibit enzyme activity, in contrast to other APOBEC family members. Despite degradation of the cellular RNA, an approximately 12-nt RNA remains bound to the enzyme, even in the presence of ssDNA. The RNA-mediated dimer is disrupted by mutating W115 on loop 7 or R175 and R176 on helix 6, but this also disrupts protein stability. In contrast, mutation of Y112 and Y113 on loop 7 also destabilizes RNA-mediated dimerization but results in a stable enzyme. Mutants unable to bind cellular RNA are unable to bind RNA oligonucleotides, oligomerize, and deaminate ssDNA in vitro, but ssDNA binding is retained. Comparison of A3H wild type and Y112A/Y113A by fluorescence polarization, single-molecule optical tweezer, and atomic force microscopy experiments demonstrates that RNA-mediated dimerization alters the interactions of A3H with ssDNA and other RNA molecules. Altogether, the biochemical analysis demonstrates that RNA binding is integral to APOBEC3H function.


Asunto(s)
Desaminasa APOBEC-3G/química , Desaminasa APOBEC-3G/metabolismo , VIH-1/fisiología , Mutación , ARN/metabolismo , Desaminasa APOBEC-3G/genética , ADN de Cadena Simple/metabolismo , Estabilidad de Enzimas , Polarización de Fluorescencia , VIH-1/genética , Humanos , Microscopía de Fuerza Atómica , Modelos Moleculares , Multimerización de Proteína , Estructura Secundaria de Proteína , ARN Viral/metabolismo , Replicación Viral
18.
Nat Commun ; 9(1): 2460, 2018 06 25.
Artículo en Inglés | MEDLINE | ID: mdl-29941968

RESUMEN

The human APOBEC3G protein is a cytidine deaminase that generates cytidine to deoxy-uridine mutations in single-stranded DNA (ssDNA), and capable of restricting replication of HIV-1 by generating mutations in viral genome. The mechanism by which APOBEC3G specifically deaminates 5'-CC motifs has remained elusive since structural studies have been hampered due to apparently weak ssDNA binding of the catalytic domain of APOBEC3G. We overcame the problem by generating a highly active variant with higher ssDNA affinity. Here, we present the crystal structure of this variant complexed with a ssDNA substrate at 1.86 Å resolution. This structure reveals atomic-level interactions by which APOBEC3G recognizes a functionally-relevant 5'-TCCCA sequence. This complex also reveals a key role of W211 in substrate recognition, implicating a similar recognition in activation-induced cytidine deaminase (AID) with a conserved tryptophan.


Asunto(s)
Desaminasa APOBEC-3G/química , Dominio Catalítico/fisiología , ADN de Cadena Simple/química , Línea Celular , Cristalografía por Rayos X , Citidina/química , Células HEK293 , VIH-1/genética , Humanos , Modelos Moleculares , Estructura Secundaria de Proteína , Replicación Viral/genética
19.
Methods Mol Biol ; 1814: 579-592, 2018.
Artículo en Inglés | MEDLINE | ID: mdl-29956256

RESUMEN

The present article describes techniques for classical simulations of proteins and protein-nucleic acid complexes, revealing their dynamics and protein-substrate binding energies. The approach is based on classical atomistic molecular dynamics (MD) simulations of the experimentally determined structures of the complexes. MD simulations can provide dynamics of complexes in realistic solvents on microsecond timescales, and the free energy methods are able to provide Gibbs free energies of binding of substrates, such as nucleic acids, to proteins. The chapter describes methodologies for the preparation of computer models of biomolecular complexes and free energy perturbation methodology for evaluating Gibbs free energies of binding. The applications are illustrated with examples of snapshots of proteins and their complexes with nucleic acids, as well as the precise Gibbs free energies of binding.


Asunto(s)
Simulación de Dinámica Molecular , Nanotecnología/métodos , Ácidos Nucleicos/química , Proteínas/química , Desaminasa APOBEC-3G/química , Dominio Catalítico , ARN/química , Termodinámica
20.
Sci Rep ; 8(1): 8067, 2018 05 23.
Artículo en Inglés | MEDLINE | ID: mdl-29795228

RESUMEN

Human APOBEC3G (hA3G) is a restriction factor that inhibits human immunodeficiency 1 virus (HIV-1) replication. The virally encoded protein Vif binds to hA3G and induces its degradation, thereby counteracting the antiviral activity of hA3G. Vif-mediated hA3G degradation clearly represents a potential target for anti-HIV drug development. Herein, we have performed virtual screening to discover small molecule inhibitors that target the binding interface of the Vif/hA3G complex. Subsequent biochemical studies have led to the identification of a small molecule inhibitor, IMB-301 that binds to hA3G, interrupts the hA3G-Vif interaction and inhibits Vif-mediated degradation of hA3G. As a result, IMB-301 strongly inhibits HIV-1 replication in a hA3G-dependent manner. Our study further demonstrates the feasibility of inhibiting HIV replication by abrogating the Vif-hA3G interaction with small molecules.


Asunto(s)
Desaminasa APOBEC-3G/metabolismo , Fármacos Anti-VIH/farmacología , Infecciones por VIH/tratamiento farmacológico , VIH-1/efectos de los fármacos , Dominios y Motivos de Interacción de Proteínas/efectos de los fármacos , Bibliotecas de Moléculas Pequeñas/farmacología , Productos del Gen vif del Virus de la Inmunodeficiencia Humana/metabolismo , Desaminasa APOBEC-3G/química , Desaminasa APOBEC-3G/genética , Infecciones por VIH/metabolismo , Infecciones por VIH/virología , Ensayos Analíticos de Alto Rendimiento , Humanos , Conformación Proteica , Replicación Viral/efectos de los fármacos , Productos del Gen vif del Virus de la Inmunodeficiencia Humana/química , Productos del Gen vif del Virus de la Inmunodeficiencia Humana/genética
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