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1.
Proc Natl Acad Sci U S A ; 121(31): e2220020121, 2024 Jul 30.
Artículo en Inglés | MEDLINE | ID: mdl-39042693

RESUMEN

Expansion of intronic GGGGCC repeats in the C9orf72 gene causes amyotrophic lateral sclerosis (ALS) and frontotemporal dementia. Transcription of the expanded repeats results in the formation of RNA-containing nuclear foci and altered RNA metabolism. In addition, repeat-associated non-AUG (RAN) translation of the expanded GGGGCC-repeat sequence results in the production of highly toxic dipeptide-repeat (DPR) proteins. GGGGCC repeat-containing transcripts form G-quadruplexes, which are associated with formation of RNA foci and RAN translation. Zfp106, an RNA-binding protein essential for motor neuron survival in mice, suppresses neurotoxicity in a Drosophila model of C9orf72 ALS. Here, we show that Zfp106 inhibits formation of RNA foci and significantly reduces RAN translation caused by GGGGCC repeats in cultured mammalian cells, and we demonstrate that Zfp106 coexpression reduces the levels of DPRs in C9orf72 patient-derived cells. Further, we show that Zfp106 binds to RNA G-quadruplexes and causes a conformational change in the G-quadruplex structure formed by GGGGCC repeats. Together, these data demonstrate that Zfp106 suppresses the formation of RNA foci and DPRs caused by GGGGCC repeats and suggest that the G-quadruplex RNA-binding function of Zfp106 contributes to its suppression of GGGGCC repeat-mediated cytotoxicity.


Asunto(s)
Esclerosis Amiotrófica Lateral , Proteína C9orf72 , G-Cuádruplex , Proteínas de Unión al ARN , ARN , Animales , Humanos , Ratones , Esclerosis Amiotrófica Lateral/genética , Esclerosis Amiotrófica Lateral/metabolismo , Proteína C9orf72/genética , Proteína C9orf72/metabolismo , Expansión de las Repeticiones de ADN , Demencia Frontotemporal/genética , Demencia Frontotemporal/metabolismo , Proteínas del Tejido Nervioso/metabolismo , Proteínas del Tejido Nervioso/genética , Unión Proteica , Biosíntesis de Proteínas , ARN/metabolismo , ARN/genética , Proteínas de Unión al ARN/metabolismo , Proteínas de Unión al ARN/genética
2.
Proc Natl Acad Sci U S A ; 119(5)2022 02 01.
Artículo en Inglés | MEDLINE | ID: mdl-35082148

RESUMEN

Triggering receptor expressed on myeloid cells 2 (TREM2) is a single-pass transmembrane receptor of the immunoglobulin superfamily that is secreted in a soluble (sTREM2) form. Mutations in TREM2 have been linked to increased risk of Alzheimer's disease (AD). A prominent neuropathological component of AD is deposition of the amyloid-ß (Aß) into plaques, particularly Aß40 and Aß42. While the membrane-bound form of TREM2 is known to facilitate uptake of Aß fibrils and the polarization of microglial processes toward amyloid plaques, the role of its soluble ectodomain, particularly in interactions with monomeric or fibrillar Aß, has been less clear. Our results demonstrate that sTREM2 does not bind to monomeric Aß40 and Aß42, even at a high micromolar concentration, while it does bind to fibrillar Aß42 and Aß40 with equal affinities (2.6 ± 0.3 µM and 2.3 ± 0.4 µM). Kinetic analysis shows that sTREM2 inhibits the secondary nucleation step in the fibrillization of Aß, while having little effect on the primary nucleation pathway. Furthermore, binding of sTREM2 to fibrils markedly enhanced uptake of fibrils into human microglial and neuroglioma derived cell lines. The disease-associated sTREM2 mutant, R47H, displayed little to no effect on fibril nucleation and binding, but it decreased uptake and functional responses markedly. We also probed the structure of the WT sTREM2-Aß fibril complex using integrative molecular modeling based primarily on the cross-linking mass spectrometry data. The model shows that sTREM2 binds fibrils along one face of the structure, leaving a second, mutation-sensitive site free to mediate cellular binding and uptake.


Asunto(s)
Péptidos beta-Amiloides/metabolismo , Amiloide/metabolismo , Glicoproteínas de Membrana/metabolismo , Receptores Inmunológicos/metabolismo , Enfermedad de Alzheimer/genética , Enfermedad de Alzheimer/metabolismo , Amiloide/genética , Péptidos beta-Amiloides/genética , Animales , Humanos , Cinética , Glicoproteínas de Membrana/genética , Ratones , Microglía/metabolismo , Mutación/genética , Fragmentos de Péptidos/genética , Fragmentos de Péptidos/metabolismo , Placa Amiloide/genética , Placa Amiloide/metabolismo , Receptores Inmunológicos/genética , Proteínas tau/genética , Proteínas tau/metabolismo
3.
Anal Chem ; 96(6): 2318-2326, 2024 02 13.
Artículo en Inglés | MEDLINE | ID: mdl-38301112

RESUMEN

Ion mobility spectrometry (IMS) coupled to mass spectrometry (MS) has become a versatile tool to fractionate complex mixtures, distinguish structural isomers, and elucidate molecular geometries. Along with the whole MS field, IMS/MS advances to ever larger species. A topical proteomic problem is the discovery and characterization of d-amino acid-containing peptides (DAACPs) that are critical to neurotransmission and toxicology. Both linear IMS and FAIMS previously disentangled d/l epimers with up to ∼30 residues. In the first study using all three most powerful IMS methodologies─trapped IMS, cyclic IMS, and FAIMS─we demonstrate baseline resolution of the largest known d/l peptides (CHH from Homarus americanus with 72 residues) with a dynamic range up to 100. This expands FAIMS analyses of isomeric modified peptides, especially using hydrogen-rich buffers, to the ∼50-100 residue range of small proteins. The spectra for d and l are unprecedentedly strikingly similar except for a uniform shift of the separation parameter, indicating the conserved epimer-specific structural elements across multiple charge states and conformers. As the interepimer resolution tracks the average for smaller DAACPs, the IMS approaches could help search for yet larger DAACPs. The a priori method to calibrate cyclic (including multipass) IMS developed here may be broadly useful.


Asunto(s)
Péptidos , Proteómica , Péptidos/química , Espectrometría de Masas/métodos , Proteínas , Espectrometría de Movilidad Iónica , Aminoácidos/química
4.
Altern Ther Health Med ; 30(1): 226-231, 2024 Jan.
Artículo en Inglés | MEDLINE | ID: mdl-37773681

RESUMEN

Objective: To assess the reliability of quantitative ultrasound (QUS) in diagnosing and screening osteoporosis in elder women. Methods: We conducted a systematic search of the online databases, including PubMed, Embase, Web of Science, and China National Knowledge, and screened the studies according to the inclusion criteria. We directly extract or calculate the value of true positive (TP), false positive (FP), false negative (FN), and true negative (TN) from eligible studies. We sought to evaluate the diagnostic parameters of QUS, containing the pooled sensitivity, specificity, positive likelihood ratio (PLR), negative likelihood ratio (NLR), diagnostic odds ratio (DOR), and area under the curve (AUC). Results: Twelve studies were included in this study with a total of 2260 women. QUS showed a pooled diagnostic odds ratio of 5.07 (95% CI 3.28-7.84), sensitivity of 0.69 (95% CI 0.65-0.72), specificity of 0.67 (95% CI 0.64-0.69), and an AUC of 0.7523 (Q*=0.6953). There was no obvious heterogeneity and threshold effect according to the Spearman correlation coefficient (P = 0.059). No significant publication bias was found through the Deek's funnel. Conclusion: Our study suggested that the diagnostic value of QUS for osteoporosis in elder women was acceptable, but the accuracy still needed to be improved, QUS can be recommended as a pre-screening tool for osteoporosis to determine whether DXA measurement was needed.


Asunto(s)
Osteoporosis , Humanos , Femenino , Anciano , Curva ROC , Reproducibilidad de los Resultados , Ultrasonografía , Osteoporosis/diagnóstico por imagen , China
5.
Anal Chem ; 95(2): 784-791, 2023 01 17.
Artículo en Inglés | MEDLINE | ID: mdl-36562749

RESUMEN

Continuing advances in proteomics highlight the ubiquity and biological importance of proteoforms─proteins with varied sequence, splicing, or distribution of post-translational modifications (PTMs). The preeminent example is histones, where the PTM pattern encodes the combinatorial language controlling the DNA transcription central to life. While the proteoforms with distinct PTM compositions are distinguishable by mass, the isomers with permuted PTMs commonly coexisting in cells generally require separation before mass-spectrometric (MS) analyses. That was accomplished on the bottom-up and middle-down levels using chromatography or ion mobility spectrometry (IMS), but proteolytic digestion obliterates the crucial PTM connectivity information. Here, we demonstrate baseline IMS resolution of intact isomeric proteoforms, specifically the acetylated H4 histones (11.3 kDa). The proteoforms with a single acetyl moiety on five alternative lysine residues (K5, K8, K12, K16, K20) known for distinct functionalities in vivo were constructed by two-step native chemical ligation and separated using trapped IMS at the resolving power up to 350 on the Bruker TIMS/ToF platform. Full resolution for several pairs was confirmed using binary mixtures and by unique fragments in tandem MS employing collision-induced dissociation. This novel capability for top-down proteoform characterization is poised to open major new avenues in proteomics and epigenetics.


Asunto(s)
Histonas , Espectrometría de Masas en Tándem , Histonas/química , Espectrometría de Masas en Tándem/métodos , Procesamiento Proteico-Postraduccional , Proteolisis , Proteómica/métodos
6.
Anal Chem ; 95(2): 846-853, 2023 01 17.
Artículo en Inglés | MEDLINE | ID: mdl-36595388

RESUMEN

Post-translational modification of proteins by Ubiquitin (Ub) and Ubiquitin-like proteins (Ubls) can be reversed by deconjugating enzymes, which have been implicated in different pathways and associated with various human diseases. To understand the activity and dynamics of deconjugating enzymes, multiple synthetic and semi-synthetic Ub/Ubl probes have been developed, and some of them have been applied to screen inhibitors of deconjugating enzymes. Since these Ub/Ubl probes are generally not cell-permeable, different strategies have been developed to deliver Ub/Ubl probes to live cells. However, till now, no Ub/Ubl probes can be expressed in live cells to directly report on the activities of deconjugating enzymes in the most relevant cellular environment. Here, we genetically encoded cross-linkable Ub/Ubl probes in live E. coli and HEK293T cells. These probes can cross-link with deconjugating enzymes in vitro and in vivo. Using these Ub probes combined with mass spectrometry, we have successfully identified endogenous deconjugating enzymes in live cells. We believe that these genetically encoded Ub/Ubl probes are valuable for investigating biological functions of deconjugating enzymes in physiological environments.


Asunto(s)
Ubiquitina , Ubiquitinas , Humanos , Ubiquitina/química , Escherichia coli/genética , Escherichia coli/metabolismo , Células HEK293 , Procesamiento Proteico-Postraduccional
7.
Small ; : e2308383, 2023 Dec 11.
Artículo en Inglés | MEDLINE | ID: mdl-38073323

RESUMEN

Acidic residues (Asp and Glu) have a high prevalence on protein surfaces, but cross-linking reactions targeting these residues are limited. Existing methods either require high-concentration coupling reagents or have low structural compatibility. Here a previously reported "plant-and-cast" strategy is extended to develop heterobifunctional cross-linkers. These cross-linkers first react rapidly with Lys sidechains and then react with Asp and Glu sidechains, in a proximity-enhanced fashion. The cross-linking reaction proceeds at neutral pH and room temperature without coupling reagents. The efficiency and robustness of cross-linking using model proteins, ranging from small monomeric proteins to large protein complexes are demonstrated. Importantly, it is shown that this type of cross-linkers are efficient at identifying protein-protein interactions involving acidic domains. The Cross-linking mass spectrometry (XL-MS) study with p53 identified 87 putative binders of the C-terminal domain of p53. Among them, SARNP, ZRAB2, and WBP11 are shown to regulate the expression and alternative splicing of p53 target genes. Thus, these carboxylate-reactive cross-linkers will further expand the power of XL-MS in the analysis of protein structures and protein-protein interactions.

8.
J Am Chem Soc ; 144(3): 1416-1430, 2022 01 26.
Artículo en Inglés | MEDLINE | ID: mdl-35015530

RESUMEN

Amyloid imaging by positron emission tomography (PET) is an important method for diagnosing neurodegenerative disorders such as Alzheimer's disease. Many 11C- and 18F-labeled PET tracers show varying binding capacities, specificities, and affinities for their target proteins. The structural basis of these variations is poorly understood. Here we employ 19F and 13C solid-state NMR to investigate the binding sites of a PET ligand, flutemetamol, to the 40-residue Alzheimer's ß-amyloid peptide (Aß40). Analytical high-performance liquid chromatography and 19F NMR spectra show that flutemetamol binds the current Aß40 fibril polymorph with a stoichiometry of one ligand per four to five peptides. Half of the ligands are tightly bound while the other half are loosely bound. 13C and 15N chemical shifts indicate that this Aß40 polymorph has an immobilized N-terminus, a non-ß-sheet His14, and a non-ß-sheet C-terminus. We measured the proximity of the ligand fluorine to peptide residues using 19F-13C and 19F-1H rotational-echo double-resonance (REDOR) experiments. The spectra show that three segments in the peptide, 12VHH14, 18VFF20, and 39VV40, lie the closest to the ligand. REDOR-constrained docking simulations indicate that these three segments form multiple binding sites, and the ligand orientations and positions at these sites are similar across different Aß polymorphs. Comparison of the flutemetamol-interacting residues in Aß40 with the small-molecule binding sites in other amyloid proteins suggest that conjugated aromatic compounds preferentially bind ß-sheet surface grooves lined by aromatic, polar, and charged residues. These motifs may explain the specificity of different PET tracers to different amyloid proteins.


Asunto(s)
Péptidos beta-Amiloides
9.
Proc Natl Acad Sci U S A ; 116(33): 16357-16366, 2019 08 13.
Artículo en Inglés | MEDLINE | ID: mdl-31358628

RESUMEN

Misfolding of the microtubule-binding protein tau into filamentous aggregates is characteristic of many neurodegenerative diseases such as Alzheimer's disease and progressive supranuclear palsy. Determining the structures and dynamics of these tau fibrils is important for designing inhibitors against tau aggregation. Tau fibrils obtained from patient brains have been found by cryo-electron microscopy to adopt disease-specific molecular conformations. However, in vitro heparin-fibrillized 2N4R tau, which contains all four microtubule-binding repeats (4R), was recently found to adopt polymorphic structures. Here we use solid-state NMR spectroscopy to investigate the global fold and dynamics of heparin-fibrillized 0N4R tau. A single set of 13C and 15N chemical shifts was observed for residues in the four repeats, indicating a single ß-sheet conformation for the fibril core. This rigid core spans the R2 and R3 repeats and adopts a hairpin-like fold that has similarities to but also clear differences from any of the polymorphic 2N4R folds. Obtaining a homogeneous fibril sample required careful purification of the protein and removal of any proteolytic fragments. A variety of experiments and polarization transfer from water and mobile side chains indicate that 0N4R tau fibrils exhibit heterogeneous dynamics: Outside the rigid R2-R3 core, the R1 and R4 repeats are semirigid even though they exhibit ß-strand character and the proline-rich domains undergo large-amplitude anisotropic motions, whereas the two termini are nearly isotropically flexible. These results have significant implications for the structure and dynamics of 4R tau fibrils in vivo.


Asunto(s)
Enfermedad de Alzheimer/genética , Citoesqueleto/ultraestructura , Proteínas Asociadas a Microtúbulos/química , Proteínas tau/química , Enfermedad de Alzheimer/patología , Secuencia de Aminoácidos/genética , Microscopía por Crioelectrón , Citoesqueleto/química , Citoesqueleto/patología , Humanos , Proteínas Asociadas a Microtúbulos/genética , Proteínas Asociadas a Microtúbulos/ultraestructura , Microtúbulos/química , Microtúbulos/genética , Resonancia Magnética Nuclear Biomolecular , Agregación Patológica de Proteínas/genética , Agregación Patológica de Proteínas/patología , Unión Proteica/genética , Conformación Proteica en Lámina beta/genética , Dominios Proteicos/genética , Estructura Secundaria de Proteína , Proteínas tau/genética , Proteínas tau/ultraestructura
10.
J Am Chem Soc ; 143(20): 7839-7851, 2021 05 26.
Artículo en Inglés | MEDLINE | ID: mdl-33983722

RESUMEN

Many neurodegenerative diseases such as Alzheimer's disease are characterized by pathological ß-sheet filaments of the tau protein, which spread in a prion-like manner in patient brains. To date, high-resolution structures of tau filaments obtained from patient brains show that the ß-sheet core only includes portions of the microtubule-binding repeat domains and excludes the C-terminal residues, indicating that the C-terminus is dynamically disordered. Here, we use solid-state NMR spectroscopy to identify the ß-sheet core of full-length 0N3R tau fibrillized using heparin. Assignment of 13C and 15N chemical shifts of the rigid core of the protein revealed a single predominant ß-sheet conformation, which spans not only the R3, R4, R' repeats but also the entire C-terminal domain (CT) of the protein. This massive ß-sheet core qualitatively differs from all other tau fibril structures known to date. Using long-range correlation NMR experiments, we found that the R3 and R4 repeats form a ß-arch, similar to that seen in some of the brain-derived tau fibrils, but the R1 and R3 domains additionally stack against the CT, reminiscent of previously reported transient interactions of the CT with the microtubule-binding repeats. This expanded ß-sheet core structure suggests that the CT may have a protective effect against the formation of pathological tau fibrils by shielding the amyloidogenic R3 and R4 domains, preventing side-on nucleation. Truncation and post-translational modification of the CT in vivo may thus play an important role in the progression of tauopathies.


Asunto(s)
Resonancia Magnética Nuclear Biomolecular , Proteínas tau/química , Humanos , Conformación Proteica en Lámina beta
11.
Proc Natl Acad Sci U S A ; 115(44): 11162-11167, 2018 10 30.
Artículo en Inglés | MEDLINE | ID: mdl-30322930

RESUMEN

Chemical cross-linking mass spectrometry (CXMS) is being increasingly used to study protein assemblies and complex protein interaction networks. Existing CXMS chemical cross-linkers target only Lys, Cys, Glu, and Asp residues, limiting the information measurable. Here we report a "plant-and-cast" cross-linking strategy that employs a heterobifunctional cross-linker that contains a highly reactive succinimide ester as well as a less reactive sulfonyl fluoride. The succinimide ester reacts rapidly with surface Lys residues "planting" the reagent at fixed locations on protein. The pendant aryl sulfonyl fluoride is then "cast" across a limited range of the protein surface, where it can react with multiple weakly nucleophilic amino acid sidechains in a proximity-enhanced sulfur-fluoride exchange (SuFEx) reaction. Using proteins of known structures, we demonstrated that the heterobifunctional agent formed cross-links between Lys residues and His, Ser, Thr, Tyr, and Lys sidechains. This geometric specificity contrasts with current bis-succinimide esters, which often generate nonspecific cross-links between lysines brought into proximity by rare thermal fluctuations. Thus, the current method can provide diverse and robust distance restraints to guide integrative modeling. This work provides a chemical cross-linker targeting unactivated Ser, Thr, His, and Tyr residues using sulfonyl fluorides. In addition, this methodology yielded a variety of cross-links when applied to the complex Escherichia coli cell lysate. Finally, in combination with genetically encoded chemical cross-linking, cross-linking using this reagent markedly increased the identification of weak and transient enzyme-substrate interactions in live cells. Proximity-dependent cross-linking will dramatically expand the scope and power of CXMS for defining the identities and structures of protein complexes.


Asunto(s)
Reactivos de Enlaces Cruzados/química , Fluoruros/química , Compuestos de Azufre/química , Aminoácidos/química , Escherichia coli/metabolismo , Lisina/química , Espectrometría de Masas/métodos , Proteínas/química , Succinimidas/química
12.
Proc Natl Acad Sci U S A ; 114(24): 6191-6196, 2017 06 13.
Artículo en Inglés | MEDLINE | ID: mdl-28566494

RESUMEN

Throughout biology, amyloids are key structures in both functional proteins and the end product of pathologic protein misfolding. Amyloids might also represent an early precursor in the evolution of life because of their small molecular size and their ability to self-purify and catalyze chemical reactions. They also provide attractive backbones for advanced materials. When ß-strands of an amyloid are arranged parallel and in register, side chains from the same position of each chain align, facilitating metal chelation when the residues are good ligands such as histidine. High-resolution structures of metalloamyloids are needed to understand the molecular bases of metal-amyloid interactions. Here we combine solid-state NMR and structural bioinformatics to determine the structure of a zinc-bound metalloamyloid that catalyzes ester hydrolysis. The peptide forms amphiphilic parallel ß-sheets that assemble into stacked bilayers with alternating hydrophobic and polar interfaces. The hydrophobic interface is stabilized by apolar side chains from adjacent sheets, whereas the hydrated polar interface houses the Zn2+-binding histidines with binding geometries unusual in proteins. Each Zn2+ has two bis-coordinated histidine ligands, which bridge adjacent strands to form an infinite metal-ligand chain along the fibril axis. A third histidine completes the protein ligand environment, leaving a free site on the Zn2+ for water activation. This structure defines a class of materials, which we call metal-peptide frameworks. The structure reveals a delicate interplay through which metal ions stabilize the amyloid structure, which in turn shapes the ligand geometry and catalytic reactivity of Zn2.


Asunto(s)
Amiloide/química , Espectroscopía de Resonancia Magnética/métodos , Zinc/química , Amiloide/metabolismo , Sitios de Unión , Biología Computacional , Histidina/química , Histidina/metabolismo , Metaloproteínas , Modelos Moleculares , Agua/química , Zinc/metabolismo
13.
Proc Natl Acad Sci U S A ; 114(41): 10852-10857, 2017 10 10.
Artículo en Inglés | MEDLINE | ID: mdl-28973862

RESUMEN

The folding of natural proteins typically relies on hydrophobic packing, metal binding, or disulfide bond formation in the protein core. Alternatively, a 3D structure can be defined by incorporating a multivalent cross-linking agent, and this approach has been successfully developed for the selection of bicyclic peptides from large random-sequence libraries. By contrast, there is no general method for the de novo computational design of multicross-linked proteins with predictable and well-defined folds, including ones not found in nature. Here we use Rosetta and Tertiary Motifs (TERMs) to design small proteins that fold around multivalent cross-linkers. The hydrophobic cross-linkers stabilize the fold by macrocyclic restraints, and they also form an integral part of a small apolar core. The designed CovCore proteins were prepared by chemical synthesis, and their structures were determined by solution NMR or X-ray crystallography. These mesosized proteins, lying between conventional proteins and small peptides, are easily accessible either through biosynthetic precursors or chemical synthesis. The unique tertiary structures and ease of synthesis of CovCore proteins indicate that they should provide versatile templates for developing inhibitors of protein-protein interactions.


Asunto(s)
Coronavirus/fisiología , Ingeniería de Proteínas/métodos , Pliegue de Proteína , Estructura Secundaria de Proteína , Proteínas del Núcleo Viral/química , Secuencia de Aminoácidos , Cristalografía por Rayos X , Humanos , Modelos Moleculares , Homología de Secuencia
14.
J Am Chem Soc ; 141(18): 7320-7326, 2019 05 08.
Artículo en Inglés | MEDLINE | ID: mdl-30998340

RESUMEN

Infrared (IR) spectroscopy has provided considerable insight into the structures, dynamics, and formation mechanisms of amyloid fibrils. IR probes, such as main chain 13C═18O, have been widely employed to obtain site-specific structural information, yet only secondary structures and strand-to-strand arrangements can be probed. Very few nonperturbative IR probes are available to report on the side-chain conformation and environments, which are critical to determining sheet-to-sheet arrangements in steric zippers within amyloids. Polar residues, such as glutamine, contribute significantly to the stability of amyloids and thus are frequently found in core regions of amyloid peptides/proteins. Furthermore, polyglutamine (polyQ) repeats form toxic aggregates in several neurodegenerative diseases. Here we report the synthesis and application of a new nonperturbative IR probe-glutamine side chain 13C═18O. We use side chain 13C═18O labeling and isotope dilution to detect the presence of intermolecularly hydrogen-bonded arrays of glutamine side chains (Gln ladders) in amyloid-forming peptides. Moreover, the line width of the 13C═18O peak is highly sensitive to its local hydration environment. The IR data from side chain labeling allows us to unambiguously determine the sheet-to-sheet arrangement in a short amyloid-forming peptide, GNNQQNY, providing insight that was otherwise inaccessible through main chain labeling. With several different fibril samples, we also show the versatility of this IR probe in studying the structures and aggregation kinetics of amyloids. Finally, we demonstrate the capability of modeling amyloid structures with IR data using the integrative modeling platform (IMP) and the potential of integrating IR with other biophysical methods for more accurate structural modeling. Together, we believe that side chain 13C═18O will complement main chain isotope labeling in future IR studies of amyloids and integrative modeling using IR data will significantly expand the power of IR spectroscopy to elucidate amyloid assemblies.


Asunto(s)
Amiloide/síntesis química , Glutamina/química , Marcaje Isotópico , Sondas Moleculares/química , Amiloide/química , Espectrofotometría Infrarroja
15.
J Am Chem Soc ; 141(11): 4526-4530, 2019 03 20.
Artículo en Inglés | MEDLINE | ID: mdl-30821975

RESUMEN

A family of proteases called caspases mediate apoptosis signaling in animals. We report a GFP-based fluorogenic protease reporter, dubbed "FlipGFP", by flipping a beta strand of the GFP. Upon protease activation and cleavage, the beta strand is restored, leading to reconstitution of the GFP and fluorescence. FlipGFP-based TEV protease reporter achieves 100-fold fluorescence change. A FlipGFP-based executioner caspase reporter visualized apoptosis in live zebrafish embryos with spatiotemporal resolution. FlipGFP also visualized apoptotic cells in the midgut of Drosophila. Thus, the FlipGFP-based caspase reporter will be useful for monitoring apoptosis during animal development and for designing reporters of proteases beyond caspases. The design strategy can be further applied to a red fluorescent protein for engineering a red fluorogenic protease reporter.


Asunto(s)
Apoptosis , Genes Reporteros/genética , Proteínas Fluorescentes Verdes/química , Proteínas Fluorescentes Verdes/genética , Imagen Molecular , Péptido Hidrolasas/química , Péptido Hidrolasas/genética , Animales , Drosophila melanogaster , Células HEK293 , Células HeLa , Humanos , Conformación Proteica en Lámina beta
16.
Chembiochem ; 19(9): 902-906, 2018 05 04.
Artículo en Inglés | MEDLINE | ID: mdl-29417711

RESUMEN

Although helices play key roles in peptide-protein and protein-protein interactions, the helical conformation is generally unstable for short peptides (10-15 residues) in aqueous solution in the absence of their binding partners. Thus, stabilizing the helical conformation of peptides can lead to increases in binding potency, specificity, and stability towards proteolytic degradation. Helices have been successfully stabilized by introducing side chain-to-side chain crosslinks within the central portion of the helix. However, this approach leaves the ends of the helix free, thus leading to fraying and exposure of the non-hydrogen-bonded amide groups to solvent. Here, we develop a "capped-strapped" peptide strategy to stabilize helices by embedding the entire length of the helix within a macrocycle, which also includes a semirigid organic template as well as end-capping interactions. We have designed a ten-residue capped-strapped helical peptide that behaves like a miniprotein, with a cooperative thermal unfolding transition and Tm ≈70 °C, unprecedented for helical peptides of this length. The NMR structure determination confirmed the design, and X-ray crystallography revealed a novel quaternary structure with implications for foldamer design.


Asunto(s)
Compuestos Macrocíclicos/química , Péptidos/química , Secuencia de Aminoácidos , Cristalografía por Rayos X , Modelos Moleculares , Conformación Proteica en Hélice alfa , Estabilidad Proteica , Desplegamiento Proteico , Temperatura
17.
Angew Chem Int Ed Engl ; 57(39): 12702-12706, 2018 09 24.
Artículo en Inglés | MEDLINE | ID: mdl-30118570

RESUMEN

Analogous to reversible post-translational protein modifications, the ability to attach and subsequently remove modifications on proteins would be valuable for protein and biological research. Although bioorthogonal functionalities have been developed to conjugate or cleave protein modifications, they are introduced into proteins on separate residues and often with bulky side chains, limiting their use to one type of control and primarily protein surface. Here we achieved dual control on one residue by genetically encoding S-propargyl-cysteine (SprC), which has bioorthogonal alkyne and propargyl groups in a compact structure, permitting usage in protein interior in addition to surface. We demonstrated its incorporation at the dimer interface of glutathione transferase for in vivo crosslinking via thiol-yne click chemistry, and at the active site of human rhinovirus 3C protease for masking and then turning on enzyme activity via Pd-cleavage of SprC into Cys. In addition, we installed biotin onto EGFP via Sonogashira coupling of SprC and then tracelessly removed it via Pd cleavage. SprC is small in size, commercially available, nontoxic, and allows for bond building and breaking on a single residue. Genetically encoded SprC will be valuable for chemically controlling proteins with an essential Cys and for reversible protein modifications.


Asunto(s)
Cisteína Endopeptidasas/metabolismo , Cisteína/química , Proteínas Fluorescentes Verdes/química , Proteínas Virales/metabolismo , Proteasas Virales 3C , Proteínas Arqueales/química , Proteínas Arqueales/genética , Proteínas Arqueales/metabolismo , Biotina/química , Catálisis , Dominio Catalítico , Química Clic , Cisteína/metabolismo , Cisteína Endopeptidasas/química , Enterovirus/enzimología , Proteínas Fluorescentes Verdes/genética , Proteínas Fluorescentes Verdes/metabolismo , Humanos , Methanosarcina/metabolismo , Mutagénesis Sitio-Dirigida , Paladio/química , Pargilina/química , Tiorredoxinas/química , Tiorredoxinas/genética , Tiorredoxinas/metabolismo , Proteínas Virales/química
18.
Angew Chem Int Ed Engl ; 55(18): 5472-6, 2016 04 25.
Artículo en Inglés | MEDLINE | ID: mdl-27080057

RESUMEN

Described for the first time is that carbon dioxide (CO2 ) can be successfully inserted into aryl C-H bonds of the backbone of a metal-organic framework (MOF) to generate free carboxylate groups, which serve as Brønsted acid sites for efficiently catalyzing the methanolysis of epoxides. The work delineates the very first example of utilizing CO2 for heterogeneous C-H activation and carboxylation reactions on MOFs, and opens a new avenue for CO2 chemical transformations under mild reaction conditions.

19.
Chemistry ; 21(6): 2501-7, 2015 Feb 02.
Artículo en Inglés | MEDLINE | ID: mdl-25504756

RESUMEN

Foldamers offer an attractive opportunity for the design of novel molecules that mimic the structures and functions of proteins and enzymes including biocatalysis and biomolecular recognition. Herein we report a new class of nonnatural helical sulfono-γ-AApeptide foldamers of varying lengths. The crystal structure of the sulfono-γ-AApeptide monomer S6 illustrates the intrinsic folding propensity of sulfono-γ-AApeptides, which likely originates from the bulkiness of tertiary sulfonamide moiety. The two-dimensional solution NMR spectroscopy data for the longest sequence S1 demonstrates a 10/16 right-handed helical structure. Optical analysis using circular dichroism further supports well- defined helical conformation of sulfono-γ-AApeptides in solution containing as few as five building blocks. Future development of sulfono-γ-AApeptides may lead to new foldamers with discrete functions, enabling expanded application in chemical biology and biomedical sciences.


Asunto(s)
Péptidos/química , Sulfonas/química , Dicroismo Circular , Cristalografía por Rayos X , Espectroscopía de Resonancia Magnética , Péptidos/síntesis química , Peptidomiméticos , Estructura Secundaria de Proteína , Estructura Terciaria de Proteína
20.
Org Biomol Chem ; 13(3): 672-6, 2015 Jan 21.
Artículo en Inglés | MEDLINE | ID: mdl-25420701

RESUMEN

We report an efficient method for the preparation of unprecedented head-to-tail cyclic sulfono-γ-AApeptides. Following this method, a number of cyclic sequences bearing two to five subunits were efficiently synthesized. In addition, the X-ray crystal structure study of a three-membered cyclic sulfono-γ-AApeptide revealed a type II ß-turn-like character.


Asunto(s)
Aminoácidos Sulfúricos/química , Péptidos Cíclicos/síntesis química , Peptidomiméticos/síntesis química , Cristalografía por Rayos X , Ciclización , Estructura Molecular , Péptidos Cíclicos/química , Peptidomiméticos/química
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