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1.
Nucleic Acids Res ; 52(10): 5792-5803, 2024 Jun 10.
Artículo en Inglés | MEDLINE | ID: mdl-38661210

RESUMEN

Nucleotide repeat expansion disorders, a group of genetic diseases characterized by the expansion of specific DNA sequences, pose significant challenges to treatment and therapy development. Here, we present a precise and programmable method called prime editor-mediated correction of nucleotide repeat expansion (PE-CORE) for correcting pathogenic nucleotide repeat expansion. PE-CORE leverages a prime editor and paired pegRNAs to achieve targeted correction of repeat sequences. We demonstrate the effectiveness of PE-CORE in HEK293T cells and patient-derived induced pluripotent stem cells (iPSCs). Specifically, we focus on spinal and bulbar muscular atrophy and spinocerebellar ataxia type, two diseases associated with nucleotide repeat expansion. Our results demonstrate the successful correction of pathogenic expansions in iPSCs and subsequent differentiation into motor neurons. Specifically, we detect distinct downshifts in the size of both the mRNA and protein, confirming the functional correction of the iPSC-derived motor neurons. These findings highlight PE-CORE as a precision tool for addressing the intricate challenges of nucleotide repeat expansion disorders, paving the way for targeted therapies and potential clinical applications.


Asunto(s)
Edición Génica , Células Madre Pluripotentes Inducidas , Humanos , Células Madre Pluripotentes Inducidas/metabolismo , Edición Génica/métodos , Células HEK293 , Neuronas Motoras/metabolismo , Diferenciación Celular/genética , Expansión de las Repeticiones de ADN/genética , Expansión de Repetición de Trinucleótido/genética
2.
Mol Ther ; 32(7): 2190-2206, 2024 Jul 03.
Artículo en Inglés | MEDLINE | ID: mdl-38796705

RESUMEN

X-linked adrenoleukodystrophy (ALD), an inherited neurometabolic disorder caused by mutations in ABCD1, which encodes the peroxisomal ABC transporter, mainly affects the brain, spinal cord, adrenal glands, and testes. In ALD patients, very-long-chain fatty acids (VLCFAs) fail to enter the peroxisome and undergo subsequent ß-oxidation, resulting in their accumulation in the body. It has not been tested whether in vivo base editing or prime editing can be harnessed to ameliorate ALD. We developed a humanized mouse model of ALD by inserting a human cDNA containing the pathogenic variant into the mouse Abcd1 locus. The humanized ALD model showed increased levels of VLCFAs. To correct the mutation, we tested both base editing and prime editing and found that base editing using ABE8e(V106W) could correct the mutation in patient-derived fibroblasts at an efficiency of 7.4%. Adeno-associated virus (AAV)-mediated systemic delivery of NG-ABE8e(V106W) enabled robust correction of the pathogenic variant in the mouse brain (correction efficiency: ∼5.5%), spinal cord (∼5.1%), and adrenal gland (∼2%), leading to a significant reduction in the plasma levels of C26:0/C22:0. This established humanized mouse model and the successful correction of the pathogenic variant using a base editor serve as a significant step toward treating human ALD disease.


Asunto(s)
Miembro 1 de la Subfamilia D de Transportador de Casetes de Unión al ATP , Adrenoleucodistrofia , Dependovirus , Modelos Animales de Enfermedad , Edición Génica , Terapia Genética , Animales , Adrenoleucodistrofia/terapia , Adrenoleucodistrofia/genética , Ratones , Humanos , Miembro 1 de la Subfamilia D de Transportador de Casetes de Unión al ATP/genética , Dependovirus/genética , Terapia Genética/métodos , Vectores Genéticos/genética , Vectores Genéticos/administración & dosificación , Adenina , Mutación , Fibroblastos/metabolismo , Ácidos Grasos/metabolismo , Encéfalo/metabolismo , Encéfalo/patología
3.
Mol Ther ; 31(1): 249-259, 2023 01 04.
Artículo en Inglés | MEDLINE | ID: mdl-36114670

RESUMEN

A variety of cancers have been found to have chromosomal rearrangements, and the genomic abnormalities often induced expression of fusion oncogenes. To date, a pair of engineered nucleases including ZFNs, TALENs, and CRISPR-Cas9 nucleases have been used to generate chromosomal rearrangement in living cells and organisms for disease modeling. However, these methods induce unwanted indel mutations at the DNA break junctions, resulting in incomplete disease modeling. Here, we developed prime editor nuclease-mediated translocation and inversion (PETI), a method for programmable chromosomal translocation and inversion using prime editor 2 nuclease (PE2 nuclease) and paired pegRNA. Using PETI method, we successfully introduced DNA recombination in episomal fluorescence reporters as well as precise chromosomal translocations in human cells. We applied PETI to create cancer-associated translocations and inversions such as NPM1-ALK and EML4-ALK in human cells. Our findings show that PETI generated chromosomal translocation and inversion in a programmable manner with efficiencies comparable of Cas9. PETI methods, we believe, could be used to create disease models or for gene therapy.


Asunto(s)
Neoplasias , Translocación Genética , Humanos , Reordenamiento Génico , Genoma , Endonucleasas , Genómica , Proteínas Tirosina Quinasas Receptoras , Edición Génica/métodos , Sistemas CRISPR-Cas
4.
Biochem Biophys Res Commun ; 552: 164-169, 2021 05 07.
Artículo en Inglés | MEDLINE | ID: mdl-33751933

RESUMEN

Human mesenchymal stem cells (MSCs) are known to have anti-inflammatory and immunomodulatory functions; thus, several MSC products have been applied as cell therapy in clinical trials worldwide. Recent studies have demonstrated that MSC spheroids have superior anti-inflammatory and immunomodulatory functions to a single cell suspension. Current methods to prepare MSC spheroids include hanging drop, concave microwell aggregation, spinner flask, and gravity circulation. However, all these methods have limitations such as low scalability, easy cell clumping, low viability, and irregular size distribution. Here, we present a nano-patterned culture plasticware named PAMcell™ 3D plate to overcome these limitations. Nano-sized silica particles (700 nm) coated with RGD peptide were arrayed into fusiform onto the PLGA film. This uniform array enabled the seeded MSCs to grow only on the silica particles, forming uniform-sized semi-spheroids within 48 h. These MSC spheroids have been shown to have enhanced stemness, anti-inflammatory, and immunomodulatory functions, as revealed by the increased expression of stem cell markers (Oct4, Sox2, and Nanog), anti-inflammatory (IL-10, TSG6, and IDO), and immunomodulatory molecules (HGF, VEGF, CXCR4) both at mRNA and protein expression levels. Furthermore, these MSC spheroids demonstrated an increased palliative effect on glycemic control in a multiple low-dose streptozotocin-induced diabetes model compared with the same number of MSC single cell suspensions. Taken together, this study presents a new method to produce uniform-sized MSC spheroids with enhanced anti-inflammatory and immunomodulatory functions in vitro and in vivo.


Asunto(s)
Tejido Adiposo/citología , Antiinflamatorios/inmunología , Técnicas de Cultivo de Célula/métodos , Factores Inmunológicos/inmunología , Células Madre Mesenquimatosas/inmunología , Esferoides Celulares/inmunología , Animales , Técnicas de Cultivo de Célula/instrumentación , Células Cultivadas , Diabetes Mellitus Experimental/inmunología , Diabetes Mellitus Experimental/terapia , Expresión Génica/inmunología , Humanos , Masculino , Trasplante de Células Madre Mesenquimatosas/métodos , Células Madre Mesenquimatosas/citología , Células Madre Mesenquimatosas/metabolismo , Ratones Endogámicos C57BL , Esferoides Celulares/metabolismo , Factores de Transcripción/genética , Factores de Transcripción/inmunología , Factores de Transcripción/metabolismo
5.
Nucleic Acids Res ; 42(9): 5937-48, 2014 May.
Artículo en Inglés | MEDLINE | ID: mdl-24682817

RESUMEN

Double-stranded ribonucleic acid-activated protein kinase (PKR) downregulates translation as a defense mechanism against viral infection. In fish species, PKZ, a PKR-like protein kinase containing left-handed deoxyribonucleic acid (Z-DNA) binding domains, performs a similar role in the antiviral response. To understand the role of PKZ in Z-DNA recognition and innate immune response, we performed structural and functional studies of the Z-DNA binding domain (Zα) of PKZ from Carassius auratus (caZαPKZ). The 1.7-Å resolution crystal structure of caZαPKZ:Z-DNA revealed that caZαPKZ shares the overall fold with other Zα, but has discrete structural features that differentiate its DNA binding mode from others. Functional analyses of caZαPKZ and its mutants revealed that caZαPKZ mediates the fastest B-to-Z transition of DNA among Zα, and the minimal interaction for Z-DNA recognition is mediated by three backbone phosphates and six residues of caZαPKZ. Structure-based mutagenesis and B-to-Z transition assays confirmed that Lys56 located in the ß-wing contributes to its fast B-to-Z transition kinetics. Investigation of the DNA binding kinetics of caZαPKZ further revealed that the B-to-Z transition rate is positively correlated with the association rate constant. Taking these results together, we conclude that the positive charge in the ß-wing largely affects fast B-to-Z transition activity by enhancing the DNA binding rate.


Asunto(s)
ADN de Forma Z/química , Proteínas de Peces/química , Carpa Dorada , eIF-2 Quinasa/química , Secuencia de Aminoácidos , Animales , Dominio Catalítico , Cristalografía por Rayos X , Enlace de Hidrógeno , Cinética , Modelos Moleculares , Datos de Secuencia Molecular , Estructura Secundaria de Proteína , Cloruro de Sodio/química
6.
Biochem Biophys Res Commun ; 461(1): 122-7, 2015 May 22.
Artículo en Inglés | MEDLINE | ID: mdl-25858319

RESUMEN

Proteins in the haloalkaloic acid dehalogenase (HAD) superfamily, which is one of the largest enzyme families, is generally composed of a catalytic core domain and a cap domain. Although proteins in this family show broad substrate specificities, the mechanisms of their substrate recognition are not well understood. In this study, we identified a new substrate binding motif of HAD proteins from structural and functional analyses, and propose that this motif might be crucial for interacting with hydrophobic rings of substrates. The crystal structure of TON_0338, one of the 17 putative HAD proteins identified in a hyperthermophilic archaeon, Thermococcus onnurineus NA1, was determined as an apo-form at 2.0 Å resolution. In addition, we determined the crystal structure TON_0338 in complex with Mg(2+) or N-cyclohexyl-2-aminoethanesulfonic acid (CHES) at 1.7 Å resolution. Examination of the apo-form and CHES-bound structures revealed that CHES is sandwiched between Trp58 and Trp61, suggesting that this Trp sandwich might function as a substrate recognition motif. In the phosphatase assay, TON_0338 was shown to have high activity for flavin mononucleotide (FMN), and the docking analysis suggested that the flavin of FMN may interact with Trp58 and Trp61 in a way similar to that observed in the crystal structure. Moreover, the replacement of these tryptophan residues significantly reduced the phosphatase activity for FMN. Our results suggest that WxxW may function as a substrate binding motif in HAD proteins, and expand the diversity of their substrate recognition mode.


Asunto(s)
Hidrolasas/química , Hidrolasas/ultraestructura , Modelos Químicos , Simulación del Acoplamiento Molecular , Monoéster Fosfórico Hidrolasas/química , Monoéster Fosfórico Hidrolasas/ultraestructura , Thermococcus/enzimología , Secuencia de Aminoácidos , Sitios de Unión , Simulación por Computador , Activación Enzimática , Estabilidad de Enzimas , Hidrolasas/aislamiento & purificación , Conformación Molecular , Datos de Secuencia Molecular , Monoéster Fosfórico Hidrolasas/aislamiento & purificación , Unión Proteica , Especificidad de la Especie , Relación Estructura-Actividad , Especificidad por Sustrato , Thermococcus/clasificación
7.
Acta Crystallogr D Biol Crystallogr ; 70(Pt 3): 694-707, 2014 Mar.
Artículo en Inglés | MEDLINE | ID: mdl-24598739

RESUMEN

Escherichia coli SdiA is a quorum-sensing (QS) receptor that responds to autoinducers produced by other bacterial species to control cell division and virulence. Crystal structures reveal that E. coli SdiA, which is composed of an N-terminal ligand-binding domain and a C-terminal DNA-binding domain (DBD), forms a symmetrical dimer. Although each domain shows structural similarity to other QS receptors, SdiA differs from them in the relative orientation of the two domains, suggesting that its ligand-binding and DNA-binding functions are independent. Consistently, in DNA gel-shift assays the binding affinity of SdiA for the ftsQP2 promoter appeared to be insensitive to the presence of autoinducers. These results suggest that autoinducers increase the functionality of SdiA by enhancing the protein stability rather than by directly affecting the DNA-binding affinity. Structural analyses of the ligand-binding pocket showed that SdiA cannot accommodate ligands with long acyl chains, which was corroborated by isothermal titration calorimetry and thermal stability analyses. The formation of an intersubunit disulfide bond that might be relevant to modulation of the DNA-binding activity was predicted from the proximal position of two Cys residues in the DBDs of dimeric SdiA. It was confirmed that the binding affinity of SdiA for the uvrY promoter was reduced under oxidizing conditions, which suggested the possibility of regulation of SdiA by multiple independent signals such as quorum-sensing inducers and the oxidation state of the cell.


Asunto(s)
Proteínas de Unión al ADN/química , Proteínas de Unión al ADN/metabolismo , Proteínas de Escherichia coli/química , Proteínas de Escherichia coli/metabolismo , Percepción de Quorum , Transactivadores/química , Transactivadores/metabolismo , Cristalografía por Rayos X , Ligandos , Ligasas/química , Ligasas/metabolismo , Unión Proteica , Transducción de Señal , Especificidad de la Especie
8.
Acta Crystallogr D Biol Crystallogr ; 70(Pt 3): 615-26, 2014 Mar.
Artículo en Inglés | MEDLINE | ID: mdl-24598731

RESUMEN

Bacterial pathogens have evolved diverse types of efficient machinery to acquire haem, the most abundant source of iron in the human body, and degrade it for the utilization of iron. Gram-positive bacteria commonly encode IsdG-family proteins as haem-degrading monooxygenases. Listeria monocytogenes is predicted to possess an IsdG-type protein (Lmo2213), but the residues involved in haem monooxygenase activity are not well conserved and there is an extra N-terminal domain in Lmo2213. Therefore, its function and mechanism of action cannot be predicted. In this study, the crystal structure of Lmo2213 was determined at 1.75 Šresolution and its haem-binding and haem-degradation activities were confirmed. Structure-based mutational and functional assays of this protein, designated as an Isd-type L. monocytogenes haem-degrading enzyme (Isd-LmHde), identified that Glu71, Tyr87 and Trp129 play important roles in haem degradation and that the N-terminal domain is also critical for its haem-degrading activity. The haem-degradation product of Isd-LmHde is verified to be biliverdin, which is also known to be the degradation product of other bacterial haem oxygenases. This study, the first structural and functional report of the haem-degradation system in L. monocytogenes, sheds light on the concealed haem-utilization system in this life-threatening human pathogen.


Asunto(s)
Proteínas de la Membrana Bacteriana Externa/química , Proteínas de la Membrana Bacteriana Externa/fisiología , Hemo/metabolismo , Listeria monocytogenes/enzimología , Oxigenasas/química , Oxigenasas/fisiología , Secuencia de Aminoácidos , Proteínas de la Membrana Bacteriana Externa/genética , Biliverdina/química , Biliverdina/metabolismo , Catálisis , Cristalografía por Rayos X , Hemo/química , Humanos , Listeria monocytogenes/genética , Listeria monocytogenes/patogenicidad , Datos de Secuencia Molecular , Mutagénesis Sitio-Dirigida , Oxigenasas/genética
9.
Mol Ther Nucleic Acids ; 35(2): 102199, 2024 Jun 11.
Artículo en Inglés | MEDLINE | ID: mdl-38766525

RESUMEN

Pathogenic structure variations (SVs) are associated with various types of cancer and rare genetic diseases. Recent studies have used Cas9 nuclease with paired guide RNAs (gRNAs) to generate targeted chromosomal rearrangements, focusing on producing fusion proteins that cause cancer, whereas research on precision genome editing for rectifying SVs is limited. In this study, we identified a novel complex genomic rearrangement (CGR), specifically an EYA1 inversion with a deletion, implicated in branchio-oto-renal/branchio-oto syndrome. To address this, two CRISPR-based approaches were tested. First, we used Cas9 nuclease and paired gRNAs tailored to the patient's genome. The dual CRISPR-Cas9 system induced efficient correction of paracentric inversion in patient-derived fibroblast, and effectively restored the expression of EYA1 mRNA and protein, along with its transcriptional activity required to regulate the target gene expression. Additionally, we used CRISPR activation (CRISPRa), which leads to the upregulation of EYA1 mRNA expression in patient-derived fibroblasts. Moreover, CRISPRa significantly improved EYA1 protein expression and transcriptional activity essential for target gene expression. This suggests that CRISPRa-based gene therapies could offer substantial translational potential for approximately 70% of disease-causing EYA1 variants responsible for haploinsufficiency. Our findings demonstrate the potential of CRISPR-guided genome editing for correcting SVs, including those with EYA1 CGR linked to haploinsufficiency.

10.
Proc Natl Acad Sci U S A ; 107(47): 20281-6, 2010 Nov 23.
Artículo en Inglés | MEDLINE | ID: mdl-21059944

RESUMEN

The receptor activator of nuclear factor-κB (RANK) and its ligand RANKL, which belong to the tumor necrosis factor (TNF) receptor-ligand family, mediate osteoclastogenesis. The crystal structure of the RANKL ectodomain (eRANKL) in complex with the RANK ectodomain (eRANK) combined with biochemical assays of RANK mutants indicated that three RANK loops (Loop1, Loop2, and Loop3) bind to the interface of a trimeric eRANKL. Loop3 is particularly notable in that it is structurally distinctive from other TNF-family receptors and forms extensive contacts with RANKL. The disulfide bond (C125-C127) at the tip of Loop3 is important for determining the unique topology of Loop3, and docking E126 close to RANKL, which was supported by the inability of C127A or E126A mutants of RANK to bind to RANKL. Inhibitory activity of RANK mutants, which contain loops of osteoprotegerin (OPG), a soluble decoy receptor to RANKL, confirmed that OPG shares the similar binding mode with RANK and OPG. Loop3 plays a key role in RANKL binding. Peptide inhibitors designed to mimic Loop3 blocked the RANKL-induced differentiation of osteoclast precursors, suggesting that they could be developed as therapeutic agents for the treatment of osteoporosis and bone-related diseases. Furthermore, some of the RANK mutations associated with autosomal recessive osteopetrosis (ARO) resulted in reduced RANKL-binding activity and failure to induce osteoclastogenesis. These results, together with structural interpretation of eRANK-eRANKL interaction, provided molecular understanding for pathogenesis of ARO.


Asunto(s)
Huesos/metabolismo , Modelos Moleculares , Oligopéptidos/farmacología , Osteopetrosis/metabolismo , Osteoprotegerina/metabolismo , Péptidos Cíclicos/farmacología , Ligando RANK/química , Animales , Diferenciación Celular/efectos de los fármacos , Diferenciación Celular/genética , Cristalografía , Ratones , Mutagénesis Sitio-Dirigida , Osteoclastos/citología , Osteoclastos/efectos de los fármacos , Osteopetrosis/genética , Ligando RANK/antagonistas & inhibidores , Receptor Activador del Factor Nuclear kappa-B/genética
11.
Commun Biol ; 6(1): 466, 2023 04 28.
Artículo en Inglés | MEDLINE | ID: mdl-37117485

RESUMEN

Huntington's disease (HD) is caused by a CAG repeat expansion in the huntingtin (HTT) gene. CRISPR-Cas9 nuclease causes double-strand breaks (DSBs) in the targeted DNA that induces toxicity, whereas CRISPR interference (CRISPRi) using dead Cas9 (dCas9) suppresses the target gene expression without DSBs. Delivery of dCas9-sgRNA targeting CAG repeat region does not damage the targeted DNA in HEK293T cells containing CAG repeats. When this study investigates whether CRISPRi can suppress mutant HTT (mHTT), CRISPRi results in reduced expression of mHTT with relative preservation of the wild-type HTT in human HD fibroblasts. Although both dCas9 and Cas9 treatments reduce mHTT by sgRNA targeting the CAG repeat region, CRISPRi delays behavioral deterioration and protects striatal neurons against cell death in HD mice. Collectively, CRISPRi can delay disease progression by suppressing mHtt, suggesting DNA DSB-free CRISPRi is a potential therapy for HD that can compensate for the shortcoming of CRISPR-Cas9 nuclease.


Asunto(s)
Enfermedad de Huntington , Ratones , Humanos , Animales , Enfermedad de Huntington/genética , Enfermedad de Huntington/terapia , Enfermedad de Huntington/metabolismo , Roturas del ADN de Doble Cadena , Células HEK293 , Cuerpo Estriado/metabolismo
12.
Mol Ther Nucleic Acids ; 30: 131-142, 2022 Dec 13.
Artículo en Inglés | MEDLINE | ID: mdl-36250202

RESUMEN

RNA-guided CRISPR-Cas12a endonucleases are promising tools for genome engineering. Here we demonstrate that LbCas12a variants derived from Lachnospiraceae bacterium show a broad PAM preference, recognizing certain non-canonical PAMs with high efficiency. Furthermore, we engineered LbABE8e to carry G532R and/or K595R mutations, altering its original PAM specificities; these variants exhibited superior base editing activity in human cells compared with wild-type LbABE8e at sites with non-canonical PAMs. Based on this finding, we utilized the most effective LbCas12a and LbABE8e variants to demonstrate multiplexed and mutant-allele-specific gene editing in oncogenes, made possible by the variant's recognition of non-canonical PAMs. Importantly, LbCas12a-G532R/K595R and LbABE8e-G532R/K595R with optimized crRNA arrays targeted to triple oncogenic mutations inhibited colon cancer cell proliferation. Taken together, these results demonstrate the potential of engineered LbCas12a and LbABE8e as tools for targeting sites with alternative PAMs for genome engineering and therapeutic editing in cancer cells.

13.
Nucleic Acids Res ; 37(2): 629-37, 2009 Feb.
Artículo en Inglés | MEDLINE | ID: mdl-19074195

RESUMEN

The Z-DNA conformation preferentially occurs at alternating purine-pyrimidine repeats, and is specifically recognized by Z alpha domains identified in several Z-DNA-binding proteins. The binding of Z alpha to foreign or chromosomal DNA in various sequence contexts is known to influence various biological functions, including the DNA-mediated innate immune response and transcriptional modulation of gene expression. For these reasons, understanding its binding mode and the conformational diversity of Z alpha bound Z-DNAs is of considerable importance. However, structural studies of Z alpha bound Z-DNA have been mostly limited to standard CG-repeat DNAs. Here, we have solved the crystal structures of three representative non-CG repeat DNAs, d(CACGTG)(2), d(CGTACG)(2) and d(CGGCCG)(2) complexed to hZ alpha(ADAR1) and compared those structures with that of hZ alpha(ADAR1)/d(CGCGCG)(2) and the Z alpha-free Z-DNAs. hZ alpha(ADAR1) bound to each of the three Z-DNAs showed a well conserved binding mode with very limited structural deviation irrespective of the DNA sequence, although varying numbers of residues were in contact with Z-DNA. Z-DNAs display less structural alterations in the Z alpha-bound state than in their free form, thereby suggesting that conformational diversities of Z-DNAs are restrained by the binding pocket of Z alpha. These data suggest that Z-DNAs are recognized by Z alpha through common conformational features regardless of the sequence and structural alterations.


Asunto(s)
Adenosina Desaminasa/química , ADN de Forma Z/química , Proteínas de Unión al ADN/química , Cristalografía por Rayos X , Humanos , Modelos Moleculares , Conformación de Ácido Nucleico , Unión Proteica , Dominios y Motivos de Interacción de Proteínas , Proteínas de Unión al ARN , Secuencias Repetitivas de Ácidos Nucleicos
14.
Proc Natl Acad Sci U S A ; 105(52): 20671-6, 2008 Dec 30.
Artículo en Inglés | MEDLINE | ID: mdl-19095800

RESUMEN

Mammalian DAI (DNA-dependent activator of IFN-regulatory factors), an activator of the innate immune response, senses cytosolic DNA by using 2 N-terminal Z-DNA binding domains (ZBDs) and a third putative DNA binding domain located next to the second ZBD. Compared with other previously known ZBDs, the second ZBD of human DAI (hZbeta(DAI)) shows significant variation in the sequence of the residues that are essential for DNA binding. In this article, the crystal structure of the hZbeta(DAI)/Z-DNA complex reveals that hZbeta(DAI) has a similar fold to that of other ZBDs, but adopts an unusual binding mode for recognition of Z-DNA. A residue in the first beta-strand rather than residues in the beta-loop contributes to DNA binding, and part of the (alpha3) recognition helix adopts a 3(10) helix conformation. The role of each residue that makes contact with DNA was confirmed by mutational analysis. The 2 ZBDs of DAI can together bind to DNA and both are necessary for full B-to-Z conversion. It is possible that binding 2 DAIs to 1 dsDNA brings about dimerization of DAI that might facilitate DNA-mediated innate immune activation.


Asunto(s)
ADN de Forma Z/química , Proteínas de Unión al ADN/química , Pliegue de Proteína , Cristalografía por Rayos X , ADN de Forma Z/genética , ADN de Forma Z/inmunología , ADN de Forma Z/metabolismo , Proteínas de Unión al ADN/genética , Proteínas de Unión al ADN/inmunología , Proteínas de Unión al ADN/metabolismo , Humanos , Inmunidad Innata/fisiología , Mutación , Unión Proteica/fisiología , Estructura Cuaternaria de Proteína/fisiología , Proteínas de Unión al ARN
15.
Biochem Biophys Res Commun ; 383(4): 386-91, 2009 Jun 12.
Artículo en Inglés | MEDLINE | ID: mdl-19268655

RESUMEN

Endoglin, an accessory membrane receptor of transforming growth factor-beta (TGF-beta)1, modulates the cellular response to TGF-beta via its interaction with type I and II TGF-beta receptors. It has been considered a promising target for the development of therapeutics and cancer markers. We have established stable CHO cell lines that efficiently secrete soluble endoglin (s-endoglin) fused with human growth hormone. Two oligomeric forms were observed in a homogeneous preparation of s-endoglin, as a dimer and a tetramer. The dimeric s-endoglin enhanced TGF-beta responsiveness in U937 cells, thus proving its potential for therapeutic applications. Small angle X-ray scattering (SAXS) experiments revealed elongated conformations of both dimeric and tetrameric s-endoglins in solution, suggesting that s-endoglin might undergo conformational adaptations upon TGF-beta binding. The current results provide important references and material for high-resolution structural studies and for medical applications of s-endoglin.


Asunto(s)
Antígenos CD/química , Antígenos CD/metabolismo , Receptores de Superficie Celular/química , Receptores de Superficie Celular/metabolismo , Factor de Crecimiento Transformador alfa/metabolismo , Animales , Antígenos CD/genética , Células CHO , Cricetinae , Cricetulus , Endoglina , Genes Reporteros , Humanos , Luciferasas/genética , Conformación Proteica , Multimerización de Proteína , Receptores de Superficie Celular/genética , Dispersión de Radiación , Rayos X
16.
Artículo en Inglés | MEDLINE | ID: mdl-19255480

RESUMEN

PKZ, a PKR-like eIF2alpha kinase, consists of a Z-DNA-specific binding domain (Zalpha) and an eIF2alpha kinase domain. The kinase activity of PKZ is modulated by the binding of Zalpha to Z-DNA. The mechanisms underlying Z-DNA binding and the subsequent stimulation of PKZ raise intriguing questions. Interestingly, the Z-DNA-binding domain of PKZ from goldfish (Carassius auratus; caZalpha(PKZ)) shows limited sequence homology to other canonical Zalpha domains, suggesting that it may have a distinct Z-DNA-recognition mode. In this study, the Z-DNA-binding activity and stoichiometry of caZalpha(PKZ) were confirmed using circular dichroism (CD). In addition, preliminary X-ray studies of the caZalpha(PKZ)-Z-DNA complex are reported as the first step in the determination of its three-dimensional structure. Bacterially expressed recombinant caZalpha(PKZ) was purified and crystallized with Z-DNA at 295 K using the microbatch method. X-ray diffraction data were collected to 1.7 A resolution with an R(merge) of 7.4%. The crystals belonged to the monoclinic space group C2, with unit-cell parameters a = 55.54, b = 49.93, c = 29.44 A, beta = 96.5 degrees . Structural analysis of caZalpha(PKZ)-Z-DNA will reveal the binding mode of caZalpha(PKZ) to Z-DNA and its relevance to other Z-DNA-binding proteins.


Asunto(s)
ADN de Forma Z/química , ADN de Forma Z/metabolismo , Carpa Dorada/metabolismo , eIF-2 Quinasa/química , eIF-2 Quinasa/metabolismo , Animales , Dicroismo Circular , Cristalización , Cristalografía por Rayos X , Unión Proteica , Estructura Terciaria de Proteína
17.
Protein Pept Lett ; 15(2): 235-7, 2008.
Artículo en Inglés | MEDLINE | ID: mdl-18289118

RESUMEN

To elucidate the molecular basis underlying their broad substrate specificity and reaction mechanism of the enzymes belonging to the haloacid dehalogenase (HAD) superfamily, TON_0559, a putative HAD subfamily protein from a hyperthermophilic archaeon Thermococcus onnurineus NA1, was expressed, purified and crystallized. X-ray diffraction data were collected to 2.0 A resolution. The space group is C2, with unit cell parameters a = 121.2 A, b = 62.9 A, c = 37.5 A and beta= 106.5 degrees .


Asunto(s)
Proteínas Arqueales/química , Thermococcus/enzimología , Proteínas Arqueales/genética , Proteínas Arqueales/metabolismo , Cristalización , Datos de Secuencia Molecular , Especificidad por Sustrato , Difracción de Rayos X
18.
Biochim Biophys Acta ; 1764(2): 320-3, 2006 Feb.
Artículo en Inglés | MEDLINE | ID: mdl-16448869

RESUMEN

ZBP1 is involved in host responses against cellular stresses, including tumorigenesis and viral infection. Structurally, it harbors two copies of the Zalpha domain containing the Zalpha motif, at its N terminus. Here, we attempted to characterize the Z-DNA binding activities of two Zalpha domains in the human ZBP1, hZalpha(ZBP1) and hZbeta(ZBP1), using circular dichroism (CD). Our results indicated that both hZalpha(ZBP1) and hZbeta(ZBP1) are viable Z-DNA binders, and their binding activities are comparable to those of previously-established Zalpha domains. Additionally, we crystallized hZbeta(ZBP1) in a complex with Z-DNA, d(TCGCGCG)2. The crystal diffracted to 1.45 angstroms, and belongs to the P2(1)2(1)2(1) space group, with the unit-cell parameters: a = 29.53 angstroms, b = 58.25 angstroms, and c = 88.61 angstroms. The delineation of this structure will provide insight into the manner in which diverse Zalpha motifs recognize Z-DNA.


Asunto(s)
ADN de Forma Z/química , Glicoproteínas/química , Secuencias de Aminoácidos , Secuencia de Aminoácidos , Sitios de Unión , Dicroismo Circular , Cristalografía por Rayos X , Proteínas de Unión al ADN , Humanos , Datos de Secuencia Molecular , Estructura Terciaria de Proteína , Proteínas de Unión al ARN
19.
Mol Cells ; 39(4): 316-21, 2016 Apr 30.
Artículo en Inglés | MEDLINE | ID: mdl-26923188

RESUMEN

The receptor activator of nuclear factor κB (RANK) and its ligand RANKL are key regulators of osteoclastogenesis and well-recognized targets in developing treatments for bone disorders associated with excessive bone resorption, such as osteoporosis. Our previous work on the structure of the RANK-RANKL complex revealed that Loop3 of RANK, specifically the non-canonical disulfide bond at the tip, performs a crucial role in specific recognition of RANKL. It also demonstrated that peptide mimics of Loop3 were capable of interfering with the function of RANKL in osteoclastogenesis. Here, we reported the structure-based design of a smaller peptide with enhanced inhibitory efficiency. The kinetic analysis and osteoclast differentiation assay showed that in addition to the sharp turn induced by the disulfide bond, two consecutive arginine residues were also important for binding to RANKL and inhibiting osteoclastogenesis. Docking and molecular dynamics simulations proposed the binding mode of the peptide to the RANKL trimer, showing that the arginine residues provide electrostatic interactions with RANKL and contribute to stabilizing the complex. These findings provided useful information for the rational design of therapeutics for bone diseases associated with RANK/RANKL function.


Asunto(s)
Osteogénesis/efectos de los fármacos , Peptidomiméticos/síntesis química , Peptidomiméticos/farmacología , Ligando RANK/metabolismo , Receptor Activador del Factor Nuclear kappa-B/química , Animales , Arginina/metabolismo , Diferenciación Celular/efectos de los fármacos , Células Cultivadas , Diseño de Fármacos , Humanos , Ratones , Simulación del Acoplamiento Molecular , Simulación de Dinámica Molecular , Osteoclastos/citología , Osteoclastos/efectos de los fármacos , Peptidomiméticos/química , Unión Proteica , Relación Estructura-Actividad
20.
Biotechnol Prog ; 21(3): 933-7, 2005.
Artículo en Inglés | MEDLINE | ID: mdl-15932276

RESUMEN

We describe the development of an efficient expression system suitable for the stable expression of recombinant genes in Chinese hamster ovary (CHO) cells using the human interferon beta SAR element. The insertion of two copies of the human interferon beta SAR element at the 5' and 3' flanking regions of the beta-galactosidase reporter gene increased the frequency of beta-galactosidase positive colonies by up to 75% and enhanced beta-galactosidase expression by 15- to 20-fold after G418 selection or 30- to 40-fold at the initial stage of the MTX selection procedure. Deletion analysis showed that the whole DNA regions of the human interferon beta SAR element are required for beta-galactosidase expression enhancement. The developed expression system was also highly effective at enhancing the stable expression of two therapeutically important proteins, namely, erythropoietin (EPO) and hepatocyte growth factor (HGF). We isolated stable colonies with expression levels of 47 microg/10(6) cells/day for EPO and 13 microg/10(6) cells/day for HGF, suggesting that the developed expression system based on the human beta SAR element is suitable for expressing high levels of recombinant proteins in CHO cells.


Asunto(s)
Células CHO/fisiología , Interferón Tipo I/genética , Interferón Tipo I/metabolismo , Ingeniería de Proteínas/métodos , Proteínas Recombinantes/biosíntesis , beta-Galactosidasa/biosíntesis , beta-Galactosidasa/genética , Animales , Células CHO/clasificación , Cricetinae , Cricetulus , Regulación de la Expresión Génica/fisiología , Humanos , Regiones Promotoras Genéticas/genética , Secuencias Reguladoras de Ácidos Nucleicos/genética
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