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1.
Cell ; 2024 Oct 21.
Artigo em Inglês | MEDLINE | ID: mdl-39447570

RESUMO

Pathogens constantly evolve and can develop mutations that evade host immunity and treatment. Addressing these escape mechanisms requires targeting evolutionarily conserved vulnerabilities, as mutations in these regions often impose fitness costs. We introduce adaptive multi-epitope targeting with enhanced avidity (AMETA), a modular and multivalent nanobody platform that conjugates potent bispecific nanobodies to a human immunoglobulin M (IgM) scaffold. AMETA can display 20+ nanobodies, enabling superior avidity binding to multiple conserved and neutralizing epitopes. By leveraging multi-epitope SARS-CoV-2 nanobodies and structure-guided design, AMETA constructs exponentially enhance antiviral potency, surpassing monomeric nanobodies by over a million-fold. These constructs demonstrate ultrapotent, broad, and durable efficacy against pathogenic sarbecoviruses, including Omicron sublineages, with robust preclinical results. Structural analysis through cryoelectron microscopy and modeling has uncovered multiple antiviral mechanisms within a single construct. At picomolar to nanomolar concentrations, AMETA efficiently induces inter-spike and inter-virus cross-linking, promoting spike post-fusion and striking viral disarmament. AMETA's modularity enables rapid, cost-effective production and adaptation to evolving pathogens.

2.
Cell ; 181(3): 688-701.e16, 2020 04 30.
Artigo em Inglês | MEDLINE | ID: mdl-32315618

RESUMO

Impairment of protein phosphatases, including the family of serine/threonine phosphatases designated PP2A, is essential for the pathogenesis of many diseases, including cancer. The ability of PP2A to dephosphorylate hundreds of proteins is regulated by over 40 specificity-determining regulatory "B" subunits that compete for assembly and activation of heterogeneous PP2A heterotrimers. Here, we reveal how a small molecule, DT-061, specifically stabilizes the B56α-PP2A holoenzyme in a fully assembled, active state to dephosphorylate selective substrates, such as its well-known oncogenic target, c-Myc. Our 3.6 Å structure identifies molecular interactions between DT-061 and all three PP2A subunits that prevent dissociation of the active enzyme and highlight inherent mechanisms of PP2A complex assembly. Thus, our findings provide fundamental insights into PP2A complex assembly and regulation, identify a unique interfacial stabilizing mode of action for therapeutic targeting, and aid in the development of phosphatase-based therapeutics tailored against disease specific phospho-protein targets.


Assuntos
Proteína Fosfatase 2/metabolismo , Sequência de Aminoácidos , Animais , Linhagem Celular Tumoral , Ativadores de Enzimas/metabolismo , Células HEK293 , Xenoenxertos , Humanos , Masculino , Camundongos , Camundongos Nus , Modelos Moleculares , Complexos Multiproteicos/metabolismo , Proteína Fosfatase 2/química , Subunidades Proteicas
3.
Nature ; 621(7977): 154-161, 2023 Sep.
Artigo em Inglês | MEDLINE | ID: mdl-37494956

RESUMO

Although eukaryotic and long prokaryotic Argonaute proteins (pAgos) cleave nucleic acids, some short pAgos lack nuclease activity and hydrolyse NAD(P)+ to induce bacterial cell death1. Here we present a hierarchical activation pathway for SPARTA, a short pAgo consisting of an Argonaute (Ago) protein and TIR-APAZ, an associated protein2. SPARTA progresses through distinct oligomeric forms, including a monomeric apo state, a monomeric RNA-DNA-bound state, two dimeric RNA-DNA-bound states and a tetrameric RNA-DNA-bound active state. These snapshots together identify oligomerization as a mechanistic principle of SPARTA activation. The RNA-DNA-binding channel of apo inactive SPARTA is occupied by an auto-inhibitory motif in TIR-APAZ. After the binding of RNA-DNA, SPARTA transitions from a monomer to a symmetric dimer and then an asymmetric dimer, in which two TIR domains interact through charge and shape complementarity. Next, two dimers assemble into a tetramer with a central TIR cluster responsible for hydrolysing NAD(P)+. In addition, we observe unique features of interactions between SPARTA and RNA-DNA, including competition between the DNA 3' end and the auto-inhibitory motif, interactions between the RNA G2 nucleotide and Ago, and splaying of the RNA-DNA duplex by two loops exclusive to short pAgos. Together, our findings provide a mechanistic basis for the activation of short pAgos, a large section of the Ago superfamily.


Assuntos
Proteínas Argonautas , Células Procarióticas , Apoproteínas/química , Apoproteínas/metabolismo , Proteínas Argonautas/química , Proteínas Argonautas/classificação , Proteínas Argonautas/metabolismo , DNA/metabolismo , Ativação Enzimática , NAD/metabolismo , Células Procarióticas/metabolismo , RNA/metabolismo
4.
PLoS Pathog ; 20(9): e1011864, 2024 Sep.
Artigo em Inglês | MEDLINE | ID: mdl-39226335

RESUMO

Although several filoviruses are dangerous human pathogens, there is conflicting evidence regarding their origins and interactions with animal hosts. Here we attempt to improve this understanding using the paleoviral record over a geological time scale, protein structure predictions, tests for evolutionary maintenance, and phylogenetic methods that alleviate sources of bias and error. We found evidence for long branch attraction bias in the L gene tree for filoviruses, and that using codon-specific models and protein structural comparisons of paleoviruses ameliorated conflict and bias. We found evidence for four ancient filoviral groups, each with extant viruses and paleoviruses with open reading frames. Furthermore, we found evidence of repeated transfers of filovirus-like elements to mouse-like rodents. A filovirus-like nucleoprotein ortholog with an open reading frame was detected in three subfamilies of spalacid rodents (present since the Miocene). We provide evidence that purifying selection is acting to maintain amino acids, protein structure and open reading frames in these elements. Our finding of extant viruses nested within phylogenetic clades of paleoviruses informs virus discovery methods and reveals the existence of Lazarus taxa among RNA viruses. Our results resolve a deep conflict in the evolutionary framework for filoviruses and reveal that genomic transfers to vertebrate hosts with potentially functional co-options have been more widespread than previously appreciated.


Assuntos
Evolução Molecular , Filoviridae , Filogenia , Vertebrados , Animais , Filoviridae/genética , Vertebrados/virologia , Vertebrados/genética , Genoma Viral , Humanos , Fases de Leitura Aberta , Genômica/métodos
5.
J Biol Chem ; 300(1): 105498, 2024 Jan.
Artigo em Inglês | MEDLINE | ID: mdl-38013087

RESUMO

Developing quantitative models of substrate specificity for RNA processing enzymes is a key step toward understanding their biology and guiding applications in biotechnology and biomedicine. Optimally, models to predict relative rate constants for alternative substrates should integrate an understanding of structures of the enzyme bound to "fast" and "slow" substrates, large datasets of rate constants for alternative substrates, and transcriptomic data identifying in vivo processing sites. Such data are either available or emerging for bacterial ribonucleoprotein RNase P a widespread and essential tRNA 5' processing endonuclease, thus making it a valuable model system for investigating principles of biological specificity. Indeed, the well-established structure and kinetics of bacterial RNase P enabled the development of high throughput measurements of rate constants for tRNA variants and provided the necessary framework for quantitative specificity modeling. Several studies document the importance of conformational changes in the precursor tRNA substrate as well as the RNA and protein subunits of bacterial RNase P during binding, although the functional roles and dynamics are still being resolved. Recently, results from cryo-EM studies of E. coli RNase P with alternative precursor tRNAs are revealing prospective mechanistic relationships between conformational changes and substrate specificity. Yet, extensive uncharted territory remains, including leveraging these advances for drug discovery, achieving a complete accounting of RNase P substrates, and understanding how the cellular context contributes to RNA processing specificity in vivo.


Assuntos
Proteínas de Bactérias , Ribonuclease P , Escherichia coli/enzimologia , Escherichia coli/genética , Conformação de Ácido Nucleico , Ribonuclease P/química , Ribonuclease P/genética , Ribonuclease P/metabolismo , Precursores de RNA/classificação , Precursores de RNA/metabolismo , RNA Bacteriano/genética , RNA Bacteriano/metabolismo , RNA de Transferência/genética , RNA de Transferência/metabolismo , Especificidade por Substrato , Proteínas de Bactérias/genética , Proteínas de Bactérias/metabolismo , Ligação Proteica
6.
PLoS Biol ; 17(4): e3000204, 2019 04.
Artigo em Inglês | MEDLINE | ID: mdl-30951520

RESUMO

Telomerase, a unique reverse transcriptase that specifically extends the ends of linear chromosomes, is up-regulated in the vast majority of cancer cells. Here, we show that an indole nucleotide analog, 5-methylcarboxyl-indolyl-2'-deoxyriboside 5'-triphosphate (5-MeCITP), functions as an inhibitor of telomerase activity. The crystal structure of 5-MeCITP bound to the Tribolium castaneum telomerase reverse transcriptase reveals an atypical interaction, in which the nucleobase is flipped in the active site. In this orientation, the methoxy group of 5-MeCITP extends out of the canonical active site to interact with a telomerase-specific hydrophobic pocket formed by motifs 1 and 2 in the fingers domain and T-motif in the RNA-binding domain of the telomerase reverse transcriptase. In vitro data show that 5-MeCITP inhibits telomerase with a similar potency as the clinically administered nucleoside analog reverse transcriptase inhibitor azidothymidine (AZT). In addition, cell-based studies show that treatment with the cell-permeable nucleoside counterpart of 5-MeCITP leads to telomere shortening in telomerase-positive cancer cells, while resulting in significantly lower cytotoxic effects in telomerase-negative cell lines when compared with AZT treatment.


Assuntos
Nucleosídeos/metabolismo , Telomerase/antagonistas & inibidores , Telomerase/fisiologia , Animais , Domínio Catalítico/efeitos dos fármacos , Células HCT116 , Células HEK293 , Células HeLa , Humanos , Modelos Moleculares , Nucleosídeos/síntese química , Nucleosídeos/fisiologia , Nucleotídeos/síntese química , Nucleotídeos/metabolismo , RNA/metabolismo , Inibidores da Transcriptase Reversa/farmacologia , Telômero , Tribolium/genética , Tribolium/metabolismo , Zidovudina/metabolismo , Zidovudina/farmacologia
7.
Proc Natl Acad Sci U S A ; 116(47): 23527-23533, 2019 11 19.
Artigo em Inglês | MEDLINE | ID: mdl-31685617

RESUMO

Telomeres cap the ends of linear chromosomes and terminate in a single-stranded DNA (ssDNA) overhang recognized by POT1-TPP1 heterodimers to help regulate telomere length homeostasis. Here hydroxyl radical footprinting coupled with mass spectrometry was employed to probe protein-protein interactions and conformational changes involved in the assembly of telomere ssDNA substrates of differing lengths bound by POT1-TPP1 heterodimers. Our data identified environmental changes surrounding residue histidine 266 of POT1 that were dependent on telomere ssDNA substrate length. We further determined that the chronic lymphocytic leukemia-associated H266L substitution significantly reduced POT1-TPP1 binding to short ssDNA substrates; however, it only moderately impaired the heterodimer binding to long ssDNA substrates containing multiple protein binding sites. Additionally, we identified a telomerase inhibitory role when several native POT1-TPP1 proteins coat physiologically relevant lengths of telomere ssDNA. This POT1-TPP1 complex-mediated inhibition of telomerase is abrogated in the context of the POT1 H266L mutation, which leads to telomere overextension in a malignant cellular environment.


Assuntos
DNA de Cadeia Simples/metabolismo , Mutação de Sentido Incorreto , Mutação Puntual , Polimorfismo de Nucleotídeo Único , Homeostase do Telômero/fisiologia , Proteínas de Ligação a Telômeros/fisiologia , Telômero/metabolismo , Substituição de Aminoácidos , Sistemas CRISPR-Cas , Células HCT116 , Humanos , Leucemia Linfocítica Crônica de Células B/genética , Leucemia Linfocítica Crônica de Células B/metabolismo , Ligação Proteica , Proteínas Recombinantes/metabolismo , Complexo Shelterina , Proteínas de Ligação a Telômeros/genética
8.
Prostate ; 81(15): 1235-1251, 2021 11.
Artigo em Inglês | MEDLINE | ID: mdl-34492133

RESUMO

BACKGROUND: To ensure replicative immortality in cancer, telomeres must be maintained through activation of telomere maintenance mechanisms (TMMs) that are dependent on telomerase or the alternative lengthening of telomeres (ALT) pathway. Although TMM pathways have traditionally been considered to be mutually exclusive, ALT hallmarks have been identified in cancers defined as being telomerase-positive, supporting TMM coexistence. In castration-resistant prostate cancer (CRPC), in vitro models were thought to be universally dependent on telomerase as the primary TMM; however, CRPC models with androgen receptor (AR) loss demonstrate ALT hallmarks with limited telomerase activity and require ALT-associated PML bodies (APBs) for sustained telomere maintenance. The TMM coexistence in AR-negative CRPC is reliant on the ALT regulator protein, SLX4IP. METHODS: To identify the regions of SLX4IP responsible for the induction of APBs and telomere preservation in CRPC models, five 3xFLAG-tagged SLX4IP constructs were designed and stably introduced into parental C4-2B, DU145, and PC-3 cells. Once generated, these cell lines were interrogated for APB abundance and SLX4IP construct localization via immunofluorescence-fluorescence in situ hybridization (IF-FISH) and coimmunoprecipitation experiments for telomeric localization. Similarly, PC-3 cells with endogenous SLX4IP knockdown and SLX4IP construct introduction were interrogated for APB abundance, telomere length preservation, and senescent rescue. RESULTS: Here, we define the N-terminus of SLX4IP as being responsible for the promotion of the ALT-like phenotype of AR-negative CRPC models. Specifically, the N-terminus of SLX4IP was sufficient for promoting APB formation to a similar degree as full-length SLX4IP across CRPC cell lines. Additionally, APB promotion by the N-terminus of SLX4IP rescued telomere shortening and senescent induction triggered by SLX4IP knockdown in AR-negative CRPC cells. Moreover, APB formation and telomere maintenance were dependent on the ability of the N-terminus to direct SLX4IP localization at telomeres and APBs. CONCLUSIONS: These findings identify the role of the uncharacterized ALT regulator SLX4IP in the promotion of TMM coexistence to perpetuate replicative immortality in CRPC in vitro.


Assuntos
Proteínas de Transporte/metabolismo , Neoplasias de Próstata Resistentes à Castração/metabolismo , Homeostase do Telômero/fisiologia , Telômero/metabolismo , Proteínas de Transporte/genética , Linhagem Celular Tumoral , Humanos , Hibridização in Situ Fluorescente , Masculino , Neoplasias de Próstata Resistentes à Castração/patologia
9.
Nucleic Acids Res ; 44(21): 10467-10479, 2016 Dec 01.
Artigo em Inglês | MEDLINE | ID: mdl-27655633

RESUMO

Telomeres are specialized nucleoprotein complexes that comprise the ends of linear chromosomes. Human telomeres end in a short, single-stranded DNA (ssDNA) overhang that is recognized and bound by two telomere proteins, POT1 and TPP1. Whereas POT1 binds directly to telomere ssDNA, its interaction with TPP1 is essential for localization of POT1 to the telomere. TPP1 also provides enhanced binding and sequence discrimination that regulates POT1-TPP1 interactions exclusively with telomere ssDNA. Finally, TPP1 recruits telomerase, the enzyme responsible for synthesis of telomere DNA, to the telomere. While the oligosaccharide-oligonucleotide-binding (OB)-fold domain of TPP1 has been solved by X-ray crystallography, the molecular interactions within the POT1-TPP1-ssDNA ternary complex and the conformational changes that contribute to its diverse functions remain ambiguous. We employed hydrogen/deuterium exchange combined with mass spectrometry to identify three peptides, all residing within the OB-fold of TPP1, that exhibit altered exchange rates upon complex formation or ssDNA binding. Mutation of these regions combined with functional assays revealed the diverse contributions of each moiety in protein-protein interactions, regulating telomerase activity or DNA-binding. Together, these functional data combined with biophysical analyses and homology modeling provide a molecular understanding of the diverse contributions of TPP1 in telomere maintenance.


Assuntos
Aminopeptidases/metabolismo , Dipeptidil Peptidases e Tripeptidil Peptidases/metabolismo , Peptídeos/metabolismo , Serina Proteases/metabolismo , Complexo Shelterina , Homeostase do Telômero , Proteínas de Ligação a Telômeros/metabolismo , Telômero/metabolismo , Sequência de Aminoácidos , Aminopeptidases/química , Aminopeptidases/genética , Animais , Dicroísmo Circular , DNA/química , DNA/metabolismo , Dipeptidil Peptidases e Tripeptidil Peptidases/química , Dipeptidil Peptidases e Tripeptidil Peptidases/genética , Humanos , Espectrometria de Massas , Modelos Moleculares , Mutação , Peptídeos/química , Peptídeos/genética , Peptídeos/farmacologia , Ligação Proteica , Conformação Proteica , Multimerização Proteica , Proteínas Recombinantes de Fusão , Serina Proteases/química , Serina Proteases/genética , Complexo Shelterina/química , Relação Estrutura-Atividade , Telomerase/metabolismo , Homeostase do Telômero/efeitos dos fármacos , Proteínas de Ligação a Telômeros/química , Proteínas de Ligação a Telômeros/genética
10.
J Biol Chem ; 291(1): 215-26, 2016 Jan 01.
Artigo em Inglês | MEDLINE | ID: mdl-26574546

RESUMO

Bacterial viruses of the P22-like family encode a specialized tail needle essential for genome stabilization after DNA packaging and implicated in Gram-negative cell envelope penetration. The atomic structure of P22 tail needle (gp26) crystallized at acidic pH reveals a slender fiber containing an N-terminal "trimer of hairpins" tip. Although the length and composition of tail needles vary significantly in Podoviridae, unexpectedly, the amino acid sequence of the N-terminal tip is exceptionally conserved in more than 200 genomes of P22-like phages and prophages. In this paper, we used x-ray crystallography and EM to investigate the neutral pH structure of three tail needles from bacteriophage P22, HK620, and Sf6. In all cases, we found that the N-terminal tip is poorly structured, in stark contrast to the compact trimer of hairpins seen in gp26 crystallized at acidic pH. Hydrogen-deuterium exchange mass spectrometry, limited proteolysis, circular dichroism spectroscopy, and gel filtration chromatography revealed that the N-terminal tip is highly dynamic in solution and unlikely to adopt a stable trimeric conformation at physiological pH. This is supported by the cryo-EM reconstruction of P22 mature virion tail, where the density of gp26 N-terminal tip is incompatible with a trimer of hairpins. We propose the tail needle N-terminal tip exists in two conformations: a pre-ejection extended conformation, which seals the portal vertex after genome packaging, and a postejection trimer of hairpins, which forms upon its release from the virion. The conformational plasticity of the tail needle N-terminal tip is built in the amino acid sequence, explaining its extraordinary conservation in nature.


Assuntos
Genoma Viral , Podoviridae/genética , Proteínas da Cauda Viral/química , Vírion/genética , Montagem de Vírus , Bacteriófagos/química , Dicroísmo Circular , Microscopia Crioeletrônica , Cristalografia por Raios X , Medição da Troca de Deutério , Concentração de Íons de Hidrogênio , Espectrometria de Massas , Coloração Negativa , Multimerização Proteica , Proteínas da Cauda Viral/ultraestrutura
11.
Biochim Biophys Acta ; 1844(9): 1550-9, 2014 Sep.
Artigo em Inglês | MEDLINE | ID: mdl-24780581

RESUMO

Telomeres are nucleoprotein complexes that cap the ends of all linear chromosomes and function to prevent aberrant repair and end-to-end chromosome fusions. In somatic cells, telomere shortening is a natural part of the aging process as it occurs with each round of cell division. In germ and stem cells, however, the enzyme telomerase synthesizes telomere DNA to counter-balance telomere shortening and help maintain cellular proliferation. Of the primary telomere end-binding proteins, TPP1 has recently emerged as a primary contributor in protecting telomere DNA and in recruiting telomerase to the telomere ends. In this review, we summarize the current knowledge regarding the role of TPP1 in telomere maintenance.


Assuntos
Telomerase/genética , Homeostase do Telômero/genética , Proteínas de Ligação a Telômeros/genética , Telômero , Animais , Cilióforos/genética , Cilióforos/metabolismo , DNA de Cadeia Simples/genética , DNA de Cadeia Simples/metabolismo , Regulação da Expressão Gênica , Humanos , Ligação Proteica , Homologia de Sequência de Aminoácidos , Complexo Shelterina , Telomerase/metabolismo , Proteínas de Ligação a Telômeros/metabolismo
12.
J Virol ; 88(16): 8783-94, 2014 Aug.
Artigo em Inglês | MEDLINE | ID: mdl-24850747

RESUMO

UNLABELLED: Bunyaviridae is a large family of RNA viruses chiefly comprised of vertebrate and plant pathogens. We discovered novel bunyavirids that are approximately equally divergent from each of the five known genera. We characterized novel genome sequences for two bunyavirids, namely, Kigluaik phantom virus (KIGV), from tundra-native phantom midges (Chaoborus), and Nome phantom virus (NOMV), from tundra-invading phantom midges, and demonstrated that these bunyavirid-like sequences belong to an infectious virus by passaging KIGV in mosquito cell culture, although the infection does not seem to be well sustained beyond a few passages. Virus and host gene sequences from individuals collected on opposite ends of North America, a region spanning 4,000 km, support a long-term, vertically transmitted infection of KIGV in Chaoborus trivittatus. KIGV-like sequences ranging from single genes to full genomes are present in transcriptomes and genomes of insects belonging to six taxonomic orders, suggesting an ancient association of this clade with insect hosts. In Drosophila, endogenous virus genes have been coopted, forming an orthologous tandem gene family that has been maintained by selection during the radiation of the host genus. Our findings indicate that bunyavirid-host interactions in nonbloodsucking arthropods have been much more extensive than previously thought. IMPORTANCE: Very little is known about the viral diversity in polar freshwater ponds, and perhaps less is known about the effects that climate-induced habitat changes in these regions will have on virus-host interactions in the coming years. Our results show that at the tundra-boreal boundary, a hidden viral landscape is being altered as infected boreal phantom midges colonize tundra ponds. Likewise, relatively little is known of the deeper evolutionary history of bunyavirids that has led to the stark lifestyle contrasts between some genera. The discovery of this novel bunyavirid group suggests that ancient and highly divergent bunyavirid lineages remain undetected in nature and may offer fresh insight into host reservoirs, potential sources of emerging disease, and major lifestyle shifts in the evolutionary history of viruses in the family Bunyaviridae.


Assuntos
Infecções por Bunyaviridae/genética , Bunyaviridae/genética , Genoma de Inseto/genética , Insetos/genética , Animais , Evolução Biológica , Infecções por Bunyaviridae/virologia , Células Cultivadas , Culicidae/genética , Culicidae/virologia , Drosophila/genética , Drosophila/virologia , Insetos/virologia , América do Norte , Filogenia , Vírus de RNA/genética
13.
J Biol Chem ; 288(23): 16361-16370, 2013 Jun 07.
Artigo em Inglês | MEDLINE | ID: mdl-23616058

RESUMO

Telomeres are macromolecular nucleoprotein complexes that protect the ends of eukaryotic chromosomes from degradation, end-to-end fusion events, and from engaging the DNA damage response. However, the assembly of this essential DNA-protein complex is poorly understood. Telomere DNA consists of the repeated double-stranded sequence 5'-TTAGGG-3' in vertebrates, followed by a single-stranded DNA overhang with the same sequence. Both double- and single-stranded regions are coated with high specificity by telomere end-binding proteins, including POT1 and TPP1, that bind as a heterodimer to single-stranded telomeric DNA. Multiple POT1-TPP1 proteins must fully coat the single-stranded telomere DNA to form a functional telomere. To better understand the mechanism of multiple binding, we mutated or deleted the two guanosine nucleotides residing between adjacent POT1-TPP1 recognition sites in single-stranded telomere DNA that are not required for multiple POT1-TPP1 binding events. Circular dichroism demonstrated that spectra from the native telomere sequence are characteristic of a G-quadruplex secondary structure, whereas the altered telomere sequences were devoid of these signatures. The altered telomere strands, however, facilitated more cooperative loading of multiple POT1-TPP1 proteins compared with the wild-type telomere sequence. Finally, we show that a 48-nucleotide DNA with a telomere sequence is more susceptible to nuclease digestion when coated with POT1-TPP1 proteins than when it is left uncoated. Together, these data suggest that POT1-TPP1 binds telomeric DNA in a coordinated manner to facilitate assembly of the nucleoprotein complexes into a state that is more accessible to enzymatic activity.


Assuntos
Cromossomos Humanos/química , DNA de Cadeia Simples/química , Proteínas de Ligação a Telômeros/química , Telômero/química , Cromossomos Humanos/genética , Cromossomos Humanos/metabolismo , Dicroísmo Circular , DNA de Cadeia Simples/genética , DNA de Cadeia Simples/metabolismo , Humanos , Ligação Proteica , Estrutura Quaternária de Proteína , Estrutura Secundária de Proteína , Complexo Shelterina , Telômero/metabolismo , Proteínas de Ligação a Telômeros/genética , Proteínas de Ligação a Telômeros/metabolismo
14.
Nat Commun ; 15(1): 6350, 2024 Jul 28.
Artigo em Inglês | MEDLINE | ID: mdl-39068213

RESUMO

The arginyl-transferase ATE1 is a tRNA-dependent enzyme that covalently attaches an arginine molecule to a protein substrate. Conserved from yeast to humans, ATE1 deficiency in mice correlates with defects in cardiovascular development and angiogenesis and results in embryonic lethality, while conditional knockouts exhibit reproductive, developmental, and neurological deficiencies. Despite the recent revelation of the tRNA binding mechanism and the catalytic cycle of yeast ATE1, the structure-function relationship of ATE1 in higher organisms is not well understood. In this study, we present the three-dimensional structure of human ATE1 in an apo-state and in complex with its tRNA cofactor and a peptide substrate. In contrast to its yeast counterpart, human ATE1 forms a symmetric homodimer, which dissociates upon binding of a substrate. Furthermore, human ATE1 includes a unique and extended loop that wraps around tRNAArg, creating extensive contacts with the T-arm of the tRNA cofactor. Substituting key residues identified in the substrate binding site of ATE1 abolishes enzymatic activity and results in the accumulation of ATE1 substrates in cells.


Assuntos
Aminoaciltransferases , Multimerização Proteica , Humanos , Aminoaciltransferases/metabolismo , Aminoaciltransferases/genética , Aminoaciltransferases/química , RNA de Transferência/metabolismo , Sítios de Ligação , RNA de Transferência de Arginina/metabolismo , RNA de Transferência de Arginina/genética , RNA de Transferência de Arginina/química , Modelos Moleculares , Ligação Proteica , Animais , Camundongos , Células HEK293
15.
Nat Commun ; 15(1): 1328, 2024 Feb 13.
Artigo em Inglês | MEDLINE | ID: mdl-38351080

RESUMO

Mitochondrial fission is a critical cellular event to maintain organelle function. This multistep process is initiated by the enhanced recruitment and oligomerization of dynamin-related protein 1 (Drp1) at the surface of mitochondria. As such, Drp1 is essential for inducing mitochondrial division in mammalian cells, and homologous proteins are found in all eukaryotes. As a member of the dynamin superfamily of proteins (DSPs), controlled Drp1 self-assembly into large helical polymers stimulates its GTPase activity to promote membrane constriction. Still, little is known about the mechanisms that regulate correct spatial and temporal assembly of the fission machinery. Here we present a cryo-EM structure of a full-length Drp1 dimer in an auto-inhibited state. This dimer reveals two key conformational rearrangements that must be unlocked through intramolecular rearrangements to achieve the assembly-competent state observed in previous structures. This structural insight provides understanding into the mechanism for regulated self-assembly of the mitochondrial fission machinery.


Assuntos
GTP Fosfo-Hidrolases , Dinâmica Mitocondrial , Animais , GTP Fosfo-Hidrolases/metabolismo , Proteínas Associadas aos Microtúbulos/metabolismo , Dinaminas/metabolismo , Mitocôndrias/metabolismo , Proteínas Mitocondriais/metabolismo , Mamíferos/metabolismo
16.
Nat Commun ; 14(1): 2232, 2023 04 19.
Artigo em Inglês | MEDLINE | ID: mdl-37076488

RESUMO

Arginyl-tRNA-protein transferase 1 (ATE1) is a master regulator of protein homeostasis, stress response, cytoskeleton maintenance, and cell migration. The diverse functions of ATE1 arise from its unique enzymatic activity to covalently attach an arginine onto its protein substrates in a tRNA-dependent manner. However, how ATE1 (and other aminoacyl-tRNA transferases) hijacks tRNA from the highly efficient ribosomal protein synthesis pathways and catalyzes the arginylation reaction remains a mystery. Here, we describe the three-dimensional structures of Saccharomyces cerevisiae ATE1 with and without its tRNA cofactor. Importantly, the putative substrate binding domain of ATE1 adopts a previously uncharacterized fold that contains an atypical zinc-binding site critical for ATE1 stability and function. The unique recognition of tRNAArg by ATE1 is coordinated through interactions with the major groove of the acceptor arm of tRNA. Binding of tRNA induces conformational changes in ATE1 that helps explain the mechanism of substrate arginylation.


Assuntos
Aminoaciltransferases , Aminoaciltransferases/genética , Proteínas/metabolismo , Saccharomyces cerevisiae/metabolismo , Movimento Celular , RNA de Transferência , Arginina/metabolismo
17.
Nat Commun ; 14(1): 2072, 2023 04 13.
Artigo em Inglês | MEDLINE | ID: mdl-37055408

RESUMO

Accurate segregation of chromosomes is required to maintain genome integrity during cell division. This feat is accomplished by the microtubule-based spindle. To build a spindle rapidly and with high fidelity, cells take advantage of branching microtubule nucleation, which rapidly amplifies microtubules during cell division. Branching microtubule nucleation relies on the hetero-octameric augmin complex, but lack of structure information about augmin has hindered understanding how it promotes branching. In this work, we combine cryo-electron microscopy, protein structural prediction, and visualization of fused bulky tags via negative stain electron microscopy to identify the location and orientation of each subunit within the augmin structure. Evolutionary analysis shows that augmin's structure is highly conserved across eukaryotes, and that augmin contains a previously unidentified microtubule binding site. Thus, our findings provide insight into the mechanism of branching microtubule nucleation.


Assuntos
Proteínas Associadas aos Microtúbulos , Microtúbulos , Animais , Proteínas Associadas aos Microtúbulos/metabolismo , Microscopia Crioeletrônica , Microtúbulos/metabolismo , Vertebrados/metabolismo , Sítios de Ligação , Fuso Acromático/metabolismo , Tubulina (Proteína)/metabolismo
18.
Cell Rep ; 42(6): 112609, 2023 06 27.
Artigo em Inglês | MEDLINE | ID: mdl-37289586

RESUMO

We applied raw human liver microsome lysate to a holey carbon grid and used cryo-electron microscopy (cryo-EM) to define its composition. From this sample we identified and simultaneously determined high-resolution structural information for ten unique human liver enzymes involved in diverse cellular processes. Notably, we determined the structure of the endoplasmic bifunctional protein H6PD, where the N- and C-terminal domains independently possess glucose-6-phosphate dehydrogenase and 6-phosphogluconolactonase enzymatic activity, respectively. We also obtained the structure of heterodimeric human GANAB, an ER glycoprotein quality-control machinery that contains a catalytic α subunit and a noncatalytic ß subunit. In addition, we observed a decameric peroxidase, PRDX4, which directly contacts a disulfide isomerase-related protein, ERp46. Structural data suggest that several glycosylations, bound endogenous compounds, and ions associate with these human liver enzymes. These results highlight the importance of cryo-EM in facilitating the elucidation of human organ proteomics at the atomic level.


Assuntos
Retículo Endoplasmático , Isomerases de Dissulfetos de Proteínas , Humanos , Retículo Endoplasmático/metabolismo , Microscopia Crioeletrônica , Isomerases de Dissulfetos de Proteínas/metabolismo , Domínio Catalítico , Fígado/metabolismo
19.
Nat Commun ; 14(1): 784, 2023 02 11.
Artigo em Inglês | MEDLINE | ID: mdl-36774348

RESUMO

15-prostaglandin dehydrogenase (15-PGDH) is a negative regulator of tissue stem cells that acts via enzymatic activity of oxidizing and degrading PGE2, and related eicosanoids, that support stem cells during tissue repair. Indeed, inhibiting 15-PGDH markedly accelerates tissue repair in multiple organs. Here we have used cryo-electron microscopy to solve the solution structure of native 15-PGDH and of 15-PGDH individually complexed with two distinct chemical inhibitors. These structures identify key 15-PGDH residues that mediate binding to both classes of inhibitors. Moreover, we identify a dynamic 15-PGDH lid domain that closes around the inhibitors, and that is likely fundamental to the physiologic 15-PGDH enzymatic mechanism. We furthermore identify two key residues, F185 and Y217, that act as hinges to regulate lid closing, and which both inhibitors exploit to capture the lid in the closed conformation, thus explaining their sub-nanomolar binding affinities. These findings provide the basis for further development of 15-PGDH targeted drugs as therapeutics for regenerative medicine.


Assuntos
Eicosanoides , Hidroxiprostaglandina Desidrogenases , Microscopia Crioeletrônica , Hidroxiprostaglandina Desidrogenases/antagonistas & inibidores
20.
Nat Commun ; 14(1): 5253, 2023 08 29.
Artigo em Inglês | MEDLINE | ID: mdl-37644036

RESUMO

Loss of the tumor suppressive activity of the protein phosphatase 2A (PP2A) is associated with cancer, but the underlying molecular mechanisms are unclear. PP2A holoenzyme comprises a heterodimeric core, a scaffolding A subunit and a catalytic C subunit, and one of over 20 distinct substrate-directing regulatory B subunits. Methylation of the C subunit regulates PP2A heterotrimerization, affecting B subunit binding and substrate specificity. Here, we report that the leucine carboxy methyltransferase (LCMT1), which methylates the L309 residue of the C subunit, acts as a suppressor of androgen receptor (AR) addicted prostate cancer (PCa). Decreased methyl-PP2A-C levels in prostate tumors is associated with biochemical recurrence and metastasis. Silencing LCMT1 increases AR activity and promotes castration-resistant prostate cancer growth. LCMT1-dependent methyl-sensitive AB56αCme heterotrimers target AR and its critical coactivator MED1 for dephosphorylation, resulting in the eviction of the AR-MED1 complex from chromatin and loss of target gene expression. Mechanistically, LCMT1 is regulated by S6K1-mediated phosphorylation-induced degradation requiring the ß-TRCP, leading to acquired resistance to anti-androgens. Finally, feedforward stabilization of LCMT1 by small molecule activator of phosphatase (SMAP) results in attenuation of AR-signaling and tumor growth inhibition in anti-androgen refractory PCa. These findings highlight methyl-PP2A-C as a prognostic marker and that the loss of LCMT1 is a major determinant in AR-addicted PCa, suggesting therapeutic potential for AR degraders or PP2A modulators in prostate cancer treatment.


Assuntos
Neoplasias da Próstata , Proteína Fosfatase 2 , Humanos , Masculino , Antagonistas de Androgênios , Leucina , Metiltransferases , Próstata , Neoplasias da Próstata/genética , Proteína Fosfatase 2/genética
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