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1.
Nucleic Acids Res ; 51(16): 8691-8710, 2023 09 08.
Artigo em Inglês | MEDLINE | ID: mdl-37395448

RESUMO

5-Methyluridine (m5U) is one of the most abundant RNA modifications found in cytosolic tRNA. tRNA methyltransferase 2 homolog A (hTRMT2A) is the dedicated mammalian enzyme for m5U formation at tRNA position 54. However, its RNA binding specificity and functional role in the cell are not well understood. Here we dissected structural and sequence requirements for binding and methylation of its RNA targets. Specificity of tRNA modification by hTRMT2A is achieved by a combination of modest binding preference and presence of a uridine in position 54 of tRNAs. Mutational analysis together with cross-linking experiments identified a large hTRMT2A-tRNA binding surface. Furthermore, complementing hTRMT2A interactome studies revealed that hTRMT2A interacts with proteins involved in RNA biogenesis. Finally, we addressed the question of the importance of hTRMT2A function by showing that its knockdown reduces translation fidelity. These findings extend the role of hTRMT2A beyond tRNA modification towards a role in translation.


Assuntos
RNA de Transferência , tRNA Metiltransferases , Animais , Humanos , Mamíferos/genética , Metilação , RNA/metabolismo , RNA de Transferência/metabolismo , tRNA Metiltransferases/metabolismo
2.
Plant Cell ; 33(3): 714-734, 2021 05 05.
Artigo em Inglês | MEDLINE | ID: mdl-33955482

RESUMO

Glucosylation modulates the biological activity of small molecules and frequently leads to their inactivation. The Arabidopsis thaliana glucosyltransferase UGT76B1 is involved in conjugating the stress hormone salicylic acid (SA) as well as isoleucic acid (ILA). Here, we show that UGT76B1 also glucosylates N-hydroxypipecolic acid (NHP), which is synthesized by FLAVIN-DEPENDENT MONOOXYGENASE 1 (FMO1) and activates systemic acquired resistance (SAR). Upon pathogen attack, Arabidopsis leaves generate two distinct NHP hexose conjugates, NHP-O-ß-glucoside and NHP glucose ester, whereupon only NHP-O-ß-glucoside formation requires a functional SA pathway. The ugt76b1 mutants specifically fail to generate the NHP-O-ß-glucoside, and recombinant UGT76B1 synthesizes NHP-O-ß-glucoside in vitro in competition with SA and ILA. The loss of UGT76B1 elevates the endogenous levels of NHP, SA, and ILA and establishes a constitutive SAR-like immune status. Introgression of the fmo1 mutant lacking NHP biosynthesis into the ugt76b1 background abolishes this SAR-like resistance. Moreover, overexpression of UGT76B1 in Arabidopsis shifts the NHP and SA pools toward O-ß-glucoside formation and abrogates pathogen-induced SAR. Our results further indicate that NHP-triggered immunity is SA-dependent and relies on UGT76B1 as a common metabolic hub. Thereby, UGT76B1-mediated glucosylation controls the levels of active NHP, SA, and ILA in concert to balance the plant immune status.


Assuntos
Proteínas de Arabidopsis/metabolismo , Arabidopsis/metabolismo , Glicosiltransferases/metabolismo , Ácidos Pipecólicos/metabolismo , Imunidade Vegetal/fisiologia , Arabidopsis/genética , Proteínas de Arabidopsis/genética , Glicosiltransferases/genética , Imunidade Vegetal/genética
3.
Nucleic Acids Res ; 48(13): 7385-7403, 2020 07 27.
Artigo em Inglês | MEDLINE | ID: mdl-32491174

RESUMO

Adenylate/uridylate-rich elements (AREs) are the most common cis-regulatory elements in the 3'-untranslated region (UTR) of mRNAs, where they fine-tune turnover by mediating mRNA decay. They increase plasticity and efficacy of mRNA regulation and are recognized by several ARE-specific RNA-binding proteins (RBPs). Typically, AREs are short linear motifs with a high content of complementary A and U nucleotides and often occur in multiple copies. Although thermodynamically rather unstable, the high AU-content might enable transient secondary structure formation and modify mRNA regulation by RBPs. We have recently suggested that the immunoregulatory RBP Roquin recognizes folded AREs as constitutive decay elements (CDEs), resulting in shape-specific ARE-mediated mRNA degradation. However, the structural evidence for a CDE-like recognition of AREs by Roquin is still lacking. We here present structures of CDE-like folded AREs, both in their free and protein-bound form. Moreover, the AREs in the UCP3 3'-UTR are additionally bound by the canonical ARE-binding protein AUF1 in their linear form, adopting an alternative binding-interface compared to the recognition of their CDE structure by Roquin. Strikingly, our findings thus suggest that AREs can be recognized in multiple ways, allowing control over mRNA regulation by adapting distinct conformational states, thus providing differential accessibility to regulatory RBPs.


Assuntos
Elementos Ricos em Adenilato e Uridilato , Proteínas de Ligação a RNA/química , Ubiquitina-Proteína Ligases/química , Sítios de Ligação , Células HEK293 , Humanos , Simulação de Acoplamento Molecular , Motivos de Nucleotídeos , Ligação Proteica , Proteínas de Ligação a RNA/metabolismo , Ubiquitina-Proteína Ligases/metabolismo
4.
Anal Chem ; 92(15): 10717-10724, 2020 08 04.
Artigo em Inglês | MEDLINE | ID: mdl-32640156

RESUMO

Optoacoustic (photoacoustic) imaging has seen marked advances in detection and data analysis, but there is less progress in understanding the photophysics of common optoacoustic contrast agents. This gap blocks the development of novel agents and the accurate analysis and interpretation of multispectral optoacoustic images. To close it, we developed a multimodal laser spectrometer (MLS) to enable the simultaneous measurement of optoacoustic, absorbance, and fluorescence spectra. Herein, we employ MLS to analyze contrast agents (methylene blue, rhodamine 800, Alexa Fluor 750, IRDye 800CW, and indocyanine green) and proteins (sfGFP, mCherry, mKate, HcRed, iRFP720, and smURFP). We found that the optical absorption spectrum does not correlate with the optoacoustic spectrum for the majority of the analytes. We determined that for dyes, the transition underlying an aggregation state has more optoacoustic signal generation efficiency than the monomer transition. For proteins we found a favored optoacoustic relaxation that stems from the neutral or zwitterionic chromophores and unreported photoswitching behavior of tdTomato and HcRed. We then crystalized HcRed in its photoswitch optoacoustic state, confirming structurally the change in isomerization with respect to HcReds' fluorescence state. Finally, on the example of the widely used label tdTomato and the dye indocyanine green, we show the importance of correct photophysical (e.g., spectral and kinetic) information as a prerequisite for spectral-unmixing for in vivo imaging.


Assuntos
Absorção Fisico-Química , Corantes/química , Proteínas Luminescentes/química , Imagem Molecular , Técnicas Fotoacústicas , Limite de Detecção , Modelos Moleculares , Conformação Proteica
5.
Mol Pharm ; 17(5): 1663-1673, 2020 05 04.
Artigo em Inglês | MEDLINE | ID: mdl-32243177

RESUMO

Glucagon-like peptide-1 (GLP-1) is an incretin (a type of metabolic hormone that stimulates a decrease in blood glucose levels), holding great potential for the treatment of type 2 diabetes mellitus (T2DM). However, its extremely short half-life of 1-2 min hampers any direct clinical application. Here, we describe the application of the heavy chain of human ferritin (HFt) nanocage as a carrier to improve the pharmacological properties of GLP-1. The GLP-HFt was designed by genetic fusion of GLP-1 to the N-terminus of HFt and was expressed in inclusion bodies in E. coli. The refolding process was developed to obtain a soluble GLP-HFt protein. The biophysical properties determined by size-exclusion chromatography (SEC), dynamic light scattering (DLS), circular dichroism (CD), transmission electron microscopy (TEM), and X-ray crystallography verified that the GLP-HFt successfully formed a 24-mer nanocage with GLP-1 displayed on the external surface of HFt. The in vivo pharmacodynamic results demonstrated that the GLP-HFt nanocage retained the bioactivity of natural GLP-1, significantly reduced the blood glucose levels for at least 24 h in a dose-dependent manner, and inhibited food intake for at least 8-10 h. The half-life of the GLP-HFt nanocage was approximately 52 h in mice after subcutaneous injection. The prolonged half-life and sustained control of blood glucose levels indicate that the GLP-HFt nanocage can be further developed for the treatment of T2DM. Meanwhile, the HFt nanocage proves its great potential as a universal carrier that improves the pharmacodynamic and pharmacokinetic properties of a wide range of therapeutic peptides and proteins.


Assuntos
Diabetes Mellitus Tipo 2 , Peptídeo 1 Semelhante ao Glucagon , Animais , Glicemia , Diabetes Mellitus Tipo 2/tratamento farmacológico , Escherichia coli/metabolismo , Ferritinas , Peptídeo 1 Semelhante ao Glucagon/farmacologia , Hipoglicemiantes/farmacocinética , Hipoglicemiantes/farmacologia , Insulina/metabolismo , Camundongos
6.
RNA Biol ; 17(9): 1228-1238, 2020 09.
Artigo em Inglês | MEDLINE | ID: mdl-32476604

RESUMO

RNA- and DNA-binding domains are essential building blocks for specific regulation of gene expression. While a number of canonical nucleic acid binding domains share sequence and structural conservation, others are less obviously linked by evolutionary traits. In this review, we describe a protein fold of about 150 aa in length, bearing a conserved ß-ß-ß-ß-α-linker-ß-ß-ß-ß-α topology and similar nucleic acid binding properties but no apparent sequence conservation. The same overall fold can also be achieved by dimerization of two proteins, each bearing a ß-ß-ß-ß-α topology. These proteins include but are not limited to the transcription factors PC4 and P24 from humans and plants, respectively, the human RNA-transport factor Pur-α (also termed PURA), as well as the ssDNA-binding SP_0782 protein from Streptococcus pneumonia and the bacteriophage coat proteins PP7 and MS2. Besides their common overall topology, these proteins share common nucleic acids binding surfaces and thus functional similarity. We conclude that these PC4-like domains include proteins from all kingdoms of life and are much more abundant than previously known.


Assuntos
Proteínas de Ligação a DNA/química , Proteínas de Ligação a DNA/metabolismo , Domínios Proteicos , Motivos de Ligação ao RNA , Proteínas de Ligação a RNA/química , Proteínas de Ligação a RNA/metabolismo , Animais , Sítios de Ligação , Evolução Biológica , DNA/química , DNA/metabolismo , Bases de Dados Genéticas , Humanos , Modelos Moleculares , Conformação Proteica , Dobramento de Proteína , Multimerização Proteica , RNA/química , RNA/metabolismo , Relação Estrutura-Atividade
7.
J Med Genet ; 55(2): 104-113, 2018 02.
Artigo em Inglês | MEDLINE | ID: mdl-29097605

RESUMO

BACKGROUND: De novo mutations in PURA have recently been described to cause PURA syndrome, a neurodevelopmental disorder characterised by severe intellectual disability (ID), epilepsy, feeding difficulties and neonatal hypotonia. OBJECTIVES: To delineate the clinical spectrum of PURA syndrome and study genotype-phenotype correlations. METHODS: Diagnostic or research-based exome or Sanger sequencing was performed in individuals with ID. We systematically collected clinical and mutation data on newly ascertained PURA syndrome individuals, evaluated data of previously reported individuals and performed a computational analysis of photographs. We classified mutations based on predicted effect using 3D in silico models of crystal structures of Drosophila-derived Pur-alpha homologues. Finally, we explored genotype-phenotype correlations by analysis of both recurrent mutations as well as mutation classes. RESULTS: We report mutations in PURA (purine-rich element binding protein A) in 32 individuals, the largest cohort described so far. Evaluation of clinical data, including 22 previously published cases, revealed that all have moderate to severe ID and neonatal-onset symptoms, including hypotonia (96%), respiratory problems (57%), feeding difficulties (77%), exaggerated startle response (44%), hypersomnolence (66%) and hypothermia (35%). Epilepsy (54%) and gastrointestinal (69%), ophthalmological (51%) and endocrine problems (42%) were observed frequently. Computational analysis of facial photographs showed subtle facial dysmorphism. No strong genotype-phenotype correlation was identified by subgrouping mutations into functional classes. CONCLUSION: We delineate the clinical spectrum of PURA syndrome with the identification of 32 additional individuals. The identification of one individual through targeted Sanger sequencing points towards the clinical recognisability of the syndrome. Genotype-phenotype analysis showed no significant correlation between mutation classes and disease severity.


Assuntos
Proteínas de Ligação a DNA/genética , Face/anormalidades , Deficiência Intelectual/genética , Mutação , Fatores de Transcrição/genética , Proteínas de Ligação a DNA/química , Proteínas de Drosophila/química , Proteínas de Drosophila/genética , Anormalidades do Olho/genética , Feminino , Estudos de Associação Genética , Humanos , Recém-Nascido , Hipotonia Muscular/etiologia , Hipotonia Muscular/genética , Gravidez , Homologia Estrutural de Proteína , Síndrome , Fatores de Transcrição/química
8.
J Struct Biol ; 204(3): 519-522, 2018 12.
Artigo em Inglês | MEDLINE | ID: mdl-30287387

RESUMO

Small, ultra-red fluorescence protein (smURFP) introduces the non-native biliverdin (BV) chromophore to phycobiliproteins (PBPs), allowing them to be used as transgenic labels for in vivo mammalian imaging. Presently, no structural information exists for PBPs bound to the non-native BV chromophore, which limits the further development of smURFP and related proteins as imaging labels or indicators. Here we describe the first crystal structure of a PBP bound to BV. The structures of smURFP-Y56R with BV and smURFP-Y56F without BV reveal unique oligomerization interfaces different from those in wild-type PBPs bound to native chromophores. Our structures suggest that the oligomerization interface affects the BV binding site, creating a link between oligomerization and chromophorylation that we confirmed through site-directed mutagenesis and that may help guide efforts to improve the notorious chromophorylation of smURFP and other PBPs engineered to bind BV.


Assuntos
Biliverdina/química , Medições Luminescentes/métodos , Proteínas Luminescentes/química , Ficobiliproteínas/química , Biliverdina/metabolismo , Sítios de Ligação/genética , Cristalização , Cristalografia por Raios X , Proteínas Luminescentes/genética , Proteínas Luminescentes/metabolismo , Modelos Moleculares , Mutagênese Sítio-Dirigida , Ficobiliproteínas/metabolismo , Ligação Proteica , Multimerização Proteica , Espectrometria de Fluorescência , Proteína Vermelha Fluorescente
9.
J Cell Sci ; 128(9): 1824-34, 2015 May 01.
Artigo em Inglês | MEDLINE | ID: mdl-25908846

RESUMO

Tubulin proteostasis is regulated by a group of molecular chaperones termed tubulin cofactors (TBC). Whereas tubulin heterodimer formation is well-characterized biochemically, its dissociation pathway is not clearly understood. Here, we carried out biochemical assays to dissect the role of the human TBCE and TBCB chaperones in α-tubulin-ß-tubulin dissociation. We used electron microscopy and image processing to determine the three-dimensional structure of the human TBCE, TBCB and α-tubulin (αEB) complex, which is formed upon α-tubulin-ß-tubulin heterodimer dissociation by the two chaperones. Docking the atomic structures of domains of these proteins, including the TBCE UBL domain, as we determined by X-ray crystallography, allowed description of the molecular architecture of the αEB complex. We found that heterodimer dissociation is an energy-independent process that takes place through a disruption of the α-tubulin-ß-tubulin interface that is caused by a steric interaction between ß-tubulin and the TBCE cytoskeleton-associated protein glycine-rich (CAP-Gly) and leucine-rich repeat (LRR) domains. The protruding arrangement of chaperone ubiquitin-like (UBL) domains in the αEB complex suggests that there is a direct interaction of this complex with the proteasome, thus mediating α-tubulin degradation.


Assuntos
Proteínas Associadas aos Microtúbulos/metabolismo , Chaperonas Moleculares/metabolismo , Multimerização Proteica , Tubulina (Proteína)/metabolismo , Motivos de Aminoácidos , Sequência de Aminoácidos , Animais , Bovinos , Cristalografia por Raios X , Proteínas de Fluorescência Verde/metabolismo , Guanosina Trifosfato , Humanos , Hidrólise , Proteínas Associadas aos Microtúbulos/química , Modelos Biológicos , Modelos Moleculares , Chaperonas Moleculares/química , Dados de Sequência Molecular , Proteínas Mutantes/química , Proteínas Mutantes/metabolismo , Ligação Proteica , Estrutura Terciária de Proteína , Proteólise , Tubulina (Proteína)/química
10.
Acta Crystallogr F Struct Biol Commun ; 80(Pt 2): 36-42, 2024 Feb 01.
Artigo em Inglês | MEDLINE | ID: mdl-38270511

RESUMO

Human tRNA (uracil-5-)-methyltransferase 2 homolog A (TRMT2A) is the dedicated enzyme for the methylation of uridine 54 in transfer RNA (tRNA). Human TRMT2A has also been described as a modifier of polyglutamine (polyQ)-derived neuronal toxicity. The corresponding human polyQ pathologies include Huntington's disease and constitute a family of devastating neurodegenerative diseases. A polyQ tract in the corresponding disease-linked protein causes neuronal death and symptoms such as impaired motor function, as well as cognitive impairment. In polyQ disease models, silencing of TRMT2A reduced polyQ-associated cell death and polyQ protein aggregation, suggesting this protein as a valid drug target against this class of disorders. In this paper, the 1.6 Šresolution crystal structure of the RNA-recognition motif (RRM) from Drosophila melanogaster, which is a homolog of human TRMT2A, is described and analysed.


Assuntos
Drosophila melanogaster , Doença de Huntington , Animais , Humanos , Drosophila melanogaster/metabolismo , Cristalografia por Raios X , Doença de Huntington/genética , Doença de Huntington/metabolismo , Doença de Huntington/patologia , RNA de Transferência/genética , RNA de Transferência/metabolismo , Metiltransferases/metabolismo
11.
Elife ; 132024 Apr 24.
Artigo em Inglês | MEDLINE | ID: mdl-38655849

RESUMO

Mutations in the human PURA gene cause the neurodevelopmental PURA syndrome. In contrast to several other monogenetic disorders, almost all reported mutations in this nucleic acid-binding protein result in the full disease penetrance. In this study, we observed that patient mutations across PURA impair its previously reported co-localization with processing bodies. These mutations either destroyed the folding integrity, RNA binding, or dimerization of PURA. We also solved the crystal structures of the N- and C-terminal PUR domains of human PURA and combined them with molecular dynamics simulations and nuclear magnetic resonance measurements. The observed unusually high dynamics and structural promiscuity of PURA indicated that this protein is particularly susceptible to mutations impairing its structural integrity. It offers an explanation why even conservative mutations across PURA result in the full penetrance of symptoms in patients with PURA syndrome.


PURA syndrome is a neurodevelopmental disorder that affects about 650 patients worldwide, resulting in a range of symptoms including neurodevelopmental delays, intellectual disability, muscle weakness, seizures, and eating difficulties. The condition is caused by a mutated gene that codes for a protein called PURA. PURA binds RNA ­ the molecule that carries genetic information so it can be translated into proteins ­ and has roles in regulating the production of new proteins. Contrary to other conditions that result from mutations in a single gene, PURA syndrome patients show 'high penetrance', meaning almost every reported mutation in the gene leads to symptoms. Proske, Janowski et al. wanted to understand the molecular basis for this high penetrance. To find out more, the researchers first examined how patient mutations affected the location of the PURA in the cell, using human cells grown in the laboratory. Normally, PURA travels to P-bodies, which are groupings of RNA and proteins involved in regulating which genes get translated into proteins. The researchers found that in cells carrying PURA syndrome mutations, PURA failed to move adequately to P-bodies. To find out how this 'mislocalization' might happen, Proske, Janowski et al. tested how different mutations affected the three-dimensional folding of PURA. These analyses showed that the mutations impair the protein's folding and thereby disrupt PURA's ability to bind RNA, which may explain why mutant PURA cannot localize correctly. Proske, Janowski et al. describe the molecular abnormalities of PURA underlying this disorder and show how molecular analysis of patient mutations can reveal the mechanisms of a disease at the cell level. The results show that the impact of mutations on the structural integrity of the protein, which affects its ability to bind RNA, are likely key to the symptoms of the syndrome. Additionally, their approach used establishes a way to predict and test mutations that will cause PURA syndrome. This may help to develop diagnostic tools for this condition.


Assuntos
Transtornos do Neurodesenvolvimento , Corpos de Processamento , Humanos , Transtornos do Neurodesenvolvimento/metabolismo , Transtornos do Neurodesenvolvimento/patologia , Corpos de Processamento/metabolismo , Corpos de Processamento/patologia , Grânulos de Estresse/metabolismo , Cristalografia por Raios X , Dimerização , Domínios Proteicos , Dicroísmo Circular , Proteínas Recombinantes , Dobramento de Proteína , Penetrância , Substituição de Aminoácidos , Mutação Puntual , Células HeLa
12.
J Virol ; 85(20): 10764-73, 2011 Oct.
Artigo em Inglês | MEDLINE | ID: mdl-21835784

RESUMO

Members of the Enterovirus genus of the Picornaviridae family are abundant, with common human pathogens that belong to the rhinovirus (HRV) and enterovirus (EV) species, including diverse echo-, coxsackie- and polioviruses. They cause a wide spectrum of clinical manifestations ranging from asymptomatic to severe diseases with neurological and/or cardiac manifestations. Pandemic outbreaks of EVs may be accompanied by meningitis and/or paralysis and can be fatal. However, no effective prophylaxis or antiviral treatment against most EVs is available. The EV RNA genome directs the synthesis of a single polyprotein that is autocatalytically processed into mature proteins at Gln↓Gly cleavage sites by the 3C protease (3C(pro)), which has narrow, conserved substrate specificity. These cleavages are essential for virus replication, making 3C(pro) an excellent target for antivirus drug development. In this study, we report the first determination of the crystal structure of 3C(pro) from an enterovirus B, EV-93, a recently identified pathogen, alone and in complex with the anti-HRV molecules compound 1 (AG7404) and rupintrivir (AG7088) at resolutions of 1.9, 1.3, and 1.5 Å, respectively. The EV-93 3C(pro) adopts a chymotrypsin-like fold with a canonically configured oxyanion hole and a substrate binding pocket similar to that of rhino-, coxsackie- and poliovirus 3C proteases. We show that compound 1 and rupintrivir are both active against EV-93 in infected cells and inhibit the proteolytic activity of EV-93 3C(pro) in vitro. These results provide a framework for further structure-guided optimization of the tested compounds to produce antiviral drugs against a broad range of EV species.


Assuntos
Antivirais/metabolismo , Cisteína Endopeptidases/química , Cisteína Endopeptidases/metabolismo , Enterovirus/química , Enterovirus/enzimologia , Inibidores Enzimáticos/metabolismo , Isoxazóis/metabolismo , Pirrolidinonas/metabolismo , Proteínas Virais/química , Proteínas Virais/metabolismo , Proteases Virais 3C , Antivirais/química , Sítios de Ligação , Cristalografia por Raios X , Inibidores Enzimáticos/química , Humanos , Isoxazóis/química , Modelos Moleculares , Fenilalanina/análogos & derivados , Ligação Proteica , Estrutura Terciária de Proteína , Pirrolidinonas/química , Valina/análogos & derivados
13.
Virulence ; 13(1): 483-501, 2022 12.
Artigo em Inglês | MEDLINE | ID: mdl-35291913

RESUMO

The genes hblC, hblD and hblA encode the components Hbl L2, L1 and B of the pore forming enterotoxin haemolysin BL of Bacillus cereus. Two variants of the operon existand the more common one additionally contains hblB downstream of hblCDA. Up to now, it was completely unclear whether the corresponding protein, Hbl B', is widely expressed among B. cereus strains and if it has a distinct function. In the present study, it was shown that the hblB gene is indeed expressed and the Hbl B' protein is secreted by nearly all analysed B. cereus strains. For the latter, a detection system was developed based on monoclonal antibody 11A5. Further, a distinct reduction of cytotoxic and haemolytic activity was observed when recombinant (r)Hbl B' was applied simultaneously with L2, L1 and B. This effect was due to direct interaction of rHbl B' with L1. D-6B. cereusAltogether, we present the first simple tool for the detection of Hbl B' in B. cereus culture supernatants. Moreover, an important regulatory function of Hbl B' in the mechanism of Hbl was determined, which is best described as an additional control of complex formation, balancing the amounts of Hbl B-L1 complexes and the corresponding free subunits.


Assuntos
Bacillus cereus , Proteínas de Bactérias , Bacillus cereus/genética , Bacillus cereus/metabolismo , Proteínas de Bactérias/metabolismo , Enterotoxinas/genética , Proteínas Hemolisinas/metabolismo , Óperon
14.
Nat Biotechnol ; 40(4): 598-605, 2022 04.
Artigo em Inglês | MEDLINE | ID: mdl-34845372

RESUMO

Reversibly photo-switchable proteins are essential for many super-resolution fluorescence microscopic and optoacoustic imaging methods. However, they have yet to be used as sensors that measure the distribution of specific analytes at the nanoscale or in the tissues of live animals. Here we constructed the prototype of a photo-switchable Ca2+ sensor based on GCaMP5G that can be switched with 405/488-nm light and describe its molecular mechanisms at the structural level, including the importance of the interaction of the core barrel structure of the fluorescent protein with the Ca2+ receptor moiety. We demonstrate super-resolution imaging of Ca2+ concentration in cultured cells and optoacoustic Ca2+ imaging in implanted tumor cells in mice under controlled Ca2+ conditions. Finally, we show the generalizability of the concept by constructing examples of photo-switching maltose and dopamine sensors based on periplasmatic binding protein and G-protein-coupled receptor-based sensors.


Assuntos
Técnicas Fotoacústicas , Animais , Linhagem Celular , Camundongos , Microscopia de Fluorescência/métodos , Técnicas Fotoacústicas/métodos
15.
Comput Struct Biotechnol J ; 20: 443-458, 2022.
Artigo em Inglês | MEDLINE | ID: mdl-35070167

RESUMO

Polyglutamine (polyQ) diseases are characterized by an expansion of cytosine-adenine-guanine (CAG) trinucleotide repeats encoding for an uninterrupted prolonged polyQ tract. We previously identified TRMT2A as a strong modifier of polyQ-induced toxicity in an unbiased large-scale screen in Drosophila melanogaster. This work aimed at identifying and validating pharmacological TRMT2A inhibitors as treatment opportunities for polyQ diseases in humans. Computer-aided drug discovery was implemented to identify human TRMT2A inhibitors. Additionally, the crystal structure of one protein domain, the RNA recognition motif (RRM), was determined, and Biacore experiments with the RRM were performed. The identified molecules were validated for their potency to reduce polyQ aggregation and polyQ-induced cell death in human HEK293T cells and patient derived fibroblasts. Our work provides a first step towards pharmacological inhibition of this enzyme and indicates TRMT2A as a viable drug target for polyQ diseases.

16.
Front Immunol ; 13: 958952, 2022.
Artigo em Inglês | MEDLINE | ID: mdl-35990627

RESUMO

The alpha-Gal epitope (α-Gal) with the determining element galactose-α1,3-galactose can lead to clinically relevant allergic reactions and rejections in xenotransplantation. These immune reactions can develop because humans are devoid of this carbohydrate due to evolutionary loss of the enzyme α1,3-galactosyltransferase (GGTA1). In addition, up to 1% of human IgG antibodies are directed against α-Gal, but the stimulus for the induction of anti-α-Gal antibodies is still unclear. Commensal bacteria have been suggested as a causal factor for this induction as α-Gal binding tools such as lectins were found to stain cultivated bacteria isolated from the intestinal tract. Currently available tools for the detection of the definite α-Gal epitope, however, are cross-reactive, or have limited affinity and, hence, offer restricted possibilities for application. In this study, we describe a novel monoclonal IgG1 antibody (27H8) specific for the α-Gal epitope. The 27H8 antibody was generated by immunization of Ggta1 knockout mice and displays a high affinity towards synthetic and naturally occurring α-Gal in various applications. Using this novel tool, we found that intestinal bacteria reported to be α-Gal positive cannot be stained with 27H8 questioning whether commensal bacteria express the native α-Gal epitope at all.


Assuntos
Galactose , Imunoglobulina G , Animais , Anticorpos Monoclonais , Bactérias , Epitopos , Humanos , Camundongos
17.
Acta Crystallogr D Biol Crystallogr ; 66(Pt 1): 61-72, 2010 Jan.
Artigo em Inglês | MEDLINE | ID: mdl-20057050

RESUMO

Dihydrodipicolinate reductase (DHDPR, DapB) is an enzyme that belongs to the L-lysine biosynthetic pathway. DHDPR reduces the alpha,beta-unsaturated cyclic imine 2,3-dihydrodipicolinic acid to yield the compound 2,3,4,5-tetrahydrodipicolinic acid in a pyridine nucleotide-dependent reaction. The substrate of this reaction is the unstable product of the preceding enzyme dihydrodipicolinate synthase (DHDPS, DapA). Here, the structure of apo-DHDPR from Mycobacterium tuberculosis is reported in two orthorhombic crystal forms, as well as the structure of DHDPR from M. tuberculosis in complex with NADH in a monoclinic crystal form. A comparison of the results with previously solved structures of this enzyme shows that DHDPR undergoes a major conformational change upon binding of its cofactor. This conformational change can be interpreted as one of the low-frequency normal modes of the structure.


Assuntos
Proteínas de Bactérias/química , Di-Hidrodipicolinato Redutase/química , Mycobacterium tuberculosis/enzimologia , NAD/química , Regulação Alostérica , Proteínas de Bactérias/metabolismo , Cristalização , Cristalografia por Raios X , Di-Hidrodipicolinato Redutase/metabolismo , Hidroliases/metabolismo , NAD/metabolismo , Ligação Proteica , Conformação Proteica , Piridinas/metabolismo
18.
Biotechnol J ; 15(11): e2000010, 2020 Nov.
Artigo em Inglês | MEDLINE | ID: mdl-32302461

RESUMO

Technical crystallization is an attractive method to purify recombinant proteins. However, it is rarely applied due to the limited crystallizability of many proteins. To overcome this limitation, single amino acid exchanges are rationally introduced to enhance intermolecular interactions at the crystal contacts of the industrially relevant biocatalyst Lactobacillus brevis alcohol dehydrogenase (LbADH). The wildtype (WT) and the best crystallizing and enzymatically active LbADH mutants K32A, D54F, Q126H, and T102E are produced with Escherichia coli and subsequently crystallized from cell lysate in stirred mL-crystallizers. Notwithstanding the high host cell protein (HCP) concentrations in the lysate, all mutants crystallize significantly faster than the WT. Combinations of mutations result in double mutants with faster crystallization kinetics than the respective single mutants, demonstrating a synergetic effect. The almost entire depletion of the soluble LbADH fraction at crystallization equilibrium is observed, proving high yields. The HCP concentration is reduced to below 0.5% after crystal dissolution and recrystallization, and thus a 100-fold HCP reduction is achieved after two successive crystallization steps. The combination of fast kinetics, high yields, and high target protein purity highlights the potential of crystal contact engineering to transform technical crystallization into an efficient protein capture and purification step in biotechnological downstream processes.


Assuntos
Biotecnologia , Oxirredutases , Álcool Desidrogenase/genética , Cristalização , Cristalografia por Raios X , Proteínas Recombinantes/genética
19.
J Struct Funct Genomics ; 10(2): 137-50, 2009 Apr.
Artigo em Inglês | MEDLINE | ID: mdl-19184528

RESUMO

Tuberculosis (TB) is a major global health threat caused by Mycobacterium tuberculosis (Mtb). It is further fueled by the HIV pandemic and by increasing incidences of multidrug resistant Mtb-strains. Rv2827c, a hypothetical protein from Mtb, has been implicated in the survival of Mtb in the macrophages of the host. The three-dimensional structure of Rv2827c has been determined by the three-wavelength anomalous diffraction technique using bromide-derivatized crystals and refined to a resolution of 1.93 A. The asymmetric unit of the orthorhombic crystals contains two independent protein molecules related by a non-crystallographic translation. The tertiary structure of Rv2827c comprises two domains: an N-terminal domain displaying a winged helix topology and a C-terminal domain, which appears to constitute a new and unique fold. Based on structural homology considerations and additional biochemical evidence, it could be established that Rv2827c is a DNA-binding protein. Once the understanding of the structure-function relationship of Rv2827c extends to the function of Rv2827c in vivo, new clues for the rational design of novel intervention strategies may be obtained.


Assuntos
Proteínas de Bactérias/química , Proteínas de Ligação a DNA/química , Mycobacterium tuberculosis/metabolismo , Proteínas de Bactérias/metabolismo , Sítios de Ligação , Clonagem Molecular , Cristalografia por Raios X , Proteínas de Ligação a DNA/metabolismo
20.
Nat Commun ; 10(1): 1659, 2019 04 10.
Artigo em Inglês | MEDLINE | ID: mdl-30971701

RESUMO

Throughout metazoans, Staufen (Stau) proteins are core factors of mRNA localization particles. They consist of three to four double-stranded RNA binding domains (dsRBDs) and a C-terminal dsRBD-like domain. Mouse Staufen2 (mStau2)-like Drosophila Stau (dmStau) contains four dsRBDs. Existing data suggest that only dsRBDs 3-4 are necessary and sufficient for mRNA binding. Here, we show that dsRBDs 1 and 2 of mStau2 bind RNA with similar affinities and kinetics as dsRBDs 3 and 4. While RNA binding by these tandem domains is transient, all four dsRBDs recognize their target RNAs with high stability. Rescue experiments in Drosophila oocytes demonstrate that mStau2 partially rescues dmStau-dependent mRNA localization. In contrast, a rescue with mStau2 bearing RNA-binding mutations in dsRBD1-2 fails, confirming the physiological relevance of our findings. In summary, our data show that the dsRBDs 1-2 play essential roles in the mRNA recognition and function of Stau-family proteins of different species.


Assuntos
Proteínas de Drosophila/metabolismo , Proteínas do Tecido Nervoso/metabolismo , Domínios Proteicos/fisiologia , RNA de Cadeia Dupla/metabolismo , RNA Mensageiro/metabolismo , Proteínas de Ligação a RNA/metabolismo , Animais , Animais Geneticamente Modificados , Proteínas de Drosophila/genética , Proteínas de Drosophila/isolamento & purificação , Drosophila melanogaster , Embrião não Mamífero , Feminino , Mutagênese Sítio-Dirigida , Mutação , Proteínas do Tecido Nervoso/genética , Proteínas do Tecido Nervoso/isolamento & purificação , Oócitos , Ligação Proteica , Proteínas de Ligação a RNA/genética , Proteínas de Ligação a RNA/isolamento & purificação , Proteínas Recombinantes/genética , Proteínas Recombinantes/isolamento & purificação , Proteínas Recombinantes/metabolismo
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