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The PKC-related kinases (PRKs, also termed PKNs) are important in cell migration, cancer, hepatitis C infection, and nutrient sensing. They belong to a group of protein kinases called AGC kinases that share common features like a C-terminal extension to the catalytic domain comprising a hydrophobic motif. PRKs are regulated by N-terminal domains, a pseudosubstrate sequence, Rho-binding domains, and a C2 domain involved in inhibition and dimerization, while Rho and lipids are activators. We investigated the allosteric regulation of PRK2 and its interaction with its upstream kinase PDK1 using a chemical biology approach. We confirmed the phosphoinositide-dependent protein kinase 1 (PDK1)-interacting fragment (PIF)-mediated docking interaction of PRK2 with PDK1 and showed that this interaction can be modulated allosterically. We showed that the polypeptide PIFtide and a small compound binding to the PIF-pocket of PRK2 were allosteric activators, by displacing the pseudosubstrate PKL region from the active site. In addition, a small compound binding to the PIF-pocket allosterically inhibited the catalytic activity of PRK2. Together, we confirmed the docking interaction and allostery between PRK2 and PDK1 and described an allosteric communication between the PIF-pocket and the active site of PRK2, both modulating the conformation of the ATP-binding site and the pseudosubstrate PKL-binding site. Our study highlights the allosteric modulation of the activity and the conformation of PRK2 in addition to the existence of at least two different complexes between PRK2 and its upstream kinase PDK1. Finally, the study highlights the potential for developing allosteric drugs to modulate PRK2 kinase conformations and catalytic activity.
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Proteína Quinase C , Piruvato Desidrogenase Quinase de Transferência de Acetil , Humanos , Regulação Alostérica , Proteína Quinase C/metabolismo , Proteína Quinase C/genética , Proteína Quinase C/química , Piruvato Desidrogenase Quinase de Transferência de Acetil/metabolismo , Piruvato Desidrogenase Quinase de Transferência de Acetil/genética , Domínio Catalítico , Simulação de Acoplamento Molecular , Proteínas Serina-Treonina Quinases/metabolismo , Proteínas Serina-Treonina Quinases/genética , Proteínas Serina-Treonina Quinases/química , Proteínas Quinases Dependentes de 3-Fosfoinositídeo/metabolismo , Proteínas Quinases Dependentes de 3-Fosfoinositídeo/genética , Proteínas Quinases Dependentes de 3-Fosfoinositídeo/química , Ligação ProteicaRESUMO
The circadian clock system coordinates metabolic, physiological, and behavioral functions across a 24-h cycle, crucial for adapting to environmental changes. Disruptions in circadian rhythms contribute to major metabolic pathologies like obesity and Type 2 diabetes. Understanding the regulatory mechanisms governing circadian control is vital for identifying therapeutic targets. It is well characterized that chromatin remodeling and 3D structure at genome regulatory elements contributes to circadian transcriptional cycles; yet the impact of rhythmic chromatin topology in metabolic disease is largely unexplored. In this study, we explore how the spatial configuration of the genome adapts to diet, rewiring circadian transcription and contributing to dysfunctional metabolism. We describe daily fluctuations in chromatin contacts between distal regulatory elements of metabolic control genes in livers from lean and obese mice and identify specific lipid-responsive regions recruiting the clock molecular machinery. Interestingly, under high-fat feeding, a distinct interactome for the clock-controlled gene Dbp strategically promotes the expression of distal metabolic genes including Fgf21. Alongside, new chromatin loops between regulatory elements from genes involved in lipid metabolism control contribute to their transcriptional activation. These enhancers are responsive to lipids through CEBPß, counteracting the circadian repressor REVERBa. Our findings highlight the intricate coupling of circadian gene expression to a dynamic nuclear environment under high-fat feeding, supporting a temporally regulated program of gene expression and transcriptional adaptation to diet.
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Cromatina , Relógios Circadianos , Ácidos Graxos , Fígado , Camundongos Endogâmicos C57BL , Camundongos Obesos , Obesidade , Animais , Cromatina/metabolismo , Cromatina/genética , Fígado/metabolismo , Camundongos , Relógios Circadianos/genética , Obesidade/metabolismo , Obesidade/genética , Ácidos Graxos/metabolismo , Masculino , Dieta Hiperlipídica/efeitos adversos , Montagem e Desmontagem da Cromatina , Ritmo Circadiano/genética , Fatores de Transcrição/metabolismo , Fatores de Transcrição/genética , Metabolismo dos Lipídeos/genética , Fatores de Crescimento de Fibroblastos/metabolismo , Fatores de Crescimento de Fibroblastos/genética , Regulação da Expressão Gênica/efeitos dos fármacos , Proteínas de Ligação a DNA/genética , Proteínas de Ligação a DNA/metabolismoRESUMO
Ewing sarcoma (ES) is a highly malignant and aggressive small round-cell tumor originating from primitive neuroepithelium and mesenchymal stem cells. It is usually seen in children and adolescents with a male predilection and a preponderance to occur in long bones. Although skeletal/soft tissue ES is encountered in clinical practice, primary ES of the genital tract, particularly bilateral primary ovarian ES, is highly uncommon, with only a handful of cases reported worldwide. Ovarian ES is occasionally reported to involve para-aortic and pelvic lymph nodes in advanced stages. Still, cervical lymph node metastasis from ovarian ES is an infrequent clinical occurrence and, when present, indicates a worse prognosis. Here, we present an intriguing case of bilateral peripheral primary ovarian ES in an adult female, recurring as metastasis in the left submandibular lymph node. This case underlines the importance of keeping metastasis from ES as a possible differential while diagnosing metastatic small round cell tumors in peripheral lymph nodes. It also highlights the usefulness of a minimally invasive diagnostic modality of fine needle aspiration cytology and cell block preparation with applied ancillary techniques of immunohistochemistry and confirmatory molecular testing by fluorescence in-situ hybridization (FISH), for an accurate and quick diagnosis of such entities. The cytological diagnosis of our patient helped in the prompt and early initiation of chemotherapy without requiring any invasive procedure.
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Chemical oxidizers and redox enzymes have traditionally been used to enhance the quality of baked goods. However, consumers now seek natural and clean-label ingredients, avoiding those with chemical-sounding names. Honey, a natural source of glucose oxidase (GOX), represents a promising alternative to purified enzymes for baking purposes. This study aimed to evaluate the effect of honey on the molecular structure and microstructure of gluten proteins in sourdough fermented by different lactic acid bacteria (LAB) strains. Four wheat-rye (1:1) sourdoughs were prepared, each supplemented with honey and inoculated with a different LAB strain. Additionally, two uninoculated doughs, one with honey (honey dough) and the other without (control dough), were prepared under identical conditions. Electronic paramagnetic resonance spectroscopy revealed the presence of hydrogen peroxide in honey solutions, indicating its role as an active source of GOX. Raman spectroscopy showed that honey addition altered the molecular structure of gluten by increasing the proportion of random coils at the expense of α-helix structures. This change is likely attributed to the competition between honey sugars and gluten proteins for water molecules in this system. Moreover, honey led to a decrease in the free sulfhydryl content of gluten compared to the control dough, suggesting an increase in disulfide crosslinking points. These enhanced protein-protein interactions were observed in scanning electron microscopy micrographs as a coarse gluten network composed of interconnected strands and fibrils. All LAB strains exhibited optimal acidification (pH < 4.3) in honey-supplemented sourdoughs, promoting the hydrolysis of gluten proteins into smaller fragments. Overall, honey-supplemented sourdoughs showed a gradual increase in the ß-sheet content while decreasing the proportion of random coils over time. This trend suggests that the polypeptide fragments interacted through interchain hydrogen bonds, leading to a more ordered structure, which likely contributes to providing dough with good baking aptitude.
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In the age of information technology and the additional computational search tools and software available, this systematic review aimed to identify potential therapeutic targets for obesity, evaluated in silico and subsequently validated in vivo. The systematic review was initially guided by the research question "What therapeutic targets have been used in in silico analysis for the treatment of obesity?" and structured based on the acronym PECo (P, problem; E, exposure; Co, context). The systematic review protocol was formulated and registered in PROSPERO (CRD42022353808) in accordance with the Preferred Reporting Items Checklist for Systematic Review and Meta-Analysis Protocols (PRISMA-P), and the PRISMA was followed for the systematic review. The studies were selected according to the eligibility criteria, aligned with PECo, in the following databases: PubMed, ScienceDirect, Scopus, Web of Science, BVS, and EMBASE. The search strategy yielded 1142 articles, from which, based on the evaluation criteria, 12 were included in the systematic review. Only seven these articles allowed the identification of both in silico and in vivo reassessed therapeutic targets. Among these targets, five were exclusively experimental, one was exclusively theoretical, and one of the targets presented an experimental portion and a portion obtained by modeling. The predominant methodology used was molecular docking and the most studied target was Human Pancreatic Lipase (HPL) (n = 4). The lack of methodological details resulted in more than 50% of the papers being categorized with an "unclear risk of bias" across eight out of the eleven evaluated criteria. From the current systematic review, it seems evident that integrating in silico methodologies into studies of potential drug targets for the exploration of new therapeutic agents provides an important tool, given the ongoing challenges in controlling obesity.
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Simulação por Computador , Obesidade , Humanos , Obesidade/tratamento farmacológico , Obesidade/metabolismo , Animais , Simulação de Acoplamento Molecular , Fármacos Antiobesidade/farmacologia , Fármacos Antiobesidade/uso terapêutico , Lipase/metabolismo , Lipase/antagonistas & inibidores , Terapia de Alvo Molecular/métodosRESUMO
Staurosporine and its analogs (STA-analogs) are indolocarbazoles (ICZs) compounds able to inhibit kinase proteins in a non-specific way, while present antimicrobial and cytostatic properties. The knowledge of molecular features associated to the complexation, including the ligand shape in solution and thermodynamics of complexation, is substantial to the development of new bioactive ICZs with improved therapeutic properties. In this context, the empirical approach of GROMOS force field is able to accurately reproduce condensed phase physicochemical properties of molecular systems after parameterization. Hence, through parameterization under GROMOS force field and molecular simulations, we assessed STA-analogs dynamics in aqueous solution, as well as its interaction with water to probe conformational and structural features involved in complexation to therapeutic targets. The coexistence of multiple conformers observed in simulations, and confirmed by metadynamics calculations, expanding the conformational space knowledge of these ligands with potential implications in understanding the ligand conformational selection during complexation. Also, changes in availability to H-bonding concerning the different substituents and water can reflect on effects at complexation free energy due to variation at the desolvation energetic costs. Based on these results, we expect the obtained structural data provide systemic framework for rational chemical modification of STA-analogs.
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Modelos Teóricos , Água , Estaurosporina/farmacologia , Ligantes , Água/química , Conformação Molecular , Termodinâmica , Simulação de Dinâmica MolecularRESUMO
ABSTRACT Ewing sarcoma (ES) is a highly malignant and aggressive small round-cell tumor originating from primitive neuroepithelium and mesenchymal stem cells. It is usually seen in children and adolescents with a male predilection and a preponderance to occur in long bones. Although skeletal/soft tissue ES is encountered in clinical practice, primary ES of the genital tract, particularly bilateral primary ovarian ES, is highly uncommon, with only a handful of cases reported worldwide. Ovarian ES is occasionally reported to involve para-aortic and pelvic lymph nodes in advanced stages. Still, cervical lymph node metastasis from ovarian ES is an infrequent clinical occurrence and, when present, indicates a worse prognosis. Here, we present an intriguing case of bilateral peripheral primary ovarian ES in an adult female, recurring as metastasis in the left submandibular lymph node. This case underlines the importance of keeping metastasis from ES as a possible differential while diagnosing metastatic small round cell tumors in peripheral lymph nodes. It also highlights the usefulness of a minimally invasive diagnostic modality of fine needle aspiration cytology and cell block preparation with applied ancillary techniques of immunohistochemistry and confirmatory molecular testing by fluorescence in-situ hybridization (FISH), for an accurate and quick diagnosis of such entities. The cytological diagnosis of our patient helped in the prompt and early initiation of chemotherapy without requiring any invasive procedure.
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The long noncoding RNA (lncRNA) AUXIN-REGULATED PROMOTER LOOP (APOLO) recognizes a subset of target loci across the Arabidopsis thaliana genome by forming RNA-DNA hybrids (R-loops) and modulating local three-dimensional chromatin conformation. Here, we show that APOLO regulates shade avoidance syndrome by dynamically modulating expression of key factors. In response to far-red (FR) light, expression of APOLO anti-correlates with that of its target BRANCHED1 (BRC1), a master regulator of shoot branching in Arabidopsis thaliana. APOLO deregulation results in BRC1 transcriptional repression and an increase in the number of branches. Accumulation of APOLO transcription fine-tunes the formation of a repressive chromatin loop encompassing the BRC1 promoter, which normally occurs only in leaves and in a late response to far-red light treatment in axillary buds. In addition, our data reveal that APOLO participates in leaf hyponasty, in agreement with its previously reported role in the control of auxin homeostasis through direct modulation of auxin synthesis gene YUCCA2, and auxin efflux genes PID and WAG2. We show that direct application of APOLO RNA to leaves results in a rapid increase in auxin signaling that is associated with changes in the plant response to far-red light. Collectively, our data support the view that lncRNAs coordinate shade avoidance syndrome in A. thaliana, and reveal their potential as exogenous bioactive molecules. Deploying exogenous RNAs that modulate plant-environment interactions may therefore become a new tool for sustainable agriculture.
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Proteínas de Arabidopsis , Arabidopsis , RNA Longo não Codificante , Arabidopsis/genética , Arabidopsis/metabolismo , RNA Longo não Codificante/genética , RNA Longo não Codificante/metabolismo , Proteínas de Arabidopsis/metabolismo , Ácidos Indolacéticos/metabolismo , Epigênese Genética , Cromatina/metabolismo , Regulação da Expressão Gênica de Plantas , Luz , Fatores de Transcrição/metabolismoRESUMO
Azithromycin (AZM) is a macrolide-type antibiotic used to prevent and treat serious infections (mycobacteria or MAC) that significantly inhibit bacterial growth. Knowledge of the predominant conformation in solution is of fundamental importance for advancing our understanding of the intermolecular interactions of AZM with biological targets. We report an extensive density functional theory (DFT) study of plausible AZM structures in solution considering implicit and explicit solvent effects. The best match between the experimental and theoretical nuclear magnetic resonance (NMR) profiles was used to assign the preferred conformer in solution, which was supported by the thermodynamic analysis. Among the 15 distinct AZM structures, conformer M14, having a short intramolecular C6-OH N H-bond, is predicted to be dominant in water and dimethyl sulfoxide (DMSO) solutions. The results indicated that the X-ray structure backbone is mostly conserved in solution, showing that large flexible molecules with several possible conformations may assume a preferential spatial orientation in solution, which is the molecular structure that ultimately interacts with biological targets.
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The protein kinase PDK1 phosphorylates at least 24 distinct substrates, all of which belong to the AGC protein kinase group. Some substrates, such as conventional PKCs, undergo phosphorylation by PDK1 during their synthesis and subsequently get activated by DAG and Calcium. On the other hand, other substrates, including members of the Akt/PKB, S6K, SGK, and RSK families, undergo phosphorylation and activation downstream of PI3-kinase signaling. This review presents two accepted molecular mechanisms that determine the precise and timely phosphorylation of different substrates by PDK1. The first mechanism involves the colocalization of PDK1 with Akt/PKB in the presence of PIP3. The second mechanism involves the regulated docking interaction between the hydrophobic motif (HM) of substrates and the PIF-pocket of PDK1. This interaction, in trans, is equivalent to the molecular mechanism that governs the activity of AGC kinases through their HMs intramolecularly. PDK1 has been instrumental in illustrating the bi-directional allosteric communication between the PIF-pocket and the ATP-binding site and the potential of the system for drug discovery. PDK1's interaction with substrates is not solely regulated by the substrates themselves. Recent research indicates that full-length PDK1 can adopt various conformations based on the positioning of the PH domain relative to the catalytic domain. These distinct conformations of full-length PDK1 can influence the interaction and phosphorylation of substrates. Finally, we critically discuss recent findings proposing that PIP3 can directly regulate the activity of PDK1, which contradicts extensive in vitro and in vivo studies conducted over the years.
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Piruvato Desidrogenase Quinase de Transferência de Acetil , Humanos , Sítios de Ligação , Fosfatidilinositol 3-Quinase , Fosforilação , Proteínas Proto-Oncogênicas c-akt , Piruvato Desidrogenase Quinase de Transferência de Acetil/metabolismoRESUMO
Activation of the extracellular signal regulated kinase-2 (ERK2) by phosphorylation has been shown to involve changes in protein dynamics, as determined by hydrogen-deuterium exchange mass spectrometry (HDX-MS) and NMR relaxation dispersion measurements. These can be described by a global exchange between two conformational states of the active kinase, named "L" and "R", where R is associated with a catalytically productive ATP-binding mode. An ATP-competitive ERK1/2 inhibitor, Vertex-11e, has properties of conformation selection for the R-state, revealing movements of the activation loop that are allosterically coupled to the kinase active site. However, the features of inhibitors important for R-state selection are unknown. Here we survey a panel of ATP-competitive ERK inhibitors using HDX-MS and NMR and identify 14 new molecules with properties of R-state selection. They reveal effects propagated to distal regions in the P+1 and helix αF segments surrounding the activation loop, as well as helix αL16. Crystal structures of inhibitor complexes with ERK2 reveal systematic shifts in the Gly loop and helix αC, mediated by a Tyr-Tyr ring stacking interaction and the conserved Lys-Glu salt bridge. The findings suggest a model for the R-state involving small movements in the N-lobe that promote compactness within the kinase active site and alter mobility surrounding the activation loop. Such properties of conformation selection might be exploited to modulate the protein docking interface used by ERK substrates and effectors.
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Over the past decade, myriads of studies have highlighted the central role of protein condensation in subcellular compartmentalization and spatiotemporal organization of biological processes. Conceptually, protein condensation stands at the highest level in protein structure hierarchy, accounting for the assembly of bodies ranging from thousands to billions of molecules and for densities ranging from dense liquids to solid materials. In size, protein condensates range from nanocondensates of hundreds of nanometers (mesoscopic clusters) to phase-separated micron-sized condensates. In this review, we focus on protein nanocondensation, a process that can occur in subsaturated solutions and can nucleate dense liquid phases, crystals, amorphous aggregates, and fibers. We discuss the nanocondensation of proteins in the light of general physical principles and examine the biophysical properties of several outstanding examples of nanocondensation. We conclude that protein nanocondensation cannot be fully explained by the conceptual framework of micron-scale biomolecular condensation. The evolution of nanocondensates through changes in density and order is currently under intense investigation, and this should lead to the development of a general theoretical framework, capable of encompassing the full range of sizes and densities found in protein condensates.
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The A-series is the most recent generation of chemical warfare nerve agents (CWA) which act directly on the inhibition of the human acetylcholinesterase (HssAChE) enzyme. These compounds lack accurate experimental data on their physicochemical properties, and there is no evidence that traditional antidotes effectively reactivate HssAChE inhibited by them. In the search for potential antidotes, we employed virtual screening, molecular docking, and molecular dynamics (MD) simulations for the theoretical assessment of the performance of a library of Mannich phenols as potential reactivators of HssAChE inhibited by the Novichok agents A-230, A-232, and A-234, in comparison with the commercial oximes pralidoxime (2-PAM), asoxime (HI-6), trimedoxime (TMB-4), and obidoxime. Following the near-attack conformation (NAC) approach, our results suggest that the compounds assessed would face difficulties in triggering the proposed nucleophilic in-line displacement mechanism. Despite this, it was observed that certain Mannich phenols presented similar or superior results to those obtained by reference oximes against A-232 and A-234 model, suggesting that these compounds can adopt more favourable conformations. Additional binding energy calculations confirmed the stability of the model/ligands complexes and the reactivating potential observed in the molecular docking and MD studies. Our findings indicate that the Mannich phenols could be alternative antidotes and that their efficacy should be evaluated experimentally against the A-series CWA.
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Substâncias para a Guerra Química , Reativadores da Colinesterase , Agentes Neurotóxicos , Humanos , Antídotos/farmacologia , Reativadores da Colinesterase/farmacologia , Acetilcolinesterase/metabolismo , Simulação de Acoplamento Molecular , Inibidores da Colinesterase/farmacologia , Inibidores da Colinesterase/química , Oximas/farmacologia , Oximas/química , Trimedoxima/química , Trimedoxima/farmacologia , Substâncias para a Guerra Química/farmacologia , Compostos de Piridínio/farmacologiaRESUMO
3D genome organization regulates gene expression in different physiological and pathological contexts. Characterization of chromatin structure at different scales has provided information about how the genome organizes in the nuclear space, from chromosome territories, compartments of euchromatin and heterochromatin, topologically associated domains to punctual chromatin loops between genomic regulatory elements and gene promoters. In recent years, chromosome conformation capture technologies have also been used to characterize structural variations (SVs) de novo in pathological conditions. The study of SVs in cancer, has brought information about transcriptional misregulation that relates directly to the incidence and prognosis of the disease. For example, gene fusions have been discovered arising from chromosomal translocations that upregulate oncogenes expression, and other types of SVs have been described that alter large genomic regions encompassing many genes. However, studying SVs in 2D cannot capture all their regulatory implications in the genome. Recently, several bioinformatic tools have been developed to identify and classify SVs from chromosome conformation capture data and clarify how they impact chromatin structure in 3D, resulting in transcriptional misregulation. Here, we review recent literature concerning bioinformatic tools to characterize SVs from chromosome conformation capture technologies and exemplify their vast potential to rebuild the 3D landscape of genomes in cancer. The study of SVs from the 3D perspective can produce essential information about drivers, molecular targets, and disease evolution.
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The measurement of morphometric traits in horses is important for determining breed qualification and is one of the main selection criteria for the species. The development of an index (HPC) that consists of principal components weighted by additive genetic values allows to explore the most relevant relationships using a reduced number of variables that explain the greatest amount of variation in the data. Genome-wide association studies (GWAS) using HPC are a relatively new approach that permits to identify regions related to a set of traits. The aim of this study was to perform GWAS using HPC for 15 linear measurements as the explanatory variable in order to identify associated genomic regions and to elucidate the biological mechanisms linked to this index in Campolina horses. For GWAS, weighted single-step GBLUP was applied to HPC. The eight genomic windows that explained the highest proportion of additive genetic variance were identified. The sum of the additive variance explained by the eight windows was 95.89%. Genes involved in bone and cartilage development were identified (SPRY2, COL9A2, MIR30C, HEYL, BMP8B, LTBP1, FAM98A, and CRIM1). They represent potential positional candidates for the HPC of the linear measurements evaluated. The HPC is an efficient alternative to reduce the 15 usually measured traits in Campolina horses. Moreover, candidate genes inserted in region that explained high additive variance of the HPC were identified and might be fine-mapped for searching putative mutation/markers.
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Estudo de Associação Genômica Ampla , Polimorfismo de Nucleotídeo Único , Animais , Cavalos/genética , Estudo de Associação Genômica Ampla/veterinária , Fenótipo , Genômica , Desenvolvimento ÓsseoRESUMO
Four new 2,4-distyrylquinolines and one 2-styryl-4-[2-(thiophen-2-yl)vinyl]quinoline have been synthesized using indium trichloride condensation reactions between aromatic aldehydes and the corresponding 2-methylquinolines, which were themselves prepared using Friedländer annulation reactions between mono- or diketones and (2-aminophenyl)chalcones: the products have all been fully characterized by spectroscopic and crystallographic methods. 2,4-Bis[(E)-styryl]quinoline, C25H19N, (IIa), and its dichloro analogue, 2-[(E)-2,4-dichlorostyryl]-4-[(E)-styryl]quinoline, C25H17Cl2N, (IIb), exhibit different orientations of the 2-styryl unit relative to the quinoline nucleus. In each of the 3-benzoyl analogues {2-[(E)-4-bromostyryl]-4-[(E)-styryl]quinolin-3-yl}(phenyl)methanone, C32H22BrNO, (IIc), {2-[(E)-4-bromostyryl]-4-[(E)-4-chlorostyryl]quinolin-3-yl}(phenyl)methanone, C32H21BrClNO, (IId), and {2-[(E)-4-bromostyryl]-4-[(E)-2-(thiophen-2-yl)vinyl]quinolin-3-yl}(phenyl)methanone, C30H20BrNOS, (IIe), the orientation of the 2-styryl unit is similar to that in (IIa), but the orientation of the 4-arylvinyl units show considerable variation. The thiophene unit in (IIe) is disordered over two sets of atomic sites having occupancies of 0.926â (3) and 0.074â (3). There are no hydrogen bonds of any kind in the structure of (IIa), but in (IId), a single C-H...O hydrogen bond links the molecules into cyclic centrosymmetric R22(20) dimers. A combination of C-H...N and C-H...π hydrogen bonds links the molecules of (IIb) into a three-dimensional framework structure. A combination of three C-H...π hydrogen bonds links the molecules of (IIc) into sheets, and a combination of C-H...O and C-H...π hydrogen bonds forms sheets in (IIe). Comparisons are made with the structures of some related compounds.
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Intrinsically disordered proteins (IDPs) have numerous dynamic conformations. Given the difficulties in tracking temporarily folded states of this kind of protein, methods such as molecular modeling and molecular dynamics (MD) simulations make the process less costly, less laborious, and more detailed. Few plant IDPs have been characterized so far, such as proteins from the Abscisic acid, Stress and Ripening (ASR) family. The present work applied, for the first time, the two above-mentioned tools to test the feasibility of determining a three-dimensional transition model of OsASR5 and to investigate the relationship between OsASR5 and zinc. We found that one of OsASR5's conformers contains α-helices, turns, and loops and that the metal binding resulted in a predominance of α-helix. This stability is possibly imperative for the transcription factor activity. The promoter region of a sugar transporter was chosen to test this hypothesis and free energy calculations showed how the ion is mandatory for this complex formation. The results produced here aim to clarify which conformation the protein in the bound state assumes and which residues are involved in the process, besides developing the understanding of how the flexibility of these proteins can contribute to the response to environmental stresses.
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Proteínas Intrinsicamente Desordenadas , Simulação de Dinâmica Molecular , Zinco , Proteínas Intrinsicamente Desordenadas/química , Entropia , Regiões Promotoras Genéticas , Conformação ProteicaRESUMO
Three new styrylquinoline-chalcone hybrids have been synthesized using a three-step pathway starting with Friedländer cyclocondensation between (2-aminophenyl)chalcones and acetone to give 2-methyl-4-styrylquinolines, followed by selective oxidation to the 2-formyl analogues, and finally Claisen-Schmidt condensation between the formyl intermediates and 1-acetylnaphthalene. All intermediates and the final products have been fully characterized by IR and 1H/13C NMR spectroscopy, and by high-resolution mass spectrometry, and the three products have been characterized by single-crystal X-ray diffraction. The molecular conformations of (E)-3-{4-[(E)-2-phenylethenyl]quinolin-2-yl}-1-(naphthalen-1-yl)prop-2-en-1-one, C30H21NO, (IVa), and (E)-3-{4-[(E)-2-(4-fluorophenyl)ethenyl]quinolin-2-yl}-1-(naphthalen-1-yl)prop-2-en-1-one, C30H20FNO, (IVb), are very similar. In each compound, the molecules are linked into a three-dimensional array by hydrogen bonds, of the C-H...O and C-H...N types in (IVa), and of the C-H...O and C-H...π types in (IVb), and by two independent π-π stacking interactions. By contrast, the conformation of the chalcone unit in (E)-3-{4-[(E)-2-(2-chlorophenyl)ethenyl]quinolin-2-yl}-1-(naphthalen-1-yl)prop-2-en-1-one, C30H20ClNO, (IVc), differs from those in (IVa) and (IVb). There are only weak hydrogen bonds in the structure of (IVc), but a single rather weak π-π stacking interaction links the molecules into chains. Comparisons are made with some related structures.
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Chalcona , Chalconas , Chalcona/química , Chalconas/química , Cristalografia por Raios X , Ligação de HidrogênioRESUMO
Fluorine is often considered the only halogen to effectively engage in hydrogen bonds, while the other halogens, particularly iodine, are not electronegative enough to participate as hydrogen bond acceptors in electrostatic interactions. 2-Fluoroethanol and 2-iodoethanol have been studied herein to test this assumption, since a highly stable gauche conformation can experience the intramolecular hydrogen bond. However, the infrared O H stretching frequency indicates that the hydroxyl group in 2-fluoroethanol is not engaged in intramolecular hydrogen bond, while the corresponding vibration mode for 2-iodoethanol suggests that not only the O H is engaged in such interaction, but also that intramolecular hydrogen bond may drive the conformational equilibrium in this molecule. Theoretical calculations support the covalent nature of this interaction, and provide evidence that intermolecular hydrogen bond with a water molecule, and probably with the polar solvents tested experimentally, occurs with the hydroxyl rather than with the iodine substituent, as conventionally, in order to keep the intramolecular hydrogen bond effective.
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Hidrogênio , Iodo , Hidrogênio/química , Ligação de HidrogênioRESUMO
The interaction between the anti-apoptotic Bcl-2 protein and its antagonist Bax is essential to the regulation of the mitochondrial pathway of apoptosis. For this work, we built models by homology of Bcl-2 full-sequence length in monomeric form (apo-Bcl-2) and in complex with the BH3 domain of Bax (holo-Bcl-2). The Bcl-2 protein was analyzed with its transmembrane domain anchored to a lipidic bilayer of DPPC, imitating physiological conditions. We performed molecular dynamics (MD) simulations using the GROMACS program. Conformational changes showed that the flexible loop domain (FLD) tends to fold on itself and move towards the main core. Furthermore, the BH3 peptide of pro-apoptotic protein Bax, showed an allosteric stabilizing effect on FLD upon being bound to the hydrophobic cleft of the anti-apoptotic protein Bcl-2, causing a reduction in its structural flexibility. However, FLD is distal from the main core of Bcl-2. Principal component analysis (PCA) showed a weak correlation between FLD residues and BH3 peptide from Bax. Upon MD simulations, several new contacts appeared between FLD and some α-helices of the core of Bcl-2, which contribute to maintaining the stability of Bcl-2. This knowledge sheds light on the behavior of Bcl-2 in the cell's native environment.Communicated by Ramaswamy H. Sarma.