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1.
Nucleic Acids Res ; 47(7): 3607-3618, 2019 04 23.
Artículo en Inglés | MEDLINE | ID: mdl-30767014

RESUMEN

The integration of the retroviral genome into the chromatin of the infected cell is catalysed by the integrase (IN)•viral DNA complex (intasome). This process requires functional association between the integration complex and the nucleosomes. Direct intasome/histone contacts have been reported to modulate the interaction between the integration complex and the target DNA (tDNA). Both prototype foamy virus (PFV) and HIV-1 integrases can directly bind histone amino-terminal tails. We have further investigated this final association by studying the effect of isolated histone tails on HIV-1 integration. We show here that the binding of HIV-1 IN to a peptide derived from the H4 tail strongly stimulates integration catalysis in vitro. This stimulation was not observed with peptide tails from other variants or with alpha-retroviral (RAV) and spuma-retroviral PFV integrases. Biochemical analyses show that the peptide tail induces both an increase in the IN oligomerization state and affinity for the target DNA, which are associated with substantial structural rearrangements in the IN carboxy-terminal domain (CTD) observed by NMR. Our data indicate that the H4 peptide tail promotes the formation of active strand transfer complexes (STCs) and support an activation step of the incoming intasome at the contact of the histone tail.


Asunto(s)
Integrasa de VIH/genética , VIH-1/genética , Histonas/genética , Integración Viral/genética , Catálisis , Cromatina/genética , Cromatina/virología , Genoma Viral/genética , VIH-1/patogenicidad , Interacciones Huésped-Patógeno/genética , Humanos , Nucleosomas/genética , Nucleosomas/virología , Spumavirus/genética
2.
J Cell Physiol ; 234(6): 8295-8315, 2019 06.
Artículo en Inglés | MEDLINE | ID: mdl-30390301

RESUMEN

Polyomavirus family consists of a highly diverse group of small DNA viruses. The founding family member (MPyV) was first discovered in the newborn mouse in the late 1950s, which induces solid tumors in a wide variety of tissue types that are the epithelial and mesenchymal origin. Later, other family members were also isolated from a number of mammalian, avian and fish species. Some of these viruses significantly contributed to our current understanding of the fundamentals of modern biology such as transcription, replication, splicing, RNA editing, and cell transformation. After the discovery of first two human polyomaviruses (JC virus [JCV] and BK virus [BKV]) in the early 1970s, there has been a rapid expansion in the number of human polyomaviruses in recent years due to the availability of the new technologies and brought the present number to 14. Some of the human polyomaviruses cause considerably serious human diseases, including progressive multifocal leukoencephalopathy, polyomavirus-associated nephropathy, Merkel cell carcinoma, and trichodysplasia spinulosa. Emerging evidence suggests that the expression of the polyomavirus genome is more complex than previously thought. In addition to encoding universally expressed regulatory and structural proteins (LT-Ag, Sm t-Ag, VP1, VP2, and VP3), some polyomaviruses express additional virus-specific regulatory proteins and microRNAs. This review summarizes the recent advances in polyomavirus genome expression with respect to the new viral proteins and microRNAs other than the universally expressed ones. In addition, a special emphasis is devoted to the recent structural and functional discoveries in the field of polyomavirus agnoprotein which is expressed only by JCV, BKV, and simian virus 40 genomes.


Asunto(s)
Genoma Viral/genética , MicroARNs/genética , Poliomavirus/genética , Proteínas Reguladoras y Accesorias Virales/genética , Carcinoma de Células de Merkel/genética , Carcinoma de Células de Merkel/virología , ADN Viral/genética , Regulación Viral de la Expresión Génica/genética , Humanos , Leucoencefalopatía Multifocal Progresiva/genética , Leucoencefalopatía Multifocal Progresiva/virología , Poliomavirus/patogenicidad , Replicación Viral/genética
3.
Org Biomol Chem ; 16(3): 459-471, 2018 01 17.
Artículo en Inglés | MEDLINE | ID: mdl-29265149

RESUMEN

Short peptides composed of naturally occurring amino acids are usually unstructured in aqueous media. The installation of covalent constraints within their side chains or backbones, resulting in the formation of macrocyclic peptides, is an appealing approach to stabilize them in defined secondary structures. Therefore, with the objective to stabilize α-turn conformation, we designed, synthesized and characterized constrained 13-membered macrocyclic peptides. Their design was inspired by previous work using the replacement of a hydrogen bond by a covalent bond, for the stabilization of α-helical secondary structures. Their synthesis employed our recently published solid-phase method based on Fukuyama-Mitsunobu alkylation reactions. We report herein an optimized synthesis leading to three water-soluble 13-membered macrocyclic peptides 10a-c, including respectively two, one and zero glycine residues. They were characterized by CD and NMR, which indicated the presence of equilibrating conformers. The detailed conformational analysis was based on extensive NMR and molecular dynamics studies. We found that the peptide without glycine residues 10c was mostly present as slowly interconverting conformers whereas the peptide with two glycine residues 10a was mostly present as rapidly interconverting conformers. We did not find a good match between the conformers of 10a and α-turns occurring in proteins, due to the high flexibility of the glycine backbone. Interestingly, we found that the major conformer of 10c accurately matched the "non-classical" or "tight" α-turn of type II-αLS, with a RMSD value of 0.42 Å for heavy atoms constituting the macrocycle. This is, to the best of our knowledge, the first molecule reported to mimic this type of α-turn found in proteins.


Asunto(s)
Péptidos Cíclicos/química , Péptidos Cíclicos/síntesis química , Péptidos/química , Péptidos/síntesis química , Agua/química , Técnicas de Química Sintética , Enlace de Hidrógeno , Simulación de Dinámica Molecular , Conformación Proteica en Hélice alfa , Estabilidad Proteica , Solubilidad
4.
J Cell Biochem ; 118(10): 3268-3280, 2017 10.
Artículo en Inglés | MEDLINE | ID: mdl-28295503

RESUMEN

Agnoprotein is an important regulatory protein of the human polyoma JC virus (JCV) and plays critical roles during the viral replication cycle. It forms highly stable dimers and oligomers through its Leu/Ile/Phe-rich domain, which is important for the stability and function of the protein. We recently resolved the partial 3D structure of this protein by NMR using a synthetic peptide encompassing amino acids Thr17 to Gln52, where the Leu/Ile/Phe- rich region was found to adopt a major alpha-helix conformation spanning amino acids 23-39. Here, we report the resolution of the 3D structure of full-length JCV agnoprotein by NMR, which not only confirmed the existence of the previously reported major α-helix domain at the same position but also revealed the presence of an additional minor α-helix region spanning amino acid residues Leu6 to lys13. The remaining regions of the protein adopt an intrinsically unstructured conformation. J. Cell. Biochem. 118: 3268-3280, 2017. © 2017 Wiley Periodicals, Inc.


Asunto(s)
Virus JC/química , Resonancia Magnética Nuclear Biomolecular , Proteínas Reguladoras y Accesorias Virales/química , Humanos , Estructura Secundaria de Proteína
5.
J Cell Physiol ; 231(10): 2115-27, 2016 10.
Artículo en Inglés | MEDLINE | ID: mdl-26831433

RESUMEN

Agnoprotein is an important regulatory protein of polyomaviruses, including JCV, BKV, and SV40. In the absence of its expression, these viruses are unable to sustain their productive life cycle. It is a highly basic phosphoprotein that localizes mostly to the perinuclear area of infected cells, although a small amount of the protein is also found in nucleus. Much has been learned about the structure and function of this important regulatory protein in recent years. It forms highly stable dimers/oligomers in vitro and in vivo through its Leu/Ile/Phe-rich domain. Structural NMR studies revealed that this domain adopts an alpha-helix conformation and plays a critical role in the stability of the protein. It associates with cellular proteins, including YB-1, p53, Ku70, FEZ1, HP1α, PP2A, AP-3, PCNA, and α-SNAP; and viral proteins, including small t antigen, large T antigen, HIV-1 Tat, and JCV VP1; and significantly contributes the viral transcription and replication. This review summarizes the recent advances in the structural and functional properties of this important regulatory protein. J. Cell. Physiol. 231: 2115-2127, 2016. © 2016 Wiley Periodicals, Inc.


Asunto(s)
Infecciones por Polyomavirus/virología , Poliomavirus/metabolismo , Factores de Transcripción/metabolismo , Proteínas Virales/metabolismo , Proteínas Reguladoras y Accesorias Virales/metabolismo , Animales , Homólogo de la Proteína Chromobox 5 , Humanos , Virus JC/aislamiento & purificación , Virus JC/metabolismo , Poliomavirus/aislamiento & purificación
6.
Biochim Biophys Acta ; 1838(8): 2026-35, 2014 Aug.
Artículo en Inglés | MEDLINE | ID: mdl-24746450

RESUMEN

Biological membranes represent a physical barrier that most viruses have to cross for replication. While enveloped viruses cross membranes through a well-characterized membrane fusion mechanism, non-enveloped viruses, such as rotaviruses, require the destabilization of the host cell membrane by processes that are still poorly understood. We have identified, in the C-terminal region of the rotavirus glycoprotein VP7, a peptide that was predicted to contain a membrane domain and to fold into an amphipathic α-helix. Its structure was confirmed by circular dichroism in media mimicking the hydrophobic environment of the membrane at both acidic and neutral pHs. The helical folding of the peptide was corroborated by ATR-FTIR spectroscopy, which suggested a transmembrane orientation of the peptide. The interaction of this peptide with artificial membranes and its affinity were assessed by plasmon waveguide resonance. We have found that the peptide was able to insert into membranes and permeabilize them while the native protein VP7 did not. Finally, NMR studies revealed that in a hydrophobic environment, this helix has amphipathic properties characteristic of membrane-perforating peptides. Surprisingly, its structure varies from that of its counterpart in the structure of the native protein VP7, as was determined by X-ray. All together, our results show that a peptide released from VP7 is capable of changing its conformation and destabilizing artificial membranes. Such peptides could play an important role by facilitating membrane crossing by non-enveloped viruses during cell infection.


Asunto(s)
Antígenos Virales/metabolismo , Proteínas de la Cápside/metabolismo , Permeabilidad de la Membrana Celular , Membranas Artificiales , Fragmentos de Péptidos/metabolismo , Antígenos Virales/química , Proteínas de la Cápside/química , Dicroismo Circular , Biología Computacional , Espectroscopía de Resonancia Magnética , Micelas , Fragmentos de Péptidos/química , Espectroscopía Infrarroja por Transformada de Fourier
8.
J Virol ; 88(12): 6556-75, 2014 Jun.
Artículo en Inglés | MEDLINE | ID: mdl-24672035

RESUMEN

UNLABELLED: Agnoprotein is a small multifunctional regulatory protein required for sustaining the productive replication of JC virus (JCV). It is a mostly cytoplasmic protein localizing in the perinuclear area and forms highly stable dimers/oligomers through a Leu/Ile/Phe-rich domain. There have been no three-dimensional structural data available for agnoprotein due to difficulties associated with the dynamic conversion from monomers to oligomers. Here, we report the first nuclear magnetic resonance (NMR) structure of a synthetic agnoprotein peptide spanning amino acids Thr17 to Glu55 where Lys23 to Phe39 encompassing the Leu/Ile/Phe-rich domain forms an amphipathic α-helix. On the basis of these structural data, a number of Ala substitution mutations were made to investigate the role of the α-helix in the structure and function of agnoprotein. Single L29A and L36A mutations exhibited a significant negative effect on both protein stability and viral replication, whereas the L32A mutation did not. In addition, the L29A mutant displayed a highly nuclear localization pattern, in contrast to the pattern for the wild type (WT). Interestingly, a triple mutant, the L29A+L32A+L36A mutant, yielded no detectable agnoprotein expression, and the replication of this JCV mutant was significantly reduced, suggesting that Leu29 and Leu36 are located at the dimer interface, contributing to the structure and stability of agnoprotein. Two other single mutations, L33A and E34A, did not perturb agnoprotein stability as drastically as that observed with the L29A and L36A mutations, but they negatively affected viral replication, suggesting that the role of these residues is functional rather than structural. Thus, the agnoprotein dimerization domain can be targeted for the development of novel drugs active against JCV infection. IMPORTANCE: Agnoprotein is a small regulatory protein of JC virus (JCV) and is required for the successful completion of the viral replication cycle. It forms highly stable dimers and oligomers through its hydrophobic (Leu/Ile/Phe-rich) domain, which has been shown to play essential roles in the stability and function of the protein. In this work, the Leu/Ile/Phe-rich domain has been further characterized by NMR studies using an agnoprotein peptide spanning amino acids T17 to Q54. Those studies revealed that the dimerization domain of the protein forms an amphipathic α-helix. Subsequent NMR structure-based mutational analysis of the region highlighted the critical importance of certain amino acids within the α-helix for the stability and function of agnoprotein. In conclusion, this study provides a solid foundation for developing effective therapeutic approaches against the dimerization domain of the protein to inhibit its critical roles in JCV infection.


Asunto(s)
Virus JC/metabolismo , Infecciones por Polyomavirus/virología , Proteínas Reguladoras y Accesorias Virales/química , Secuencia de Aminoácidos , Línea Celular , Dimerización , Humanos , Virus JC/química , Virus JC/genética , Espectroscopía de Resonancia Magnética , Modelos Moleculares , Datos de Secuencia Molecular , Mutación Missense , Estabilidad Proteica , Estructura Secundaria de Proteína , Estructura Terciaria de Proteína , Proteínas Reguladoras y Accesorias Virales/genética , Proteínas Reguladoras y Accesorias Virales/metabolismo , Replicación Viral
9.
Microbes Infect ; : 105297, 2024 Jan 09.
Artículo en Inglés | MEDLINE | ID: mdl-38199267

RESUMEN

Small molecule drugs have an important role to play in combating viral infections, and biophysics support has been central for contributing to the discovery and design of direct acting antivirals. Perhaps one of the most successful biophysical tools for this purpose is NMR spectroscopy when utilized strategically and pragmatically within team workflows and timelines. This report describes some clear examples of how NMR applications contributed to the design of antivirals when combined with medicinal chemistry, biochemistry, X-ray crystallography and computational chemistry. Overall, these multidisciplinary approaches allowed teams to reveal and expose compound physical properties from which design ideas were spawned and tested to achieve the desired successes. Examples are discussed for the discovery of antivirals that target HCV, HIV and SARS-CoV-2.

10.
J Mol Biol ; 436(2): 168359, 2024 01 15.
Artículo en Inglés | MEDLINE | ID: mdl-37952768

RESUMEN

Nucleic acid sequences containing guanine tracts are able to form non-canonical DNA or RNA structures known as G-quadruplexes (or G4s). These structures, based on the stacking of G-tetrads, are involved in various biological processes such as gene expression regulation. Here, we investigated a G4 forming sequence, HIVpro2, derived from the HIV-1 promoter. This motif is located 60 nucleotides upstream of the proviral Transcription Starting Site (TSS) and overlaps with two SP1 transcription factor binding sites. Using NMR spectroscopy, we determined that HIVpro2 forms a hybrid type G4 structure with a core that is interrupted by a single nucleotide bulge. An additional reverse-Hoogsteen AT base pair is stacked on top of the tetrad. SP1 transcription factor is known to regulate transcription activity of many genes through the recognition of Guanine-rich duplex motifs. Here, the formation of HIVpro2 G4 may modulate SP1 binding sites architecture by competing with the formation of the canonical duplex structure. Such DNA structural switch potentially participates to the regulation of viral transcription and may also interfere with HIV-1 reactivation or viral latency.


Asunto(s)
G-Cuádruplex , VIH-1 , Factor de Transcripción Sp1 , Sitios de Unión , ADN/química , Guanina/química , VIH-1/genética , VIH-1/metabolismo , Factor de Transcripción Sp1/genética , Factor de Transcripción Sp1/metabolismo , Humanos , Regulación Viral de la Expresión Génica
11.
PLoS Pathog ; 7(9): e1002221, 2011 Sep.
Artículo en Inglés | MEDLINE | ID: mdl-21966267

RESUMEN

Myeloid cells play numerous roles in HIV-1 pathogenesis serving as a vehicle for viral spread and as a viral reservoir. Yet, cells of this lineage generally resist HIV-1 infection when compared to cells of other lineages, a phenomenon particularly acute during the early phases of infection. Here, we explore the role of APOBEC3A on these steps. APOBEC3A is a member of the APOBEC3 family that is highly expressed in myeloid cells, but so far lacks a known antiviral effect against retroviruses. Using ectopic expression of APOBEC3A in established cell lines and specific silencing in primary macrophages and dendritic cells, we demonstrate that the pool of APOBEC3A in target cells inhibits the early phases of HIV-1 infection and the spread of replication-competent R5-tropic HIV-1, specifically in cells of myeloid origins. In these cells, APOBEC3A affects the amount of vDNA synthesized over the course of infection. The susceptibility to the antiviral effect of APOBEC3A is conserved among primate lentiviruses, although the viral protein Vpx coded by members of the SIV(SM)/HIV-2 lineage provides partial protection from APOBEC3A during infection. Our results indicate that APOBEC3A is a previously unrecognized antiviral factor that targets primate lentiviruses specifically in myeloid cells and that acts during the early phases of infection directly in target cells. The findings presented here open up new venues on the role of APOBEC3A during HIV infection and pathogenesis, on the role of the cellular context in the regulation of the antiviral activities of members of the APOBEC3 family and more generally on the natural functions of APOBEC3A.


Asunto(s)
Citidina Desaminasa/farmacología , VIH-1/efectos de los fármacos , Proteínas/farmacología , Línea Celular , Citidina Desaminasa/biosíntesis , ADN Viral/biosíntesis , ADN Viral/efectos de los fármacos , Células HEK293 , VIH-1/fisiología , Células HeLa , Humanos , Lentivirus de los Primates/efectos de los fármacos , Células Mieloides/virología
12.
Pharmaceutics ; 14(3)2022 Mar 04.
Artículo en Inglés | MEDLINE | ID: mdl-35335945

RESUMEN

Facial angiofibromas (FA) are one of the most obvious cutaneous manifestations of tuberous sclerosis complex. Topical rapamycin for angiofibromas has been reported as a promising treatment. Several types of vehicles have been used hitherto, but polymeric micelles and especially those made of d-α-tocopherol polyethylene glycol 1000 succinate (TPGS) seem to have shown better skin bioavailability of rapamycin than the so far commonly used ointments. To better understand the influence of polymeric micelles on the behavior of rapamycin, we explored it through mixed polymeric micelles combining TPGS and poloxamer, evaluating stability and skin bioavailability to define an optimized formulation to effectively treat FA. Our studies have shown that TPGS improves the physicochemical behavior of rapamycin, i.e., its solubility and stability, due to a strong inclusion in micelles, while poloxamer P123 has a more significant influence on skin bioavailability. Accordingly, we formulated mixed-micelle hydrogels containing 0.1% rapamycin, and the optimized formulation was found to be stable for up to 3 months at 2-8 °C. In addition, compared to hydroalcoholic gel formulations, the studied system allows for better biodistribution on human skin.

13.
Cell Death Dis ; 13(11): 959, 2022 11 15.
Artículo en Inglés | MEDLINE | ID: mdl-36379916

RESUMEN

Caspase-2 (Casp2) is a promising therapeutic target in several human diseases, including nonalcoholic steatohepatitis (NASH) and Alzheimer's disease (AD). However, the design of an active-site-directed inhibitor selective to individual caspase family members is challenging because caspases have extremely similar active sites. Here we present new peptidomimetics derived from the VDVAD pentapeptide structure, harboring non-natural modifications at the P2 position and an irreversible warhead. Enzyme kinetics show that these new compounds, such as LJ2 or its specific isomers LJ2a, and LJ3a, strongly and irreversibly inhibit Casp2 with genuine selectivity. In agreement with the established role of Casp2 in cellular stress responses, LJ2 inhibits cell death induced by microtubule destabilization or hydroxamic acid-based deacetylase inhibition. The most potent peptidomimetic, LJ2a, inhibits human Casp2 with a remarkably high inactivation rate (k3/Ki ~5,500,000 M-1 s-1), and the most selective inhibitor, LJ3a, has close to a 1000 times higher inactivation rate on Casp2 as compared to Casp3. Structural analysis of LJ3a shows that the spatial configuration of Cα at the P2 position determines inhibitor efficacy. In transfected human cell lines overexpressing site-1 protease (S1P), sterol regulatory element-binding protein 2 (SREBP2) and Casp2, LJ2a and LJ3a fully inhibit Casp2-mediated S1P cleavage and thus SREBP2 activation, suggesting a potential to prevent NASH development. Furthermore, in primary hippocampal neurons treated with ß-amyloid oligomers, submicromolar concentrations of LJ2a and of LJ3a prevent synapse loss, indicating a potential for further investigations in AD treatment.


Asunto(s)
Enfermedad del Hígado Graso no Alcohólico , Peptidomiméticos , Humanos , Caspasa 2/metabolismo , Caspasa 3/metabolismo , Neuronas/metabolismo , Enfermedad del Hígado Graso no Alcohólico/tratamiento farmacológico , Enfermedad del Hígado Graso no Alcohólico/metabolismo , Peptidomiméticos/farmacología , Peptidomiméticos/metabolismo
14.
J Biol Chem ; 285(25): 19409-21, 2010 Jun 18.
Artículo en Inglés | MEDLINE | ID: mdl-20385550

RESUMEN

Nonenveloped virus must penetrate the cellular membrane to access the cytoplasm without the benefit of membrane fusion. For birnavirus, one of the peptides present in the virus capsid, pep46 for infectious bursal disease virus, is able to induce pores into membranes as an intermediate step of the birnavirus-penetration pathway. Using osmotic protection experiments, we demonstrate here that pep46 and its pore-forming N-terminal moiety (pep22) form pores of different diameters, 5-8 and 2-4 nm, respectively, showing that both pep46 moieties participate to pore formation. The solution structures of pep46, pep22, and pep24 (the pep46 C-terminal moiety) in different hydrophobic environments and micelles determined by (1)H NMR studies provide structural insights of the pep46 domain interaction. In CDCl(3)/CD(3)OH mixture and in dodecylphosphocholine micelles, the N-terminal domain of pep46 is structured in a long kinked helix, although the C terminus is structured in one or two helices depending upon the solvents used. We also show that the folding and the proline isomerization status of pep46 depend on the type of hydrophobic environment. NMR spectroscopy with labeled phospholipid micelles, differential scanning calorimetry, and plasmon waveguide resonance studies show the peptides lie parallel to the lipid-water interface, perturbing the fatty acid chain packing. All these data lead to a model in which the two domains of pep46 interact with the membrane to form pores.


Asunto(s)
Birnaviridae/metabolismo , Espectroscopía de Resonancia Magnética/métodos , Membranas Artificiales , Péptidos/química , Animales , Rastreo Diferencial de Calorimetría/métodos , Eritrocitos/citología , Eritrocitos/virología , Ácidos Grasos/química , Hemólisis , Interacciones Hidrofóbicas e Hidrofílicas , Lípidos/química , Micelas , Estructura Terciaria de Proteína , Proteínas/química , Ovinos , Solventes/química
15.
Biomol NMR Assign ; 15(2): 267-271, 2021 10.
Artículo en Inglés | MEDLINE | ID: mdl-33754285

RESUMEN

During the maturation of the HIV-1 particle, the Gag polyprotein is cleaved by the viral protease into several proteins: matrix (MA), capsid (CA), spacer peptide 1 (SP1), nucleocapsid (NC), spacer peptide 2 (SP2) and p6. After cleavage, these proteins rearrange to form infectious viral particles. The final cleavage by the protease occurs between CA and SP1 and is the limiting step for the maturation of the particle. The CA-SP1 junction is the target of HIV-1 maturation inhibitors. CA is responsible for the formation of the viral capsid which protects the viral RNA inside. The SP1 domain is essential for viral assembly and infectivity, it is flexible and in helix-coil equilibrium. The presence of NC allows the SP1 domain to be less dynamic. The perturbation of the natural coil-helix equilibrium to helix interferes with protease cleavage and leads to non-completion of viral maturation. In this work, two mutations, W316A and M317A, that abolish the oligomerization of CA were introduced into the protein. The HIV-1 CACTDW316A, M317A-SP1-NC which contains the C-terminal monomeric mutant of CA, SP1 and NC was produced to study the mechanism of action of HIV-1 maturation inhibitors. Here we report the backbone assignment of the protein CACTDW316A, M317A-SP1-NC. These results will be useful to study the interaction between HIV-1 Gag and HIV-1 maturation inhibitors.


Asunto(s)
VIH-1
16.
Protein Sci ; 30(11): 2324-2332, 2021 11.
Artículo en Inglés | MEDLINE | ID: mdl-34462977

RESUMEN

Detergent-soluble proteins (DSPs) are commonly dissolved in lipid buffers for NMR experiments, but the huge lipid proton signal prevents recording of high-quality spectra. The use of costly deuterated lipids is thus required to replace nondeuterated ones. With conventional methods, detergents like dodecylphosphocholine (DPC) cannot be fully exchanged due to their high binding affinity to hydrophobic proteins. We propose an original and simple protocol which combines the use of acetonitrile, dialysis and lyophilization to disrupt the binding of lipids to the protein and allow their indirect replacement by their deuterated equivalents, while maintaining the native structure of the protein. Moreover, by this protocol, the detergent-to-protein molar ratio can be controlled as it challenges the protein structure. This protocol was applied to solubilize the Vpx protein that was followed upon addition of DPC-d38 by 1 H-15 N SOFAST-HMQC spectra and the best detergent-to-DSPs molar ratio was obtained for structural studies.


Asunto(s)
Acetonitrilos/química , Detergentes/química , Proteínas de la Membrana/química , Resonancia Magnética Nuclear Biomolecular , Fosforilcolina/análogos & derivados , Fosforilcolina/química
17.
Microbiol Spectr ; 9(2): e0047121, 2021 10 31.
Artículo en Inglés | MEDLINE | ID: mdl-34704807

RESUMEN

Staphylococci are pathogenic biofilm-forming bacteria and a source of multidrug resistance and/or tolerance causing a broad spectrum of infections. These bacteria are enclosed in a matrix that allows them to colonize medical devices, such as catheters and tissues, and that protects against antibiotics and immune systems. Advances in antibiofilm strategies for targeting this matrix are therefore extremely relevant. Here, we describe the development of the Capsicum pepper bioinspired peptide "capsicumicine." By using microbiological, microscopic, and nuclear magnetic resonance (NMR) approaches, we demonstrate that capsicumicine strongly prevents methicillin-resistant Staphylococcus epidermidis biofilm via an extracellular "matrix anti-assembly" mechanism of action. The results were confirmed in vivo in a translational preclinical model that mimics medical device-related infection. Since capsicumicine is not cytotoxic, it is a promising candidate for complementary treatment of infectious diseases. IMPORTANCE Pathogenic biofilms are a global health care concern, as they can cause extensive antibiotic resistance, morbidity, mortality, and thereby substantial economic loss. So far, no effective treatments targeting the bacteria in biofilms have been developed. Plants are constantly attacked by a wide range of pathogens and have protective factors, such as peptides, to defend themselves. These peptides are common components in Capsicum baccatum (red pepper). Here, we provide insights into an antibiofilm strategy based on the development of capsicumicine, a natural peptide that strongly controls biofilm formation by Staphylococcus epidermidis, the most prevalent pathogen in device-related infections.


Asunto(s)
Antibacterianos/farmacología , Biopelículas/efectos de los fármacos , Capsicum/química , Staphylococcus aureus Resistente a Meticilina/efectos de los fármacos , Péptidos/farmacología , Antibacterianos/química , Humanos , Staphylococcus aureus Resistente a Meticilina/genética , Staphylococcus aureus Resistente a Meticilina/fisiología , Pruebas de Sensibilidad Microbiana , Péptidos/química , Infecciones Estafilocócicas/microbiología
18.
Eur J Med Chem ; 204: 112634, 2020 Oct 15.
Artículo en Inglés | MEDLINE | ID: mdl-32717487

RESUMEN

During the maturation of HIV-1 particle, the Gag polyprotein is cleaved into several proteins by the HIV-1 protease. These proteins rearrange to form infectious virus particles. In this study, the solution structure and dynamics of a monomeric mutated domain encompassing the C-terminal of capsid, the spacer peptide SP1 and the nucleocapsid from Gag was characterized by Nuclear Magnetic Resonance in the presence of maturation inhibitor EP39, a more hydro-soluble derivative of BVM. We show that the binding of EP39 decreases the dynamics of CA-SP1 junction, especially the QVT motif in SP1, and perturbs the natural coil-helix equilibrium on both sides of the SP1 domain by stabilizing the transient alpha helical structure. Our results provide new insight into the structure and dynamics of the SP1 domain and how HIV-1 maturation inhibitors interfere with this domain. They offer additional clues for the development of new second generation inhibitors targeting HIV-1 maturation.


Asunto(s)
Fármacos Anti-VIH/farmacología , Productos del Gen gag/metabolismo , VIH-1/efectos de los fármacos , Secuencia de Aminoácidos , Sitios de Unión , Dimerización , Productos del Gen gag/química , VIH-1/fisiología , Humanos , Resonancia Magnética Nuclear Biomolecular , Factor de Transcripción Sp1/química , Factor de Transcripción Sp1/metabolismo
19.
J Chem Theory Comput ; 16(4): 2013-2020, 2020 Apr 14.
Artículo en Inglés | MEDLINE | ID: mdl-32178519

RESUMEN

Using polarizable (AMOEBA) and nonpolarizable (CHARMM) force fields, we compare the relative free energy stability of two extreme conformations of the HIV-1 nucleocapsid protein NCp7 that had been previously experimentally advocated to prevail in solution. Using accelerated sampling techniques, we show that they differ in stability by no more than 0.75-1.9 kcal/mol depending on the reference protein sequence. While the extended form appears to be the most probable structure, both forms should thus coexist in water explaining the differing NMR findings.


Asunto(s)
Productos del Gen gag del Virus de la Inmunodeficiencia Humana/química , Entropía , Espectroscopía de Resonancia Magnética , Simulación de Dinámica Molecular
20.
Biochemistry ; 48(11): 2355-67, 2009 Mar 24.
Artículo en Inglés | MEDLINE | ID: mdl-19254034

RESUMEN

The ability of human immunodeficiency virus type 1 (HIV-1) to egress from human cells by budding with the cell membrane remains a complex phenomenon of unclear steps. HIV-1 viral protein R (Vpr) incorporation in sorting virions relies greatly on the interaction with the group-specific antigen (Gag) C-terminal region, which encompasses protein p6. The complete role of p6 is still undetermined; however, it is thought that p6 interacts with protein core elements from the endosomal sorting complex ESCRT-1, known to sort ubiquitinated cargo into multivesicular bodies (MVB). The three-dimensional structure of the p6 C-terminus (p6ct) comprising amino acids 32-52, determined in this study using NMR methods, includes the region thought to interact with Vpr, i.e., the LXXLF sequence. Here we present new results indicating that the region which interacts with Vpr is the ELY(36) sequence, in the same region where mutational studies revealed that replacing Y36 with a phenylalanine would increase the infectivity of virions by 300-fold. The interaction of Vpr with an egg PC bilayer in the presence of p6ct measured by plasmon waveguide resonance (PWR) is approximately 0.8 microM, approximately 100 times stronger in the absence of p6ct. Our results suggests an interaction based on an ELYP(37) sequence bearing similarities with recently published results, which elegantly demonstrated that the HIV-1 Gag LYPx(n)LxxL motif interacts with Alix 364-702. Moreover, we performed a 60 ns molecular dynamics (MD) simulation of p6ct in DPC micelles. The MD results, supported by differential scanning calorimetry measurements in DMPC, show that p6ct adsorbs onto the DPC micelle surface by adopting a rather stable alpha-helix. Our results provide insights regarding the HIV-1 virion sorting mechanism, specifically concerning the interaction between p6 and Vpr. We also suggest that Gag p6 may adsorb onto the surface of membranes during the sorting process, a property so far only attributed to the N-terminal portion of Gag matrix (MA), which is myristylated. The implications of such a novel event provide an alternative direction toward understanding the assembly and escape mechanisms of virions, which have been undetected so far.


Asunto(s)
Productos del Gen gag del Virus de la Inmunodeficiencia Humana/química , Productos del Gen vpr del Virus de la Inmunodeficiencia Humana/química , Secuencia de Aminoácidos , Espectroscopía de Resonancia Magnética , Conformación Molecular , Datos de Secuencia Molecular , Unión Proteica
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