Toggle Switch Research Articles

Cardiac contractility structure-activity relationship and ligand-receptor interactions; the discovery of unique and novel molecular switches in myosuppressin signaling.

Peptidergic signaling regulates cardiac contractility; thus, identifying molecular switches, ligand-receptor contacts, and antagonists aids in exploring the underlying mechanisms to influence health. Myosuppressin (MS), a decapeptide, diminishes cardiac contractility and gut motility. Myosuppressin binds to G protein-coupled receptor (GPCR) proteins. Two Drosophila melanogaster myosuppressin receptors (DrmMS-Rs) exist; however, no mechanism underlying MS-R activation is reported. We predicted DrmMS-Rs contained molecular switches that resembled those of Rhodopsin. Additionally, we believed DrmMS-DrmMS-R1 and DrmMS-DrmMS-R2 interactions would reflect our structure-activity relationship (SAR) data. We hypothesized agonist- and antagonist-receptor contacts would differ from one another depending on activity. Lastly, we expected our study to apply to other species; we tested this hypothesis in Rhodnius prolixus, the Chagas disease vector. Searching DrmMS-Rs for molecular switches led to the discovery of a unique ionic lock and a novel 3–6 lock, as well as transmission and tyrosine toggle switches. The DrmMS-DrmMS-R1 and DrmMS-DrmMS-R2 contacts suggested tissue-specific signaling existed, which was in line with our SAR data. We identified R. prolixus (Rhp)MS-R and discovered it, too, contained the unique myosuppressin ionic lock and novel 3–6 lock found in DrmMS-Rs as well as transmission and tyrosine toggle switches. Further, these motifs were present in red flour beetle, common water flea, honey bee, domestic silkworm, and termite MS-Rs. RhpMS and DrmMS decreased R. prolixus cardiac contractility dose dependently with EC50 values of 140 nM and 50 nM. Based on ligand-receptor contacts, we designed RhpMS analogs believed to be an active core and antagonist; testing on heart confirmed these predictions. The active core docking mimicked RhpMS, however, the antagonist did not. Together, these data were consistent with the unique ionic lock, novel 3–6 lock, transmission switch, and tyrosine toggle switch being involved in mechanisms underlying TM movement and MS-R activation, and the ability of MS agonists and antagonists to influence physiology.

Jagged–Delta asymmetry in Notch signaling can give rise to a Sender/Receiver hybrid phenotype

Notch signaling pathway mediates cell-fate determination during embryonic development, wound healing, and tumorigenesis. This pathway is activated when the ligand Delta or the ligand Jagged of one cell interacts with the Notch receptor of its neighboring cell, releasing the Notch Intracellular Domain (NICD) that activates many downstream target genes. NICD affects ligand production asymmetrically--it represses Delta, but activates Jagged. Although the dynamical role of Notch-Jagged signaling remains elusive, it is widely recognized that Notch-Delta signaling behaves as an intercellular toggle switch, giving rise to two distinct fates that neighboring cells adopt--Sender (high ligand, low receptor) and Receiver (low ligand, high receptor). Here, we devise a specific theoretical framework that incorporates both Delta and Jagged in Notch signaling circuit to explore the functional role of Jagged in cell-fate determination. We find that the asymmetric effect of NICD renders the circuit to behave as a three-way switch, giving rise to an additional state--a hybrid Sender/Receiver (medium ligand, medium receptor). This phenotype allows neighboring cells to both send and receive signals, thereby attaining similar fates. We also show that due to the asymmetric effect of the glycosyltransferase Fringe, different outcomes are generated depending on which ligand is dominant: Delta-mediated signaling drives neighboring cells to have an opposite fate; Jagged-mediated signaling drives the cell to maintain a similar fate to that of its neighbor. We elucidate the role of Jagged in cell-fate determination and discuss its possible implications in understanding tumor-stroma cross-talk, which frequently entails Notch-Jagged communication.

On stability analysis of genetic regulatory networks represented by delay-differential equations

The purpose of this note is to give a short presentation of a general method for the stability analysis of the steady-states of genetic regulatory networks represented by delay- differential equations. Two complementary ways are investigated: a frequency domain approach which applies to linearized models and gives necessary and sufficient conditions for the local steady-state stability, a Lyapunov approach derived from the viewpoint of hyperbolic PDE systems which gives sufficient conditions for global stability. These methods are illustrated with the example of the “toggle switch”.

An insight into antagonist binding and induced conformational dynamics of class B GPCR corticotropin-releasing factor receptor 1.

The human corticotropin-releasing factor receptor type 1 (CRF1R) is a class B G-protein-coupled receptor (GPCR), which mediates the response to stress and has been considered as a drug target for depression and anxiety. Based on the CRF1R-antagonist crystal structure, we study the binding mechanism of two distinct antagonists, CP-376395 and MTIP, and the dynamics behaviors of CRF1R induced by an antagonist binding. Key residues interacting with both antagonists and residues specifically binding to one of them are identified. Both antagonists interact with Asn283, Phe203, Met206, Leu280, Tyr316, Leu323, Leu287, Phe284, Val279, Leu319, Phe207, Gly210 and Phe362. CP-376395 specifically binds to Glu209 and Phe160, while MTIP specifically binds to Leu320, Leu213, Ile290, Phe162 and Val313. The total binding free energy of MTIP is lower than that of CP-376395; this is consistent with the experimental observation that MTIP shows higher binding affinity than CP-376395. The conformational dynamic behaviors of antagonist bound holo-CRF1R were found to be different from those of apo-CRF1R in three aspects: (i) the "ionic lock" between side chains of Arg151 in TM2 and Glu209 in TM3 was broken in apo-CRF1R, but was formed in holo-CRF1Rs; (ii) Phe203 in TM3 and Tyr327 in TM6 were in close proximity to each other in apo-CRF1R, while they were far apart resulting from the shift of TM6 in holo-CRF1Rs; and (iii) the "rotamer toggle switch", Tyr327/Leu323/Phe284, adopted different rotameric conformations in apo-CRF1R and holo-CRF1Rs. We hope that our results could be helpful in further development of the drug design of CRF1R.

Noise Treatment in Models of Genetic Switches

Mathematical modeling plays a key role in understanding and characterization of critical chemical processes underlying the dynamics of cellular decision-making. Deterministic modeling of relevant processes in complex genetic networks through a set of biochemical reactions is generally thought to predict an average kinetic behavior. Stochastic kinetic methods, accounting for random fluctuations, become essential to characterize intrinsic heterogeneity due to low copy numbers and noisy environments present in these systems. While in certain regulatory constructs, it has been shown that a fully discrete stochastic treatment of fluctuations through the Chemical Master Equation yields multi-stability when deterministic treatment predicts monostability; deterministic or continuous approaches continues to be the most widespread method for modeling the behavior of cell populations. We explore stochastic variability in cellular dynamics through a varied treatment of intrinsic noise, the randomness arising either at the level of a single reaction, single molecule or as a drift in concentration of the involved species. Our study involves modeling of a genetic toggle switch which is a set of two mutually repressing genes, acting as a cellular “memory device” during cell differentiation process, deciding the final cell fate. We simulate the complex switching dynamics between the multi-attractor states in these systems through direct sampling using continuous stochastic approaches Langevin dynamics and Fokker Plank equation as well as discrete stochastic methods Gillespie's Stochastic Simulation Algorithm and numerical solution of the Chemical Master Equation. The stochastic trajectories obtained through numerical simulations not only unveil the complex dynamics leading to multi-stability, they also help explore rigorously the variations, if any, in the dynamics of transitions. Our results can further be used to compare the statistics of switching events and hence to benchmark the various computational methods available to model stochasticity in such systems.

Web-based software tool for constraint-based design specification of synthetic biological systems.

miniEugene provides computational support for solving combinatorial design problems, enabling users to specify and enumerate designs for novel biological systems based on sets of biological constraints. This technical note presents a brief tutorial for biologists and software engineers in the field of synthetic biology on how to use miniEugene. After reading this technical note, users should know which biological constraints are available in miniEugene, understand the syntax and semantics of these constraints, and be able to follow a step-by-step guide to specify the design of a classical synthetic biological system-the genetic toggle switch.1 We also provide links and references to more information on the miniEugene web application and the integration of the miniEugene software library into sophisticated Computer-Aided Design (CAD) tools for synthetic biology ( www.eugenecad.org ).

Noises-induced toggle switch and stability in a gene regulation network

It is well-known that noises are inevitable in gene regulatory networks due to the low-copy numbers of molecules and environmental fluctuations. In this paper, we investigate the stationary probability distribution (SPD) between both low (OFF state) and high (ON state) protein levels and mean first passage time (MFPT) in an abstract model of the Myc/E2F/miR-17-92 network presented by Aguda et al., PNAS 105, 19678 (2008), where the gene expression is assumed to be disturbed simultaneously by intrinsic and extrinsic noises that were correlated. Our results show that (i) the OFF state is enhanced by the extrinsic noise (D), while the ON state is enhanced by the intrinsic noise (Q) or cross-correlation between two noises (λ); (ii) for the cases of negative or no cross-correlation (λ⩽0.0), the increase of the noise intensity (D or Q) leads to a decline of the MFPT and enhances the probability of toggle switch to the OFF state; (iii) but for the case of positive cross-correlation (λ>0.0), the MFPT as a function of the noise intensity (D or Q) exhibits a maximum, this maximum for MFPT identifies the characteristic of noise enhanced stability of the ON state and (iv) the cross-correlation between two noises can enhance stability of the ON state.

Piecewise linear and Boolean models of chemical reaction networks.

Models of biochemical networks are frequently complex and high-dimensional. Reduction methods that preserve important dynamical properties are therefore essential for their study. Interactions in biochemical networks are frequently modeled using Hill functions ([Formula: see text]). Reduced ODEs and Boolean approximations of such model networks have been studied extensively when the exponent [Formula: see text] is large. However, while the case of small constant [Formula: see text] appears in practice, it is not well understood. We provide a mathematical analysis of this limit and show that a reduction to a set of piecewise linear ODEs and Boolean networks can be mathematically justified. The piecewise linear systems have closed-form solutions that closely track those of the fully nonlinear model. The simpler, Boolean network can be used to study the qualitative behavior of the original system. We justify the reduction using geometric singular perturbation theory and compact convergence, and illustrate the results in network models of a toggle switch and an oscillator.

Period doubling induced by thermal noise amplification in genetic circuits.

Rhythms of life are dictated by oscillations, which take place in a wide rage of biological scales. In bacteria, for example, oscillations have been proven to control many fundamental processes, ranging from gene expression to cell divisions. In genetic circuits, oscillations originate from elemental block such as autorepressors and toggle switches, which produce robust and noise-free cycles with well defined frequency. In some circumstances, the oscillation period of biological functions may double, thus generating bistable behaviors whose ultimate origin is at the basis of intense investigations. Motivated by brain studies, we here study an “elemental” genetic circuit, where a simple nonlinear process interacts with a noisy environment. In the proposed system, nonlinearity naturally arises from the mechanism of cooperative stability, which regulates the concentration of a protein produced during a transcription process. In this elemental model, bistability results from the coherent amplification of environmental fluctuations due to a stochastic resonance of nonlinear origin. This suggests that the period doubling observed in many biological functions might result from the intrinsic interplay between nonlinearity and thermal noise.

W246(6.48) opens a gate for a continuous intrinsic water pathway during activation of the adenosine A2A receptor.

The question how G-protein-coupled receptors transduce an extracellular signal by a sequence of transmembrane conformational transitions into an intracellular response remains to be solved at molecular detail. Herein, we use molecular dynamics simulations to reveal distinct conformational transitions of the adenosine A2A receptor, and we found that the conserved W246(6.48) residue in transmembrane helix TM6 performs a key rotamer toggle switch. Agonist binding induces the sidechain of W246(6.48) to fluctuate between two distinct conformations enabling the diffusion of water molecules from the bulk into the center of the receptor. After passing the W246(6.48) gate, the internal water molecules induce another conserved residue, Y288(7.53), to switch to a distinct rotamer conformation establishing a continuous transmembrane water pathway. Further, structural changes of TM6 and TM7 induce local structural changes of the adjacent lipid bilayer.

W2466.48 Opens a Gate for a Continuous Intrinsic Water Pathway during Activation of the Adenosine A2A Receptor

AbstractThe question how G‐protein‐coupled receptors transduce an extracellular signal by a sequence of transmembrane conformational transitions into an intracellular response remains to be solved at molecular detail. Herein, we use molecular dynamics simulations to reveal distinct conformational transitions of the adenosine A2A receptor, and we found that the conserved W2466.48 residue in transmembrane helix TM6 performs a key rotamer toggle switch. Agonist binding induces the sidechain of W2466.48 to fluctuate between two distinct conformations enabling the diffusion of water molecules from the bulk into the center of the receptor. After passing the W2466.48 gate, the internal water molecules induce another conserved residue, Y2887.53, to switch to a distinct rotamer conformation establishing a continuous transmembrane water pathway. Further, structural changes of TM6 and TM7 induce local structural changes of the adjacent lipid bilayer.

A toggle switch of visual awareness?

Major clues to the human brain mechanisms of spatial attention and visual awareness have come from the syndrome of neglect, where patients ignore one half of space. A longstanding puzzle, though, is that neglect almost always comes from right-hemisphere damage, which suggests that the two sides of the brain play distinct roles. But tests of attention in healthy people have revealed only slight differences between the hemispheres. Here we show that major differences emerge if we look at the timing of brain activity in a task optimized to identify attentional functions. Using EEG to map cortical activity on a millisecond timescale, we found transient (20–30 ms) periods of interhemispheric competition, followed by short phases of marked right-sided activity in the ventral attentional network. Our data are the first to show interhemispheric interactions that, much like a toggle switch, quickly allocate neural resources to one or the other hemisphere.

Networks of coupled circuits: from a versatile toggle switch to collective coherent behavior.

We study the versatile performance of networks of coupled circuits. Each of these circuits is composed of a positive and a negative feedback loop in a motif that is frequently found in genetic and neural networks. When two of these circuits are coupled with mutual repression, the system can function as a toggle switch. The variety of its states can be controlled by two parameters as we demonstrate by a detailed bifurcation analysis. In the bistable regimes, switches between the coexisting attractors can be induced by noise. When we couple larger sets of these units, we numerically observe collective coherent modes of individual fixed-point and limit-cycle behavior. It is there that the monotonic change of a single bifurcation parameter allows one to control the onset and arrest of the synchronized oscillations. This mechanism may play a role in biological applications, in particular, in connection with the segmentation clock. While tuning the bifurcation parameter, also a variety of transient patterns emerges upon approaching the stationary states, in particular, a self-organized pacemaker in a completely uniformly equipped ensemble, so that the symmetry breaking happens dynamically.

Motif for controllable toggle switch in gene regulatory networks

Toggle switch as a common phenomenon in gene regulatory networks has been recognized important for biological functions. Despite much effort dedicated to understanding the toggle switch and designing synthetic biology circuit to achieve the biological function, we still lack a comprehensive understanding of the intrinsic dynamics behind such phenomenon and the minimum structure that is imperative for producing toggle switch. In this paper, we discover a minimum structure, a motif that enables a controllable toggle switch. In particular, the motif consists of a transformative double negative feedback loop (DNFL) that is regulated by an additional driver node. By enumerating all possible regulatory configurations from the driver node, we identify two types of motifs associated with the toggle switch that is captured by the existence of bistable states. The toggle switch is controllable in the sense that the gap between the bistable states is adjustable as determined by the regulatory strength from the driver nodes. We test the effect of the motifs in self-oscillating gene regulatory network (SON) with respect to the interplay between the motifs and the other genes, and find that the switching dynamics of the whole network can be successfully controlled insofar as the network contains a single motif. Our findings are important to uncover the underlying nonlinear dynamics of controllable toggle switch and can have implications in devising biology circuit in the field of synthetic biology.

CB2-Selective Cannabinoid Receptor Ligands: Synthesis, Pharmacological Evaluation, and Molecular Modeling Investigation of 1,8-Naphthyridin-2(1H)-one-3-carboxamides

We have recently identified 1,8-naphthyridin-2(1H)-one-3-carboxamide as a new scaffold very suitable for the development of new CB2 receptor potent and selective ligands. In this paper we describe a number of additional derivatives in which the same central scaffold has been variously functionalized in position 1 or 6. All new compounds showed high selectivity and affinity in the nanomolar range for the CB2 receptor. Furthermore, we found that their functional activity is controlled by the presence of the substituents at position C-6 of the naphthyridine scaffold. In fact, the introduction of substituents in this position determined a functionality switch from agonist to antagonists/inverse agonists. Finally, docking studies showed that the difference between the pharmacology of these ligands may be in the ability/inability to block the Toggle Switch W6.48(258) (χ1 g+ → trans) transition.

A bistable genetic switch based on designable DNA-binding domains.

Bistable switches are fundamental regulatory elements of complex systems, ranging from electronics to living cells. Designed genetic toggle switches have been constructed from pairs of natural transcriptional repressors wired to inhibit one another. The complexity of the engineered regulatory circuits can be increased using orthogonal transcriptional regulators based on designed DNA-binding domains. However, a mutual repressor-based toggle switch comprising DNA-binding domains of transcription-activator-like effectors (TALEs) did not support bistability in mammalian cells. Here, the challenge of engineering a bistable switch based on monomeric DNA-binding domains is solved via the introduction of a positive feedback loop composed of activators based on the same TALE domains as their opposing repressors and competition for the same DNA operator site. This design introduces nonlinearity and results in epigenetic bistability. This principle could be used to employ other monomeric DNA-binding domains such as CRISPR for applications ranging from reprogramming cells to building digital biological memory.

Regulated assembly and disassembly of the yeast telomerase quaternary complex

The enzyme telomerase, which elongates chromosome termini, is a critical factor in determining long-term cellular proliferation and tissue renewal. Hence, even small differences in telomerase levels can have substantial consequences for human health. In budding yeast, telomerase consists of the catalytic Est2 protein and two regulatory subunits (Est1 and Est3) in association with the TLC1 RNA, with each of the four subunits essential for in vivo telomerase function. We show here that a hierarchy of assembly and disassembly results in limiting amounts of the quaternary complex late in the cell cycle, following completion of DNA replication. The assembly pathway, which is driven by interaction of the Est3 telomerase subunit with a previously formed Est1-TLC1-Est2 preassembly complex, is highly regulated, involving Est3-binding sites on both Est2 and Est1 as well as an interface on Est3 itself that functions as a toggle switch. Telomerase subsequently disassembles by a mechanistically distinct pathway due to dissociation of the catalytic subunit from the complex in every cell cycle. The balance between the assembly and disassembly pathways, which dictate the levels of the active holoenzyme in the cell, reveals a novel mechanism by which telomerase (and hence telomere homeostasis) is regulated.

Investigating the functional implications of reinforcing feedback loops in transcriptional regulatory networks.

Transcription factors (TFs) and microRNAs (miRNAs) can jointly regulate transcriptional networks in the form of recurrent circuits or motifs. A motif can be divided into a feedforward loop (FFL) and a feedback loop (FBL). Incoherent FFLs have been the recent focus due to their potential to dampen gene expression noise in maintaining physiological norms. However, a cell is not only able to manage noise but also able to exploit it during development or tumorigenesis to initiate radical transformation such as cell differentiation or metastasis. A plausible mechanism may involve reinforcing FBLs (rFBLs), which amplify changes to a sufficient level in order to complete the state transition. To study the behaviour of rFBLs, we developed a novel theoretical framework based on biochemical kinetics. The proposed rFBL follows a parsimonious design, involving two TFs and two miRNAs. A simulation study based on our model suggested that a system with rFBLs is robust to only a certain level of fluctuation but prone to a complete paradigm shift when the change exceeds a threshold level. To investigate the natural occurrence of rFBLs, we performed a rigorous network motif analysis using a recently available TF/miRNA regulatory network from the Encyclopedia of DNA Elements (ENCODE). Our analysis suggested that the rFBL is significantly depleted in the observed network. Nonetheless, we identified 9 rFBL instances. Among them, we found a double-rFBL involving three TFs SUZ12/BCLAF1/ZBTB33 and three miRNAs miR-9/19a/129-5p, which together serve as an intriguing toggle switch between nerve development and telomere maintenance. Additionally, we investigated the interactions implicated in the rFBLs using expression profiles of cancer patients from The Cancer Genome Atlas (TCGA). Together, we provided a novel and comprehensive view of the profound impacts of rFBLs and highlighted several TFs and miRNAs as the leverage points for potential therapeutic targets in cancers due to their eminent roles in the identified rFBLs.

Switch dynamics for stochastic model of genetic toggle switch

Recently, more and more biological experiments have indicated that noise plays an important role in bistable systems, such as the case of the bimodal population distribution in the genetic toggle switch. In this paper, we further verify that noises in degradation rates can indeed induce switching in the genetic toggle switch. Meanwhile, we apply the theory of mean first passage time (MFPT) in high dimensional system to the above stochastic model. According to our assumption, the high order finite difference method is used to compute the MFPT (that the average time switching from one steady state to the other) and we find that the relationship between the MFPT and noise intensity is negative correlation. The result is also verified through another numerical simulation method.

Exact computation of probability landscape of stochastic networks of Single Input and Coupled Toggle Switch Modules.

Gene regulatory networks depict the interactions between genes, proteins, and other components of the cell. These interactions often are stochastic that can influence behavior of the cells. Discrete Chemical Master Equation (dCME) provides a general framework for understanding the stochastic nature of these networks. However solving dCME is challenging due to the enormous state space, one effective approach is to study the behavior of individual modules of the stochastic network. Here we used the finite buffer dCME method and directly calculated the exact steady state probability landscape for the two stochastic networks of Single Input and Coupled Toggle Switch Modules. The first example is a switch network consisting of three genes, and the second example is a double switching network consisting of four coupled genes. Our results show complex switching behavior of these networks can be quantified.