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1.
Cell ; 187(13): 3427-3444.e21, 2024 Jun 20.
Artigo em Inglês | MEDLINE | ID: mdl-38733990

RESUMO

Many behaviors require the coordinated actions of somatic and autonomic functions. However, the underlying mechanisms remain elusive. By opto-stimulating different populations of descending spinal projecting neurons (SPNs) in anesthetized mice, we show that stimulation of excitatory SPNs in the rostral ventromedial medulla (rVMM) resulted in a simultaneous increase in somatomotor and sympathetic activities. Conversely, opto-stimulation of rVMM inhibitory SPNs decreased both activities. Anatomically, these SPNs innervate both sympathetic preganglionic neurons and motor-related regions in the spinal cord. Fiber-photometry recording indicated that the activities of rVMM SPNs correlate with different levels of muscle and sympathetic tone during distinct arousal states. Inhibiting rVMM excitatory SPNs reduced basal muscle and sympathetic tone, impairing locomotion initiation and high-speed performance. In contrast, silencing the inhibitory population abolished muscle atonia and sympathetic hypoactivity during rapid eye movement (REM) sleep. Together, these results identify rVMM SPNs as descending spinal projecting pathways controlling the tone of both the somatomotor and sympathetic systems.


Assuntos
Bulbo , Medula Espinal , Sistema Nervoso Simpático , Animais , Masculino , Camundongos , Locomoção/fisiologia , Bulbo/fisiologia , Camundongos Endogâmicos C57BL , Neurônios Motores/fisiologia , Neurônios/fisiologia , Sono REM/fisiologia , Medula Espinal/fisiologia , Sistema Nervoso Simpático/fisiologia , Comportamento Animal , Contagem de Células , Músculo Esquelético
2.
Cell ; 185(16): 2853-2878, 2022 08 04.
Artigo em Inglês | MEDLINE | ID: mdl-35931019

RESUMO

The surprising discovery that the diatomic gas nitric oxide (NO) is generated by mammalian cells and serves to regulate a multitude of physiological processes has continued to fascinate biologists for almost four decades. The biochemistry of NO is complex, and novel insights into the control of NO biosynthesis and mechanisms of signal transduction are continuously emerging. NO is a key regulator of cardiovascular function, metabolism, neurotransmission, immunity, and more, and aberrant NO signaling is a central feature of many major disorders including cardiovascular disease, diabetes, and cancer. Here, we discuss the basics of NO biology emphasizing recent advances in the field including novel means of increasing NO bioactivity with therapeutic and nutritional implications.


Assuntos
Doenças Cardiovasculares , Nitritos , Animais , Doenças Cardiovasculares/tratamento farmacológico , Fenômenos Fisiológicos Cardiovasculares , Humanos , Mamíferos/metabolismo , Óxido Nítrico/metabolismo , Nitritos/metabolismo , Nitritos/uso terapêutico , Transdução de Sinais
3.
Annu Rev Cell Dev Biol ; 38: 375-394, 2022 10 06.
Artigo em Inglês | MEDLINE | ID: mdl-35804476

RESUMO

During organismal development, organs and systems are built following a genetic blueprint that produces structures capable of performing specific physiological functions. Interestingly, we have learned that the physiological activities of developing tissues also contribute to their own morphogenesis. Specifically, physiological activities such as fluid secretion and cell contractility generate hydrostatic pressure that can act as a morphogenetic force. Here, we first review the role of hydrostatic pressure in tube formation during animal development and discuss mathematical models of lumen formation. We then illustrate specific roles of the notochord as a hydrostatic scaffold in anterior-posterior axis development in chordates. Finally, we cover some examples of how fluid flows influence morphogenetic processes in other developmental contexts. Understanding how fluid forces act during development will be key for uncovering the self-organizing principles that control morphogenesis.


Assuntos
Notocorda , Animais , Pressão Hidrostática , Morfogênese
4.
Cell ; 179(2): 498-513.e22, 2019 10 03.
Artigo em Inglês | MEDLINE | ID: mdl-31585084

RESUMO

Neuromodulators bind to pre- and postsynaptic G protein-coupled receptors (GPCRs), are able to quickly change intracellular cyclic AMP (cAMP) and Ca2+ levels, and are thought to play important roles in neuropsychiatric and neurodegenerative diseases. Here, we discovered in human neurons an unanticipated presynaptic mechanism that acutely changes synaptic ultrastructure and regulates synaptic communication. Activation of neuromodulator receptors bidirectionally controlled synaptic vesicle numbers within nerve terminals. This control correlated with changes in the levels of cAMP-dependent protein kinase A-mediated phosphorylation of synapsin-1. Using a conditional deletion approach, we reveal that the neuromodulator-induced control of synaptic vesicle numbers was largely dependent on synapsin-1. We propose a mechanism whereby non-phosphorylated synapsin-1 "latches" synaptic vesicles to presynaptic clusters at the active zone. cAMP-dependent phosphorylation of synapsin-1 then removes the vesicles. cAMP-independent dephosphorylation of synapsin-1 in turn recruits vesicles. Synapsin-1 thereby bidirectionally regulates synaptic vesicle numbers and modifies presynaptic neurotransmitter release as an effector of neuromodulator signaling in human neurons.


Assuntos
Proteínas Quinases Dependentes de AMP Cíclico/metabolismo , Terminações Pré-Sinápticas/metabolismo , Sinapsinas/metabolismo , Transmissão Sináptica , Vesículas Sinápticas/metabolismo , Animais , Células Cultivadas , Células HEK293 , Humanos , Camundongos , Camundongos Endogâmicos C57BL , Neurotransmissores/metabolismo , Receptores de Neurotransmissores/metabolismo , Transdução de Sinais
5.
Cell ; 172(4): 758-770.e14, 2018 02 08.
Artigo em Inglês | MEDLINE | ID: mdl-29425492

RESUMO

The means by which the physicochemical properties of different cellular components together determine bacterial cell shape remain poorly understood. Here, we investigate a programmed cell-shape change during Bacillus subtilis sporulation, when a rod-shaped vegetative cell is transformed to an ovoid spore. Asymmetric cell division generates a bigger mother cell and a smaller, hemispherical forespore. The septum traps the forespore chromosome, which is translocated to the forespore by SpoIIIE. Simultaneously, forespore size increases as it is reshaped into an ovoid. Using genetics, timelapse microscopy, cryo-electron tomography, and mathematical modeling, we demonstrate that forespore growth relies on membrane synthesis and SpoIIIE-mediated chromosome translocation, but not on peptidoglycan or protein synthesis. Our data suggest that the hydrated nucleoid swells and inflates the forespore, displacing ribosomes to the cell periphery, stretching septal peptidoglycan, and reshaping the forespore. Our results illustrate how simple biophysical interactions between core cellular components contribute to cellular morphology.


Assuntos
Divisão Celular Assimétrica/fisiologia , Bacillus subtilis/fisiologia , Cromossomos Bacterianos/metabolismo , Esporos Bacterianos/metabolismo , Translocação Genética , Bacillus subtilis/ultraestrutura , Proteínas de Bactérias/genética , Proteínas de Bactérias/metabolismo , Cromossomos Bacterianos/genética , Peptidoglicano/biossíntese , Peptidoglicano/genética , Biossíntese de Proteínas/fisiologia , Esporos Bacterianos/genética , Esporos Bacterianos/ultraestrutura
6.
Physiol Rev ; 104(1): 199-251, 2024 Jan 01.
Artigo em Inglês | MEDLINE | ID: mdl-37477622

RESUMO

The teleology of sex differences has been argued since at least as early as Aristotle's controversial Generation of Animals more than 300 years BC, which reflects the sex bias of the time to contemporary readers. Although the question "why are the sexes different" remains a topic of debate in the present day in metaphysics, the recent emphasis on sex comparison in research studies has led to the question "how are the sexes different" being addressed in health science through numerous observational studies in both health and disease susceptibility, including blood pressure regulation and hypertension. These efforts have resulted in better understanding of differences in males and females at the molecular level that partially explain their differences in vascular function and renal sodium handling and hence blood pressure and the consequential cardiovascular and kidney disease risks in hypertension. This review focuses on clinical studies comparing differences between men and women in blood pressure over the life span and response to dietary sodium and highlights experimental models investigating sexual dimorphism in the renin-angiotensin-aldosterone, vascular, sympathetic nervous, and immune systems, endothelin, the major renal sodium transporters/exchangers/channels, and the impact of sex hormones on these systems in blood pressure homeostasis. Understanding the mechanisms governing sex differences in blood pressure regulation could guide novel therapeutic approaches in a sex-specific manner to lower cardiovascular risks in hypertension and advance personalized medicine.


Assuntos
Hipertensão , Caracteres Sexuais , Animais , Feminino , Humanos , Masculino , Pressão Sanguínea/fisiologia , Rim , Hemodinâmica , Sódio
7.
Annu Rev Cell Dev Biol ; 31: 373-97, 2015.
Artigo em Inglês | MEDLINE | ID: mdl-26407212

RESUMO

Mechanotransduction translates mechanical signals into biochemical signals. It is based on the soft-matter properties of biomolecules or membranes that deform in response to mechanical loads to trigger activation of biochemical reactions. The study of mechanotransductive processes in cell-structure organization has been initiated in vitro in many biological contexts, such as examining cells' response to substrate rigidity increases associated with tumor fibrosis and to blood flow pressure. In vivo, the study of mechanotransduction in regulating physiological processes has focused primarily on the context of embryogenesis, with an increasing number of examples demonstrating its importance for both differentiation and morphogenesis. The conservation across species of mechanical induction in early embryonic patterning now suggests that major animal transitions, such as mesoderm emergence, may have been based on mechanotransduction pathways. In adult animal tissues, permanent stiffness and tissue growth pressure contribute to tumorigenesis and appear to reactivate such conserved embryonic mechanosensitive pathways.


Assuntos
Carcinogênese/patologia , Mecanotransdução Celular/fisiologia , Morfogênese/fisiologia , Animais , Evolução Biológica , Desenvolvimento Embrionário/fisiologia , Humanos
8.
Trends Biochem Sci ; 49(4): 333-345, 2024 Apr.
Artigo em Inglês | MEDLINE | ID: mdl-38355393

RESUMO

Plasma membranes utilize free energy to maintain highly asymmetric, non-equilibrium distributions of lipids and proteins between their two leaflets. In this review we discuss recent progress in quantitative research enabled by using compositionally controlled asymmetric model membranes. Both experimental and computational studies have shed light on the nuanced mechanisms that govern the structural and dynamic coupling between compositionally distinct bilayer leaflets. This coupling can increase the membrane bending rigidity and induce order - or lipid domains - across the membrane. Furthermore, emerging evidence indicates that integral membrane proteins not only respond to asymmetric lipid distributions but also exhibit intriguing asymmetric properties themselves. We propose strategies to advance experimental research, aiming for a deeper, quantitative understanding of membrane asymmetry, which carries profound implications for cellular physiology.


Assuntos
Bicamadas Lipídicas , Proteínas de Membrana , Bicamadas Lipídicas/química , Proteínas de Membrana/metabolismo , Membrana Celular/metabolismo
9.
Physiol Rev ; 100(3): 1119-1147, 2020 07 01.
Artigo em Inglês | MEDLINE | ID: mdl-32347156

RESUMO

Intercalated cells (ICs) are found in the connecting tubule and the collecting duct. Of the three IC subtypes identified, type B intercalated cells are one of the best characterized and known to mediate Cl- absorption and HCO3- secretion, largely through the anion exchanger pendrin. This exchanger is thought to act in tandem with the Na+-dependent Cl-/HCO3- exchanger, NDCBE, to mediate net NaCl absorption. Pendrin is stimulated by angiotensin II and aldosterone administration via the angiotensin type 1a and the mineralocorticoid receptors, respectively. It is also stimulated in models of metabolic alkalosis, such as with NaHCO3 administration. In some rodent models, pendrin-mediated HCO3- secretion modulates acid-base balance. However, of probably more physiological or clinical significance is the role of these pendrin-positive ICs in blood pressure regulation, which occurs, at least in part, through pendrin-mediated renal Cl- absorption, as well as their effect on the epithelial Na+ channel, ENaC. Aldosterone stimulates ENaC directly through principal cell mineralocorticoid hormone receptor (ligand) binding and also indirectly through its effect on pendrin expression and function. In so doing, pendrin contributes to the aldosterone pressor response. Pendrin may also modulate blood pressure in part through its action in the adrenal medulla, where it modulates the release of catecholamines, or through an indirect effect on vascular contractile force. In addition to its role in Na+ and Cl- balance, pendrin affects the balance of other ions, such as K+ and I-. This review describes how aldosterone and angiotensin II-induced signaling regulate pendrin and the contribution of pendrin-positive ICs in the kidney to distal nephron function and blood pressure.


Assuntos
Rim/citologia , Rim/fisiologia , Transportadores de Sulfato/metabolismo , Equilíbrio Ácido-Base/efeitos dos fármacos , Equilíbrio Ácido-Base/fisiologia , Aldosterona/farmacologia , Angiotensina II/farmacologia , Animais , Regulação da Expressão Gênica/efeitos dos fármacos , Regulação da Expressão Gênica/fisiologia , Humanos
10.
Am J Hum Genet ; 111(5): 954-965, 2024 May 02.
Artigo em Inglês | MEDLINE | ID: mdl-38614075

RESUMO

Variability in quantitative traits has clinical, ecological, and evolutionary significance. Most genetic variants identified for complex quantitative traits have only a detectable effect on the mean of trait. We have developed the mean-variance test (MVtest) to simultaneously model the mean and log-variance of a quantitative trait as functions of genotypes and covariates by using estimating equations. The advantages of MVtest include the facts that it can detect effect modification, that multiple testing can follow conventional thresholds, that it is robust to non-normal outcomes, and that association statistics can be meta-analyzed. In simulations, we show control of type I error of MVtest over several alternatives. We identified 51 and 37 previously unreported associations for effects on blood-pressure variance and mean, respectively, in the UK Biobank. Transcriptome-wide association studies revealed 633 significant unique gene associations with blood-pressure mean variance. MVtest is broadly applicable to studies of complex quantitative traits and provides an important opportunity to detect novel loci.


Assuntos
Pressão Sanguínea , Estudo de Associação Genômica Ampla , Locos de Características Quantitativas , Humanos , Pressão Sanguínea/genética , Polimorfismo de Nucleotídeo Único , Modelos Genéticos , Genótipo , Variação Genética , Simulação por Computador , Fenótipo
11.
Proc Natl Acad Sci U S A ; 121(26): e2401840121, 2024 Jun 25.
Artigo em Inglês | MEDLINE | ID: mdl-38900793

RESUMO

The recent theory-driven discovery of a class of clathrate hydrides (e.g., CaH6, YH6, YH9, and LaH10) with superconducting critical temperatures (Tc) well above 200 K has opened the prospects for "hot" superconductivity above room temperature under pressure. Recent efforts focus on the search for superconductors among ternary hydrides that accommodate more diverse material types and configurations compared to binary hydrides. Through extensive computational searches, we report the prediction of a unique class of thermodynamically stable clathrate hydrides structures consisting of two previously unreported H24 and H30 hydrogen clathrate cages at megabar pressures. Among these phases, LaSc2H24 shows potential hot superconductivity at the thermodynamically stable pressure range of 167 to 300 GPa, with calculated Tcs up to 331 K at 250 GPa and 316 K at 167 GPa when the important effects of anharmonicity are included. The very high critical temperatures are attributed to an unusually large hydrogen-derived density of states at the Fermi level arising from the newly reported peculiar H30 as well as H24 cages in the structure. Our predicted introduction of Sc in the La-H system is expected to facilitate future design and realization of hot superconductors in ternary clathrate superhydrides.

12.
Proc Natl Acad Sci U S A ; 121(23): e2403726121, 2024 Jun 04.
Artigo em Inglês | MEDLINE | ID: mdl-38805293

RESUMO

The key of heterostructure is the combinations created by stacking various vdW materials, which can modify interlayer coupling and electronic properties, providing exciting opportunities for designer devices. However, this simple stacking does not create chemical bonds, making it difficult to fundamentally alter the electronic structure. Here, we demonstrate that interlayer interactions in heterostructures can be fundamentally controlled using hydrostatic pressure, providing a bonding method to modify electronic structures. By covering graphene with boron nitride and inducing an irreversible phase transition, the conditions for graphene lattice-matching bonding (IMB) were created. We demonstrate that the increased bandgap of graphene under pressure is well maintained in ambient due to the IMB in the interface. Comparison to theoretical modeling emphasizes the process of pressure-induced interfacial bonding, systematically generalizes, and predicts this model. Our results demonstrate that pressure can irreversibly control interlayer bonding, providing opportunities for high-pressure technology in ambient applications and IMB engineering in heterostructures.

13.
Proc Natl Acad Sci U S A ; 121(22): e2319880121, 2024 May 28.
Artigo em Inglês | MEDLINE | ID: mdl-38768353

RESUMO

Elevated interstitial fluid pressure (IFP) within pathological tissues (e.g., tumors, obstructed kidneys, and cirrhotic livers) creates a significant hindrance to the transport of nanomedicine, ultimately impairing the therapeutic efficiency. Among these tissues, solid tumors present the most challenging scenario. While several strategies through reducing tumor IFP have been devised to enhance nanoparticle delivery, few approaches focus on modulating the intrinsic properties of nanoparticles to effectively counteract IFP during extravasation and penetration, which are precisely the stages obstructed by elevated IFP. Herein, we propose an innovative solution by engineering nanoparticles with a fusiform shape of high curvature, enabling efficient surmounting of IFP barriers during extravasation and penetration within tumor tissues. Through experimental and theoretical analyses, we demonstrate that the elongated nanoparticles with the highest mean curvature outperform spherical and rod-shaped counterparts against elevated IFP, leading to superior intratumoral accumulation and antitumor efficacy. Super-resolution microscopy and molecular dynamics simulations uncover the underlying mechanisms in which the high curvature contributes to diminished drag force in surmounting high-pressure differentials during extravasation. Simultaneously, the facilitated rotational movement augments the hopping frequency during penetration. This study effectively addresses the limitations posed by high-pressure impediments, uncovers the mutual interactions between the physical properties of NPs and their environment, and presents a promising avenue for advancing cancer treatment through nanomedicine.


Assuntos
Sistemas de Liberação de Medicamentos , Líquido Extracelular , Nanopartículas , Pressão , Nanopartículas/química , Líquido Extracelular/metabolismo , Animais , Sistemas de Liberação de Medicamentos/métodos , Camundongos , Humanos , Neoplasias/tratamento farmacológico , Neoplasias/metabolismo , Linhagem Celular Tumoral , Extravasamento de Materiais Terapêuticos e Diagnósticos , Simulação de Dinâmica Molecular , Antineoplásicos/farmacocinética , Antineoplásicos/administração & dosagem , Antineoplásicos/química
14.
Proc Natl Acad Sci U S A ; 121(9): e2316580121, 2024 Feb 27.
Artigo em Inglês | MEDLINE | ID: mdl-38377204

RESUMO

Achieving high-performance materials with superior mechanical properties and electrical conductivity, especially in large-sized bulk forms, has always been the goal. However, it remains a grand challenge due to the inherent trade-off between these properties. Herein, by employing nanodiamonds as precursors, centimeter-sized diamond/graphene composites were synthesized under moderate pressure and temperature conditions (12 GPa and 1,300 to 1,500 °C), and the composites consisted of ultrafine diamond grains and few-layer graphene domains interconnected through covalently bonded interfaces. The composites exhibit a remarkable electrical conductivity of 2.0 × 104 S m-1 at room temperature, a Vickers hardness of up to ~55.8 GPa, and a toughness of 10.8 to 19.8 MPa m1/2. Theoretical calculations indicate that the transformation energy barrier for the graphitization of diamond surface is lower than that for diamond growth directly from conventional sp2 carbon materials, allowing the synthesis of such diamond composites under mild conditions. The above results pave the way for realizing large-sized diamond-based materials with ultrahigh electrical conductivity and superior mechanical properties simultaneously under moderate synthesis conditions, which will facilitate their large-scale applications in a variety of fields.

15.
Proc Natl Acad Sci U S A ; 121(14): e2318978121, 2024 Apr 02.
Artigo em Inglês | MEDLINE | ID: mdl-38536755

RESUMO

Pressure-induced transformations in an archetypal chalcogenide glass (GeSe2) have been investigated up to 157 GPa by X-ray absorption spectroscopy (XAS) and molecular dynamics (MD) simulations. Ge and Se K-edge XAS data allowed simultaneous tracking of the correlated local structural and electronic changes at both Ge and Se sites. Thanks to the simultaneous analysis of extended X-ray absorption fine structure (EXAFS) signals of both edges, reliable quantitative information about the evolution of the first neighbor Ge-Se distribution could be obtained. It also allowed to account for contributions of the Ge-Ge and Se-Se bond distributions (chemical disorder). The low-density to high-density amorphous-amorphous transformation was found to occur within 10 to 30 GPa pressure range, but the conversion from tetrahedral to octahedral coordination of the Ge sites is completed above [Formula: see text] 80 GPa. No convincing evidence of another high-density amorphous state with coordination number larger than six was found within the investigated pressure range. The number of short Ge-Ge and Se-Se "wrong" bonds was found to increase upon pressurization. Experimental XAS results are confirmed by MD simulations, indicating the increase of chemical disorder under high pressure.

16.
Proc Natl Acad Sci U S A ; 121(14): e2319663121, 2024 Apr 02.
Artigo em Inglês | MEDLINE | ID: mdl-38547059

RESUMO

The structure of dislocation cores, the fundamental knowledge on crystal plasticity, remains largely unexplored in covalent crystals. Here, we conducted atomically resolved characterizations of dislocation core structures in a plastically deformed diamond anvil cell tip that was unloaded from an exceptionally high pressure of 360 GPa. Our observations unveiled a series of nonequilibrium dislocation cores that deviate from the commonly accepted "five-seven-membered ring" dislocation core model found in FCC-structured covalent crystals. The nonequilibrium dislocation cores were generated through a process known as "mechanical quenching," analogous to the quenching process where a high-energy state is rapidly frozen. The density functional theory-based molecular dynamic simulations reveal that the phenomenon of mechanical quenching in diamond arises from the challenging relaxation of the nonequilibrium configuration, necessitating a large critical strain of 25% that is difficult to maintain. Further electronic-scale analysis suggested that such large critical strain is spent on the excitation of valance electrons for bond breaking and rebonding during relaxation. These findings establish a foundation for the plasticity theory of covalent materials and provide insights into the design of electrical and luminescent properties in diamond, which are intimately linked to the dislocation core structure.

17.
Proc Natl Acad Sci U S A ; 121(5): e2312571121, 2024 Jan 30.
Artigo em Inglês | MEDLINE | ID: mdl-38266049

RESUMO

We combine synchrotron-based infrared absorption and Raman scattering spectroscopies with diamond anvil cell techniques and first-principles calculations to explore the properties of hafnia under compression. We find that pressure drives HfO[Formula: see text]:7%Y from the mixed monoclinic ([Formula: see text]) [Formula: see text] antipolar orthorhombic ([Formula: see text]) phase to pure antipolar orthorhombic ([Formula: see text]) phase at approximately 6.3 GPa. This transformation is irreversible, meaning that upon release, the material is kinetically trapped in the [Formula: see text] metastable state at 300 K. Compression also drives polar orthorhombic ([Formula: see text]) hafnia into the tetragonal ([Formula: see text]) phase, although the latter is not metastable upon release. These results are unified by an analysis of the energy landscape. The fact that pressure allows us to stabilize targeted metastable structures with less Y stabilizer is important to preserving the flat phonon band physics of pure HfO[Formula: see text].

18.
Proc Natl Acad Sci U S A ; 121(28): e2320222121, 2024 Jul 09.
Artigo em Inglês | MEDLINE | ID: mdl-38954542

RESUMO

Artificial skins or flexible pressure sensors that mimic human cutaneous mechanoreceptors transduce tactile stimuli to quantitative electrical signals. Conventional trial-and-error designs for such devices follow a forward structure-to-property routine, which is usually time-consuming and determines one possible solution in one run. Data-driven inverse design can precisely target desired functions while showing far higher productivity, however, it is still absent for flexible pressure sensors because of the difficulties in acquiring a large amount of data. Here, we report a property-to-structure inverse design of flexible pressure sensors, exhibiting a significantly greater efficiency than the conventional routine. We use a reduced-order model that analytically constrains the design scope and an iterative "jumping-selection" method together with a surrogate model that enhances data screening. As an exemplary scenario, hundreds of solutions that overcome the intrinsic signal saturation have been predicted by the inverse method, validating for a variety of material systems. The success in property design on multiple indicators demonstrates that the proposed inverse design is an efficient and powerful tool to target multifarious applications of flexible pressure sensors, which can potentially advance the fields of intelligent robots, advanced healthcare, and human-machine interfaces.

19.
Proc Natl Acad Sci U S A ; 121(3): e2312029121, 2024 Jan 16.
Artigo em Inglês | MEDLINE | ID: mdl-38194446

RESUMO

Understanding natural protein evolution and designing novel proteins are motivating interest in development of high-throughput methods to explore large sequence spaces. In this work, we demonstrate the application of multisite λ dynamics (MSλD), a rigorous free energy simulation method, and chemical denaturation experiments to quantify evolutionary selection pressure from sequence-stability relationships and to address questions of design. This study examines a mesophilic phylogenetic clade of ribonuclease H (RNase H), furthering its extensive characterization in earlier studies, focusing on E. coli RNase H (ecRNH) and a more stable consensus sequence (AncCcons) differing at 15 positions. The stabilities of 32,768 chimeras between these two sequences were computed using the MSλD framework. The most stable and least stable chimeras were predicted and tested along with several other sequences, revealing a designed chimera with approximately the same stability increase as AncCcons, but requiring only half the mutations. Comparing the computed stabilities with experiment for 12 sequences reveals a Pearson correlation of 0.86 and root mean squared error of 1.18 kcal/mol, an unprecedented level of accuracy well beyond less rigorous computational design methods. We then quantified selection pressure using a simple evolutionary model in which sequences are selected according to the Boltzmann factor of their stability. Selection temperatures from 110 to 168 K are estimated in three ways by comparing experimental and computational results to evolutionary models. These estimates indicate selection pressure is high, which has implications for evolutionary dynamics and for the accuracy required for design, and suggests accurate high-throughput computational methods like MSλD may enable more effective protein design.


Assuntos
Escherichia coli , Ribonuclease H , Escherichia coli/genética , Filogenia , Simulação por Computador , Sequência Consenso , Ribonuclease H/genética
20.
Proc Natl Acad Sci U S A ; 121(12): e2321540121, 2024 Mar 19.
Artigo em Inglês | MEDLINE | ID: mdl-38483993

RESUMO

Nitrogen doped lutetium hydride has drawn global attention in the pursuit of room-temperature superconductivity near ambient pressure and temperature. However, variable synthesis techniques and uncertainty surrounding nitrogen concentration have contributed to extensive debate within the scientific community about this material and its properties. We used a solid-state approach to synthesize nitrogen doped lutetium hydride at high pressure and temperature (HPT) and analyzed the residual starting materials to determine its nitrogen content. High temperature oxide melt solution calorimetry determined the formation enthalpy of LuH1.96N0.02 (LHN) from LuH2 and LuN to be -28.4 ± 11.4 kJ/mol. Magnetic measurements indicated diamagnetism which increased with nitrogen content. Ambient pressure conductivity measurements observed metallic behavior from 5 to 350 K, and the constant and parabolic magnetoresistance changed with increasing temperature. High pressure conductivity measurements revealed that LHN does not exhibit superconductivity up to 26.6 GPa. We compressed LHN in a diamond anvil cell to 13.7 GPa and measured the Raman signal at each step, with no evidence of any phase transition. Despite the absence of superconductivity, a color change from blue to purple to red was observed with increasing pressure. Thus, our findings confirm the thermodynamic stability of LHN, do not support superconductivity, and provide insights into the origins of its diamagnetism.

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