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1.
J Mol Biol ; 435(16): 168153, 2023 08 15.
Artigo em Inglês | MEDLINE | ID: mdl-37210029

RESUMO

Viral factories of liquid-like nature serve as sites for transcription and replication in most viruses. The respiratory syncytial virus factories include replication proteins, brought together by the phosphoprotein (P) RNA polymerase cofactor, present across non-segmented negative stranded RNA viruses. Homotypic liquid-liquid phase separation of RSV-P is governed by an α-helical molten globule domain, and strongly self-downmodulated by adjacent sequences. Condensation of P with the nucleoprotein N is stoichiometrically tuned, defining aggregate-droplet and droplet-dissolution boundaries. Time course analysis show small N-P nuclei gradually coalescing into large granules in transfected cells. This behavior is recapitulated in infection, with small puncta evolving to large viral factories, strongly suggesting that P-N nucleation-condensation sequentially drives viral factories. Thus, the tendency of P to undergo phase separation is moderate and latent in the full-length protein but unleashed in the presence of N or when neighboring disordered sequences are deleted. This, together with its capacity to rescue nucleoprotein-RNA aggregates suggests a role as a "solvent-protein".


Assuntos
Nucleoproteínas , Vírus Sincicial Respiratório Humano , Compartimentos de Replicação Viral , Proteínas Estruturais Virais , RNA Polimerases Dirigidas por DNA/metabolismo , Nucleoproteínas/metabolismo , Vírus Sincicial Respiratório Humano/metabolismo , Vírus Sincicial Respiratório Humano/fisiologia , Compartimentos de Replicação Viral/metabolismo , Replicação Viral , Proteínas Estruturais Virais/metabolismo , Humanos
2.
J Mol Biol ; 435(16): 167889, 2023 08 15.
Artigo em Inglês | MEDLINE | ID: mdl-36402224

RESUMO

p53 exerts its tumour suppressor activity by modulating hundreds of genes and it can also repress viral replication. Such is the case of human papillomavirus (HPV) through targeting the E2 master regulator, but the biochemical mechanism is not known. We show that the C-terminal DNA binding domain of HPV16 E2 protein (E2C) triggers heterotypic condensation with p53 at a precise 2/1 E2C/p53 stoichiometry at the onset for demixing, yielding large regular spherical droplets that increase in size with E2C concentration. Interestingly, transfection experiments show that E2 co-localizes with p53 in the nucleus with a grainy pattern, and recruits p53 to chromatin-associated foci, a function independent of the DNA binding capacity of p53 as judged by a DNA binding impaired mutant. Depending on the length, DNA can either completely dissolve or reshape heterotypic droplets into irregular condensates containing p53, E2C, and DNA, and reminiscent of that observed linked to chromatin. We propose that p53 is a scaffold for condensation in line with its structural and functional features, in particular as a promiscuous hub that binds multiple cellular proteins. E2 appears as both client and modulator, likely based on its homodimeric DNA binding nature. Our results, in line with the known role of condensation in eukaryotic gene enhancement and silencing, point at biomolecular condensation of E2 with p53 as a means to modulate HPV gene function, strictly dependent on host cell replication and transcription machinery.


Assuntos
Condensados Biomoleculares , Replicação do DNA , Proteínas de Ligação a DNA , Papillomavirus Humano 16 , Proteínas Oncogênicas Virais , Proteína Supressora de Tumor p53 , Replicação Viral , Humanos , Linhagem Celular Tumoral , Cromatina/química , Cromatina/metabolismo , DNA/química , DNA/metabolismo , Proteínas de Ligação a DNA/química , Proteínas de Ligação a DNA/metabolismo , Papillomavirus Humano 16/fisiologia , Proteínas Oncogênicas Virais/química , Proteínas Oncogênicas Virais/metabolismo , Infecções por Papillomavirus/virologia , Domínios Proteicos , Proteína Supressora de Tumor p53/genética , Proteína Supressora de Tumor p53/metabolismo , Replicação Viral/fisiologia , Condensados Biomoleculares/metabolismo , Condensados Biomoleculares/virologia
3.
Nat Struct Mol Biol ; 29(8): 781-790, 2022 08.
Artigo em Inglês | MEDLINE | ID: mdl-35948766

RESUMO

Many disordered proteins conserve essential functions in the face of extensive sequence variation, making it challenging to identify the mechanisms responsible for functional selection. Here we identify the molecular mechanism of functional selection for the disordered adenovirus early gene 1A (E1A) protein. E1A competes with host factors to bind the retinoblastoma (Rb) protein, subverting cell cycle regulation. We show that two binding motifs tethered by a hypervariable disordered linker drive picomolar affinity Rb binding and host factor displacement. Compensatory changes in amino acid sequence composition and sequence length lead to conservation of optimal tethering across a large family of E1A linkers. We refer to this compensatory mechanism as conformational buffering. We also detect coevolution of the motifs and linker, which can preserve or eliminate the tethering mechanism. Conformational buffering and motif-linker coevolution explain robust functional encoding within hypervariable disordered linkers and could underlie functional selection of many disordered protein regions.


Assuntos
Proteínas Intrinsicamente Desordenadas , Proteínas E1A de Adenovirus/química , Proteínas E1A de Adenovirus/genética , Proteínas E1A de Adenovirus/metabolismo , Sequência de Aminoácidos , Proteínas Intrinsicamente Desordenadas/química , Ligação Proteica , Domínios Proteicos , Proteína do Retinoblastoma/metabolismo
4.
Proteins ; 88(1): 106-112, 2020 01.
Artigo em Inglês | MEDLINE | ID: mdl-31299114

RESUMO

Bovine papillomavirus proteins were extensively studied as a prototype for the human papillomavirus. Here, the crystal structure of the extended E2 DNA-binding domain of the dominant transcription regulator from the bovine papillomavirus strain 1 is described in the space group P31 21. We found two protein functional dimers packed in the asymmetric unit. This new protein arrangement inside the crystal led to the reduction of the mobility of a previously unobserved loop directly involved in the protein-DNA interaction, which was then modeled for the first time.


Assuntos
Papillomavirus Bovino 1/química , Proteínas de Ligação a DNA/química , Proteínas Virais/química , Animais , Bovinos/virologia , Doenças dos Bovinos/virologia , Cristalografia por Raios X , Modelos Moleculares , Infecções por Papillomavirus/veterinária , Infecções por Papillomavirus/virologia , Conformação Proteica , Domínios Proteicos , Multimerização Proteica
5.
Mol Biol Evol ; 36(7): 1521-1532, 2019 07 01.
Artigo em Inglês | MEDLINE | ID: mdl-30982925

RESUMO

Redox regulation in biology is largely operated by cysteine chemistry in response to a variety of cell environmental and intracellular stimuli. The high chemical reactivity of cysteines determines their conservation in functional roles, but their presence can also result in harmful oxidation limiting their general use by proteins. Papillomaviruses constitute a unique system for studying protein sequence evolution since there are hundreds of anciently evolved stable genomes. E7, the viral transforming factor, is a dimeric, cysteine-rich oncoprotein that shows both conserved structural and variable regulatory cysteines constituting an excellent model for uncovering the mechanism that drives the acquisition of redox-sensitive groups. By analyzing over 300 E7 sequences, we found that although noncanonical cysteines show no obvious sequence conservation pattern, they are nonrandomly distributed based on topological constrains. Regulatory residues are strictly excluded from six positions stabilizing the hydrophobic core while they are enriched in key positions located at the dimerization interface or around the Zn+2 ion. Oxidation of regulatory cysteines is linked to dimer dissociation, acting as a reversible redox-sensing mechanism that triggers a conformational switch. Based on comparative sequence analysis, molecular dynamics simulations and biophysical analysis, we propose a model in which the occurrence of cysteine-rich positions is dictated by topological constrains, providing an explanation to why a degenerate pattern of cysteines can be achieved in a family of homologs. Thus, topological principles should enable the possibility to identify hidden regulatory cysteines that are not accurately detected using sequence based methodology.


Assuntos
Cisteína , Evolução Molecular , Proteínas E7 de Papillomavirus/genética , Sequência de Aminoácidos , Dimerização
6.
Virology ; 525: 117-131, 2018 12.
Artigo em Inglês | MEDLINE | ID: mdl-30265888

RESUMO

E1A is the main transforming protein in mastadenoviruses. This work uses bioinformatics to extrapolate experimental knowledge from Human adenovirus serotype 5 and 12 E1A proteins to all known serotypes. A conserved domain architecture with a high degree of intrinsic disorder acts as a scaffold for multiple linear motifs with variable occurrence mediating the interaction with over fifty host proteins. While linear motifs contribute strongly to sequence conservation within intrinsically disordered E1A regions, motif repertoires can deviate significantly from those found in prototypical serotypes. Close to one hundred predicted residue-residue contacts suggest the presence of stable structure in the CR3 domain and of specific conformational ensembles involving both short- and long-range intramolecular interactions. Our computational results suggest that E1A sequence conservation and co-evolution reflect the evolutionary pressure to maintain a mainly disordered, yet non-random conformation harboring a high number of binding motifs that mediate viral hijacking of the cell machinery.


Assuntos
Proteínas E1A de Adenovirus/metabolismo , Adenovírus Humanos/metabolismo , Proteínas E1A de Adenovirus/química , Proteínas E1A de Adenovirus/genética , Motivos de Aminoácidos , Sequência de Aminoácidos , Humanos , Conformação Proteica , Domínios Proteicos , Modificação Traducional de Proteínas
7.
Biochemistry ; 56(41): 5560-5569, 2017 10 17.
Artigo em Inglês | MEDLINE | ID: mdl-28952717

RESUMO

Intrinsic disorder is a major structural category in biology, accounting for more than 30% of coding regions across the domains of life, yet consists of conformational ensembles in equilibrium, a major challenge in protein chemistry. Anciently evolved papillomavirus genomes constitute an unparalleled case for sequence to structure-function correlation in cases in which there are no folded structures. E7, the major transforming oncoprotein of human papillomaviruses, is a paradigmatic example among the intrinsically disordered proteins. Analysis of a large number of sequences of the same viral protein allowed for the identification of a handful of residues with absolute conservation, scattered along the sequence of its N-terminal intrinsically disordered domain, which intriguingly are mostly leucine residues. Mutation of these led to a pronounced increase in both α-helix and ß-sheet structural content, reflected by drastic effects on equilibrium propensities and oligomerization kinetics, and uncovers the existence of local structural elements that oppose canonical folding. These folding relays suggest the existence of yet undefined hidden structural codes behind intrinsic disorder in this model protein. Thus, evolution pinpoints conformational hot spots that could have not been identified by direct experimental methods for analyzing or perturbing the equilibrium of an intrinsically disordered protein ensemble.


Assuntos
Papillomavirus Humano 16/metabolismo , Proteínas Intrinsicamente Desordenadas/química , Modelos Moleculares , Proteínas E7 de Papillomavirus/química , Sequência de Aminoácidos , Substituição de Aminoácidos , Sequência de Bases , Sequência Conservada , DNA Viral/química , DNA Viral/metabolismo , Deleção de Genes , Concentração de Íons de Hidrogênio , Proteínas Intrinsicamente Desordenadas/genética , Proteínas Intrinsicamente Desordenadas/metabolismo , Leucina/química , Mutagênese Sítio-Dirigida , Proteínas E7 de Papillomavirus/genética , Proteínas E7 de Papillomavirus/metabolismo , Fragmentos de Peptídeos/química , Fragmentos de Peptídeos/genética , Fragmentos de Peptídeos/metabolismo , Mutação Puntual , Conformação Proteica , Conformação Proteica em alfa-Hélice , Conformação Proteica em Folha beta , Dobramento de Proteína , Estabilidade Proteica , Proteínas Recombinantes/química , Proteínas Recombinantes/metabolismo , Alinhamento de Sequência
8.
Redox Biol ; 11: 38-50, 2017 04.
Artigo em Inglês | MEDLINE | ID: mdl-27863297

RESUMO

Infection with oncogenic human papillomavirus induces deregulation of cellular redox homeostasis. Virus replication and papillomavirus-induced cell transformation require persistent expression of viral oncoproteins E7 and E6 that must retain their functionality in a persistent oxidative environment. Here, we dissected the molecular mechanisms by which E7 oncoprotein can sense and manage the potentially harmful oxidative environment of the papillomavirus-infected cell. The carboxy terminal domain of E7 protein from most of the 79 papillomavirus viral types of alpha genus, which encloses all the tumorigenic viral types, is a cysteine rich domain that contains two classes of cysteines: strictly conserved low reactive Zn+2 binding and degenerate reactive cysteine residues that can sense reactive oxygen species (ROS). Based on experimental data obtained from E7 proteins from the prototypical viral types 16, 18 and 11, we identified a couple of low pKa nucleophilic cysteines that can form a disulfide bridge upon the exposure to ROS and regulate the cytoplasm to nucleus transport. From sequence analysis and phylogenetic reconstruction of redox sensing states we propose that reactive cysteine acquisition through evolution leads to three separate E7s protein families that differ in the ROS sensing mechanism: non ROS-sensitive E7s; ROS-sensitive E7s using only a single or multiple reactive cysteine sensing mechanisms and ROS-sensitive E7s using a reactive-resolutive cysteine couple sensing mechanism.


Assuntos
Cisteína/metabolismo , Neoplasias/genética , Estresse Oxidativo/genética , Proteínas E7 de Papillomavirus/metabolismo , Nucléolo Celular/metabolismo , Transformação Celular Neoplásica/genética , Transformação Celular Neoplásica/patologia , Cisteína/genética , Citoplasma/metabolismo , Dissulfetos/metabolismo , Neoplasias/metabolismo , Neoplasias/patologia , Oxirredução , Proteínas E7 de Papillomavirus/genética , Transporte Proteico/genética , Replicação Viral/genética
9.
Curr Opin Struct Biol ; 32: 91-101, 2015 Jun.
Artigo em Inglês | MEDLINE | ID: mdl-25863584

RESUMO

Pathogen linear motif mimics are highly evolvable elements that facilitate rewiring of host protein interaction networks. Host linear motifs and pathogen mimics differ in sequence, leading to thermodynamic and structural differences in the resulting protein-protein interactions. Moreover, the functional output of a mimic depends on the motif and domain repertoire of the pathogen protein. Regulatory evolution mediated by linear motifs can be understood by measuring evolutionary rates, quantifying positive and negative selection and performing phylogenetic reconstructions of linear motif natural history. Convergent evolution of linear motif mimics is widespread among unrelated proteins from viral, prokaryotic and eukaryotic pathogens and can also take place within individual protein phylogenies. Statistics, biochemistry and laboratory models of infection link pathogen linear motifs to phenotypic traits such as tropism, virulence and oncogenicity. In vitro evolution experiments and analysis of natural sequences suggest that changes in linear motif composition underlie pathogen adaptation to a changing environment.


Assuntos
Interações Hospedeiro-Patógeno , Mimetismo Molecular , Mapas de Interação de Proteínas , Proteínas/química , Proteínas/metabolismo , Motivos de Aminoácidos , Animais , Evolução Molecular , Humanos , Modelos Moleculares , Conformação Proteica , Proteínas/genética
10.
Biochemistry ; 53(10): 1680-96, 2014 Mar 18.
Artigo em Inglês | MEDLINE | ID: mdl-24559112

RESUMO

The E7 protein from high-risk human papillomavirus is essential for cell transformation in cervical, oropharyngeal, and other HPV-related cancers, mainly through the inactivation of the retinoblastoma (Rb) tumor suppressor. Its high cysteine content (~7%) and the observation that HPV-transformed cells are under oxidative stress prompted us to investigate the redox properties of the HPV16 E7 protein under biologically compatible oxidative conditions. The seven cysteines in HPV16 E7 remain reduced in conditions resembling the basal reduced state of a cell. However, under oxidative stress, a stable disulfide bridge forms between cysteines 59 and 68. Residue 59 has a protective effect on the other cysteines, and its mutation leads to an overall increase in the oxidation propensity of E7, including cysteine 24 central to the Rb binding motif. Gluthationylation of Cys 24 abolishes Rb binding, which is reversibly recovered upon reduction. Cysteines 59 and 68 are located 18.6 Å apart, and the formation of the disulfide bridge leads to a large structural rearrangement while retaining strong Zn association. These conformational and covalent changes are fully reversible upon restoration of the reductive environment. In addition, this is the first evidence of an interaction between the N-terminal intrinsically disordered and the C-terminal globular domains, known to be highly and separately conserved among human papillomaviruses. The significant conservation of such noncanonical cysteines in HPV E7 proteins leads us to propose a functional redox activity. Such an activity adds to the previously discovered chaperone activity of E7 and supports the picture of a moonlighting pathological role of this paradigmatic viral oncoprotein.


Assuntos
Cisteína/química , Papillomavirus Humano 16/metabolismo , Proteínas E7 de Papillomavirus/metabolismo , Infecções por Papillomavirus/metabolismo , Motivos de Aminoácidos , Sequência de Aminoácidos , Cisteína/genética , Cisteína/metabolismo , Papillomavirus Humano 16/química , Papillomavirus Humano 16/genética , Humanos , Modelos Moleculares , Dados de Sequência Molecular , Estresse Oxidativo , Proteínas E7 de Papillomavirus/química , Proteínas E7 de Papillomavirus/genética , Infecções por Papillomavirus/virologia , Alinhamento de Sequência , Dedos de Zinco
11.
PLoS One ; 8(9): e72760, 2013.
Artigo em Inglês | MEDLINE | ID: mdl-24086265

RESUMO

Intrinsic disorder is abundant in viral genomes and provides conformational plasticity to its protein products. In order to gain insight into its structure-function relationships, we carried out a comprehensive analysis of structural propensities within the intrinsically disordered N-terminal domain from the human papillomavirus type-16 E7 oncoprotein (E7N). Two E7N segments located within the conserved CR1 and CR2 regions present transient α-helix structure. The helix in the CR1 region spans residues L8 to L13 and overlaps with the E2F mimic linear motif. The second helix, located within the highly acidic CR2 region, presents a pH-dependent structural transition. At neutral pH the helix spans residues P17 to N29, which include the retinoblastoma tumor suppressor LxCxE binding motif (residues 21-29), while the acidic CKII-PEST region spanning residues E33 to I38 populates polyproline type II (PII) structure. At pH 5.0, the CR2 helix propagates up to residue I38 at the expense of loss of PII due to charge neutralization of acidic residues. Using truncated forms of HPV-16 E7, we confirmed that pH-induced changes in α-helix content are governed by the intrinsically disordered E7N domain. Interestingly, while at both pH the region encompassing the LxCxE motif adopts α-helical structure, the isolated 21-29 fragment including this stretch is unable to populate an α-helix even at high TFE concentrations. Thus, the E7N domain can populate dynamic but discrete structural ensembles by sampling α-helix-coil-PII-ß-sheet structures. This high plasticity may modulate the exposure of linear binding motifs responsible for its multi-target binding properties, leading to interference with key cell signaling pathways and eventually to cellular transformation by the virus.


Assuntos
Transformação Celular Neoplásica , Proteínas Intrinsicamente Desordenadas/química , Proteínas Oncogênicas Virais/química , Papillomaviridae/química , Sequência de Aminoácidos , Dicroísmo Circular , Concentração de Íons de Hidrogênio , Dados de Sequência Molecular , Ressonância Magnética Nuclear Biomolecular , Conformação Proteica , Espectrofotometria Ultravioleta
12.
Biochemistry ; 52(39): 6779-89, 2013 Oct 01.
Artigo em Inglês | MEDLINE | ID: mdl-23984912

RESUMO

Human respiratory syncytial virus (hRSV) is a worldwide distributed pathogen that causes respiratory disease mostly in infants and the elderly. The M2-1 protein of hRSV functions as a transcription antiterminator and partakes in virus particle budding. It is present only in Pneumovirinae, namely, Pneumovirus (RSV) and Metapneumovirus, making it an interesting target for specific antivirals. hRSV M2-1 is a tight tetramer bearing a Cys3-His1 zinc-binding motif, present in Ebola VP30 protein and some eukaryotic proteins, whose integrity was shown to be essential for protein function but without a biochemical mechanistic basis. We showed that removal of the zinc atom causes dissociation to a monomeric apo-M2-1 species. Surprisingly, the secondary structure and stability of the apo-monomer is indistinguishable from that of the M2-1 tetramer. Dissociation reported by a highly sensitive tryptophan residue is much increased at pH 5.0 compared to pH 7.0, suggesting a histidine protonation cooperating in zinc removal. The monomeric apo form binds RNA at least as well as the tetramer, and this interaction is outcompeted by the phosphoprotein P, the RNA polymerase cofactor. The role of zinc goes beyond stabilization of local structure, finely tuning dissociation to a fully folded and binding competent monomer. Removal of zinc is equivalent to the disruption of the motif by mutation, only that the former is potentially reversible in the cellular context. Thus, this process could be triggered by a natural chelator such as glutathione or thioneins, where reversibility strongly suggests a modulatory role in the participation of M2-1 in the assembly of the polymerase complex or in virion budding.


Assuntos
Cisteína/química , Histidina/química , Vírus Sincicial Respiratório Humano/química , Proteínas Virais/química , Zinco/metabolismo , Motivos de Aminoácidos , Cisteína/metabolismo , Histidina/metabolismo , Humanos , Concentração de Íons de Hidrogênio , Estrutura Quaternária de Proteína , Vírus Sincicial Respiratório Humano/genética , Vírus Sincicial Respiratório Humano/metabolismo , Proteínas Virais/metabolismo , Zinco/química , Zinco/deficiência
13.
J Biol Chem ; 288(26): 18923-38, 2013 Jun 28.
Artigo em Inglês | MEDLINE | ID: mdl-23632018

RESUMO

The retinoblastoma tumor suppressor (Rb) controls the proliferation, differentiation, and survival of cells in most eukaryotes with a role in the fate of stem cells. Its inactivation by mutation or oncogenic viruses is required for cellular transformation and eventually carcinogenesis. The high conservation of the Rb cyclin fold prompted us to investigate the link between conformational stability and ligand binding properties of the RbAB pocket domain. RbAB unfolding presents a three-state transition involving cooperative secondary and tertiary structure changes and a partially folded intermediate that can oligomerize. The first transition corresponds to unfolding of the metastable B subdomain containing the binding site for the LXCXE motif present in cellular and viral targets, and the second transition corresponds to the stable A subdomain. The low thermodynamic stability of RbAB translates into a propensity to rapidly oligomerize and aggregate at 37 °C (T50 = 28 min) that is suppressed by human papillomavirus E7 and E2F peptide ligands, suggesting that Rb is likely stabilized in vivo through binding to target proteins. We propose that marginal stability and associated oligomerization may be conserved for function as a "hub" protein, allowing the formation of multiprotein complexes, which could constitute a robust mechanism to retain its cell cycle regulatory role throughout evolution. Decreased stability and oligomerization are shared with the p53 tumor suppressor, suggesting a link between folding and function in these two essential cell regulators that are inactivated in most cancers and operate within multitarget signaling pathways.


Assuntos
Ciclinas/química , Dobramento de Proteína , Proteína do Retinoblastoma/química , Sítios de Ligação , Diferenciação Celular , Dicroísmo Circular , Proteínas de Ligação a DNA/química , Fatores de Transcrição E2F/química , Humanos , Ligantes , Modelos Moleculares , Proteínas Oncogênicas Virais/química , Proteínas E7 de Papillomavirus/química , Ligação Proteica , Estrutura Terciária de Proteína , Transdução de Sinais , Temperatura , Proteína Supressora de Tumor p53/química
14.
J Biol Chem ; 288(18): 13110-23, 2013 May 03.
Artigo em Inglês | MEDLINE | ID: mdl-23504368

RESUMO

Conformational rearrangements in antibody·antigen recognition are essential events where kinetic discrimination of isomers expands the universe of combinations. We investigated the interaction mechanism of a monoclonal antibody, M1, raised against E7 from human papillomavirus, a prototypic viral oncoprotein and a model intrinsically disordered protein. The mapped 12-amino acid immunodominant epitope lies within a "hinge" region between the N-terminal intrinsically disordered and the C-terminal globular domains. Kinetic experiments show that despite being within an intrinsically disordered region, the hinge E7 epitope has at least two populations separated by a high energy barrier. Nuclear magnetic resonance traced the origin of this barrier to a very slow (t(1/2)∼4 min) trans-cis prolyl isomerization event involving changes in secondary structure. The less populated (10%) cis isomer is the binding-competent species, thus requiring the 90% of molecules in the trans configuration to isomerize before binding. The association rate for the cis isomer approaches 6 × 10(7) M(-1) s(-1), a ceiling for antigen-antibody interactions. Mutagenesis experiments showed that Pro-41 in E7Ep was required for both binding and isomerization. After a slow postbinding unimolecular rearrangement, a consolidated complex with K(D) = 1.2 × 10(-7) M is reached. Our results suggest that presentation of this viral epitope by the antigen-presenting cells would have to be "locked" in the cis conformation, in opposition to the most populated trans isomer, in order to select the specific antibody clone that goes through affinity and kinetic maturation.


Assuntos
Anticorpos Monoclonais Murinos/química , Anticorpos Antivirais/química , Especificidade de Anticorpos , Papillomavirus Humano 16/química , Proteínas E7 de Papillomavirus/química , Animais , Anticorpos Monoclonais Murinos/imunologia , Anticorpos Antivirais/imunologia , Epitopos , Papillomavirus Humano 16/genética , Papillomavirus Humano 16/imunologia , Humanos , Camundongos , Ressonância Magnética Nuclear Biomolecular , Proteínas E7 de Papillomavirus/genética , Proteínas E7 de Papillomavirus/imunologia , Estrutura Secundária de Proteína
15.
PLoS One ; 7(10): e47661, 2012.
Artigo em Inglês | MEDLINE | ID: mdl-23118886

RESUMO

In the present work, we have used the papillomavirus E7 oncoprotein to pursue structure-function and evolutionary studies that take into account intrinsic disorder and the conformational diversity of globular domains. The intrinsically disordered (E7N) and globular (E7C) domains of E7 show similar degrees of conservation and co-evolution. We found that E7N can be described in terms of conserved and coevolving linear motifs separated by variable linkers, while sequence evolution of E7C is compatible with the known homodimeric structure yet suggests other activities for the domain. Within E7N, inter-residue relationships such as residue co-evolution and restricted intermotif distances map functional coupling and co-occurrence of linear motifs that evolve in a coordinate manner. Within E7C, additional cysteine residues proximal to the zinc-binding site may allow redox regulation of E7 function. Moreover, we describe a conserved binding site for disordered domains on the surface of E7C and suggest a putative target linear motif. Both homodimerization and peptide binding activities of E7C are also present in the distantly related host PHD domains, showing that these two proteins share not only structural homology but also functional similarities, and strengthening the view that they evolved from a common ancestor. Finally, we integrate the multiple activities and conformations of E7 into a hierarchy of structure-function relationships.


Assuntos
Motivos de Aminoácidos , Evolução Molecular , Proteínas E7 de Papillomavirus , Relação Estrutura-Atividade , Sequência de Aminoácidos , Sítios de Ligação , Dimerização , Humanos , Proteínas E7 de Papillomavirus/química , Proteínas E7 de Papillomavirus/genética , Conformação Proteica , Estrutura Terciária de Proteína , Alinhamento de Sequência , Zinco/química
16.
Biochemistry ; 51(41): 8100-10, 2012 Oct 16.
Artigo em Inglês | MEDLINE | ID: mdl-22978633

RESUMO

Paramyxoviruses share the essential RNA polymerase complex components, namely, the polymerase (L), phosphoprotein (P), and nucleoprotein (N). Human respiratory syncytial virus (RSV) P is the smallest polypeptide among the family, sharing a coiled coil tetramerization domain, which disruption renders the virus inactive. We show that unfolding of P displays a first transition with low cooperativity but substantial loss of α-helix content and accessibility to hydrophobic sites, indicative of loose chain packing and fluctuating tertiary structure, typical of molten globules. The lack of unfolding baseline indicates a native state in conformational exchange and metastable at 20 °C. The second transition starts from a true intermediate state, with only the tetramerization domain remaining folded. The tetramerization domain undergoes a two-state dissociation/unfolding reaction (37.3 kcal mol(-1)). The M(2-1) transcription antiterminator, unique to RSV and Metapneumovirus, forms a nonglobular P:M(2-1) complex with a 1:1 stoichiometry and a K(D) of 8.1 nM determined by fluorescence anisotropy, far from the strikingly coincident dissociation range of P and M(2-1) tetramers (10(-28) M(3)). The M(2-1) binding region has been previously mapped to the N-terminal module of P, strongly suggesting the latter as the metastable molten globule domain. Folding, oligomerization, and assembly events between proteins and with RNA are coupled in the RNA polymerase complex. Quantitative assessment of the hierarchy of these interactions and their mechanisms contribute to the general understanding of RNA replication and transcription in Paramyxoviruses. In particular, the unique P-M(2-1) interface present in RSV provides a valuable antiviral target for this worldwide spread human pathogen.


Assuntos
Biopolímeros/metabolismo , Fosfoproteínas/metabolismo , Desnaturação Proteica , Vírus Sincicial Respiratório Humano/metabolismo , Biopolímeros/química , Cromatografia em Gel , Dicroísmo Circular , Fosfoproteínas/química , Conformação Proteica , Dobramento de Proteína , Espectrometria de Fluorescência
17.
Methods Mol Biol ; 895: 387-404, 2012.
Artigo em Inglês | MEDLINE | ID: mdl-22760329

RESUMO

Circular dichroism (CD) spectroscopy is a simple and powerful technique, which allows for the assessment of the conformational properties of a protein or protein domain. Intrinsically disordered proteins (IDPs), as discussed throughout this series, differ from random coil polypeptides in that different regions present specific conformational preferences, exhibiting dynamic secondary structure content [1]. These dynamic secondary structure elements can be stabilized or perturbed by different chemical (solvent, ionic strength, pH) or physical (temperature) agents, by posttranslational modifications, and by ligands. This information is important for defining ID nature. As IDPs present dynamic conformations, circular dichroism measurements (and other approaches as well) should be carried out not as single spectra performed in unique conditions, but instead changing the chemical conditions and observing the behavior, as part of the determination of the ID nature.In this chapter, we present the basic methodology for performing Far-UV CD measurements on a protein of interest and for identifying and characterizing intrinsically disordered regions, and several protocols for the analysis of residual secondary structure present in the protein under study. These techniques are straightforward to perform; they require minimal training and can be preliminary to more complex methodologies such as NMR.


Assuntos
Dicroísmo Circular , Proteínas E7 de Papillomavirus/química , Algoritmos , Modelos Moleculares , Peptídeos/química , Fosforilação , Estrutura Secundária de Proteína , Estrutura Terciária de Proteína
18.
J Mol Biol ; 422(3): 336-46, 2012 Sep 21.
Artigo em Inglês | MEDLINE | ID: mdl-22683353

RESUMO

Many protein functions can be traced to linear sequence motifs of less than five residues, which are often found within intrinsically disordered domains. In spite of their prevalence, their role in protein evolution is only beginning to be understood. The study of papillomaviruses has provided many insights on the evolution of protein structure and function. We have chosen the papillomavirus E7 oncoprotein as a model system for the evolution of functional linear motifs. The multiple functions of E7 proteins from paradigmatic papillomavirus types can be explained to a large extent in terms of five linear motifs within the intrinsically disordered N-terminal domain and two linear motifs within the globular homodimeric C-terminal domain. We examined the motif inventory of E7 proteins from over 200 known papillomavirus types and found that the motifs reported for paradigmatic papillomavirus types are absent from many uncharacterized E7 proteins. Several motif pairs occur more often than expected, suggesting that linear motifs may evolve and function in a cooperative manner. The E7 linear motifs have appeared or disappeared multiple times during papillomavirus evolution, confirming the evolutionary plasticity of short functional sequences. Four of the motifs appeared several times during papillomavirus evolution, providing direct evidence for convergent evolution. Interestingly, the evolution pattern of a motif is independent of its location in a globular or disordered domain. The correlation between the presence of some motifs and virus host specificity and tissue tropism suggests that linear motifs play a role in the adaptive evolution of papillomaviruses.


Assuntos
Papillomaviridae/genética , Proteínas E7 de Papillomavirus/química , Proteínas E7 de Papillomavirus/genética , Motivos de Aminoácidos , Sequência de Aminoácidos , Evolução Molecular , Dados de Sequência Molecular , Papillomaviridae/metabolismo , Proteínas E7 de Papillomavirus/metabolismo , Estrutura Terciária de Proteína , Alinhamento de Sequência
19.
PLoS One ; 7(5): e36457, 2012.
Artigo em Inglês | MEDLINE | ID: mdl-22590549

RESUMO

BACKGROUND: Self-assembly is a common theme in proteins of unrelated sequences or functions. The human papillomavirus E7 oncoprotein is an extended dimer with an intrinsically disordered domain, that can form large spherical oligomers. These are the major species in the cytosol of HPV transformed and cancerous cells. E7 binds to a large number of targets, some of which lead to cell transformation. Thus, the assembly process not only is of biological relevance, but represents a model system to investigate a widely distributed mechanism. METHODOLOGY/PRINCIPAL FINDINGS: Using various techniques, we monitored changes in secondary, tertiary and quaternary structure in a time course manner. By applying a robust kinetic model developed by Zlotnik, we determined the slow formation of a monomeric "Z-nucleus" after zinc removal, followed by an elongation phase consisting of sequential second-order events whereby one monomer is added at a time. This elongation process takes place at a strikingly slow overall average rate of one monomer added every 28 seconds at 20 µM protein concentration, strongly suggesting either a rearrangement of the growing complex after binding of each monomer or the existence of a "conformation editing" mechanism through which the monomer binds and releases until the appropriate conformation is adopted. The oligomerization determinant lies within its small 5 kDa C-terminal globular domain and, remarkably, the E7 N-terminal intrinsically disordered domain stabilizes the oligomer, preventing an insoluble amyloid route. CONCLUSION: We described a controlled ordered mechanism with features in common with soluble amyloid precursors, chaperones, and other spherical oligomers, thus sharing determining factors for symmetry, size and shape. In addition, such a controlled and discrete polymerization reaction provides a valuable tool for nanotechnological applications. Finally, its increased immunogenicity related to its supramolecular structure is the basis for the development of a promising therapeutic vaccine candidate for treating HPV cancerous lesions.


Assuntos
Papillomavirus Humano 16/química , Proteínas E7 de Papillomavirus/química , Multimerização Proteica , Zinco/química , Papillomavirus Humano 16/genética , Papillomavirus Humano 16/metabolismo , Humanos , Proteínas E7 de Papillomavirus/genética , Proteínas E7 de Papillomavirus/metabolismo , Estabilidade Proteica , Estrutura Quaternária de Proteína , Estrutura Terciária de Proteína , Zinco/metabolismo
20.
Int J Cancer ; 130(8): 1813-20, 2012 Apr 15.
Artigo em Inglês | MEDLINE | ID: mdl-21780110

RESUMO

Cervical cancer and many other anogenital and oropharyngeal carcinomas are strongly associated with high-risk human papillomavirus (HPV) persistent infections. HPV E7 oncoprotein is the major viral transforming factor, emerging as a natural candidate for immunotherapy, since it is constitutively expressed in HPV-induced cancer cells. We have previously shown that E7 can self-assemble into soluble and homogeneous spherical oligomers, named E7 soluble oligomers (E7SOs). These are highly resistant to thermal denaturation, providing an additional advantage given the demand for highly stable vaccine formulations. Here, we present a new chemically stabilized form of the E7SOs (E7SOx) and analyzed its effect in a murine HPV-tumor model. Vaccination of female mice with low doses of E7SOx combined with a CpG-rich oligonucleotide (ODN) as adjuvant elicits a strong long-lasting protection against E7-expressing tumor cells, preventing tumor outgrowth after rechallenge 90-days later. Therapeutic experiments showed that E7SOx/ODN vaccination significantly delays tumor growth and extends the time of survival of the treated mice in a dose-dependent manner. These proof-of-principle preclinical experiments denote the potential applicability of our E7SOx-based vaccine to the treatment of cervical cancer and other mucosal HPV-related neoplastic lesions. In addition to thermal, chemical and proteolysis stability, the combined recombinant and chemical modification nature of the E7SOx vaccine candidate, results in low-cost, of particular interest in developing countries, where most of the cervical cancer cases occur and the most affected population is at reproductive age.


Assuntos
Vacinas Anticâncer/imunologia , Neoplasias/imunologia , Proteínas E7 de Papillomavirus/imunologia , Infecções por Papillomavirus/imunologia , Vacinas contra Papillomavirus/imunologia , Neoplasias do Colo do Útero/imunologia , Adjuvantes Imunológicos/administração & dosagem , Animais , Vacinas Anticâncer/administração & dosagem , Relação Dose-Resposta a Droga , Feminino , Humanos , Imunoterapia/métodos , Estimativa de Kaplan-Meier , Camundongos , Camundongos Endogâmicos C57BL , Microscopia Eletrônica , Neoplasias/terapia , Neoplasias/virologia , Oligodesoxirribonucleotídeos/administração & dosagem , Oligodesoxirribonucleotídeos/imunologia , Proteínas E7 de Papillomavirus/química , Proteínas E7 de Papillomavirus/ultraestrutura , Infecções por Papillomavirus/induzido quimicamente , Infecções por Papillomavirus/terapia , Vacinas contra Papillomavirus/administração & dosagem , Multimerização Proteica , Estabilidade Proteica , Resultado do Tratamento , Neoplasias do Colo do Útero/terapia , Neoplasias do Colo do Útero/virologia , Vacinação/métodos
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