RESUMEN
Dynamic interactions between transcription factors govern changes in gene expression that mediate changes in cell state accompanying injury response and regeneration. Transcription factors frequently function as obligate dimers whose activity is often modulated by post-translational modifications. These critical and often transient interactions are not easily detected by traditional methods to investigate protein-protein interactions. This chapter discusses the design and validation of a fusion protein involving a transcription factor tethered to a proximity labeling ligase, APEX2. In this technique, proteins are biotinylated within a small radius of the transcription factor of interest, regardless of time of interaction. Here we discuss the validations required to ensure proper functioning of the transcription factor proximity labeling tool and the sample preparation of biotinylated proteins for mass spectrometry analysis of putative protein interactors.
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Biotinilación , ADN-(Sitio Apurínico o Apirimidínico) Liasa , Mapeo de Interacción de Proteínas , Factores de Transcripción , Mapeo de Interacción de Proteínas/métodos , Humanos , Factores de Transcripción/metabolismo , ADN-(Sitio Apurínico o Apirimidínico) Liasa/metabolismo , ADN-(Sitio Apurínico o Apirimidínico) Liasa/química , Proteínas Recombinantes de Fusión/metabolismo , Proteínas Recombinantes de Fusión/genética , Unión Proteica , Espectrometría de Masas/métodos , Procesamiento Proteico-Postraduccional , Endonucleasas , Enzimas MultifuncionalesRESUMEN
Yeast two-hybrid (YTH) technology is a powerful tool for studying protein interactions and has been widely used in various fields of molecular biology, including the study of antiviral innate immunity. This chapter presents detailed information and experimental procedures for identifying virus-host protein interactions involved in immune regulation using yeast two-hybrid technology.
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Interacciones Huésped-Patógeno , Inmunidad Innata , Técnicas del Sistema de Dos Híbridos , Humanos , Interacciones Huésped-Patógeno/inmunología , Proteínas Virales/inmunología , Proteínas Virales/metabolismo , Saccharomyces cerevisiae/inmunología , Saccharomyces cerevisiae/genética , Unión Proteica , Mapeo de Interacción de Proteínas/métodosRESUMEN
Sturgeon, with 4 times higher lipid content than silver carp (ubiquitously applied for surimi production in China), affects surimi gelling properties. However, how the flesh lipids affect gelling properties remains unclear. This study investigated how flesh lipids impact surimi gelling properties and elucidated the interaction mechanism between lipids and proteins. Results revealed yellow meat contains 7 times higher lipids than white meat. Stronger ionic protein-protein interactions were replaced by weaker hydrophobic forces and hydrogen bonds in protein-lipid interaction. Protein-lipid interaction zones encapsulated lipid particles, changing protein structure from α-helix to ß-sheet structure thereby gel structure becomes flexible and disordered, significantly diminishing surimi gel strength. Docking analysis validated fatty acid mainly binding at Ala577, Ile461, Arg231, Phe165, His665, and His663 of myosin. This study first reported the weakened surimi gelling properties from the perspective of free fatty acids and myosin interactions, offering a theoretical basis for sturgeon surimi production.
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Proteínas de Peces , Peces , Geles , Lípidos , Animales , Geles/química , Lípidos/química , Proteínas de Peces/química , Proteínas de Peces/metabolismo , Productos Pesqueros/análisis , Interacciones Hidrofóbicas e Hidrofílicas , Enlace de Hidrógeno , Miosinas/química , Miosinas/metabolismo , Simulación del Acoplamiento Molecular , Ácidos Grasos/química , Ácidos Grasos/metabolismo , Carpas/metabolismo , Unión ProteicaRESUMEN
In this study, the interaction of the human hemoglobin with cost effective and chemically fabricated CdS quantum dots (QDs) (average sizes ≈3nm) has been investigated. The semiconductor QDs showed maximum visible absorption at 445 nm with excitonic formation and band gap of ≈ 2.88 eV along with hexagonal crystalline phase. The binding of QDs-Hb occurs through corona formation to the ground sate complex formation. The life time of the heme pocket binding and reorganization were found to be t1 = 43 min and t2 = 642 min, respectively. The emission quenching of the Hb has been indicated large energy transfer between CdS QDs and Hb with tertiary deformation of Hb. The binding thermodynamics showed highly exothermic nature. The ultrafast decay during corona formation was studied from TCSPC. The results showed that the energy transfer efficiency increases with the increase of the QDs concentration and maximum ≈71.5 % energy transfer occurs and average ultrafast lifetime varies from 5.45 ns to1.51 ns. The deformation and unfolding of the secondary structure of Hb with changes of the α-helix (≈74 % to ≈51.07 %) and ß-sheets (≈8.63 % to ≈10.25 %) have been observed from circular dichroism spectrum. The SAXS spectrum showed that the radius of gyration of CdS QDs-Hb bioconjugate increased (up to 23 ± 0.45 nm) with the increase of the concentration of QDs compare with pure Hb (11 ± 0.23 nm) and Hb becoming more unfolded.
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Compuestos de Cadmio , Transferencia de Energía , Hemoglobinas , Desplegamiento Proteico , Puntos Cuánticos , Sulfuros , Puntos Cuánticos/química , Humanos , Compuestos de Cadmio/química , Sulfuros/química , Sulfuros/metabolismo , Hemoglobinas/química , Hemoglobinas/metabolismo , Unión Proteica , Termodinámica , Espectrometría de Fluorescencia , Dicroismo CircularRESUMEN
Co-immunoprecipitation is a technique widely utilized to isolate protein complexes and study protein-protein interactions. Ubiquitinated proteins could be identified by combining co-immunoprecipitation with SDS-PAGE followed by immunoblotting. In this chapter, we use Herpes Simplex Virus 1 immediate-early protein ICP0-mediated polyubiquitination of p50 as an example to describe the method to identify a ubiquitinated adaptor protein by a viral E3 ligase by co-immunoprecipitation.
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Proteínas Inmediatas-Precoces , Inmunoprecipitación , Ubiquitina-Proteína Ligasas , Ubiquitinación , Ubiquitina-Proteína Ligasas/metabolismo , Inmunoprecipitación/métodos , Humanos , Proteínas Inmediatas-Precoces/metabolismo , Unión Proteica , Proteínas Ubiquitinadas/metabolismo , Herpesvirus Humano 1/metabolismo , Electroforesis en Gel de Poliacrilamida/métodos , Proteínas Virales/metabolismoRESUMEN
The dynamic interplay between intramammary IgG, formation of antigen-IgG complexes and effector immune cell function is essential for immune homeostasis within the bovine mammary gland. We explore how changes in the recognition and binding of anti-LPS IgG to the glycolipid "functional" core in milk from healthy or clinically diagnosed Escherichia coli (E. coli) mastitis cows' controls endotoxin function. In colostrum, we found a varied anti-LPS IgG repertoire and novel soluble LPS/IgG complexes with direct IgG binding to the LPS glycolipid core. These soluble complexes, absent in milk from healthy lactating cows, were evident in cows diagnosed with E. coli mastitis and correlated with endotoxin-driven inflammation. E. coli mastitis milk displayed a proportional reduction in anti-LPS glycolipid core IgG compared to colostrum. Milk IgG extracts showed that only colostrum IgG attenuated LPS induced endotoxin activity. Furthermore, LPS-stimulated reactive oxygen species (ROS) in milk granulocytes was only suppressed by colostrum IgG, while IgG extracts of neither colostrum nor E. coli mastitis milk influenced N-formylmethionine-leucyl-phenylalanine (fMLP)-stimulated ROS in LPS primed granulocytes. Our findings support bovine intramammary IgG diversity in health and in response to E. coli infection generate milk anti-LPS IgG repertoires that coordinate appropriate LPS innate-adaptive immune responses essential for animal health.
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Calostro , Infecciones por Escherichia coli , Escherichia coli , Glucolípidos , Inmunoglobulina G , Lipopolisacáridos , Mastitis Bovina , Leche , Animales , Bovinos , Femenino , Calostro/inmunología , Calostro/metabolismo , Inmunoglobulina G/inmunología , Inmunoglobulina G/metabolismo , Mastitis Bovina/inmunología , Mastitis Bovina/microbiología , Escherichia coli/inmunología , Lipopolisacáridos/inmunología , Leche/inmunología , Glucolípidos/metabolismo , Glucolípidos/inmunología , Infecciones por Escherichia coli/inmunología , Endotoxinas/inmunología , Endotoxinas/metabolismo , Especies Reactivas de Oxígeno/metabolismo , Granulocitos/inmunología , Granulocitos/metabolismo , Unión Proteica , Glándulas Mamarias Animales/inmunología , Glándulas Mamarias Animales/metabolismoRESUMEN
High-affinity and specific agents are widely applied in various areas, including diagnostics, scientific research, and disease therapy (as drugs and drug delivery systems). It takes significant time to develop them. For this reason, development of high-affinity agents extensively utilizes computer methods at various stages for the analysis and modeling of these molecules. The review describes the main affinity and specific agents, such as monoclonal antibodies and their fragments, antibody mimetics, aptamers, and molecularly imprinted polymers. The methods of their obtaining as well as their main advantages and disadvantages are briefly described, with special attention focused on the molecular modeling methods used for their analysis and development.
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Anticuerpos Monoclonales , Anticuerpos Monoclonales/química , Aptámeros de Nucleótidos/química , Modelos Moleculares , Humanos , Unión Proteica , Polímeros Impresos Molecularmente/químicaRESUMEN
Knowledge of protein-ligand complexes is essential for efficient drug design. Virtual docking can bring important information on putative complexes but it is still far from being simultaneously fast and accurate. Receptors are flexible and adapt to the incoming small molecules while docking is highly sensitive to small conformational deviations. Conformation ensemble is providing a mean to simulate protein flexibility. However, modeling multiple protein structures for many targets is seldom connected to ligand screening in an efficient and straightforward manner. @TOME-3 is an updated version of our former pipeline @TOME-2, in which protein structure modeling is now directly interfaced with flexible ligand docking. Sequence-sequence profile comparisons identify suitable PDB templates for structure modeling and ligands from these templates are used to deduce binding sites to be screened. In addition, bound ligand can be used as pharmacophoric restraint during the virtual docking. The latter is performed by PLANTS while the docking poses are analysed through multiple chemoinformatics functions. This unique combination of tools allows rapid and efficient ligand docking on multiple receptor conformations in parallel. @TOME-3 is freely available on the web at https://atome.cbs.cnrs.fr.
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Simulación del Acoplamiento Molecular , Conformación Proteica , Proteínas , Ligandos , Proteínas/química , Proteínas/metabolismo , Sitios de Unión , Unión Proteica , Programas Informáticos , Diseño de Fármacos , Modelos MolecularesRESUMEN
The DockThor-VS platform (https://dockthor.lncc.br/v2/) is a free protein-ligand docking server conceptualized to facilitate and assist drug discovery projects to perform docking-based virtual screening experiments accurately and using high-performance computing. The DockThor docking engine is a grid-based method designed for flexible-ligand and rigid-receptor docking. It employs a multiple-solution genetic algorithm and the MMFF94S molecular force field scoring function for pose prediction. This engine was engineered to handle highly flexible ligands, such as peptides. Affinity prediction and ranking of protein-ligand complexes are performed with the linear empirical scoring function DockTScore. The main steps of the ligand and protein preparation are available on the DockThor Portal, making it possible to change the protonation states of the amino acid residues, and include cofactors as rigid entities. The user can also customize and visualize the main parameters of the grid box. The results of docking experiments are automatically clustered and ordered, providing users with a diverse array of meaningful binding modes. The platform DockThor-VS offers a user-friendly interface and powerful algorithms, enabling researchers to conduct virtual screening experiments efficiently and accurately. The DockThor Portal utilizes the computational strength of the Brazilian high-performance platform SDumont, further amplifying the efficiency and speed of docking experiments. Additionally, the web server facilitates and enhances virtual screening experiments by offering curated structures of potential targets and compound datasets, such as proteins related to COVID-19 and FDA-approved drugs for repurposing studies. In summary, DockThor-VS is a dynamic and evolving solution for docking-based virtual screening to be applied in drug discovery projects.
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Simulación del Acoplamiento Molecular , Programas Informáticos , Ligandos , Algoritmos , Descubrimiento de Drogas/métodos , Unión Proteica , Humanos , Proteínas/química , Proteínas/metabolismo , Interfaz Usuario-ComputadorRESUMEN
Small-molecule drug design hinges on obtaining co-crystallized ligand-protein structures. Despite AlphaFold2's strides in protein native structure prediction, its focus on apo structures overlooks ligands and associated holo structures. Moreover, designing selective drugs often benefits from the targeting of diverse metastable conformations. Therefore, direct application of AlphaFold2 models in virtual screening and drug discovery remains tentative. Here, we demonstrate an AlphaFold2-based framework combined with all-atom enhanced sampling molecular dynamics and Induced Fit docking, named AF2RAVE-Glide, to conduct computational model-based small-molecule binding of metastable protein kinase conformations, initiated from protein sequences. We demonstrate the AF2RAVE-Glide workflow on three different mammalian protein kinases and their type I and II inhibitors, with special emphasis on binding of known type II kinase inhibitors which target the metastable classical DFG-out state. These states are not easy to sample from AlphaFold2. Here, we demonstrate how with AF2RAVE these metastable conformations can be sampled for different kinases with high enough accuracy to enable subsequent docking of known type II kinase inhibitors with more than 50% success rates across docking calculations. We believe the protocol should be deployable for other kinases and more proteins generally.
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Descubrimiento de Drogas , Conformación Proteica , Descubrimiento de Drogas/métodos , Simulación del Acoplamiento Molecular , Unión Proteica , Simulación de Dinámica Molecular , Humanos , Inhibidores de Proteínas Quinasas/farmacología , Inhibidores de Proteínas Quinasas/química , Ligandos , Proteínas Quinasas/química , Proteínas Quinasas/metabolismoRESUMEN
Peptides are valuable for therapeutic development, with multicyclic peptides showing promise in mimicking antigen-binding potency of antibodies. However, our capability to engineer multicyclic peptide scaffolds, particularly for the construction of large combinatorial libraries, is still limited. Here, we study the interplay of disulfide pairing between three biscysteine motifs, and designed a range of triscysteine motifs with unique disulfide-directing capability for regulating the oxidative folding of multicyclic peptides. We demonstrate that incorporating these motifs into random sequences allows the design of disulfide-directed multicyclic peptide (DDMP) libraries with up to four disulfide bonds, which have been applied for the successful discovery of peptide binders with nanomolar affinity to several challenging targets. This study encourages the use of more diverse disulfide-directing motifs for creating multicyclic peptide libraries and opens an avenue for discovering functional peptides in sequence and structural space beyond existing peptide scaffolds, potentially advancing the field of peptide drug discovery.
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Cisteína , Disulfuros , Biblioteca de Péptidos , Disulfuros/química , Cisteína/química , Secuencias de Aminoácidos , Descubrimiento de Drogas/métodos , Secuencia de Aminoácidos , Péptidos/química , Péptidos/metabolismo , Péptidos Cíclicos/química , Péptidos Cíclicos/metabolismo , Unión Proteica , Humanos , Oxidación-Reducción , Pliegue de ProteínaRESUMEN
Increasing the binding affinity of an antibody to its target antigen is a crucial task in antibody therapeutics development. This paper presents a pretrainable geometric graph neural network, GearBind, and explores its potential in in silico affinity maturation. Leveraging multi-relational graph construction, multi-level geometric message passing and contrastive pretraining on mass-scale, unlabeled protein structural data, GearBind outperforms previous state-of-the-art approaches on SKEMPI and an independent test set. A powerful ensemble model based on GearBind is then derived and used to successfully enhance the binding of two antibodies with distinct formats and target antigens. ELISA EC50 values of the designed antibody mutants are decreased by up to 17 fold, and KD values by up to 6.1 fold. These promising results underscore the utility of geometric deep learning and effective pretraining in macromolecule interaction modeling tasks.
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Afinidad de Anticuerpos , Redes Neurales de la Computación , Humanos , Anticuerpos/inmunología , Anticuerpos/química , Simulación por Computador , Aprendizaje Profundo , Antígenos/inmunología , Unión Proteica , Ensayo de Inmunoadsorción Enzimática , Modelos MolecularesRESUMEN
Chromatin remodelling complexes (CRC) are ATP-dependent molecular machines important for the dynamic organization of nucleosomes along eukaryotic DNA. CRCs SWI/SNF, RSC and INO80 can move positioned nucleosomes in promoter DNA, leading to nucleosome-depleted regions which facilitate access of general transcription factors. This function is strongly supported by transcriptional activators being able to interact with subunits of various CRCs. In this work we show that SWI/SNF subunits Swi1, Swi2, Snf5 and Snf6 can bind to activation domains of Ino2 required for expression of phospholipid biosynthetic genes in yeast. We identify an activator binding domain (ABD) of ATPase Swi2 and show that this ABD is functionally dispensable, presumably because ABDs of other SWI/SNF subunits can compensate for the loss. In contrast, mutational characterization of the ABD of the Swi2-related ATPase Sth1 revealed that some conserved basic and hydrophobic amino acids within this domain are essential for the function of Sth1. While ABDs of Swi2 and Sth1 define separate functional protein domains, mapping of an ABD within ATPase Ino80 showed co-localization with its HSA domain also required for binding actin-related proteins. Comparative interaction studies finally demonstrated that several unrelated activators each exhibit a specific binding pattern with ABDs of Swi2, Sth1 and Ino80.
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Adenosina Trifosfatasas , Ensamble y Desensamble de Cromatina , Proteínas de Unión al ADN , Unión Proteica , Proteínas de Saccharomyces cerevisiae , Saccharomyces cerevisiae , Factores de Transcripción , Activación Transcripcional , Proteínas de Saccharomyces cerevisiae/genética , Proteínas de Saccharomyces cerevisiae/metabolismo , Adenosina Trifosfatasas/genética , Adenosina Trifosfatasas/metabolismo , Factores de Transcripción/genética , Factores de Transcripción/metabolismo , Saccharomyces cerevisiae/genética , Saccharomyces cerevisiae/metabolismo , Ensamble y Desensamble de Cromatina/genética , Proteínas de Unión al ADN/genética , Proteínas de Unión al ADN/metabolismo , Proteínas Cromosómicas no Histona/genética , Proteínas Cromosómicas no Histona/metabolismo , Regulación Fúngica de la Expresión Génica , Dominios Proteicos , Proteínas Nucleares , Proteínas de Ciclo Celular , Factores de Transcripción con Motivo Hélice-Asa-Hélice BásicoRESUMEN
Intercellular protein-protein interactions (PPIs) have pivotal roles in biological functions and diseases. Membrane proteins are therefore a major class of drug targets. However, studying such intercellular PPIs is challenging because of the properties of membrane proteins. Current methods commonly use purified or modified proteins that are not physiologically relevant and hence might mischaracterize interactions occurring in vivo. Here, we describe Cell-Int: a cell interaction assay for studying plasma membrane PPIs. The interaction signal is measured through conjugate formation between two populations of cells each expressing either a ligand or a receptor. In these settings, membrane proteins are in their native environment thus being physiologically relevant. Cell-Int has been applied to the study of diverse protein partners, and enables to investigate the inhibitory potential of blocking antibodies, as well as the retargeting of fusion proteins for therapeutic development. The assay was also validated for screening applications and could serve as a platform for identifying new protein interactors.
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Comunicación Celular , Membrana Celular , Proteínas de la Membrana , Unión Proteica , Mapeo de Interacción de Proteínas , Humanos , Proteínas de la Membrana/metabolismo , Mapeo de Interacción de Proteínas/métodos , Membrana Celular/metabolismo , Animales , Células HEK293 , Bioensayo/métodosRESUMEN
Structure-based virtual screening is a key tool in early drug discovery, with growing interest in the screening of multi-billion chemical compound libraries. However, the success of virtual screening crucially depends on the accuracy of the binding pose and binding affinity predicted by computational docking. Here we develop a highly accurate structure-based virtual screen method, RosettaVS, for predicting docking poses and binding affinities. Our approach outperforms other state-of-the-art methods on a wide range of benchmarks, partially due to our ability to model receptor flexibility. We incorporate this into a new open-source artificial intelligence accelerated virtual screening platform for drug discovery. Using this platform, we screen multi-billion compound libraries against two unrelated targets, a ubiquitin ligase target KLHDC2 and the human voltage-gated sodium channel NaV1.7. For both targets, we discover hit compounds, including seven hits (14% hit rate) to KLHDC2 and four hits (44% hit rate) to NaV1.7, all with single digit micromolar binding affinities. Screening in both cases is completed in less than seven days. Finally, a high resolution X-ray crystallographic structure validates the predicted docking pose for the KLHDC2 ligand complex, demonstrating the effectiveness of our method in lead discovery.
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Inteligencia Artificial , Descubrimiento de Drogas , Simulación del Acoplamiento Molecular , Descubrimiento de Drogas/métodos , Humanos , Canal de Sodio Activado por Voltaje NAV1.7/metabolismo , Canal de Sodio Activado por Voltaje NAV1.7/química , Unión Proteica , Cristalografía por Rayos X , Ligandos , Ubiquitina-Proteína Ligasas/metabolismo , Ubiquitina-Proteína Ligasas/química , Bibliotecas de Moléculas Pequeñas/química , Bibliotecas de Moléculas Pequeñas/farmacología , Evaluación Preclínica de Medicamentos/métodosRESUMEN
Although aminergic GPCRs are the target for ~25% of approved drugs, developing subtype selective drugs is a major challenge due to the high sequence conservation at their orthosteric binding site. Bitopic ligands are covalently joined orthosteric and allosteric pharmacophores with the potential to boost receptor selectivity and improve current medications by reducing off-target side effects. However, the lack of structural information on their binding mode impedes rational design. Here we determine the cryo-EM structure of the hD3R:GαOßγ complex bound to the D3R selective bitopic agonist FOB02-04A. Structural, functional and computational analyses provide insights into its binding mode and point to a new TM2-ECL1-TM1 region, which requires the N-terminal ordering of TM1, as a major determinant of subtype selectivity in aminergic GPCRs. This region is underexploited in drug development, expands the established secondary binding pocket in aminergic GPCRs and could potentially be used to design novel and subtype selective drugs.
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Microscopía por Crioelectrón , Receptores de Dopamina D3 , Humanos , Sitios de Unión , Receptores de Dopamina D3/metabolismo , Receptores de Dopamina D3/química , Receptores de Dopamina D3/agonistas , Células HEK293 , Ligandos , Unión Proteica , Animales , Modelos MolecularesRESUMEN
We here introduce Ensemble Optimizer (EnOpt), a machine-learning tool to improve the accuracy and interpretability of ensemble virtual screening (VS). Ensemble VS is an established method for predicting protein/small-molecule (ligand) binding. Unlike traditional VS, which focuses on a single protein conformation, ensemble VS better accounts for protein flexibility by predicting binding to multiple protein conformations. Each compound is thus associated with a spectrum of scores (one score per protein conformation) rather than a single score. To effectively rank and prioritize the molecules for further evaluation (including experimental testing), researchers must select which protein conformations to consider and how best to map each compound's spectrum of scores to a single value, decisions that are system-specific. EnOpt uses machine learning to address these challenges. We perform benchmark VS to show that for many systems, EnOpt ranking distinguishes active compounds from inactive or decoy molecules more effectively than traditional ensemble VS methods. To encourage broad adoption, we release EnOpt free of charge under the terms of the MIT license.
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Aprendizaje Automático , Simulación del Acoplamiento Molecular , Proteínas , Simulación del Acoplamiento Molecular/métodos , Proteínas/química , Proteínas/metabolismo , Unión Proteica , Ligandos , Conformación Proteica , Programas InformáticosRESUMEN
Background: Previous studies have highlighted the catalytic activity of Escherichia coli alcohol dehydrogenase YahK in the presence of coenzyme nicotinamide adenine dinucleotide (NAD) and metal zinc. Notably, competitive interaction between iron and zinc ligands has been shown to influence the catalytic efficiency of several key proteases. This study aims to unravel the intricate mechanisms underlying YahK's catalytic action, with a particular focus on the pivotal roles played by metal ions zinc and iron. Methods: The purified YahK protein from E. coli cells cultivated in LB medium was utilized to investigate its metal-binding properties through UV-visible absorption measurements and determination of metal content. Subsequently, the effects of excess zinc and iron on the metal-binding ability and alcohol dehydrogenase activity of the YahK protein were explored using M9 minimal medium. Furthermore, site-directed mutagenesis technology was employed to determine the iron-binding site location within the YahK protein. Polyacrylamide gel electrophoresis was conducted to examine the relationship between iron and zinc with respect to the YahK protein. Results: The study confirmed the presence of iron and zinc in the YahK protein, with the zinc-bound form exhibiting enhanced catalytic activity in alcohol dehydrogenation reactions. Conversely, the presence of iron appears to play a pivotal role in maintaining overall stability of the YahK protein. Furthermore, experimental findings indicate that excessive zinc within M9 minimal medium can competitively bind to iron-binding sites on YahK, thereby augmenting its alcohol dehydrogenase activity. Conclusion: The dynamic binding of YahK to iron and zinc unveils its intricate regulatory mechanism as an alcohol dehydrogenase, thereby highlighting the possible physiological role of YahK in E. coli and its significance in governing cellular metabolic processes. This discovery provides a novel perspective for further investigating the specific impact of metal ion binding on YahK and E. coli cell metabolism.
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Alcohol Deshidrogenasa , Escherichia coli , Hierro , Zinc , Zinc/metabolismo , Alcohol Deshidrogenasa/metabolismo , Alcohol Deshidrogenasa/genética , Escherichia coli/genética , Escherichia coli/metabolismo , Escherichia coli/enzimología , Hierro/metabolismo , Proteínas de Escherichia coli/metabolismo , Proteínas de Escherichia coli/genética , Sitios de Unión , Unión Proteica , Mutagénesis Sitio-DirigidaRESUMEN
In eukaryotes, RNAs transcribed by RNA Pol II are modified at the 5' end with a 7-methylguanosine (m7G) cap, which is recognized by the nuclear cap binding complex (CBC). The CBC plays multiple important roles in mRNA metabolism, including transcription, splicing, polyadenylation, and export. It promotes mRNA export through direct interaction with a key mRNA export factor, ALYREF, which in turn links the TRanscription and EXport (TREX) complex to the 5' end of mRNA. However, the molecular mechanism for CBC-mediated recruitment of the mRNA export machinery is not well understood. Here, we present the first structure of the CBC in complex with an mRNA export factor, ALYREF. The cryo-EM structure of CBC-ALYREF reveals that the RRM domain of ALYREF makes direct contact with both the NCBP1 and NCBP2 subunits of the CBC. Comparing CBC-ALYREF with other cellular complexes containing CBC and/or ALYREF components provides insights into the coordinated events during mRNA transcription, splicing, and export.
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Microscopía por Crioelectrón , Complejo Proteico Nuclear de Unión a la Caperuza/metabolismo , Complejo Proteico Nuclear de Unión a la Caperuza/química , Humanos , ARN Mensajero/metabolismo , ARN Mensajero/química , ARN Mensajero/genética , Conformación Proteica , Unión ProteicaRESUMEN
Experimental detection of residues critical for protein-protein interactions (PPI) is a time-consuming, costly, and labor-intensive process. Hence, high-throughput PPI-hot spot prediction methods have been developed, but they have been validated using relatively small datasets, which may compromise their predictive reliability. Here, we introduce PPI-hotspotID, a novel method for identifying PPI-hot spots using the free protein structure, and validated it on the largest collection of experimentally confirmed PPI-hot spots to date. We explored the possibility of detecting PPI-hot spots using (i) FTMap in the PPI mode, which identifies hot spots on protein-protein interfaces from the free protein structure, and (ii) the interface residues predicted by AlphaFold-Multimer. PPI-hotspotID yielded better performance than FTMap and SPOTONE, a webserver for predicting PPI-hot spots given the protein sequence. When combined with the AlphaFold-Multimer-predicted interface residues, PPI-hotspotID yielded better performance than either method alone. Furthermore, we experimentally verified several PPI-hotspotID-predicted PPI-hot spots of eukaryotic elongation factor 2. Notably, PPI-hotspotID can reveal PPI-hot spots not obvious from complex structures, including those in indirect contact with binding partners. PPI-hotspotID serves as a valuable tool for understanding PPI mechanisms and aiding drug design. It is available as a web server (https://ppihotspotid.limlab.dnsalias.org/) and open-source code (https://github.com/wrigjz/ppihotspotid/).