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1.
Methods Mol Biol ; 2856: 293-308, 2025.
Artículo en Inglés | MEDLINE | ID: mdl-39283460

RESUMEN

In order to analyze the three-dimensional genome architecture, it is important to simulate how the genome is structured through the cell cycle progression. In this chapter, we present the usage of our computation codes for simulating how the human genome is formed as the cell transforms from anaphase to interphase. We do not use the global Hi-C data as an input into the genome simulation but represent all chromosomes as linear polymers annotated by the neighboring region contact index (NCI), which classifies the A/B type of each local chromatin region. The simulated mitotic chromosomes heterogeneously expand upon entry to the G1 phase, which induces phase separation of A and B chromatin regions, establishing chromosome territories, compartments, and lamina and nucleolus associations in the interphase nucleus. When the appropriate one-dimensional chromosomal annotation is possible, using the protocol of this chapter, one can quantitatively simulate the three-dimensional genome structure and dynamics of human cells of interest.


Asunto(s)
Anafase , Cromatina , Genoma Humano , Interfase , Humanos , Anafase/genética , Interfase/genética , Cromatina/genética , Cromatina/metabolismo , Simulación por Computador , Cromosomas Humanos/genética , Mitosis/genética
2.
Proc Natl Acad Sci U S A ; 121(36): e2403153121, 2024 Sep 03.
Artículo en Inglés | MEDLINE | ID: mdl-39190347

RESUMEN

Genomic information must be faithfully transmitted into two daughter cells during mitosis. To ensure the transmission process, interphase chromatin is further condensed into mitotic chromosomes. Although protein factors like condensins and topoisomerase IIα are involved in the assembly of mitotic chromosomes, the physical bases of the condensation process remain unclear. Depletion attraction/macromolecular crowding, an effective attractive force that arises between large structures in crowded environments around chromosomes, may contribute to the condensation process. To approach this issue, we investigated the "chromosome milieu" during mitosis of living human cells using an orientation-independent-differential interference contrast module combined with a confocal laser scanning microscope, which is capable of precisely mapping optical path differences and estimating molecular densities. We found that the molecular density surrounding chromosomes increased with the progression from prophase to anaphase, concurring with chromosome condensation. However, the molecular density went down in telophase, when chromosome decondensation began. Changes in the molecular density around chromosomes by hypotonic or hypertonic treatment consistently altered the condensation levels of chromosomes. In vitro, native chromatin was converted into liquid droplets of chromatin in the presence of cations and a macromolecular crowder. Additional crowder made the chromatin droplets stiffer and more solid-like. These results suggest that a transient rise in depletion attraction, likely triggered by the relocation of macromolecules (proteins, RNAs, and others) via nuclear envelope breakdown and by a subsequent decrease in cell volumes, contributes to mitotic chromosome condensation, shedding light on a different aspect of the condensation mechanism in living human cells.


Asunto(s)
Cromatina , Cromosomas Humanos , Mitosis , Humanos , Células HeLa , Cromatina/metabolismo , Cromosomas Humanos/metabolismo , Cromosomas Humanos/genética , Microscopía Confocal , Complejos Multiproteicos/metabolismo , Adenosina Trifosfatasas , Proteínas de Unión al ADN
3.
Nutrients ; 16(14)2024 Jul 10.
Artículo en Inglés | MEDLINE | ID: mdl-39064634

RESUMEN

Probiotic-fermented milk is commonly used to maintain intestinal health. However, the effects of heat-treated fermented milk, which does not contain live microorganisms, on intestinal function are not yet fully understood. This study aimed to investigate whether heat-treated Lactobacillus helveticus CP790-fermented milk affects fecal microbiota and gut health as a "postbiotic". A randomized, double-blind, placebo-controlled trial was conducted in healthy Japanese individuals aged 20-59 years with a tendency toward constipation. Participants consumed 100 mL of either the test beverage (n = 60) or placebo beverage (n = 60) for four weeks. The test beverages were prepared with heat-treated CP790-fermented milk, while the placebo beverages were prepared with nonfermented milk flavored with lactic acid. Fecal samples were analyzed using 16S rRNA gene sequencing. Constipation symptoms were assessed using defecation logs and the Patient Assessment of Constipation Symptoms (PAC-SYM) questionnaire. Mood state was also assessed using the Profile of Mood States 2 (POMS2) questionnaire to explore its potential as a "psychobiotic". Desulfobacterota were significantly decreased by CP790-fermented milk intake. PICRUSt2 analysis predicted a decrease in the proportion of genes involved in the sulfate reduction pathway following the consumption of CP790-fermented milk. The CP790-fermented milk intervention significantly improved stool consistency and straining during defecation. These improvements were correlated with a decrease in Desulfobacterota. After the intervention, overall mood, expressed as total mood disturbance, and depression-dejection were significantly better in the CP790 group than in the placebo group. These results suggest that the intake of CP790-fermented milk could be effective in modulating gut microbiota and improving constipation symptoms and mood states.


Asunto(s)
Estreñimiento , Productos Lácteos Cultivados , Heces , Microbioma Gastrointestinal , Calor , Lactobacillus helveticus , Probióticos , Humanos , Método Doble Ciego , Adulto , Femenino , Masculino , Persona de Mediana Edad , Probióticos/administración & dosificación , Adulto Joven , Heces/microbiología , Estreñimiento/microbiología , Estreñimiento/terapia , Productos Lácteos Cultivados/microbiología , Animales , Leche/microbiología , Fermentación
4.
J Agric Food Chem ; 72(22): 12719-12724, 2024 Jun 05.
Artículo en Inglés | MEDLINE | ID: mdl-38789103

RESUMEN

Lactononadecapeptide (LNDP; NIPPLTQTPVVVPPFLQPE), a casein-derived peptide comprising 19 residues, is known for its capacity to enhance cognitive function. This study aimed to explore the transepithelial transport and stability of LNDP. Results showed that LNDP retained over 90% stability after 2 h of treatment with gastrointestinal enzymes. The stability of LNDP on Caco-2 cell monolayers ranged from 93.4% ± 0.9% to 101.1% ± 1.2% over a period of 15-60 min, with no significant differences at each time point. The permeability of LNDP across an artificial lipid membrane was very low with the effective permeability of 3.6 × 10-11 cm/s. The Caco-2 assay demonstrated that LNDP could traverse the intestinal epithelium, with an apparent permeability of 1.22 × 10-6 cm/s. Its transport was significantly inhibited to 67.9% ± 5.0% of the control by Gly-Pro, a competitor of peptide transporter 1 (PEPT1). Furthermore, PEPT1 knockdown using siRNA significantly inhibited LNDP transport by 77.6% ± 1.9% in Caco-2 cell monolayers. The LNDP uptake in PEPT1-expressing HEK293 cells was significantly higher (54.5% ± 14.6%) than that in mock cells. These findings suggest that PEPT1 plays a crucial role in LNDP transport, and LNDP exhibits good resistance to gastrointestinal enzymes.


Asunto(s)
Caseínas , Humanos , Células CACO-2 , Transporte Biológico , Caseínas/metabolismo , Caseínas/química , Caseínas/genética , Transportador de Péptidos 1/genética , Transportador de Péptidos 1/metabolismo , Mucosa Intestinal/metabolismo , Estabilidad de Enzimas , Péptidos/química , Péptidos/metabolismo
5.
Sci Adv ; 9(14): eadf1488, 2023 04 05.
Artículo en Inglés | MEDLINE | ID: mdl-37018405

RESUMEN

In eukaryotes, higher-order chromatin organization is spatiotemporally regulated as domains, for various cellular functions. However, their physical nature in living cells remains unclear (e.g., condensed domains or extended fiber loops; liquid-like or solid-like). Using novel approaches combining genomics, single-nucleosome imaging, and computational modeling, we investigated the physical organization and behavior of early DNA replicated regions in human cells, which correspond to Hi-C contact domains with active chromatin marks. Motion correlation analysis of two neighbor nucleosomes shows that nucleosomes form physically condensed domains with ~150-nm diameters, even in active chromatin regions. The mean-square displacement analysis between two neighbor nucleosomes demonstrates that nucleosomes behave like a liquid in the condensed domain on the ~150 nm/~0.5 s spatiotemporal scale, which facilitates chromatin accessibility. Beyond the micrometers/minutes scale, chromatin seems solid-like, which may contribute to maintaining genome integrity. Our study reveals the viscoelastic principle of the chromatin polymer; chromatin is locally dynamic and reactive but globally stable.


Asunto(s)
Cromatina , Nucleosomas , Humanos , ADN , Eucariontes , Ensamble y Desensamble de Cromatina
6.
Nutrients ; 16(1)2023 Dec 31.
Artículo en Inglés | MEDLINE | ID: mdl-38201970

RESUMEN

Human gut health is closely related to sleep. We aimed to evaluate the efficacy of yeast mannan (YM) in improving bowel habits and sleep quality, along with metabolomics in fecal samples. A total of 40 healthy adults (age range, 22-64 years) with discomfort in defecation were enrolled and randomly allocated to receive either YM (n = 20; 1.1 g/day) or placebo (n = 20) for four weeks. Participants recorded their defecation habits throughout the test periods. Sleep electroencephalogram (EEG) recording using an EEG device and fecal sampling were performed pre- and post-treatment. The YM group significantly increased defecation frequency and stool volumes compared to the placebo group. After 4 weeks of treatment, the non-REM sleep stage 3 (N3) duration in the YM group was significantly higher than that in the placebo group. YM ingestion significantly lengthened total time in bed (TIB) and significantly shortened N3 latency compared to placebo intake during the trial. The metabolomics analysis found a total of 20 metabolite differences between the YM and placebo groups. As a result of stepwise linear regression, changes in fecal propionate and gamma-aminobutyric acid (GABA) levels were identified as the primary factors explaining changes in TIB and N3 latency, respectively. Our findings suggest that the prebiotic YM could be beneficial to gut health and sleep quality.


Asunto(s)
Mananos , Calidad del Sueño , Adulto , Humanos , Adulto Joven , Persona de Mediana Edad , Mananos/farmacología , Saccharomyces cerevisiae , Sueño , Método Doble Ciego , Prebióticos
7.
J Phys Chem B ; 126(38): 7262-7270, 2022 09 29.
Artículo en Inglés | MEDLINE | ID: mdl-36107864

RESUMEN

Myosin VI dimer walks toward the minus end of the actin filament with a large and variable step size of 25-36 nm. Two competing models have been put forward to explain this large step size. The Spudich model assumes that the myosin VI dimer associates at a distal tail near the cargo-binding domain, which makes two full-length single α-helix (SAH) domains serve as long legs. In contrast, the Houdusse-Sweeney model assumes that the association occurs in the middle (between residues 913 and 940) of the SAH domain and that the three-helix bundles unfold to ensure the large step size. Their consistency with the observation of stepping motion with a large and variable step size has not been examined in detail. To compare the two proposed models of myosin VI, we computationally characterized the free energy landscape experienced by the leading head during the stepping movement along the actin filament using the elastic network model of two heads and an implicit model of the SAH domains. Our results showed that the Spudich model is more consistent with the 25-36 nm step size than the Houdusse-Sweeney model. The unfolding of the three-helix bundles gives rise to the free energy bias toward a shorter distance between two heads. Besides, the stiffness of the SAH domain is a key factor for giving strong energetic bias toward the longer distance of stepping. Free energy analysis of the stepping motion complements the visual inspection of static structures and enables a deeper understanding of underlying mechanisms of molecular motors.


Asunto(s)
Actinas , Cadenas Pesadas de Miosina , Citoesqueleto de Actina , Actinas/química , Movimiento , Cadenas Pesadas de Miosina/química
8.
PLoS Comput Biol ; 18(9): e1010494, 2022 09.
Artículo en Inglés | MEDLINE | ID: mdl-36067222

RESUMEN

When the mixture solution of cyanobacterial proteins, KaiA, KaiB, and KaiC, is incubated with ATP in vitro, the phosphorylation level of KaiC shows stable oscillations with the temperature-compensated circadian period. Elucidating this temperature compensation is essential for understanding the KaiABC circadian clock, but its mechanism has remained a mystery. We analyzed the KaiABC temperature compensation by developing a theoretical model describing the feedback relations among reactions and structural transitions in the KaiC molecule. The model showed that the reduced structural cooperativity should weaken the negative feedback coupling among reactions and structural transitions, which enlarges the oscillation amplitude and period, explaining the observed significant period extension upon single amino-acid residue substitution. We propose that an increase in thermal fluctuations similarly attenuates the reaction-structure feedback, explaining the temperature compensation in the KaiABC clock. The model explained the experimentally observed responses of the oscillation phase to the temperature shift or the ADP-concentration change and suggested that the ATPase reactions in the CI domain of KaiC affect the period depending on how the reaction rates are modulated. The KaiABC clock provides a unique opportunity to analyze how the reaction-structure coupling regulates the system-level synchronized oscillations of molecules.


Asunto(s)
Relojes Circadianos , Péptidos y Proteínas de Señalización del Ritmo Circadiano , Adenosina Difosfato/metabolismo , Adenosina Trifosfatasas/metabolismo , Adenosina Trifosfato/metabolismo , Proteínas Bacterianas/metabolismo , Relojes Circadianos/fisiología , Ritmo Circadiano , Péptidos y Proteínas de Señalización del Ritmo Circadiano/metabolismo , Fosforilación , Temperatura
9.
Molecules ; 27(11)2022 May 31.
Artículo en Inglés | MEDLINE | ID: mdl-35684484

RESUMEN

Superfolds are folds commonly observed among evolutionarily unrelated multiple superfamilies of proteins. Since discovering superfolds almost two decades ago, structural rules distinguishing superfolds from the other ordinary folds have been explored but remained elusive. Here, we analyzed a typical superfold, the ferredoxin fold, and the fold which reverses the N to C terminus direction from the ferredoxin fold as a case study to find the rule to distinguish superfolds from the other folds. Though all the known structural characteristics for superfolds apply to both the ferredoxin fold and the reverse ferredoxin fold, the reverse fold has been found only in a single superfamily. The database analyses in the present study revealed the structural preferences of αß- and ßα-units; the preferences separate two α-helices in the ferredoxin fold, preventing their collision and stabilizing the fold. In contrast, in the reverse ferredoxin fold, the preferences bring two helices near each other, inducing structural conflict. The Rosetta folding simulations suggested that the ferredoxin fold is physically much more realizable than the reverse ferredoxin fold. Therefore, we propose that minimal structural conflict or minimal frustration among secondary structures is the rule to distinguish a superfold from ordinary folds. Intriguingly, the database analyses revealed that a most stringent structural rule in proteins, the right-handedness of the ßαß-unit, is broken in a set of structures to prevent the frustration, suggesting the proposed rule of minimum frustration among secondary structural units is comparably strong as the right-handedness rule of the ßαß-unit.


Asunto(s)
Ferredoxinas , Pliegue de Proteína , Ferredoxinas/metabolismo , Conformación Proteica , Estructura Secundaria de Proteína , Proteínas/química
10.
Proc Natl Acad Sci U S A ; 119(22): e2109838119, 2022 05 31.
Artículo en Inglés | MEDLINE | ID: mdl-35617433

RESUMEN

Three-dimensional genome structure and dynamics play critical roles in regulating DNA functions. Flexible chromatin structure and movements suggested that the genome is dynamically phase separated to form A (active) and B (inactive) compartments in interphase nuclei. Here, we examine this hypothesis by developing a polymer model of the whole genome of human cells and assessing the impact of phase separation on genome structure. Upon entry to the G1 phase, the simulated genome expanded according to heterogeneous repulsion among chromatin chains, which moved chromatin heterogeneously, inducing phase separation of chromatin. This repulsion-driven phase separation quantitatively reproduces the experimentally observed chromatin domains, A/B compartments, lamina-associated domains, and nucleolus-associated domains, consistently explaining nuclei of different human cells and predicting their dynamic fluctuations. We propose that phase separation induced by heterogeneous repulsive interactions among chromatin chains largely determines dynamic genome organization.


Asunto(s)
Cromatina , Fase G1 , Genoma Humano , Núcleo Celular/genética , Núcleo Celular/metabolismo , Cromatina/química , Cromatina/genética , Humanos , Dominios Proteicos
11.
Sci Rep ; 11(1): 4713, 2021 02 25.
Artículo en Inglés | MEDLINE | ID: mdl-33633230

RESUMEN

The cyanobacterial circadian clock can be reconstituted by mixing three proteins, KaiA, KaiB, and KaiC, in vitro. In this protein mixture, oscillations of the phosphorylation level of KaiC molecules are synchronized to show the coherent oscillations of the ensemble of many molecules. However, the molecular mechanism of this synchronization has not yet been fully elucidated. In this paper, we explain a theoretical model that considers the multifold feedback relations among the structure and reactions of KaiC. The simulated KaiC hexamers show stochastic switch-like transitions at the level of single molecules, which are synchronized in the ensemble through the sequestration of KaiA into the KaiC-KaiB-KaiA complexes. The proposed mechanism quantitatively reproduces the synchronization that was observed by mixing two solutions oscillating in different phases. The model results suggest that biochemical assays with varying concentrations of KaiA or KaiB can be used to test this hypothesis.


Asunto(s)
Proteínas Bacterianas/metabolismo , Péptidos y Proteínas de Señalización del Ritmo Circadiano/metabolismo , Cianobacterias/metabolismo , Ritmo Circadiano , Modelos Biológicos , Fosforilación , Procesos Estocásticos
12.
Biosci Biotechnol Biochem ; 85(4): 948-956, 2021 Mar 24.
Artículo en Inglés | MEDLINE | ID: mdl-33580692

RESUMEN

Lactononadecapeptide (LNDP; NIPPLTQTPVVVPPFLQPE) is a memory-improving peptide. The current study aimed to determine the effects of a single dose of tablets containing LNDP on cognitive function in healthy Japanese men aged 30-59 years. A randomized, double-blind, cross-over, placebo-controlled trial was conducted in participants randomly assigned to receive LNDP or placebo tablets. The Uchida-Kraepelin test was used to induce cognitive load in participants as a model of work load. Cognitive function was evaluated using the Japanese version of the CNS Vital Signs. Composite memory and verbal memory were significantly higher following consumption of LNDP than placebo tablets. Carryover effects were observed in attention and concentration domains so that period 1 data was analyzed. LNDP consumption led to higher processing speed, executive function, and cognitive flexibility than placebo. Thus, supplementation with a single dose of LNDP tablets may improve cognitive functions including memory, attention, concentration, and information processing in daily life.


Asunto(s)
Cognición/efectos de los fármacos , Oligopéptidos/farmacología , Comprimidos , Estudios Cruzados , Método Doble Ciego , Humanos , Lactonas/química , Oligopéptidos/química
13.
Phys Rev E ; 102(4-1): 042408, 2020 Oct.
Artículo en Inglés | MEDLINE | ID: mdl-33212709

RESUMEN

Epigenetic modifications of histones crucially affect eukaryotic gene activity, while the epigenetic histone state is largely determined by the binding of specific factors such as the transcription factors (TFs) to DNA. Here, the way in which the TFs and the histone state are dynamically correlated is not obvious when the TF synthesis is regulated by the histone state. This type of feedback regulatory relation is ubiquitous in gene networks to determine cell fate in differentiation and other cell transformations. To gain insights into such dynamical feedback regulations, we theoretically analyze a model of epigenetic gene switching by extending the Doi-Peliti operator formalism of reaction kinetics to the problem of coupled molecular processes. Spin-1 and spin-1/2 coherent-state representations are introduced to describe stochastic reactions of histones and binding or unbinding of TFs in a unified way, which provides a concise view of the effects of timescale difference among these molecular processes; even in the case that binding or unbinding of TFs to or from DNA is adiabatically fast, the slow nonadiabatic histone dynamics gives rise to a distinct circular flow of the probability flux around basins in the landscape of the gene state distribution, which leads to hysteresis in gene switching. In contrast to the general belief that the change in the amount of TF precedes the histone state change, flux drives histones to be modified prior to the change in the amount of TF in self-regulating circuits. Flux-landscape analyses shed light on the nonlinear nonadiabatic mechanism of epigenetic cell fate decision making.


Asunto(s)
Epigénesis Genética , Modelos Genéticos , Diferenciación Celular/genética , Retroalimentación Fisiológica , Redes Reguladoras de Genes/genética , Histonas/metabolismo , Procesos Estocásticos , Factores de Transcripción/metabolismo
14.
Food Funct ; 11(11): 9489-9494, 2020 Nov 18.
Artículo en Inglés | MEDLINE | ID: mdl-33064120

RESUMEN

We recently found that a peptide that activates the cholecystokinin (CCK) system effectively reduces blood pressure in spontaneously hypertensive rats (SHR) after the development of hypertension, after which hypotensive drugs are sometimes less effective. In this study, we investigated the vasorelaxation and antihypertensive effects of a peptide derived from a milk protein in SHR with advanced hypertension. The vasorelaxing activity was measured using the mesenteric artery isolated from SHR and the systemic blood pressure was measured by the tail-cuff method. KFWGK was released from bovine serum albumin (BSA) and the model peptide after subtilisin digestion. KFWGK relaxed the mesenteric artery and this vasorelaxation activity was inhibited by lorglumide, an antagonist of the CCK1 receptor. KFWGK more potently relaxed the artery from advanced-stage SHR than that from early-stage SHR. Orally administered KFWGK exhibited potent and long-lasting antihypertensive effects in SHR after the development of hypertension (the minimum effective dose was 5 µg kg-1). The KFWGK-induced antihypertensive effects were also blocked by a CCK antagonist, suggesting that it activates the CCK system. In conclusion, KFWGK, a CCK-dependent vasorelaxant peptide, exhibited potent antihypertensive effects in SHR after the development of hypertension.


Asunto(s)
Antihipertensivos/farmacología , Colecistoquinina/metabolismo , Leche/química , Péptidos/farmacología , Vasodilatación/efectos de los fármacos , Administración Oral , Animales , Antihipertensivos/administración & dosificación , Presión Sanguínea/efectos de los fármacos , Relación Dosis-Respuesta a Droga , Masculino , Arterias Mesentéricas/efectos de los fármacos , Péptidos/administración & dosificación , Ratas , Ratas Endogámicas SHR
15.
Biophys Rev ; 12(2): 461-468, 2020 Apr.
Artículo en Inglés | MEDLINE | ID: mdl-32206982

RESUMEN

Eukaryotic chromatin is a complex of genome DNA and associated proteins, and its structure and dynamics play a crucial role in regulating DNA functions. Chromatin takes rather irregular structures in the nucleus and exhibits heterogeneous sub-diffusive movements as polymers fluctuating in a fluid state. Using genome-wide single-nucleosome tracking data, heterogeneity of movements was statistically analyzed, which categorized chromatin into two types: slow chromatin that moves under structurally constrained environments and fast chromatin that moves with less constraints. Interactions of chromatin to various protein factors determine the motional constraints. For example, loss of the cohesin complex that bundles the chromatin chains reduces the motional constraints and increases the population of fast chromatin. Another example is the transcriptional machinery. While it was previously thought that the transcriptional activity is associated with more open and dynamic chromatin structure, recent studies suggested a more nuanced role of transcription in chromatin dynamics: dynamic association/dissociation of active RNA polymerase II (RNAPII) and other transcription factors and Mediators (TF-Meds) transiently bridges transcriptionally active DNA regions, which forms a loose network of chromatin and constrains chromatin movement, enhancing the slow chromatin population. This new view on the dynamical effects of transcription urges a reflection on the traditional model of transcription factories and invites the more recent models of condensates/phase-separated liquid droplets of RNAPII, transcription factors, and Mediators. The combined procedure of genome-wide single-nucleosome tracking and its statistical analysis would unveil heterogeneity in the chromatin movement, which should provide a key to understanding the relations among chromatin dynamics, structure, and function.

16.
Aging (Albany NY) ; 11(21): 9492-9499, 2019 11 04.
Artículo en Inglés | MEDLINE | ID: mdl-31685714

RESUMEN

To understand the changes in physiological responses due to aging, a number of bioactive probes based on different signal transduction pathways are necessary. In this study, we comprehensively and systematically investigated changes in blood vessel function with age using a 336-dipeptide library. In the early stage of hypertension, the most potent vasorelaxant dipeptide was Ser-Tyr (SY) in the mesenteric artery isolated from spontaneously hypertensive rats (SHR). SY-induced vasorelaxation and anti-hypertensive effects were blocked by L-NAME, an inhibitor of nitric oxide synthase (NOS), suggesting that SY activates the NO system. On the other hand, the patterns of dipeptides with vasorelaxation activity in early and advanced stages of hypertension were different. In the advanced stage, the most potent vasorelaxing dipeptide was Asn-Ala (NA). Orally administered NA (1.5 mg/kg) reduced the blood pressure in the advanced stage, at which drugs were sometimes less effective, and the anti-hypertensive effects lasted for 6 hr. The NA-induced vasorelaxation and anti-hypertensive activity was blocked by lorglumide, an antagonist of the cholecystokinin CCK1 receptor, suggesting that NA activated the CCK system. Taken together, in the early and advanced stages of hypertension, SY and NA exhibited vasorelaxing and anti-hypertensive effects via the NO and CCK systems, respectively.


Asunto(s)
Envejecimiento/fisiología , Antihipertensivos/farmacología , Presión Sanguínea/efectos de los fármacos , Dipéptidos/farmacología , Vasodilatación/efectos de los fármacos , Secuencia de Aminoácidos , Animales , Antihipertensivos/química , Presión Sanguínea/fisiología , Colecistoquinina/fisiología , Dipéptidos/química , Evaluación Preclínica de Medicamentos , Hipertensión/tratamiento farmacológico , Hipertensión/fisiopatología , Masculino , Arterias Mesentéricas/efectos de los fármacos , Arterias Mesentéricas/fisiología , Óxido Nítrico/metabolismo , Biblioteca de Péptidos , Proglumida/análogos & derivados , Proglumida/farmacología , Ratas , Ratas Endogámicas SHR , Receptores de Colecistoquinina/antagonistas & inhibidores , Receptores de Colecistoquinina/metabolismo , Vasodilatación/fisiología , Vasodilatadores/química , Vasodilatadores/farmacología
17.
Proc Natl Acad Sci U S A ; 116(40): 19939-19944, 2019 10 01.
Artículo en Inglés | MEDLINE | ID: mdl-31527274

RESUMEN

Understanding chromatin organization and dynamics is important, since they crucially affect DNA functions. In this study, we investigate chromatin dynamics by statistically analyzing single-nucleosome movement in living human cells. Bimodal nature of the mean square displacement distribution of nucleosomes allows for a natural categorization of the nucleosomes as fast and slow. Analyses of the nucleosome-nucleosome correlation functions within these categories along with the density of vibrational modes show that the nucleosomes form dynamically correlated fluid regions (i.e., dynamic domains of fast and slow nucleosomes). Perturbed nucleosome dynamics by global histone acetylation or cohesin inactivation indicate that nucleosome-nucleosome interactions along with tethering of chromatin chains organize nucleosomes into fast and slow dynamic domains. A simple polymer model is introduced, which shows the consistency of this dynamic domain picture. Statistical analyses of single-nucleosome movement provide rich information on how chromatin is dynamically organized in a fluid manner in living cells.


Asunto(s)
Ensamble y Desensamble de Cromatina , Cromatina/química , Nucleosomas/química , Polímeros/química , Acetilación , Proteínas de Ciclo Celular , Proteínas Cromosómicas no Histona , ADN , Histonas/química , Humanos , Oscilometría , Dominios Proteicos , Cohesinas
18.
J Cell Biol ; 218(5): 1511-1530, 2019 05 06.
Artículo en Inglés | MEDLINE | ID: mdl-30824489

RESUMEN

Although chromatin organization and dynamics play a critical role in gene transcription, how they interplay remains unclear. To approach this issue, we investigated genome-wide chromatin behavior under various transcriptional conditions in living human cells using single-nucleosome imaging. While transcription by RNA polymerase II (RNAPII) is generally thought to need more open and dynamic chromatin, surprisingly, we found that active RNAPII globally constrains chromatin movements. RNAPII inhibition or its rapid depletion released the chromatin constraints and increased chromatin dynamics. Perturbation experiments of P-TEFb clusters, which are associated with active RNAPII, had similar results. Furthermore, chromatin mobility also increased in resting G0 cells and UV-irradiated cells, which are transcriptionally less active. Our results demonstrated that chromatin is globally stabilized by loose connections through active RNAPII, which is compatible with models of classical transcription factories or liquid droplet formation of transcription-related factors. Together with our computational modeling, we propose the existence of loose chromatin domain networks for various intra-/interchromosomal contacts via active RNAPII clusters/droplets.


Asunto(s)
Cromatina/metabolismo , Histonas/metabolismo , Procesamiento de Imagen Asistido por Computador/métodos , Nucleosomas/metabolismo , ARN Polimerasa II/metabolismo , Epitelio Pigmentado de la Retina/metabolismo , Transcripción Genética , Células Cultivadas , Cromatina/genética , Simulación por Computador , Genoma Humano , Histonas/genética , Humanos , Microscopía Fluorescente , Nucleosomas/genética , ARN Polimerasa II/genética , Epitelio Pigmentado de la Retina/citología
19.
J Phys Chem B ; 123(3): 702-713, 2019 01 24.
Artículo en Inglés | MEDLINE | ID: mdl-30629448

RESUMEN

How do many constituent molecules in a biochemical system synchronize, giving rise to coherent system-level oscillations? One system that is particularly suitable for use in studying this problem is a mixture solution of three cyanobacterial proteins, KaiA, KaiB, and KaiC: the phosphorylation level of KaiC shows stable oscillations with a period of approximately 24 h when these three Kai proteins are incubated with ATP in vitro. Here, we analyze the mechanism behind synchronization in the KaiABC system theoretically by enhancing a model previously developed by the present author. Our simulation results suggest that positive feedback between stochastic ATP hydrolysis and the allosteric structural transitions in KaiC molecules drives oscillations of individual molecules and promotes synchronization of oscillations of many KaiC molecules. Our simulations also show that the ATPase activity of KaiC is correlated with the oscillation frequency of an ensemble of KaiC molecules. These results suggest that stochastic ATP hydrolysis in each KaiC molecule plays an important role in regulating the coherent system-level oscillations. This property is robust against changes in the binding and unbinding rate constants for KaiA to/from KaiC or KaiB, but the oscillations are sensitive to the rate constants of the KaiC phosphorylation and dephosphorylation reactions.


Asunto(s)
Proteínas Bacterianas/metabolismo , Relojes Circadianos , Péptidos y Proteínas de Señalización del Ritmo Circadiano/metabolismo , Adenosina Trifosfato/química , Adenosina Trifosfato/metabolismo , Regulación Alostérica , Proteínas Bacterianas/química , Sitios de Unión , Péptidos y Proteínas de Señalización del Ritmo Circadiano/química , Hidrólisis , Modelos Biológicos , Modelos Moleculares , Unión Proteica , Procesos Estocásticos , Synechococcus/química
20.
Biochem Biophys Res Commun ; 503(2): 1070-1074, 2018 09 05.
Artículo en Inglés | MEDLINE | ID: mdl-29936178

RESUMEN

We previously reported that an orally administered dipeptide, Arg-Phe (RF), which causes enteroendocrine cell responses, lowered blood pressure in spontaneously hypertensive rats (SHRs). In this study, we found that Phe-Trp (FW), induced the most potent enteroendocrine cell responses out of total 338 dipeptides. An FW analogue, Phe-Trp-Gly-Lys (FWGK), which was effectively produced by tryptic digestion of bovine serum albumin, decreased blood pressure after oral administration. The minimum effective dose of FWGK (50 µg/kg) was 1/300 of that of RF (15 mg/kg). FWGK stimulated cholecystokinin (CCK) secretion in the enteroendocrine cells and exhibited vasorelaxing and antihypertensive effects via the CCK1 system.


Asunto(s)
Antihipertensivos/farmacología , Dipéptidos/farmacología , Células Enteroendocrinas/efectos de los fármacos , Vasodilatadores/farmacología , Administración Oral , Animales , Antihipertensivos/administración & dosificación , Antihipertensivos/química , Presión Sanguínea/efectos de los fármacos , Línea Celular , Colecistoquinina/metabolismo , Dipéptidos/administración & dosificación , Dipéptidos/química , Células Enteroendocrinas/metabolismo , Masculino , Ratones , Ratas Endogámicas SHR , Vasodilatadores/administración & dosificación , Vasodilatadores/química
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