RESUMO
Desensitization of G-protein-coupled receptors (GPCR) is a general regulatory mechanism adopted by biological organisms against overstimulation of G protein signaling. Although the details of the mechanism are extensively studied, it is not easy to gain an overarching understanding of the process constituted by a multitude of molecular events with vastly differing time scales. To offer a semiquantitative yet predictive understanding of the mechanism, we formulate a kinetic model for the G protein signaling and desensitization by considering essential biochemical steps from ligand binding to receptor internalization. The internalization, followed by receptor depletion from the plasma membrane, attenuates the downstream signal. Together with the kinetic model and its full numerics of the expression derived for the dose-response relation, an approximated form of the expression clarifies the role played by the individual biochemical processes and allows us to identify four distinct regimes for the downregulation that emerge from the balance between phosphorylation, dephosphorylation, and the cellular level of ß-arrestin.
Assuntos
Receptores Acoplados a Proteínas G , Transdução de Sinais , Receptores Acoplados a Proteínas G/metabolismo , Cinética , Fosforilação , beta-Arrestinas/metabolismo , Membrana Celular/metabolismo , Modelos Biológicos , LigantesRESUMO
We propose a high-throughput chromosome conformation capture data-based many-polymer model that allows us to generate an ensemble of multi-scale genome structures. We demonstrate the efficacy of our model by validating the generated structures against experimental measurements and employ them to address key questions regarding genome organization. Our model first confirms a significant correlation between chromosome size and nuclear positioning. Specifically, smaller chromosomes are distributed at the core region, whereas larger chromosomes are at the periphery, interacting with the nuclear envelope. The spatial distribution of A- and B-type compartments, which is nontrivial to infer from the corresponding high-throughput chromosome conformation capture maps alone, can also be elucidated using our model, accounting for an issue such as the effect of chromatin-lamina interaction on the compartmentalization of conventional and inverted nuclei. In accordance with imaging data, the overall shape of the 3D genome structures generated from our model displays significant variation. As a case study, we apply our method to the yellow fever mosquito genome, finding that the predicted morphology displays, on average, a more globular shape than the previously suggested spindle-like organization and that our prediction better aligns with the fluorescence in situ hybridization data. Our model has great potential to be extended to investigate many outstanding issues concerning 3D genome organization.
Assuntos
Modelos Moleculares , Animais , Cromossomos/metabolismo , Genoma , Cromatina/metabolismo , Cromatina/química , Cromatina/genéticaRESUMO
Lipid rafts, which are dynamic nanodomains in the plasma membrane, play a crucial role in intermembrane processes by clustering together and growing in size within the plane of the membrane while also aligning with each other across different membranes. However, the physical origin of layer by layer alignment of lipid rafts remains to be elucidated. Here, by using fluorescence imaging and synchrotron X-ray reflectivity in a phase-separated multilayer system, we find that the alignment of raft-mimicking Lo domains is regulated by the distance between bilayers. Molecular dynamics simulations reveal that the aligned state is energetically preferred when the intermembrane distance is small due to its ability to minimize the volume of surface water, which has fewer water hydrogen bonds (HBs) compared to bulk water. Our results suggest that water HB-driven alignment of lipid rafts plays a role as a precursor of intermembrane processes such as cell-cell fusion, virus entry, and signaling.
Assuntos
Ligação de Hidrogênio , Microdomínios da Membrana , Simulação de Dinâmica Molecular , Água , Água/química , Microdomínios da Membrana/química , Bicamadas Lipídicas/química , Bicamadas Lipídicas/metabolismoRESUMO
In many living organisms displaying circadian rhythms, the intake of energy often occurs in a periodic manner. Glycolysis is a prototypical biochemical reaction that exhibits a self-sustained oscillation under continuous injection of glucose. Here we study the effect of periodic injection of glucose on the glycolytic oscillation from a dynamical systems perspective. In particular, we employ Goldbeter's allosteric model of phosphofructokinase as a model system for glycolytic oscillations, and explore the effect of periodic substrate influx of varying frequencies and amplitudes by building the phase diagrams of Lyapunov exponents and oscillatory periods. When the frequency of driving is tuned around the harmonic and sub/super-harmonic conditions of the natural frequency, the system is entrained to a frequency-locked state, forming an entrainment band that broadens with an increasing amplitude of driving. On the other hand, if the amplitude is substantial, the system may transition, albeit infrequent, to a chaotic state which defies prediction of dynamical behaviour. Our study offers in-depth understandings into the controllability of glycolytic oscillation as well as explaining physical underpinnings that enable the synchronous oscillations among a dense population of cells.
Assuntos
Ritmo Circadiano , Modelos Biológicos , Fosfofrutoquinase-1/metabolismo , Glicólise , GlucoseRESUMO
This work presents a general chemical reaction network theory for olfactory sensing processes that employ G-protein-coupled receptors as olfactory receptors (ORs). The theory can be applied to general mixtures of odorants and an arbitrary number of ORs. Reactions of ORs with G-proteins, in both the presence and absence of odorants, are explicitly considered. A unique feature of the theory is the definition of an odor activity vector consisting of strengths of odorant-induced signals from ORs relative to those due to background G-protein activity in the absence of odorants. It is demonstrated that each component of the odor activity defined this way reduces to a Michaelis-Menten form capable of accounting for cooperation or competition effects between different odorants. The main features of the theory are illustrated for a two-odorant mixture. Known and potential mixture effects, such as suppression, shadowing, inhibition, and synergy, are quantitatively described. Effects of relative values of rate constants, basal activity, and G-protein concentration are also demonstrated.
Assuntos
Neurônios Receptores Olfatórios , Receptores Odorantes , Odorantes , Neurônios Receptores Olfatórios/fisiologia , Olfato/fisiologia , Receptores Acoplados a Proteínas GRESUMO
Trimethylamine N-oxide (TMAO) is an osmolyte that accumulates in cells in response to osmotic stress. TMAO stabilizes proteins by the entropic stabilization mechanism, which pictures TMAO as a nanocrowder that predominantly destabilizes the unfolded state. However, the mechanism of action of TMAO on RNA is much less understood. Here, we use all-atom molecular dynamics simulations to investigate how TMAO interacts with a 12-nt RNA hairpin with a high melting temperature, and an 8-nt RNA hairpin, which has a relatively fluid native basin in the absence of TMAO. The use of the two hairpins with different free energy of stabilization allows us to probe the origin of the destabilization effect of TMAO on RNA molecules without the possibility of forming tertiary interactions. We generated multiple trajectories using all-atom molecular dynamics (MD) simulations in explicit water by employing AMBER and CHARMM force fields, both in the absence and presence of TMAO. We observed qualitatively similar RNA-TMAO interaction profiles from the simulations using the two force fields. TMAO hydrogen bond interactions are largely depleted around the paired RNA bases and ribose sugars. In contrast, we show that the oxygen atom in TMAO, the hydrogen bond acceptor, preferentially interacts with the hydrogen bond donors in the solvent exposed bases, such as those in the stem-loop and the destabilized base stacks in the unfolded state, especially in the marginally stable 8-nt RNA hairpin. The predicted destabilization mechanism through TMAO-RNA hydrogen bond interactions could be tested using two-dimensional IR spectroscopy. Since TMAO does not significantly interact with the hydroxyl group of the ribose sugars, we predict that similar results must also hold for DNA.
Assuntos
RNA , Ribose , Ligação de Hidrogênio , RNA/química , Metilaminas/química , Água/químicaRESUMO
Recognizing that diverse morphologies of neurons are reminiscent of structures of branched polymers, we put forward a principled and systematic way of classifying neurons that employs the ideas of polymer physics. In particular, we use 3D coordinates of individual neurons, which are accessible in recent neuron reconstruction datasets from electron microscope images. We numerically calculate the form factor, F(q), a Fourier transform of the distance distribution of particles comprising an object of interest, which is routinely measured in scattering experiments to quantitatively characterize the structure of materials. For a polymer-like object consisting of n monomers spanning over a length scale of r, F(q) scales with the wavenumber [Formula: see text] as [Formula: see text] at an intermediate range of q, where [Formula: see text] is the fractal dimension or the inverse scaling exponent ([Formula: see text]) characterizing the geometrical feature ([Formula: see text]) of the object. F(q) can be used to describe a neuron morphology in terms of its size ([Formula: see text]) and the extent of branching quantified by [Formula: see text]. By defining the distance between F(q)s as a measure of similarity between two neuronal morphologies, we tackle the neuron classification problem. In comparison with other existing classification methods for neuronal morphologies, our F(q)-based classification rests solely on 3D coordinates of neurons with no prior knowledge of morphological features. When applied to publicly available neuron datasets from three different organisms, our method not only complements other methods but also offers a physical picture of how the dendritic and axonal branches of an individual neuron fill the space of dense neural networks inside the brain.
Assuntos
Neurônios , Polímeros , Neurônios/fisiologia , Axônios , Redes Neurais de Computação , EncéfaloRESUMO
CYT-19 is a DEAD-box protein whose adenosine-triphosphate (ATP)-dependent helicase activity facilitates the folding of group I introns in precursor RNA (pre-RNA) of Neurospora crassa (N. crassa). In the process, they consume a substantial amount of ATP. While much of the mechanistic insight into CYT-19 activity has been gained through the studies on the folding of Tetrahymena group I intron ribozyme, the more biologically relevant issue, namely the effect of CYT-19 on the self-splicing of pre-RNA, remains largely unexplored. Here, we employ a kinetic network model, based on the generalized iterative annealing mechanism (IAM), to investigate the relation between CYT-19 activity, rate of ribozyme folding, and the kinetics of the self-splicing reaction. The network rate parameters are extracted by analyzing the recent biochemical data for CYT-19-facilitated folding of Tetrahymena ribozyme. We then build extended models to explore the metabolism of pre-RNA. We show that the timescales of chaperone-mediated folding of group I ribozyme and self-splicing reaction compete with each other. As a consequence, in order to maximize the self-splicing yield of group I introns in pre-RNA, the chaperone activity must be sufficiently large to unfold the misfolded structures, but not too large to unfold the native structures prior to the self-splicing event. We discover that despite the promiscuous action on structured RNAs, the helicase activity of CYT-19 on group I ribozyme gives rise to self-splicing yields that are close to the maximum.
Assuntos
RNA Catalítico , Tetrahymena , Precursores de RNA , RNA Catalítico/genética , Splicing de RNA , RNA/genética , Tetrahymena/genética , Trifosfato de AdenosinaRESUMO
Confined in two-dimensional planes, polymer chains comprising dense monolayer solutions are segregated from each other because of topological interaction. Although the segregation is inherent in two dimensions (2D), the solution may display different properties depending on the solvent quality. Among others, it is well-known in both theory and experiment that the osmotic pressure (Π) in the semidilute regime displays solvent quality dependent increases with the area fraction (Ï) (or monomer concentration, ρ), that is, Π â¼ Ï3 for good solvents and Π â¼ Ï8 for Θ solvents. The osmotic pressure can be associated with the Flory exponent (or the correlation length exponent) for the chain size and the pair distribution function of monomers; however, they do not necessarily offer a detailed microscopic picture leading to the difference. To gain microscopic understanding into the different surface pressure isotherms of polymer solutions under the two distinct solvent conditions, we study the chain configurations of the polymer solution based on our numerical simulations that semiquantitatively reproduce the expected scaling behaviors. Notably, at the same value of Ï, polymer chains in a Θ solvent occupy the surface in a more inhomogeneous manner than the chains in good solvent, yielding on average a greater and more heterogeneous interstitial void size, which is related to the fact that the polymer in the Θ solvent has a greater correlation length. The polymer configurations and interstitial voids visualized and quantitatively analyzed in this study offer microscopic understanding to the origin of the solvent quality dependent osmotic pressure of 2D polymer solutions.
Assuntos
Polímeros , Solventes , Pressão OsmóticaRESUMO
The projection neurons (PNs), reconstructed from electron microscope (EM) images of the Drosophila olfactory system, offer a detailed view of neuronal anatomy, providing glimpses into information flow in the brain. About 150 uPNs constituting 58 glomeruli in the antennal lobe (AL) are bundled together in the axonal extension, routing the olfactory signal received at AL to mushroom body (MB) calyx and lateral horn (LH). Here we quantify the neuronal organization in terms of the inter-PN distances and examine its relationship with the odor types sensed by Drosophila. The homotypic uPNs that constitute glomeruli are tightly bundled and stereotyped in position throughout the neuropils, even though the glomerular PN organization in AL is no longer sustained in the higher brain center. Instead, odor-type dependent clusters consisting of multiple homotypes innervate the MB calyx and LH. Pheromone-encoding and hygro/thermo-sensing homotypes are spatially segregated in MB calyx, whereas two distinct clusters of food-related homotypes are found in LH in addition to the segregation of pheromone-encoding and hygro/thermo-sensing homotypes. We find that there are statistically significant associations between the spatial organization among a group of homotypic uPNs and certain stereotyped olfactory responses. Additionally, the signals from some of the tightly bundled homotypes converge to a specific group of lateral horn neurons (LHNs), which indicates that homotype (or odor type) specific integration of signals occurs at the synaptic interface between PNs and LHNs. Our findings suggest that before neural computation in the inner brain, some of the olfactory information are already encoded in the spatial organization of uPNs, illuminating that a certain degree of labeled-line strategy is at work in the Drosophila olfactory system.
Assuntos
Drosophila , Neurônios Receptores Olfatórios , Animais , Olfato/fisiologia , Corpos Pedunculados/fisiologia , Odorantes , Neurônios/fisiologia , Feromônios , Condutos Olfatórios/fisiologia , Neurônios Receptores Olfatórios/fisiologiaRESUMO
Genome architecture mapping (GAM) is a recently developed methodology that offers the cosegregation probability of two genomic segments from an ensemble of thinly sliced nuclear profiles, enabling us to probe and decipher three-dimensional chromatin organization. The cosegregation probability from GAM binned at 1 Mb, which thus probes the length scale associated with the genomic separation greater than 1 Mb, is, however, not identical to the contact probability obtained from Hi-C, and its correlation with interlocus distance measured with fluorescence in situ hybridization is not so good as the contact probability. In this study, by using a polymer-based model of chromatins, we derive a theoretical expression of the cosegregation probability as well as that of the contact probability and carry out quantitative analyses of how they differ from each other. The results from our study, validated with in silico GAM analysis on three-dimensional genome structures from fluorescence in situ hybridization, suggest that to attain strong correlation with the interlocus distance, a properly normalized version of cosegregation probability needs to be calculated based on a large number of nuclear slices (n>103).
Assuntos
Cromatina , Polímeros , Hibridização in Situ Fluorescente/métodos , Mapeamento Cromossômico/métodos , Cromatina/genética , ProbabilidadeRESUMO
The (2,2,6,6-tetramethylpiperidin-1-yl)oxyl (TEMPO) moiety tethered to the headgroup of phosphatidylcholine (PC) lipid is employed in spin labeling electron paramagnetic resonance spectroscopy to probe the water dynamics near lipid bilayer interfaces. Due to its amphiphilic character, however, TEMPO spin label could partition between aqueous and lipid phases, and may even be stabilized in the lipid phase. Accurate assessment of the TEMPO-PC configuration in bilayer membranes is essential for correctly interpreting the data from measurements. Here, we carry out all-atom molecular dynamics (MD) simulations of TEMPO-PC probe in single-component lipid bilayers at varying temperatures, using two standard MD force fields. We find that, for a dipalmitoylphosphatidylcholine (DPPC) membrane whose gel-to-fluid lipid phase transition occurs at 314 K, while the TEMPO spin label is stabilized above the bilayer interface in the gel phase, there is a preferential location of TEMPO below the membrane interface in the fluid phase. For bilayers made of unsaturated lipids, 1,2-Dioleoyl-sn-glycero-3-phosphocholine (DOPC) and 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (POPC), which adopt the fluid phase at ambient temperature, TEMPO is unequivocally stabilized inside the bilayers. Our finding of membrane phase-dependent positioning of the TEMPO moiety highlights the importance of assessing the packing order and fluidity of lipids under a given measurement condition.
Assuntos
1,2-Dipalmitoilfosfatidilcolina , Fosfatidilcolinas , 1,2-Dipalmitoilfosfatidilcolina/química , Óxidos N-Cíclicos , Bicamadas Lipídicas/química , Fosfatidilcolinas/química , Marcadores de Spin , Água/químicaRESUMO
There is a growing realization that multi-way chromatin contacts formed in chromosome structures are fundamental units of gene regulation. However, due to the paucity and complexity of such contacts, it is challenging to detect and identify them using experiments. Based on an assumption that chromosome structures can be mapped onto a network of Gaussian polymer, here we derive analytic expressions for n-body contact probabilities (n > 2) among chromatin loci based on pairwise genomic contact frequencies available in Hi-C, and show that multi-way contact probability maps can in principle be extracted from Hi-C. The three-body (triplet) contact probabilities, calculated from our theory, are in good correlation with those from measurements including Tri-C, MC-4C and SPRITE. Maps of multi-way chromatin contacts calculated from our analytic expressions can not only complement experimental measurements, but also can offer better understanding of the related issues, such as cell-line dependent assemblies of multiple genes and enhancers to chromatin hubs, competition between long-range and short-range multi-way contacts, and condensates of multiple CTCF anchors.
Assuntos
Cromatina , Mapeamento Cromossômico/métodos , Regulação da Expressão Gênica/genética , Sequenciamento de Nucleotídeos em Larga Escala/métodos , Cromatina/química , Cromatina/genética , Cromatina/metabolismo , DNA/química , DNA/metabolismo , Elementos Facilitadores Genéticos/genética , Genes/genética , Genômica , HumanosRESUMO
Thermodynamic uncertainty relations (TURs), originally discovered for classical systems, dictate the tradeoff between dissipation and fluctuations of irreversible current, specifying a minimal bound that constrains the two quantities. In a series of efforts to extend the relation to the one under more generalized conditions, it has been noticed that the bound is less tight in open quantum processes. To study the origin of the loose bounds, we consider an external field-driven transition dynamics of a two-level quantum system weakly coupled to the bosonic bath as a model of an open quantum system. The model makes it explicit that the imaginary part of quantum coherence, which contributes to dissipation to the environment, is responsible for loosening the TUR bound by suppressing the relative fluctuations in the irreversible current of transitions, whereas the real part of the coherence tightens it. Our study offers a better understanding of how quantum nature affects the TUR bound.
RESUMO
Spatial boundaries formed during animal development originate from the pre-patterning of tissues by signaling molecules, called morphogens. The accuracy of boundary location is limited by the fluctuations of morphogen concentration that thresholds the expression level of target gene. Producing more morphogen molecules, which gives rise to smaller relative fluctuations, would better serve to shape more precise target boundaries; however, it incurs more thermodynamic cost. In the classical diffusion-depletion model of morphogen profile formation, the morphogen molecules synthesized from a local source display an exponentially decaying concentration profile with a characteristic length λ. Our theory suggests that in order to attain a precise profile with the minimal cost, λ should be roughly half the distance to the target boundary position from the source. Remarkably, we find that the profiles of morphogens that pattern the Drosophila embryo and wing imaginal disk are formed with nearly optimal λ. Our finding underscores the cost-effectiveness of precise morphogen profile formation in Drosophila development.
Assuntos
Padronização Corporal , Proteínas de Drosophila/metabolismo , Drosophila melanogaster/metabolismo , Modelos Biológicos , Animais , Difusão , Proteínas de Drosophila/genética , Drosophila melanogaster/embriologia , Drosophila melanogaster/genética , Embrião não Mamífero/metabolismo , Regulação da Expressão Gênica no Desenvolvimento , Discos Imaginais/metabolismo , Transdução de Sinais , Fatores de Tempo , Asas de Animais/embriologia , Asas de Animais/metabolismoRESUMO
We investigate the effect of mobile polymer brushes on proteins embedded in biological membranes by employing both Asakura-Oosawa type of theoretical model and coarse-grained molecular dynamics simulations. The brush polymer-induced depletion attraction between proteins changes non-monotonically with the size of brush. The depletion interaction, which is determined by the ratio of the protein size to the grafting distance between brush polymers, increases linearly with the brush size as long as the polymer brush height is shorter than the protein size. When the brush height exceeds the protein size, however, the depletion attraction among proteins is slightly reduced. We also explore the possibility of the brush polymer-induced assembly of a large protein cluster, which can be related to one of many molecular mechanisms underlying recent experimental observations of integrin nanocluster formation and signaling.
Assuntos
Proteínas de Membrana/química , Polímeros/química , Análise por Conglomerados , Simulação de Dinâmica MolecularRESUMO
Temporal order in living matters reflects the self-organizing nature of dynamical processes driven out of thermodynamic equilibrium. Because of functional reasons, the period of a biochemical oscillation must be tuned to a specific value with precision; however, according to the thermodynamic uncertainty relation (TUR), the precision of the oscillatory period is constrained by the thermodynamic cost of generating it. After reviewing the basics of chemical oscillations using the Brusselator as a model system, we study the glycolytic oscillation generated by octameric phosphofructokinase (PFK), which is known to display a period of several minutes. By exploring the phase space of glycolytic oscillations, we find that the glycolytic oscillation under the cellular condition is realized in a cost-effective manner. Specifically, over the biologically relevant range of parameter values of glycolysis and octameric PFK, the entropy production from the glycolytic oscillation is minimal when the oscillation period is (5-10) min. Furthermore, the glycolytic oscillation is found at work near the phase boundary of limit cycles, suggesting that a moderate increase of glucose injection rate leads to the loss of oscillatory dynamics, which is reminiscent of the loss of pulsatile insulin release resulting from elevated blood glucose level.
Assuntos
Glicólise , Fosfofrutoquinase-1 , Modelos Biológicos , Fosfofrutoquinase-1/metabolismo , Fosfofrutoquinases , TermodinâmicaRESUMO
Fueled by ATP hydrolysis in N-ethylmaleimide sensitive factor (NSF), the 20S complex disassembles rigid SNARE (soluble NSF attachment protein receptor) complexes in single unraveling step. This global disassembly distinguishes NSF from other molecular motors that make incremental and processive motions, but the molecular underpinnings of its remarkable energy efficiency remain largely unknown. Using multiple single-molecule methods, we found remarkable cooperativity in mechanical connection between NSF and the SNARE complex, which prevents dysfunctional 20S complexes that consume ATP without productive disassembly. We also constructed ATP hydrolysis cycle of the 20S complex, in which NSF largely shows randomness in ATP binding but switches to perfect ATP hydrolysis synchronization to induce global SNARE disassembly, minimizing ATP hydrolysis by non-20S complex-forming NSF molecules. These two mechanisms work in concert to concentrate ATP consumption into functional 20S complexes, suggesting evolutionary adaptations by the 20S complex to the energetically expensive mechanical task of SNARE complex disassembly.
Assuntos
Trifosfato de Adenosina/metabolismo , Complexo de Endopeptidases do Proteassoma/metabolismo , Proteínas SNARE/metabolismo , Animais , Bovinos , Cricetulus , Hidrólise , Modelos Moleculares , Proteínas Sensíveis a N-Etilmaleimida/isolamento & purificação , Proteínas Sensíveis a N-Etilmaleimida/metabolismo , Complexo de Endopeptidases do Proteassoma/genética , Complexo de Endopeptidases do Proteassoma/isolamento & purificação , Ligação Proteica , Multimerização Proteica , Proteínas Recombinantes/genética , Proteínas Recombinantes/isolamento & purificação , Proteínas Recombinantes/metabolismo , Proteínas SNARE/genética , Proteínas SNARE/isolamento & purificação , Imagem Individual de Molécula , Proteínas de Ligação a Fator Solúvel Sensível a N-Etilmaleimida/genética , Proteínas de Ligação a Fator Solúvel Sensível a N-Etilmaleimida/isolamento & purificação , Proteínas de Ligação a Fator Solúvel Sensível a N-Etilmaleimida/metabolismoRESUMO
We review the trade-offs between speed, fluctuations, and thermodynamic cost involved with biological processes in nonequilibrium states and discuss how optimal these processes are in light of the universal bound set by the thermodynamic uncertainty relation (TUR). The values of the uncertainty product Q of TUR, which can be used as a measure of the precision of enzymatic processes realized for a given thermodynamic cost, are suboptimal when the substrate concentration is at the Michaelis constant, and some of the key biological processes are found to work around this condition. We illustrate the utility of Q in assessing how close the molecular motors and biomass producing machineries are to the TUR bound, and for the cases of biomass production (or biological copying processes), we discuss how their optimality quantified in terms of Q is balanced with the error rate in the information transfer process. We also touch upon the trade-offs in other error-minimizing processes in biology, such as gene regulation and chaperone-assisted protein folding. A spectrum of Q recapitulating the biological processes surveyed here provides glimpses into how biological systems are evolved to optimize and balance the conflicting functional requirements.