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1.
BMC Bioinformatics ; 22(1): 68, 2021 Feb 12.
Artículo en Inglés | MEDLINE | ID: mdl-33579189

RESUMEN

BACKGROUND: The clustering of data produced by liquid chromatography coupled to mass spectrometry analyses (LC-MS data) has recently gained interest to extract meaningful chemical or biological patterns. However, recent instrumental pipelines deliver data which size, dimensionality and expected number of clusters are too large to be processed by classical machine learning algorithms, so that most of the state-of-the-art relies on single pass linkage-based algorithms. RESULTS: We propose a clustering algorithm that solves the powerful but computationally demanding kernel k-means objective function in a scalable way. As a result, it can process LC-MS data in an acceptable time on a multicore machine. To do so, we combine three essential features: a compressive data representation, Nyström approximation and a hierarchical strategy. In addition, we propose new kernels based on optimal transport, which interprets as intuitive similarity measures between chromatographic elution profiles. CONCLUSIONS: Our method, referred to as CHICKN, is evaluated on proteomics data produced in our lab, as well as on benchmark data coming from the literature. From a computational viewpoint, it is particularly efficient on raw LC-MS data. From a data analysis viewpoint, it provides clusters which differ from those resulting from state-of-the-art methods, while achieving similar performances. This highlights the complementarity of differently principle algorithms to extract the best from complex LC-MS data.


Asunto(s)
Algoritmos , Análisis por Conglomerados , Péptidos , Proteómica , Cromatografía Liquida , Compresión de Datos , Espectrometría de Masas , Péptidos/química , Proteómica/métodos
2.
Nat Commun ; 12(1): 815, 2021 02 05.
Artículo en Inglés | MEDLINE | ID: mdl-33547286

RESUMEN

Narcolepsy type 1 (NT1) is a chronic neurological disorder that impairs the brain's ability to control sleep-wake cycles. Current therapies are limited to the management of symptoms with modest effectiveness and substantial adverse effects. Agonists of the orexin receptor 2 (OX2R) have shown promise as novel therapeutics that directly target the pathophysiology of the disease. However, identification of drug-like OX2R agonists has proven difficult. Here we report cryo-electron microscopy structures of active-state OX2R bound to an endogenous peptide agonist and a small-molecule agonist. The extended carboxy-terminal segment of the peptide reaches into the core of OX2R to stabilize an active conformation, while the small-molecule agonist binds deep inside the orthosteric pocket, making similar key interactions. Comparison with antagonist-bound OX2R suggests a molecular mechanism that rationalizes both receptor activation and inhibition. Our results enable structure-based discovery of therapeutic orexin agonists for the treatment of NT1 and other hypersomnia disorders.


Asunto(s)
Aminopiridinas/química , Azepinas/química , Antagonistas de los Receptores de Orexina/química , Receptores de Orexina/química , Péptidos/química , Fármacos Inductores del Sueño/química , Sulfonamidas/química , Triazoles/química , Aminopiridinas/metabolismo , Azepinas/metabolismo , Sitios de Unión , Clonación Molecular , Microscopía por Crioelectrón , Escherichia coli/genética , Escherichia coli/metabolismo , Expresión Génica , Vectores Genéticos/química , Vectores Genéticos/metabolismo , Células HEK293 , Humanos , Simulación de Dinámica Molecular , Antagonistas de los Receptores de Orexina/metabolismo , Receptores de Orexina/agonistas , Receptores de Orexina/metabolismo , Péptidos/metabolismo , Unión Proteica , Conformación Proteica en Hélice alfa , Conformación Proteica en Lámina beta , Dominios y Motivos de Interacción de Proteínas , Proteínas Recombinantes/química , Proteínas Recombinantes/genética , Proteínas Recombinantes/metabolismo , Fármacos Inductores del Sueño/metabolismo , Sulfonamidas/metabolismo , Triazoles/metabolismo
3.
Nat Commun ; 12(1): 870, 2021 02 08.
Artículo en Inglés | MEDLINE | ID: mdl-33558523

RESUMEN

Despite six decades of efforts to synthesize peptides and proteins bearing multiple disulfide bonds, this synthetic challenge remains an unsolved problem in most targets (e.g., knotted mini proteins). Here we show a de novo general synthetic strategy for the ultrafast, high-yielding formation of two and three disulfide bonds in peptides and proteins. We develop an approach based on the combination of a small molecule, ultraviolet-light, and palladium for chemo- and regio-selective activation of cysteine, which enables the one-pot formation of multiple disulfide bonds in various peptides and proteins. We prepare bioactive targets of high therapeutic potential, including conotoxin, RANTES, EETI-II, and plectasin peptides and the linaclotide drug. We anticipate that this strategy will be a game-changer in preparing millions of inaccessible targets for drug discovery.


Asunto(s)
Disulfuros/química , Disulfuros/metabolismo , Péptidos/metabolismo , Proteínas/metabolismo , Cromatografía Líquida de Alta Presión , Péptidos/síntesis química , Péptidos/química , Proteínas/síntesis química , Proteínas/química , Espectrometría de Masa por Ionización de Electrospray , Estereoisomerismo
4.
Nat Commun ; 12(1): 62, 2021 01 04.
Artículo en Inglés | MEDLINE | ID: mdl-33397936

RESUMEN

Histones control gene expression by regulating chromatin structure and function. The posttranslational modifications (PTMs) on the side chains of histones form the epigenetic landscape, which is tightly controlled by epigenetic modulator enzymes and further recognized by so-called reader domains. Histone microarrays have been widely applied to investigate histone-reader interactions, but not the transient interactions of Zn2+-dependent histone deacetylase (HDAC) eraser enzymes. Here, we synthesize hydroxamic acid-modified histone peptides and use them in femtomolar microarrays for the direct capture and detection of the four class I HDAC isozymes. Follow-up functional assays in solution provide insights into their suitability to discover HDAC substrates and inhibitors with nanomolar potency and activity in cellular assays. We conclude that similar hydroxamic acid-modified histone peptide microarrays and libraries could find broad application to identify class I HDAC isozyme-specific substrates and facilitate the development of isozyme-selective HDAC inhibitors and probes.


Asunto(s)
Inhibidores de Histona Desacetilasas/farmacología , Ácidos Hidroxámicos/metabolismo , Péptidos/metabolismo , Secuencia de Aminoácidos , Células HEK293 , Histonas/metabolismo , Humanos , Isoenzimas/metabolismo , Análisis por Micromatrices , Péptidos/química , Procesamiento Proteico-Postraduccional/efectos de los fármacos , Zinc/metabolismo
5.
BMC Bioinformatics ; 22(1): 7, 2021 Jan 06.
Artículo en Inglés | MEDLINE | ID: mdl-33407098

RESUMEN

BACKGROUND: Accurate prediction of binding between class I human leukocyte antigen (HLA) and neoepitope is critical for target identification within personalized T-cell based immunotherapy. Many recent prediction tools developed upon the deep learning algorithms and mass spectrometry data have indeed showed improvement on the average predicting power for class I HLA-peptide interaction. However, their prediction performances show great variability over individual HLA alleles and peptides with different lengths, which is particularly the case for HLA-C alleles due to the limited amount of experimental data. To meet the increasing demand for attaining the most accurate HLA-peptide binding prediction for individual patient in the real-world clinical studies, more advanced deep learning framework with higher prediction accuracy for HLA-C alleles and longer peptides is highly desirable. RESULTS: We present a pan-allele HLA-peptide binding prediction framework-MATHLA which integrates bi-directional long short-term memory network and multiple head attention mechanism. This model achieves better prediction accuracy in both fivefold cross-validation test and independent test dataset. In addition, this model is superior over existing tools regarding to the prediction accuracy for longer ligand ranging from 11 to 15 amino acids. Moreover, our model also shows a significant improvement for HLA-C-peptide-binding prediction. By investigating multiple-head attention weight scores, we depicted possible interaction patterns between three HLA I supergroups and their cognate peptides. CONCLUSION: Our method demonstrates the necessity of further development of deep learning algorithm in improving and interpreting HLA-peptide binding prediction in parallel to increasing the amount of high-quality HLA ligandome data.


Asunto(s)
Biología Computacional/métodos , Antígenos de Histocompatibilidad Clase I , Redes Neurales de la Computación , Péptidos , Unión Proteica , Algoritmos , Antígenos de Histocompatibilidad Clase I/química , Antígenos de Histocompatibilidad Clase I/metabolismo , Humanos , Modelos Estadísticos , Péptidos/química , Péptidos/metabolismo
6.
Nat Commun ; 12(1): 696, 2021 01 29.
Artículo en Inglés | MEDLINE | ID: mdl-33514734

RESUMEN

Azoles are five-membered heterocycles often found in the backbones of peptidic natural products and synthetic peptidomimetics. Here, we report a method of ribosomal synthesis of azole-containing peptides involving specific ribosomal incorporation of a bromovinylglycine derivative into the nascent peptide chain and its chemoselective conversion to a unique azole structure. The chemoselective conversion was achieved by posttranslational dehydrobromination of the bromovinyl group and isomerization in aqueous media under fairly mild conditions. This method enables us to install exotic azole groups, oxazole and thiazole, at designated positions in the peptide chain with both linear and macrocyclic scaffolds and thereby expand the repertoire of building blocks in the mRNA-templated synthesis of designer peptides.


Asunto(s)
Azoles/metabolismo , Biomimética/métodos , Biosíntesis de Péptidos , Péptidos/metabolismo , Procesamiento Proteico-Postraduccional , Azoles/química , Diseño de Fármacos , Péptidos/química , Peptidomiméticos/química , Peptidomiméticos/metabolismo
7.
J Proteome Res ; 20(2): 1296-1303, 2021 02 05.
Artículo en Inglés | MEDLINE | ID: mdl-33472369

RESUMEN

SARS-CoV-2, a novel coronavirus causing overwhelming death and infection worldwide, has emerged as a pandemic. Compared to its predecessor SARS-CoV, SARS-CoV-2 is more infective for being highly contagious and exhibiting tighter binding with host angiotensin-converting enzyme 2 (hACE-2). The entry of the virus into host cells is mediated by the interaction of its spike protein with hACE-2. Thus, a peptide that has a resemblance to hACE-2 but can overpower the spike protein-hACE-2 interaction will be a potential therapeutic to contain this virus. The non-interacting residues in the receptor-binding domain of hACE-2 have been mutated to generate a library of 136 new peptides. Out of this library, docking and virtual screening discover seven peptides that can exert a stronger interaction with the spike protein than hACE-2. A peptide derived from simultaneous mutation of all the non-interacting residues of hACE-2 yields almost three-fold stronger interaction than hACE-2 and thus turns out here to be the best peptide inhibitor of the novel coronavirus. The binding of the best peptide inhibitor with the spike protein is explored further by molecular dynamics, free energy, and principal component analysis, which demonstrate its efficacy compared to hACE-2. The delivery of the screened inhibitors with nanocarriers like metal-organic frameworks will be worthy of further consideration to boost their efficacy.


Asunto(s)
/metabolismo , Antivirales/farmacología , Materiales Biomiméticos/farmacología , Péptidos/farmacología , Glicoproteína de la Espiga del Coronavirus/antagonistas & inhibidores , /química , Antivirales/química , Materiales Biomiméticos/química , /prevención & control , Humanos , Simulación del Acoplamiento Molecular , Simulación de Dinámica Molecular , Pandemias , Péptidos/química , Unión Proteica/efectos de los fármacos , /metabolismo , Glicoproteína de la Espiga del Coronavirus/metabolismo
8.
Food Chem ; 343: 128406, 2021 May 01.
Artículo en Inglés | MEDLINE | ID: mdl-33406571

RESUMEN

This study was the first to examine the effects of γ-[Glu](1≤n≤5)-Gln (GGP, a taste enhancer; added at 0.5% or 5.0%) on the breadmaking using frozen dough. γ-[Glu](1≤n≤5)-Gln was produced using the method established in our research center. The addition of GGP at either level increased yeast viability, freezable water content and storage and loss moduli, decreased the free sulfhydryl content of dough during the frozen storage and freeze-thaw cycles, and improved the microstructure of frozen dough and texture of the baked bread. The addition of GGP at 0.5% led to a dough having the highest extensibility, and most complete and uniform starch-gluten network, and a baked bread crumb with the lowest hardness, best texture, and most uniform organization. These results indicated that GGP has great potential as a food-derived cryoprotectant/antifreeze agent for the baking industry.


Asunto(s)
Pan/análisis , Culinaria/métodos , Péptidos/química , Harina/análisis , Congelación , Dureza , Espectroscopía de Resonancia Magnética , Microscopía Electrónica de Rastreo , Reología , Compuestos de Sulfhidrilo/análisis , Agua/análisis , Levaduras/fisiología
9.
Molecules ; 26(2)2021 Jan 15.
Artículo en Inglés | MEDLINE | ID: mdl-33467522

RESUMEN

Peptides are fragments of proteins that carry out biological functions. They act as signaling entities via all domains of life and interfere with protein-protein interactions, which are indispensable in bio-processes. Short peptides include fundamental molecular information for a prelude to the symphony of life. They have aroused considerable interest due to their unique features and great promise in innovative bio-therapies. This work focusing on the current state-of-the-art short peptide-based therapeutical developments is the first global review written by researchers from all continents, as a celebration of 100 years of peptide therapeutics since the commencement of insulin therapy in the 1920s. Peptide "drugs" initially played only the role of hormone analogs to balance disorders. Nowadays, they achieve numerous biomedical tasks, can cross membranes, or reach intracellular targets. The role of peptides in bio-processes can hardly be mimicked by other chemical substances. The article is divided into independent sections, which are related to either the progress in short peptide-based theranostics or the problems posing challenge to bio-medicine. In particular, the SWOT analysis of short peptides, their relevance in therapies of diverse diseases, improvements in (bio)synthesis platforms, advanced nano-supramolecular technologies, aptamers, altered peptide ligands and in silico methodologies to overcome peptide limitations, modern smart bio-functional materials, vaccines, and drug/gene-targeted delivery systems are discussed.


Asunto(s)
Antiinfecciosos/farmacología , Antivirales/farmacología , Péptidos/química , Péptidos/farmacología , Péptidos/uso terapéutico , Aminoácidos/química , Antiinfecciosos/química , Antivirales/química , Simulación por Computador , Cosmecéuticos/química , Cosmecéuticos/uso terapéutico , Suplementos Dietéticos , Técnicas de Transferencia de Gen , Humanos , Lactoferrina/química , Membrana Dobles de Lípidos , Nanoestructuras/administración & dosificación , Nanoestructuras/química , Péptidos/administración & dosificación , Células Madre , Vacunas de Subunidad/química , Vacunas de Subunidad/farmacología
10.
BMC Bioinformatics ; 22(1): 1, 2021 Jan 02.
Artículo en Inglés | MEDLINE | ID: mdl-33388027

RESUMEN

BACKGROUND: Protein-peptide interactions play a fundamental role in a wide variety of biological processes, such as cell signaling, regulatory networks, immune responses, and enzyme inhibition. Peptides are characterized by low toxicity and small interface areas; therefore, they are good targets for therapeutic strategies, rational drug planning and protein inhibition. Approximately 10% of the ethical pharmaceutical market is protein/peptide-based. Furthermore, it is estimated that 40% of protein interactions are mediated by peptides. Despite the fast increase in the volume of biological data, particularly on sequences and structures, there remains a lack of broad and comprehensive protein-peptide databases and tools that allow the retrieval, characterization and understanding of protein-peptide recognition and consequently support peptide design. RESULTS: We introduce Propedia, a comprehensive and up-to-date database with a web interface that permits clustering, searching and visualizing of protein-peptide complexes according to varied criteria. Propedia comprises over 19,000 high-resolution structures from the Protein Data Bank including structural and sequence information from protein-peptide complexes. The main advantage of Propedia over other peptide databases is that it allows a more comprehensive analysis of similarity and redundancy. It was constructed based on a hybrid clustering algorithm that compares and groups peptides by sequences, interface structures and binding sites. Propedia is available through a graphical, user-friendly and functional interface where users can retrieve, and analyze complexes and download each search data set. We performed case studies and verified that the utility of Propedia scores to rank promissing interacting peptides. In a study involving predicting peptides to inhibit SARS-CoV-2 main protease, we showed that Propedia scores related to similarity between different peptide complexes with SARS-CoV-2 main protease are in agreement with molecular dynamics free energy calculation. CONCLUSIONS: Propedia is a database and tool to support structure-based rational design of peptides for special purposes. Protein-peptide interactions can be useful to predict, classifying and scoring complexes or for designing new molecules as well. Propedia is up-to-date as a ready-to-use webserver with a friendly and resourceful interface and is available at: https://bioinfo.dcc.ufmg.br/propedia.


Asunto(s)
Sistemas de Administración de Bases de Datos , Bases de Datos de Proteínas , Péptidos/química , Proteínas/química , Algoritmos , Humanos
11.
Nat Commun ; 12(1): 149, 2021 01 08.
Artículo en Inglés | MEDLINE | ID: mdl-33420053

RESUMEN

Intrinsically disordered proteins have dramatically changed the structure-function paradigm of proteins in the 21st century. Resilin is a native elastic insect protein, which features intrinsically disordered structure, unusual multi-stimuli responsiveness and outstanding resilience. Advances in computational techniques, polypeptide synthesis methods and modular protein engineering routines have led to the development of novel resilin-like polypeptides (RLPs) including modular RLPs, expanding their applications in tissue engineering, drug delivery, bioimaging, biosensors, catalysis and bioelectronics. However, how the responsive behaviour of RLPs is encoded in the amino acid sequence level remains elusive. This review summarises the milestones of RLPs, and discusses the development of modular RLP-based biomaterials, their current applications, challenges and future perspectives. A perspective of future research is that sequence and responsiveness profiling of RLPs can provide a new platform for the design and development of new modular RLP-based biomaterials with programmable structure, properties and functions.


Asunto(s)
Materiales Biomiméticos/química , Proteínas de Insectos/química , Péptidos/química , Materiales inteligentes/química , Secuencia de Aminoácidos , Técnicas Biosensibles/instrumentación , Sistemas de Liberación de Medicamentos/instrumentación , Elasticidad , Proteínas de Insectos/genética , Péptidos/genética , Reología , Ingeniería de Tejidos/instrumentación
12.
J Chem Inf Model ; 61(1): 423-431, 2021 01 25.
Artículo en Inglés | MEDLINE | ID: mdl-33412850

RESUMEN

Membrane fusion, a key step in the early stages of virus propagation, allows the release of the viral genome in the host cell cytoplasm. The process is initiated by fusion peptides that are small, hydrophobic components of viral membrane-embedded glycoproteins and are typically conserved within virus families. Here, we attempted to identify the correct fusion peptide region in the Spike protein of SARS-CoV-2 by all-atom molecular dynamics simulations of dual membrane systems with varied oligomeric units of putative candidate peptides. Of all of the systems tested, only a trimeric unit of a 40-amino-acid region (residues 816-855 of SARS-CoV-2 Spike) was effective in triggering the initial stages of membrane fusion, within 200 ns of simulation time. Association of this trimeric unit with dual membranes resulted in the migration of lipids from the upper leaflet of the lower bilayer toward the lower leaflet of the upper bilayer to create a structural unit reminiscent of a fusion bridge. We submit that residues 816-855 of Spike represent the bona fide fusion peptide of SARS-CoV-2 and that computational methods represent an effective way to identify fusion peptides in viral glycoproteins.


Asunto(s)
/metabolismo , Fusión de Membrana , Glicoproteína de la Espiga del Coronavirus/metabolismo , Internalización del Virus , Secuencia de Aminoácidos , Interacciones Huésped-Patógeno , Humanos , Simulación de Dinámica Molecular , Péptidos/química , Péptidos/metabolismo , Multimerización de Proteína , Glicoproteína de la Espiga del Coronavirus/química
13.
Nat Commun ; 12(1): 305, 2021 01 12.
Artículo en Inglés | MEDLINE | ID: mdl-33436646

RESUMEN

Apelin and arginine-vasopressin (AVP) are conversely regulated by osmotic stimuli. We therefore hypothesized that activating the apelin receptor (apelin-R) with LIT01-196, a metabolically stable apelin-17 analog, may be beneficial for treating the Syndrome of Inappropriate Antidiuresis, in which AVP hypersecretion leads to hyponatremia. We show that LIT01-196, which behaves as a potent full agonist for the apelin-R, has an in vivo half-life of 156 minutes in the bloodstream after subcutaneous administration in control rats. In collecting ducts, LIT01-196 decreases dDAVP-induced cAMP production and apical cell surface expression of phosphorylated aquaporin 2 via AVP type 2 receptors, leading to an increase in aqueous diuresis. In a rat experimental model of AVP-induced hyponatremia, LIT01-196 subcutaneously administered blocks the antidiuretic effect of AVP and the AVP-induced increase in urinary osmolality and induces a progressive improvement of hyponatremia. Our data suggest that apelin-R activation constitutes an original approach for hyponatremia treatment.


Asunto(s)
Apelina/análogos & derivados , Apelina/metabolismo , Arginina Vasopresina/efectos adversos , Diuresis , Hiponatremia/patología , Hiponatremia/fisiopatología , Secuencia de Aminoácidos , Animales , Apelina/administración & dosificación , Apelina/sangre , Receptores de Apelina/metabolismo , Arginina Vasopresina/sangre , Glucemia/metabolismo , Presión Sanguínea/efectos de los fármacos , Línea Celular , Colforsina/farmacología , AMP Cíclico/biosíntesis , Desamino Arginina Vasopresina/farmacología , Modelos Animales de Enfermedad , Diuresis/efectos de los fármacos , Electrólitos/sangre , Semivida , Hiponatremia/sangre , Hiponatremia/orina , Túbulos Renales Colectores/efectos de los fármacos , Túbulos Renales Colectores/metabolismo , Túbulos Renales Colectores/fisiopatología , Masculino , Ratones , Modelos Biológicos , Contracción Miocárdica/efectos de los fármacos , Péptidos/química , Péptidos/farmacología , Fosforilación/efectos de los fármacos , Ratas Sprague-Dawley , Tolvaptán/farmacología
14.
Biochem Biophys Res Commun ; 535: 47-53, 2021 01 08.
Artículo en Inglés | MEDLINE | ID: mdl-33340765

RESUMEN

The interaction of the multifunctional cytokine interleukin (IL)-6 and its receptor (IL-6R) is involved in various diseases, including not only autoimmune diseases such as rheumatoid arthritis but also cancer and cytokine storms in coronavirus disease 2019 (COVID-19). In this study, systematic evolution of ligands by exponential enrichment (SELEX) against human IL-6R from mRNA-displayed unnatural peptide library ribosomally initiated and cyclized with m-(chloromethyl)benzoic acid (mClPh) incorporated by genetic code expansion (sense suppression) was performed using the PURE (Protein synthesis Using Recombinant Elements) system. A novel 13-mer unnatural mClPh-cyclized peptide that binds to the extracellular domain of IL-6R was discovered from an extremely diverse random peptide library. In vitro affinity maturation of IL-6R-binding unnatural mClPh-cyclized peptide from focused libraries was performed, identifying two IL-6R-binding unnatural mClPh-cyclized peptides by next-generation sequencing. Because cyclization can increase the protease resistance of peptides, novel IL-6R-binding mClPh-cyclized peptides discovered in this study have the potential to be used for a variety of research, therapeutic, and diagnostic applications involving IL-6/IL-6R signaling.


Asunto(s)
Ácido Benzoico/química , Péptidos/química , Receptores de Interleucina-6/química , Ribosomas/química , Ciclización , Código Genético , Humanos , Biblioteca de Péptidos , ARN Mensajero , Técnica SELEX de Producción de Aptámeros
15.
Biochim Biophys Acta Gen Subj ; 1865(1): 129729, 2021 01.
Artículo en Inglés | MEDLINE | ID: mdl-32916204

RESUMEN

BACKGROUND: Amyloids are highly ordered polypeptide aggregates stabilized by a beta-sheet structural core. Though classically associated to pathology, reports on novel functional roles of these proteins have increasingly emerged in the past decade. Moreover, the recent discovery that amyloids formed with rationally designed small peptides can exhibit catalytic reactivity has opened up new opportunities in both biology and biotechnology. The observed activities typically require the binding of divalent metals, giving rise to active metal-amyloid complexes. METHODS: Peptide (SDIDVFI) was aggregated in vitro. The structure of the self-assembled species was analyzed using fluorescence, transmission electron microscopy, circular dichroism and computational modeling. A kinetic characterization of the emerging catalytic activity was performed. RESULTS: The peptide self-assembled into canonical amyloids that exhibited catalytic activity towards hydrolysis of the phosphoanhydride bonds of adenosine triphosphate (ATP), partially mimicking an ATPase-like enzyme. Both amyloid formation and activity are shown to depend on manganese (Mn2+) binding. The activity was not restricted to ATP but also affected all other ribonucleotides (GTP, CTP and UTP). Peptides carrying a single aspartate exhibited a similar activity. CONCLUSIONS: The phosphoanhydride bonds appear as the main specificity target of the Mn2+-amyloid complex. A single aspartate per peptide is sufficient to enable the hydrolytic activity. GENERAL SIGNIFICANCE: Catalytic amyloids are shown for the first time to catalyze the hydrolysis of all four ribonucleotides. Our results should contribute towards understanding the biological implications of amyloid-mediated reactivity as well as in the design of future catalytic amyloids for biotechnological applications.


Asunto(s)
Adenosina Trifosfatasas/metabolismo , Adenosina Trifosfato/metabolismo , Amiloide/metabolismo , Péptidos/metabolismo , Adenosina Trifosfatasas/química , Secuencia de Aminoácidos , Amiloide/química , Amiloide/ultraestructura , Hidrólisis , Modelos Moleculares , Péptidos/química , Especificidad por Sustrato
16.
Biochim Biophys Acta Gen Subj ; 1865(1): 129775, 2021 01.
Artículo en Inglés | MEDLINE | ID: mdl-33122085

RESUMEN

BACKGROUND: Intrinsically disordered regions (IDRs) in proteins can regulate their activity by facilitating protein-protein interactions (PPIs) as exemplified in the recruitment of the eukaryotic translation initiation factor 4E (eIF4E) protein by the protein eIF4G. Deregulation of this PPI module is central to a broad spectrum of cancer related malignancies and its targeted inhibition through bioactive peptides is a promising strategy for therapeutic intervention. METHODS: We employed molecular dynamics simulations coupled with biophysical assays to rationally develop peptide derivatives from the intrinsically disordered eIF4G scaffold by incorporating non-natural amino acids that facilitates disorder-to-order transition. RESULTS: The conformational heterogeneity of these peptides and the degree of structural reorganization required to adopt the optimum mode of interaction with eIF4E underscores their differential binding affinities. The presence of a pre-structured local helical element in the ensemble of structures was instrumental in the efficient docking of the peptides on to the protein surface. The formation of Y4: P38 hydrogen-bond interaction between the peptide and eIF4E is a rate limiting event in the efficient recognition of the protein since it occurs through the disordered region of the peptide. CONCLUSIONS: These insights were exploited to further design features into the peptide to propagate bound-state conformations in solution which resulted in the generation of a potent eIF4E binder. GENERAL SIGNIFICANCE: The study illustrates the molecular basis of eIF4E recognition by a disordered epitope from eIF4G and its modulation to generate peptides that can potentially attenuate translation initiation in oncology.


Asunto(s)
Factor 4G Eucariótico de Iniciación/química , Proteínas Intrínsecamente Desordenadas/química , Iniciación de la Cadena Peptídica Traduccional , Péptidos/química , Factor 4E Eucariótico de Iniciación/metabolismo , Factor 4G Eucariótico de Iniciación/metabolismo , Humanos , Proteínas Intrínsecamente Desordenadas/metabolismo , Péptidos/metabolismo , Unión Proteica , Conformación Proteica , Proteínas Recombinantes/metabolismo
17.
Food Chem ; 339: 128047, 2021 Mar 01.
Artículo en Inglés | MEDLINE | ID: mdl-32949916

RESUMEN

The antioxidative activity of natural products has commonly been studied by free radical scavenging methods. However, the mechanisms by which antioxidation is explored by free radical scavenging methods remain largely unknown. This study analyzed the composition of walnut-derived pentapeptides PW5 with potential biological activity and its oxidation reaction products in 2,2'-Azinobis-(3-ethylbenzthiazoline-6-sulphonate) (ABTS) test by nuclear magnetic resonance (NMR) spectroscopy. The amino acid sequence of PW5 peptide successfully characterized as Proline-Proline-Lysine-Asparagine-Tryptophan exhibited significant antioxidant activity with lower IC50 value (0.2210 ± 0.0032 mM) compared to glutathione (GSH, 0.2567 ± 0.0023 mM, p < 0.001). Furthermore, we found that the tryptophan residue was the only residue in PW5 with obvious alteration after treatment with ABTS free radicals, which was linked to its potential antioxidant properties. These findings revealed how NMR-characterized structures and oxidation reaction products may be used to explore the antioxidative mechanisms of food-derived peptides as well as other natural products.


Asunto(s)
Antioxidantes/química , Juglans/química , Péptidos/química , Secuencia de Aminoácidos , Depuradores de Radicales Libres/química , Radicales Libres/química , Espectroscopía de Resonancia Magnética , Nueces/química , Oxidación-Reducción , Proteínas de Plantas/química
18.
Food Chem ; 337: 128069, 2021 Feb 01.
Artículo en Inglés | MEDLINE | ID: mdl-32950762

RESUMEN

Selective enrichment of the highly active antioxidant peptides is required as the lack of an efficient method leads to long screening processes, hampering the research of antioxidant peptides. A simple synthetic metal-organic framework MIL-53 (Cr) was initially applied to extract specific antioxidant peptides from rice dreg protein hydrolysate. The highest active fraction was further purified by reversed-phase high-performance liquid chromatography. The antioxidant peptides with the highest antioxidant activities were identified as Gly-Asp-Met-Asn-Pro and Leu-Leu-Leu-Arg-Trp by LC-MS. These two peptides were synthesized and also exhibited good scavenging activity on the DPPH free radical, superoxide anion free radical and hydroxyl radical, and good chelating ability on Fe2+. The results confirmed that the angling method was effective for antioxidant peptide enrichment from protein hydrolysates.


Asunto(s)
Antioxidantes/química , Oryza/química , Péptidos/química , Proteínas de Plantas/química , Hidrolisados de Proteína/química , Cromatografía Liquida , Espectrometría de Masas
19.
Phys Chem Chem Phys ; 23(1): 607-616, 2021 Jan 06.
Artículo en Inglés | MEDLINE | ID: mdl-33331371

RESUMEN

Cyclization is commonly employed in efforts to improve the target binding affinity of peptide-based probes and therapeutics. Many structural motifs have been identified at protein-protein interfaces and provide promising targets for inhibitor design using cyclic peptides. Cyclized peptides are generally assumed to be rigidified relative to their linear counterparts. This rigidification potentially pre-organizes the molecules to interact properly with their targets. However, the actual impact of cyclization on, for example, peptide configurational entropy, is currently poorly understood in terms of both its magnitude and molecular-level origins. Moreover, even with thousands of desired structural motifs at hand, it is currently not possible to a priori identify the ones that are most promising to mimic using cyclic peptides nor to select the ideal linker length. Instead, labor-intensive chemical synthesis and experimental characterization of various cyclic peptide designs are required, in hopes of finding one with improved target affinity. Herein, using molecular dynamics simulations of polyglycines, we elucidated how head-to-tail cyclization impacts peptide backbone dihedral entropy and developed a simple strategy to rapidly screen for structures that can be reliably mimicked by preorganized cyclic peptides. As expected, cyclization generally led to a reduction in backbone dihedral entropy; notably, however, this effect was minimal when the length of polyglycines was >9 residues. We also found that the reduction in backbone dihedral entropy upon cyclization of small polyglycine peptides does not result from more restricted distributions of the dihedrals; rather, it was the correlations between specific dihedrals that caused the decrease in configurational entropy in the cyclic peptides. Using our comprehensive cyclo-Gn structural ensembles, we obtained a holistic picture of what conformations are accessible to cyclic peptides. Using "hot loops" recently identified at protein-protein interfaces as an example, we provide clear guidelines for choosing the "easiest" hot loops for cyclic peptides to mimic and for identifying appropriate cyclic peptide lengths. In conclusion, our results provide an understanding of the thermodynamics and structures of this interesting class of molecules. This information should prove particularly useful for designing cyclic peptide inhibitors of protein-protein interactions.


Asunto(s)
Péptidos Cíclicos/química , Péptidos/química , Entropía , Simulación de Dinámica Molecular , Conformación Proteica
20.
J Phys Chem Lett ; 12(1): 368-378, 2021 Jan 14.
Artículo en Inglés | MEDLINE | ID: mdl-33356290

RESUMEN

Increasing experiments suggest that amyloid peptides can undergo liquid-liquid phase separation (LLPS) before the formation of amyloid fibrils. However, the exact role of LLPS in amyloid aggregation at the molecular level remains elusive. Here, we investigated the LLPS and amyloid fibrillization of a coarse-grained peptide, capable of capturing fundamental properties of amyloid aggregation over a wide range of concentrations in molecular dynamics simulations. On the basis of the Flory-Huggins theory of polymer solutions, we determined the binodal and spinodal concentrations of LLPS in the low-concentration regime, ϕBL and ϕSL, respectively. Only at concentrations above ϕBL, peptides formed metastable or stable oligomers corresponding to the high-density liquid phase (HDLP) in LLPS, out of which the nucleated conformational conversion to fibril seeds occurred. Below ϕSL, the HDLP was metastable and transient, and the subsequent fibrillization process followed the traditional nucleation and elongation mechanisms. Only above ϕSL, the HDLP became stable, and the initial fibril nucleation and growth were governed by the high local peptide concentrations. The predicted saturation of amyloid aggregation half-times with increasing peptide concentration to a constant, instead of the traditional power-law scaling to zero, was confirmed by simulations and by a thioflavin-T kinetic assay and the transmission electron microscopy of islet amyloid polypeptide (IAPP) aggregation. Our study provides a unified picture of amyloid aggregation for a wide range of concentrations within the framework of LLPS, which may help us better understand the etiology of amyloid diseases, where the amyloid protein concentration can vary by ∼9 orders of magnitude depending on the organ location and facilitate the engineering of novel amyloid-based functional materials.


Asunto(s)
Amiloide/química , Simulación de Dinámica Molecular , Péptidos/química , Agregado de Proteínas , Conformación Proteica
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