Conformational spread: the propagation of allosteric states in large multiprotein complexes

Determining subunit-subunit interaction from statistics of cryo-EM images: observation of nearest-neighbor coupling in a circadian clock protein complex

Biological processes are typically actuated by dynamic multi-subunit molecular complexes. However, interactions between subunits, which govern the functions of these complexes, are hard to measure directly. Here, we develop a general approach combining cryo-EM imaging technology and statistical modeling and apply it to study the hexameric clock protein KaiC in Cyanobacteria. By clustering millions of KaiC monomer images, we identify two major conformational states of KaiC monomers. We then classify the conformational states of (>160,000) KaiC hexamers by the thirteen distinct spatial arrangements of these two subunit states in the hexamer ring. We find that distributions of the thirteen hexamer conformational patterns for two KaiC phosphorylation mutants can be fitted quantitatively by an Ising model, which reveals a significant cooperativity between neighboring subunits with phosphorylation shifting the probability of subunit conformation. Our results show that a KaiC hexamer can respond in a switch-like manner to changes in its phosphorylation level.

Spatial biology of Ising-like synthetic genetic networks

BACKGROUND

Understanding how spatial patterns of gene expression emerge from the interaction of individual gene networks is a fundamental challenge in biology. Developing a synthetic experimental system with a common theoretical framework that captures the emergence of short- and long-range spatial correlations (and anti-correlations) from interacting gene networks could serve to uncover generic scaling properties of these ubiquitous phenomena.

RESULTS

Here, we combine synthetic biology, statistical mechanics models, and computational simulations to study the spatial behavior of synthetic gene networks (SGNs) in Escherichia coli quasi-2D colonies growing on hard agar surfaces. Guided by the combined mechanisms of the contact process lattice simulation and two-dimensional Ising model (CPIM), we describe the spatial behavior of bi-stable and chemically coupled SGNs that self-organize into patterns of long-range correlations with power-law scaling or short-range anti-correlations. These patterns, resembling ferromagnetic and anti-ferromagnetic configurations of the Ising model near critical points, maintain their scaling properties upon changes in growth rate and cell shape.

CONCLUSIONS

Our findings shed light on the spatial biology of coupled and bistable gene networks in growing cell populations. This emergent spatial behavior could provide insights into the study and engineering of self-organizing gene patterns in eukaryotic tissues and bacterial consortia.

The role of subunit cooperativity on ryanodine receptor 2 calcium signaling

The ryanodine receptor type 2 (RyR2) is composed of four subunits that control calcium (Ca) release in cardiac cells. RyR2 serves primarily as a Ca sensor and can respond to rapid sub-millisecond pulses of Ca while remaining shut at resting concentrations. However, it is not known how the four subunits interact for the RyR2 to function as an effective Ca sensor. To address this question, and to understand the role of subunit cooperativity in Ca-mediated signal transduction, we have developed a computational model of the RyR2 composed of four interacting subunits. We first analyze the statistical properties of a single RyR2 tetramer, where each subunit can exist in a closed or open conformation. Our findings indicate that the number of subunits in the open state is a crucial parameter that dictates RyR2 kinetics. We find that three or four open subunits are required for the RyR2 to harness cooperative interactions to respond to sub-millisecond changes in Ca, while at the same time remaining shut at the resting Ca levels in the cardiac cell. If the required number of open subunits is lowered to one or two, the RyR2 cannot serve as a robust Ca sensor, as the large cooperativity required to stabilize the closed state prevents channel activation. Using this four-subunit model, we analyze the kinetics of Ca release from a RyR2 cluster. We show that the closure of a cluster of RyR2 channels is highly sensitive to the balance of cooperative interactions between closed and open subunits. Based on this result, we analyze how specific interactions between RyR2 subunits can induce persistent Ca leak from the sarcoplasmic reticulum (SR), which is believed to be arrhythmogenic. Thus, these results provide a framework to analyze how a pharmacologic or genetic modification of RyR2 subunit cooperativity can induce abnormal Ca cycling that can potentially lead to life-threatening arrhythmias.

Understanding the separation of timescales in bacterial proteasome core particle assembly

The 20S proteasome core particle (CP) is a molecular machine that is a key component of cellular protein degradation pathways. Like other molecular machines, it is not synthesized in an active form but rather as a set of subunits that assemble into a functional complex. The CP is conserved across all domains of life and is composed of 28 subunits, 14 α and 14 β, arranged in four stacked seven-member rings (α7β7β7α7). While details of CP assembly vary across species, the final step in the assembly process is universally conserved: two half proteasomes (HPs; α7β7) dimerize to form the CP. In the bacterium Rhodococcus erythropolis, experiments have shown that the formation of the HP is completed within minutes, while the dimerization process takes hours. The N-terminal propeptide of the β subunit, which is autocatalytically cleaved off after CP formation, plays a key role in regulating this separation of timescales. However, the detailed molecular mechanism of how the propeptide achieves this regulation is unclear. In this work, we used molecular dynamics simulations to characterize HP conformations and found that the HP exists in two states: one where the propeptide interacts with key residues in the HP dimerization interface and likely blocks dimerization, and one where this interface is free. Furthermore, we found that a propeptide mutant that dimerizes extremely slowly is essentially always in the nondimerizable state, while the wild-type rapidly transitions between the two. Based on these simulations, we designed a propeptide mutant that favored the dimerizable state in molecular dynamics simulations. In vitro assembly experiments confirmed that this mutant dimerizes significantly faster than wild-type. Our work thus provides unprecedented insight into how this critical step in CP assembly is regulated, with implications both for efforts to inhibit proteasome assembly and for the evolution of hierarchical assembly pathways.

Bacterial Proprioception: Can a Bacterium Sense Its Movement?

The evolution of the bacterial flagellum gave rise to motility and repurposing of a signaling network, now termed the chemotaxis network, enabled biasing of cell movements. This made it possible for the bacterium to seek out favorable chemical environments. To enable chemotaxis, the chemotaxis network sensitively detects extracellular chemical stimuli and appropriately modulates flagellar functions. Additionally, the flagellar motor itself is capable of detecting mechanical stimuli and adapts its structure and function in response, likely triggering a transition from planktonic to surface-associated lifestyles. Recent work has shown a link between the flagellar motor's response to mechanical stimuli and the chemotactic output. Here, we elaborate on this link and discuss how it likely helps the cell sense and adapt to changes in its swimming speeds in different environments. We discuss the mechanism whereby the motor precisely tunes its chemotaxis output under different mechanical loads, analogous to proprioception in higher order organisms. We speculate on the roles bacterial proprioception might play in a variety of phenomena including the transition to surface-associated lifestyles such as swarming and biofilms.

Insights into Phosphorylation-Induced Protein Allostery and Conformational Dynamics of Glycogen Phosphorylase via Integrative Structural Mass Spectrometry and In Silico Modeling

Allosteric regulation plays a fundamental role in innumerable biological processes. Understanding its dynamic mechanism and impact at the molecular level is of great importance in disease diagnosis and drug discovery. Glycogen phosphorylase (GP) is a phosphoprotein responding to allosteric regulation and has significant biological importance to glycogen metabolism. Although the atomic structures of GP have been previously solved, the conformational dynamics of GP related to allostery regulation remain largely elusive due to its macromolecular size (∼196 kDa). Here, we integrated native top-down mass spectrometry (nTD-MS), hydrogen-deuterium exchange MS (HDX-MS), protection factor (PF) analysis, molecular dynamics (MD) simulations, and allostery signaling analysis to examine the structural basis and dynamics for the allosteric regulation of GP by phosphorylation. nTD-MS reveals differences in structural stability as well as oligomeric state between the unphosphorylated (GPb) and phosphorylated (GPa) forms. HDX-MS, PF analysis, and MD simulations further pinpoint the structural differences between GPb and GPa involving the binding interfaces (the N-terminal and tower-tower helices), catalytic site, and PLP-binding region. More importantly, it also allowed us to complete the missing link of the long-range communication process from the N-terminal tail to the catalytic site caused by phosphorylation. This integrative MS and in silico-based platform is highly complementary to biophysical approaches and yields valuable insights into protein structures and dynamic regulation.

Potential allosteric sites captured in glycolytic enzymes via residue-based network models: Phosphofructokinase, glyceraldehyde-3-phosphate dehydrogenase and pyruvate kinase

Likelihood of new allosteric sites for glycolytic enzymes, phosphofructokinase (PFK), glyceraldehyde-3-phosphate dehydrogenase (GADPH) and pyruvate kinase (PK) was evaluated for bacterial, parasitic and human species. Allosteric effect of a ligand binding at a site was revealed on the basis of low-frequency normal modes via C_α-harmonic residue network model. In bacterial PFK, perturbation of the proposed allosteric site outperformed the known allosteric one, producing a high amount of stabilization or reduced dynamics, on all catalytic regions. Another proposed allosteric spot at the dimer interface in parasitic PFK exhibited major stabilization effect on catalytic regions. In parasitic GADPH, the most desired allosteric response was observed upon perturbation of its tunnel region which incorporated key residues for functional regulation. Proposed allosteric site in bacterial PK produced a satisfactory allosteric response on all catalytic regions, whereas in human and parasitic PKs, a partial inhibition was observed. Residue network model based solely on contact topology identified the 'hub residues' with high betweenness tracing plausible allosteric communication pathways between distant functional sites. For both bacterial PFK and PK, proposed sites accommodated hub residues twice as much as the known allosteric site. Tunnel region in parasitic GADPH with the strongest allosteric effect among species, incorporated the highest number of hub residues. These results clearly suggest a one-to-one correspondence between the degree of allosteric effect and the number of hub residues in that perturbation site, which increases the likelihood of its allosteric nature.

Optimal ligand discrimination by asymmetric dimerization and turnover of interferon receptors

In multicellular organisms, antiviral defense mechanisms evoke a reliable collective immune response despite the noisy nature of biochemical communication between tissue cells. A molecular hub of this response, the interferon I receptor (IFNAR), discriminates between ligand types by their affinity regardless of concentration. To understand how ligand type can be decoded robustly by a single receptor, we frame ligand discrimination as an information-theoretic problem and systematically compare the major classes of receptor architectures: allosteric, homodimerizing, and heterodimerizing. We demonstrate that asymmetric heterodimers achieve the best discrimination power over the entire physiological range of local ligand concentrations. This design enables sensing of ligand presence and type, and it buffers against moderate concentration fluctuations. In addition, receptor turnover, which drives the receptor system out of thermodynamic equilibrium, allows alignment of activation points for ligands of different affinities and thereby makes ligand discrimination practically independent of concentration. IFNAR exhibits this optimal architecture, and our findings thus suggest that this specialized receptor can robustly decode digital messages carried by its different ligands.

Protein-Lipid Interplay at the Neuromuscular Junction

Many new structures of membrane proteins have been determined over the last decade, yet the nature of protein–lipid interplay has received scant attention. The postsynaptic membrane of the neuromuscular junction and Torpedo electrocytes has a regular architecture, opening an opportunity to illuminate how proteins and lipids act together in a native membrane setting. Cryo electron microscopy (Cryo-EM) images show that cholesterol segregates preferentially around the constituent ion channel, the nicotinic acetylcholine receptor, interacting with specific sites in both leaflets of the bilayer. In addition to maintaining the transmembrane α-helical architecture, cholesterol forms microdomains – bridges of rigid sterol groups that link one channel to the next. This article discusses the whole protein–lipid organization of the cholinergic postsynaptic membrane, its physiological implications and how the observed details relate to our current concept of the membrane structure. I suggest that cooperative interactions, facilitated by the regular protein–lipid arrangement, help to spread channel activation into regions distant from the sites of neurotransmitter release, thereby enhancing the postsynaptic response.

Investigating Conformational Dynamics and Allostery in the p53 DNA-Binding Domain Using Molecular Simulations

The p53 tumor suppressor is a multifaceted context-dependent protein, which is involved in multiple cellular pathways, with the ability to either keep the cells alive or to kill them through mechanisms such as apoptosis. To complicate this picture, cancer cells that express mutant p53 becomes addicted to the mutant activity, so that the mutant variant features a myriad of gain-of-function activities, opening different venues for therapy. This makes essential to think outside the box and apply new approaches to the study of p53 structure-(mis)function relationship to find new critical components of its pathway or to understand how known parts are interconnected, compete, or cooperate. In this context, I will here illustrate how to integrate different computational methods to the identification of possible allosteric effects transmitted from the DNA binding interface of p53 to regions for cofactor recruitment. The protocol can be extended to any other cases of study. Indeed, it does not necessarily apply only to the study of DNA-induced effects, but more broadly to the investigation of long-range effects induced by a biological partner that binds to a biomolecule of interest.

Protein-lipid architecture of a cholinergic postsynaptic membrane

The cholinergic postsynaptic membrane is an acetyl-choline receptor-rich membrane mediating fast chemical communication at the nerve-muscle synapse. Here, cryo-EM is used to examine the protein-lipid architecture of this membrane in tubular vesicles obtained from the (muscle-derived) electric organ of the Torpedo ray. As reported earlier, the helical arrangement of the protein component of the vesicles facilitates image averaging and enables us to determine how cholesterol and phospho-lipid molecules are distributed in the surrounding matrix, using headgroup size as a means to discriminate between the two kinds of lipid. It is shown that cholesterol segregates preferentially around the receptors in both leaflets of the lipid bilayer, interacting robustly with specific transmembrane sites and creating a network of bridging microdomains. Cholesterol interactions with the receptor are apparently essential for stabilizing and maintaining its physiological architecture, since the transmembrane structure contracts, involving displacements of the helices at the outer membrane surface by ∼2 Å (1-3 Å), when this lipid is extracted. The microdomains may promote cooperativity between neighbouring receptors, leading to an enhanced postsynaptic response.

Filament formation by metabolic enzymes-A new twist on regulation

Compartmentalization of metabolic enzymes through protein-protein interactions is an emerging mechanism for localizing and regulating metabolic activity. Self-assembly into linear filaments is a common strategy for cellular compartmentalization of enzymes. Polymerization is often driven by changes in the metabolic state of the cell, suggesting that it is a strategy for shifting metabolic flux in response to cellular demand. Although polymerization of metabolic enzymes is widespread, observed from bacteria to humans, we are just beginning to appreciate their role in regulating cellular metabolism. In most cases, one functional role of metabolic enzyme filaments is allosteric control of enzyme activity. Here, we highlight recent findings, providing insight into the structural and functional significance of filamentation of metabolic enzymes in cells.

Constraints and limitations on the transcriptional response downstream of the Bicoid morphogen gradient

The regulation of the hunchback promoter expression by the maternal Bicoid gradient has been studied as a model system in development for many years. Yet, at the level of quantitative agreement between data and theoretical models, even the first step of this regulation, transcription, continues to be challenging. This situation is slowly progressing, thanks to quantitative live-imaging techniques coupled to advanced statistical data analysis and modeling. Here, we outline the current state of our knowledge of this apparently "simple" step, highlighting the newly appreciated role of bursty transcription dynamics and its regulation.

Coupled structural transitions enable highly cooperative regulation of human CTPS2 filaments

Many enzymes assemble into defined oligomers, providing a mechanism for cooperatively regulating activity. Recent studies have described a mode of regulation in which enzyme activity is modulated by polymerization into large-scale filaments. Here we describe an ultrasensitive form of polymerization-based regulation employed by human CTP synthase 2 (CTPS2). Cryo-EM structures reveal that CTPS2 filaments dynamically switch between active and inactive forms in response to changes in substrate and product levels. Linking the conformational state of many CTPS2 subunits in a filament results in highly cooperative regulation, greatly exceeding the limits of cooperativity for the CTPS2 tetramer alone. The structures reveal a link between conformation and control of ammonia channeling between the enzyme’s active sites, and explain differences in regulation of human CTPS isoforms. This filament-based mechanism of enhanced cooperativity demonstrates how the widespread phenomenon of enzyme polymerization can be adapted to achieve different regulatory outcomes.

Chemotaxis as a navigation strategy to boost range expansion

Bacterial chemotaxis, the directed movement of cells along gradients of chemoattractants, is among the best-characterized subjects in molecular biology^1-10, but much less is known about its physiological roles¹¹. It is commonly seen as a starvation response when nutrients run out, or as an escape response from harmful situations^12-16. Here we identify an alternative role of chemotaxis by systematically examining the spatiotemporal dynamics of Escherichia coli in soft agar^12,17,18. Chemotaxis in nutrient-replete conditions promotes the expansion of bacterial populations into unoccupied territories well before nutrients run out in the current environment. Low levels of chemoattractants act as aroma-like cues in this process, establishing the direction and enhancing the speed of population movement along the self-generated attractant gradients. This process of navigated range expansion spreads faster and yields larger population gains than unguided expansion following the canonical Fisher-Kolmogorov dynamics^19,20 and is therefore a general strategy to promote population growth in spatially extended, nutrient-replete environments.

Spreading of perturbations in myosin group kinetics along actin filaments

Global changes in the state of spatially distributed systems can often be traced back to perturbations that arise locally. Whether such local perturbations grow into global changes depends on the system geometry and the spatial spreading of these perturbations. Here, we investigate how different spreading behaviors of local perturbations determine their global impact in 1-dimensional systems of different size. Specifically, we assessed sliding arrest events in in vitro motility assays where myosins propel actin, and simulated the underlying mechanochemistry of myosins that bind along the actin filament. We observed spontaneous sliding arrest events that occurred more frequently for shorter actin filaments. This observation could be explained by spontaneous local arrest of myosin kinetics that stabilizes once it spreads throughout an entire actin filament. When we introduced intermediate concentrations of the actin cross-linker filamin, longer actin was arrested more frequently. This observation was reproduced by simulations where filamin binding induces persistent local arrest of myosin kinetics, which subsequently spreads throughout the actin filament. A spin chain model with nearest-neighbor coupling reproduced key features of our experiments and simulations, thus extending to other linear systems with nearest-neighbor coupling the following conclusions: 1) perturbations that are persistent only once they spread throughout the system are more effective in smaller systems, and 2) perturbations that are persistent upon their establishment are more effective in larger systems. Beyond these general conclusions, our work also provides a theoretical model of collective myosin kinetics with a finite range of mechanical coupling along the actin filament.

Dynamics of a Protein Chain Motor Driving Helical Bacteria under Stress

The wall-less, helical bacterial genus Spiroplasma has a unique propulsion system; it is not driven by propeller-like flagella but by a membrane-bound, cytoplasmic, linear motor that consists of a contractile chain of identical proteins spanning the entire cell length. By a coordinated spread of conformational changes of the proteins, kinks propagate in pairs along the cell body. However, the mechanisms for the initiation or delay of kinks and their coordinated spread remain unclear. Here, we show how we manipulate the initiation of kinks, their propagation velocities, and the time between two kinks for a single cell trapped in an optical line potential. By interferometric three-dimensional shape tracking, we measured the cells' deformations in response to various external stress situations. We observed a significant dependency of force generation on the cells' local ligand concentrations (likely ATP) and ligand hydrolysis, which we altered in different ways. We developed a mechanistic, mathematical model based on Kramer's rates, describing the subsequent cooperative and conformational switching of the chain's proteins. The model reproduces our experimental observations and can explain deformation characteristics even when the motor is driven to its extreme. Nature has invented a set of minimalistic mechanical driving concepts. To understand or even rebuild them, it is essential to reveal the molecular mechanisms of such protein chain motors, which need only two components-coupled proteins and ligands-to function.

Transferring information without distortion

Despite employing diverse molecular mechanisms, many different cell signaling systems avoid losing information by transmitting it in a linear manner.

The ASIC3/P2X3 cognate receptor is a pain-relevant and ligand-gated cationic channel

Two subclasses of acid-sensing ion channels (ASIC3) and of ATP-sensitive P2X receptors (P2X3Rs) show a partially overlapping expression in sensory neurons. Here we report that both recombinant and native receptors interact with each other in multiple ways. Current measurements with the patch-clamp technique prove that ASIC3 stimulation strongly inhibits the P2X3R current partly by a Ca²⁺-dependent mechanism. The proton-binding site is critical for this effect and the two receptor channels appear to switch their ionic permeabilities during activation. Co-immunoprecipation proves the close association of the two protein structures. BN-PAGE and SDS-PAGE analysis is also best reconciled with the view that ASIC3 and P2X3Rs form a multiprotein structure. Finally, in vivo measurements in rats reveal the summation of pH and purinergically induced pain. In conclusion, the receptor subunits do not appear to form a heteromeric channel, but tightly associate with each other to form a protein complex, mediating unidirectional inhibition.

Two subclasses of ligand-gated ion channels (ASIC3 and P2X3) are both present at sensory neurons and might be therefore subject to receptor crosstalk. Here authors use electrophysiology, biochemistry and co-immunoprecipitation to show that the two ion channels interact and affect P2X3 currents.

Cooperative mechanosensitivity and allostery of focal adhesion clusters

We analyse the role of cooperative interaction between neighbouring adhesion-mechanosensor complexes by constructing an Ising-like Hamiltonian describing the free energy of cell adhesion on a substrate as a lattice of 3-state mechanosensing sites involving focal adhesion kinase (FAK). We use a Monte Carlo stochastic algorithm to find equilibrium configurations of these mechanosensors in two representative geometries: on a 1D ring representing the rim of a cell on a flat surface, and a 2D bounded surface representing the whole area of cell contact with a flat surface. The level of FAK activation depends on the pulling force applied to the individual FAK-integrin via actin-myosin contractile networks, and the details of the coupling between individual sensors in a cluster. Strong coupling is shown to make the FAK sensors experience a sharp on-off behaviour in their activation, while at low coupling the activation/autoinhibition transition occurs over a broad range of pulling force. We find that the activation/autoinhibition transition of FAK in the 2D system with strong coupling occurs with a hysteresis, the width of which depends on the rate of change of force. The effect of introducing a regulating protein (such as Src) in a limited quantity to control FAK activation is explored, and visualizations of clustering in both topologies are presented. In particular the results on the bounded 2D surface indicate that clustering of active FAK occurs preferentially at the boundary, in agreement with experimental observations of focal adhesions in cells.

Reversible unfolding of infectious prion assemblies reveals the existence of an oligomeric elementary brick

Mammalian prions, the pathogens that cause transmissible spongiform encephalopathies, propagate by self-perpetuating the structural information stored in the abnormally folded, aggregated conformer (PrP^Sc) of the host-encoded prion protein (PrP^C). To date, no structural model related to prion assembly organization satisfactorily describes how strain-specified structural information is encoded and by which mechanism this information is transferred to PrP^C. To achieve progress on this issue, we correlated the PrP^Sc quaternary structural transition from three distinct prion strains during unfolding and refolding with their templating activity. We reveal the existence of a mesoscopic organization in PrP^Sc through the packing of a highly stable oligomeric elementary subunit (suPrP), in which the strain structural determinant (SSD) is encoded. Once kinetically trapped, this elementary subunit reversibly loses all replicative information. We demonstrate that acquisition of the templating interface and infectivity requires structural rearrangement of suPrP, in concert with its condensation. The existence of such an elementary brick scales down the SSD support to a small oligomer and provide a basis of reflexion for prion templating process and propagation.

Prions are self-propagating assemblies with all necessary and sufficient replicative information stored in the 3D structure of the misfolded form of PrP called PrP^Sc. Since the emergence of the prion theory in the 80s, many attempts have been done to identify prion replicative information at molecular scale. Different models have been constructed based on a broad panel of experimental observations and some of them predict the existence of periodic elements constituting prion assemblies. Here, by using partial unfolding approaches, we trapped an oligomeric conformer that we called suPrP, which could constitute the elementary brick of prion assemblies. Once isolated, this elementary brick is devoid of infectivity. However, it becomes infectious once condensated into larger assemblies. The identification of the elementary PrP building block provides a new structural basis for understanding prion replicative information storage and spreading.

A model of cell surface receptor aggregation

In this paper we construct and analyze a model of cell receptor aggregation. Experiments have shown that receptors in an aggregated state have greatly reduced mobility. We model the effects of this reduced mobility with a density dependent diffusion and study the impact of density dependent diffusion on aggregate formation in a one-dimensional domain. Critical values of receptor diffusivity and receptor activation are found and compared with numerical simulations. We find that the role of density dependant diffusion is quite limited in the formation of aggregate structures. In the case of receptor activation, the analytical results agree very well with the numerical calculations. Finally, we consider our model in higher dimensional domains. In this case our analysis is primarily numerical.

DNA-binding protects p53 from interactions with cofactors involved in transcription-independent functions

Binding-induced conformational changes of a protein at regions distant from the binding site may play crucial roles in protein function and regulation. The p53 tumour suppressor is an example of such an allosterically regulated protein. Little is known, however, about how DNA binding can affect distal sites for transcription factors. Furthermore, the molecular details of how a local perturbation is transmitted through a protein structure are generally elusive and occur on timescales hard to explore by simulations. Thus, we employed state-of-the-art enhanced sampling atomistic simulations to unveil DNA-induced effects on p53 structure and dynamics that modulate the recruitment of cofactors and the impact of phosphorylation at Ser215. We show that DNA interaction promotes a conformational change in a region 3 nm away from the DNA binding site. Specifically, binding to DNA increases the population of an occluded minor state at this distal site by more than 4-fold, whereas phosphorylation traps the protein in its major state. In the minor conformation, the interface of p53 that binds biological partners related to p53 transcription-independent functions is not accessible. Significantly, our study reveals a mechanism of DNA-mediated protection of p53 from interactions with partners involved in the p53 transcription-independent signalling. This also suggests that conformational dynamics is tightly related to p53 signalling.

Bidirectional Allosteric Communication between the ATP-Binding Site and the Regulatory PIF Pocket in PDK1 Protein Kinase

Allostery is a phenomenon observed in many proteins where binding of a macromolecular partner or a small-molecule ligand at one location leads to specific perturbations at a site not in direct contact with the region where the binding occurs. The list of proteins under allosteric regulation includes AGC protein kinases. AGC kinases have a conserved allosteric site, the phosphoinositide-dependent protein kinase 1 (PDK1)-interacting fragment (PIF) pocket, which regulates protein ATP-binding, activity, and interaction with substrates. In this study, we identify small molecules that bind to the ATP-binding site and affect the PIF pocket of AGC kinase family members, PDK1 and Aurora kinase. We describe the mechanistic details and show that although PDK1 and Aurora kinase inhibitors bind to the conserved ATP-binding site, they differentially modulate physiological interactions at the PIF-pocket site. Our work outlines a strategy for developing bidirectional small-molecule allosteric modulators of protein kinases and other signaling proteins.

Computational approaches to investigating allostery

Allosteric regulation plays a key role in many biological processes, such as signal transduction, transcriptional regulation, and many more. It is rooted in fundamental thermodynamic and dynamic properties of macromolecular systems that are still poorly understood and are moreover modulated by the cellular context. Here we review the computational approaches used in the investigation of allosteric processes in protein systems. We outline how the models of allostery have evolved from their initial formulation in the sixties to the current views, which more fully account for the roles of the thermodynamic and dynamic properties of the system. We then describe the major classes of computational approaches employed to elucidate the mechanisms of allostery, the insights they have provided, as well as their limitations. We complement this analysis by highlighting the role of computational approaches in promising practical applications, such as the engineering of regulatory modules and identifying allosteric binding sites.

The composition and organization of Drosophila heterochromatin are heterogeneous and dynamic

Heterochromatin is enriched for specific epigenetic factors including Heterochromatin Protein 1a (HP1a), and is essential for many organismal functions. To elucidate heterochromatin organization and regulation, we purified Drosophila melanogaster HP1a interactors, and performed a genome-wide RNAi screen to identify genes that impact HP1a levels or localization. The majority of the over four hundred putative HP1a interactors and regulators identified were previously unknown. We found that 13 of 16 tested candidates (83%) are required for gene silencing, providing a substantial increase in the number of identified components that impact heterochromatin properties. Surprisingly, image analysis revealed that although some HP1a interactors and regulators are broadly distributed within the heterochromatin domain, most localize to discrete subdomains that display dynamic localization patterns during the cell cycle. We conclude that heterochromatin composition and architecture is more spatially complex and dynamic than previously suggested, and propose that a network of subdomains regulates diverse heterochromatin functions.

The Gearbox of the Bacterial Flagellar Motor Switch

Switching of flagellar motor rotation sense dictates bacterial chemotaxis. Multi-subunit FliM-FliG rotor rings couple signal protein binding in FliM with reversal of a distant FliG C-terminal (FliG_C) helix involved in stator contacts. Subunit dynamics were examined in conformer ensembles generated by molecular simulations from the X-ray structures. Principal component analysis extracted collective motions. Interfacial loop immobilization by complex formation coupled elastic fluctuations of the FliM middle (FliM_M) and FliG middle (FliG_M) domains. Coevolved mutations captured interfacial dynamics as well as contacts. FliG_M rotation was amplified via two central hinges to the FliG_C helix. Intrinsic flexibility, reported by the FliG_MC ensembles, reconciled conformers with opposite FliG_C helix orientations. FliG domain stacking deformed the inter-domain linker and reduced flexibility; but conformational changes were not triggered by engineered linker deletions that cause a rotation-locked phenotype. These facts suggest that binary rotation states arise from conformational selection by stacking interactions.

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Switch complex exploits differential subunit stiffness for mechanical amplification

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Distinct rotor protein X-ray structures generate overlapping conformer ensembles

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Stacking constraints on a flexible helix linker could select diverse rotation states

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Non-contact elastic couplings at the subunit interface in the complex have coevolved

Conditions for duality between fluxes and concentrations in biochemical networks

Mathematical and computational modelling of biochemical networks is often done in terms of either the concentrations of molecular species or the fluxes of biochemical reactions. When is mathematical modelling from either perspective equivalent to the other? Mathematical duality translates concepts, theorems or mathematical structures into other concepts, theorems or structures, in a one-to-one manner. We present a novel stoichiometric condition that is necessary and sufficient for duality between unidirectional fluxes and concentrations. Our numerical experiments, with computational models derived from a range of genome-scale biochemical networks, suggest that this flux-concentration duality is a pervasive property of biochemical networks. We also provide a combinatorial characterisation that is sufficient to ensure flux-concentration duality.The condition prescribes that, for every two disjoint sets of molecular species, there is at least one reaction complex that involves species from only one of the two sets. When unidirectional fluxes and molecular species concentrations are dual vectors, this implies that the behaviour of the corresponding biochemical network can be described entirely in terms of either concentrations or unidirectional fluxes.

Statistical mechanics of the Huxley-Simmons model

The chemomechanical model of Huxley and Simmons (HS) [A. F. Huxley and R. M. Simmons, Nature 233, 533 (1971)NATUAS0028-083610.1038/233533a0] provides a paradigmatic description of mechanically induced collective conformational changes relevant in a variety of biological contexts, from muscles power stroke and hair cell gating to integrin binding and hairpin unzipping. We develop a statistical mechanical perspective on the HS model by exploiting a formal analogy with a paramagnetic Ising model. We first study the equilibrium HS model with a finite number of elements and compute explicitly its mechanical and thermal properties. To model kinetics, we derive a master equation and solve it for several loading protocols. The developed formalism is applicable to a broad range of allosteric systems with mean-field interactions.

Hysteresis in DNA compaction by Dps is described by an Ising model

In all organisms, DNA molecules are tightly compacted into a dynamic 3D nucleoprotein complex. In bacteria, this compaction is governed by the family of nucleoid-associated proteins (NAPs). Under conditions of stress and starvation, an NAP called Dps (DNA-binding protein from starved cells) becomes highly up-regulated and can massively reorganize the bacterial chromosome. Although static structures of Dps-DNA complexes have been documented, little is known about the dynamics of their assembly. Here, we use fluorescence microscopy and magnetic-tweezers measurements to resolve the process of DNA compaction by Dps. Real-time in vitro studies demonstrated a highly cooperative process of Dps binding characterized by an abrupt collapse of the DNA extension, even under applied tension. Surprisingly, we also discovered a reproducible hysteresis in the process of compaction and decompaction of the Dps-DNA complex. This hysteresis is extremely stable over hour-long timescales despite the rapid binding and dissociation rates of Dps. A modified Ising model is successfully applied to fit these kinetic features. We find that long-lived hysteresis arises naturally as a consequence of protein cooperativity in large complexes and provides a useful mechanism for cells to adopt unique epigenetic states.

Bilayer-thickness-mediated interactions between integral membrane proteins

Hydrophobic thickness mismatch between integral membrane proteins and the surrounding lipid bilayer can produce lipid bilayer thickness deformations. Experiment and theory have shown that protein-induced lipid bilayer thickness deformations can yield energetically favorable bilayer-mediated interactions between integral membrane proteins, and large-scale organization of integral membrane proteins into protein clusters in cell membranes. Within the continuum elasticity theory of membranes, the energy cost of protein-induced bilayer thickness deformations can be captured by considering compression and expansion of the bilayer hydrophobic core, membrane tension, and bilayer bending, resulting in biharmonic equilibrium equations describing the shape of lipid bilayers for a given set of bilayer-protein boundary conditions. Here we develop a combined analytic and numerical methodology for the solution of the equilibrium elastic equations associated with protein-induced lipid bilayer deformations. Our methodology allows accurate prediction of thickness-mediated protein interactions for arbitrary protein symmetries at arbitrary protein separations and relative orientations. We provide exact analytic solutions for cylindrical integral membrane proteins with constant and varying hydrophobic thickness, and develop perturbative analytic solutions for noncylindrical protein shapes. We complement these analytic solutions, and assess their accuracy, by developing both finite element and finite difference numerical solution schemes. We provide error estimates of our numerical solution schemes and systematically assess their convergence properties. Taken together, the work presented here puts into place an analytic and numerical framework which allows calculation of bilayer-mediated elastic interactions between integral membrane proteins for the complicated protein shapes suggested by structural biology and at the small protein separations most relevant for the crowded membrane environments provided by living cells.

Computational approaches to detect allosteric pathways in transmembrane molecular machines

Many of the functions of transmembrane proteins involved in signal processing and transduction across the cell membrane are determined by allosteric couplings that propagate the functional effects well beyond the original site of activation. Data gathered from breakthroughs in biochemistry, crystallography, and single molecule fluorescence have established a rich basis of information for the study of molecular mechanisms in the allosteric couplings of such transmembrane proteins. The mechanistic details of these couplings, many of which have therapeutic implications, however, have only become accessible in synergy with molecular modeling and simulations. Here, we review some recent computational approaches that analyze allosteric coupling networks (ACNs) in transmembrane proteins, and in particular the recently developed Protein Interaction Analyzer (PIA) designed to study ACNs in the structural ensembles sampled by molecular dynamics simulations. The power of these computational approaches in interrogating the functional mechanisms of transmembrane proteins is illustrated with selected examples of recent experimental and computational studies pursued synergistically in the investigation of secondary active transporters and GPCRs. This article is part of a Special Issue entitled: Membrane Proteins edited by J.C. Gumbart and Sergei Noskov.

Architecture and Function of Mechanosensitive Membrane Protein Lattices

Experiments have revealed that membrane proteins can form two-dimensional clusters with regular translational and orientational protein arrangements, which may allow cells to modulate protein function. However, the physical mechanisms yielding supramolecular organization and collective function of membrane proteins remain largely unknown. Here we show that bilayer-mediated elastic interactions between membrane proteins can yield regular and distinctive lattice architectures of protein clusters, and may provide a link between lattice architecture and lattice function. Using the mechanosensitive channel of large conductance (MscL) as a model system, we obtain relations between the shape of MscL and the supramolecular architecture of MscL lattices. We predict that the tetrameric and pentameric MscL symmetries observed in previous structural studies yield distinct lattice architectures of MscL clusters and that, in turn, these distinct MscL lattice architectures yield distinct lattice activation barriers. Our results suggest general physical mechanisms linking protein symmetry, the lattice architecture of membrane protein clusters, and the collective function of membrane protein lattices.

The principle of conformational signaling

Specific conformations of signaling proteins can serve as “signals” in signal transduction by being recognized by receptors.

Flagellar Motor Switching in Caulobacter Crescentus Obeys First Passage Time Statistics

A Caulobacter crescentus swarmer cell is propelled by a helical flagellum, which is rotated by a motor at its base. The motor alternates between rotating in clockwise and counterclockwise directions and spends variable intervals of time in each state. We measure the distributions of these intervals for cells either free swimming or tethered to a glass slide. A peak time of around one second is observed in the distributions for both motor directions with counterclockwise intervals more sharply peaked and clockwise intervals displaying a larger tail at long times. We show that distributions of rotation intervals fit first passage time statistics for a biased random walker and the dynamic binding of CheY-P to FliM motor subunits accounts for this behavior. Our results also suggest that the presence of multiple CheY proteins in C. crescentus may be responsible for differences between its switching behavior and that of the extensively studied E. coli.

Signaling and Adaptation Modulate the Dynamics of the Photosensoric Complex of Natronomonas pharaonis

Motile bacteria and archaea respond to chemical and physical stimuli seeking optimal conditions for survival. To this end transmembrane chemo- and photoreceptors organized in large arrays initiate signaling cascades and ultimately regulate the rotation of flagellar motors. To unravel the molecular mechanism of signaling in an archaeal phototaxis complex we performed coarse-grained molecular dynamics simulations of a trimer of receptor/transducer dimers, namely NpSRII/NpHtrII from Natronomonas pharaonis. Signaling is regulated by a reversible methylation mechanism called adaptation, which also influences the level of basal receptor activation. Mimicking two extreme methylation states in our simulations we found conformational changes for the transmembrane region of NpSRII/NpHtrII which resemble experimentally observed light-induced changes. Further downstream in the cytoplasmic domain of the transducer the signal propagates via distinct changes in the dynamics of HAMP1, HAMP2, the adaptation domain and the binding region for the kinase CheA, where conformational rearrangements were found to be subtle. Overall these observations suggest a signaling mechanism based on dynamic allostery resembling models previously proposed for E. coli chemoreceptors, indicating similar properties of signal transduction for archaeal photoreceptors and bacterial chemoreceptors.

Achaea and bacteria can “see” and “sniffle”, they have photo- and chemosensors that measure the environment. On the cell poles, these sensor proteins form large arrays built of several thousands of different receptors. The receptors comprise extracellular or transmembrane sensory domains and elongated homodimeric coiled-coil bundles, which transduce the signals from the membrane across ~20 nm to a conserved cytoplasmic signaling subdomain in an unknown manner. In our study we performed coarse-grained molecular dynamics simulations of the phototactic receptor/transducer complex from Natronomonas pharaonis. Comparing fully methylated and demethylated complexes reveals an interconversion between states of different dynamics along the coiled-coil bundle, which might represent the essential characteristics of the signal transfer from the membrane to the binding sites of the downstream kinase CheA.

Targets of drugs are generally, and targets of drugs having side effects are specifically good spreaders of human interactome perturbations

Network-based methods are playing an increasingly important role in drug design. Our main question in this paper was whether the efficiency of drug target proteins to spread perturbations in the human interactome is larger if the binding drugs have side effects, as compared to those which have no reported side effects. Our results showed that in general, drug targets were better spreaders of perturbations than non-target proteins, and in particular, targets of drugs with side effects were also better spreaders of perturbations than targets of drugs having no reported side effects in human protein-protein interaction networks. Colorectal cancer-related proteins were good spreaders and had a high centrality, while type 2 diabetes-related proteins showed an average spreading efficiency and had an average centrality in the human interactome. Moreover, the interactome-distance between drug targets and disease-related proteins was higher in diabetes than in colorectal cancer. Our results may help a better understanding of the network position and dynamics of drug targets and disease-related proteins, and may contribute to develop additional, network-based tests to increase the potential safety of drug candidates.

AIM for Allostery: Using the Ising Model to Understand Information Processing and Transmission in Allosteric Biomolecular Systems

In performing their biological functions, molecular machines must process and transmit information with high fidelity. Information transmission requires dynamic coupling between the conformations of discrete structural components within the protein positioned far from one another on the molecular scale. This type of biomolecular “action at a distance” is termed allostery. Although allostery is ubiquitous in biological regulation and signal transduction, its treatment in theoretical models has mostly eschewed quantitative descriptions involving the system's underlying structural components and their interactions. Here, we show how Ising models can be used to formulate an approach to allostery in a structural context of interactions between the constitutive components by building simple allosteric constructs we termed Allosteric Ising Models (AIMs). We introduce the use of AIMs in analytical and numerical calculations that relate thermodynamic descriptions of allostery to the structural context, and then show that many fundamental properties of allostery, such as the multiplicative property of parallel allosteric channels, are revealed from the analysis of such models. The power of exploring mechanistic structural models of allosteric function in more complex systems by using AIMs is demonstrated by building a model of allosteric signaling for an experimentally well-characterized asymmetric homodimer of the dopamine D2 receptor.

Dynamic membrane patterning, signal localization and polarity in living cells

We review the molecular and physical aspects of the dynamic localization of signaling molecules on the plasma membranes of living cells. At the nanoscale, clusters of receptors and signaling proteins play an essential role in the processing of extracellular signals. At the microscale, "soft" and highly dynamic signaling domains control the interaction of individual cells with their environment. At the multicellular scale, individual polarity patterns control the forces that shape multicellular aggregates and tissues.

The role of membrane-mediated interactions in the assembly and architecture of chemoreceptor lattices

In vivo fluorescence microscopy and electron cryo-tomography have revealed that chemoreceptors self-assemble into extended honeycomb lattices of chemoreceptor trimers with a well-defined relative orientation of trimers. The signaling response of the observed chemoreceptor lattices is remarkable for its extreme sensitivity, which relies crucially on cooperative interactions among chemoreceptor trimers. In common with other membrane proteins, chemoreceptor trimers are expected to deform the surrounding lipid bilayer, inducing membrane-mediated anisotropic interactions between neighboring trimers. Here we introduce a biophysical model of bilayer-chemoreceptor interactions, which allows us to quantify the role of membrane-mediated interactions in the assembly and architecture of chemoreceptor lattices. We find that, even in the absence of direct protein-protein interactions, membrane-mediated interactions can yield assembly of chemoreceptor lattices at very dilute trimer concentrations. The model correctly predicts the observed honeycomb architecture of chemoreceptor lattices as well as the observed relative orientation of chemoreceptor trimers, suggests a series of “gateway” states for chemoreceptor lattice assembly, and provides a simple mechanism for the localization of large chemoreceptor lattices to the cell poles. Our model of bilayer-chemoreceptor interactions also helps to explain the observed dependence of chemotactic signaling on lipid bilayer properties. Finally, we consider the possibility that membrane-mediated interactions might contribute to cooperativity among neighboring chemoreceptor trimers.

The chemotaxis system allows bacteria to respond to minute changes in chemical concentration, and serves as a paradigm for biological signal processing and the self-assembly of large protein lattices in living cells. The sensitivity of the chemotaxis system relies crucially on cooperative interactions among chemoreceptor trimers, which are organized into intricate honeycomb lattices. Chemoreceptors are membrane proteins and, hence, are expected to deform the surrounding lipid bilayer, leading to membrane-mediated interactions between chemoreceptor trimers. Using a biophysical model of bilayer-chemoreceptor interactions we show that the membrane-mediated interactions induced by chemoreceptor trimers provide a mechanism for the observed self-assembly of chemoreceptor lattices. We find that the directionality of membrane-mediated interactions between trimers complements protein-protein interactions in the stabilization of the observed honeycomb architecture of chemoreceptor lattices. Our results suggest that the symmetry of membrane protein complexes such as chemoreceptor trimers is reflected in the anisotropy of membrane-mediated interactions, yielding a general mechanism for the self-assembly of ordered protein lattices in cell membranes.

Subtype-specific mechanisms for functional interaction between α6β4* nicotinic acetylcholine receptors and P2X receptors

P2X receptors and nicotinic acetylcholine receptors (nAChRs) display functional and physical interactions in many cell types and heterologous expression systems, but interactions between α6β4-containing (α6β4*) nAChRs and P2X2 receptors and/or P2X3 receptors have not been fully characterized. We measured several types of crosstalk in oocytes coexpressing α6β4 nAChRs and P2X2, P2X3, or P2X2/3 receptors. A novel form of crosstalk occurs between α6β4 nAChRs and P2X2 receptors. P2X2 receptors were forced into a prolonged desensitized state upon activation by ATP through a mechanism that does not depend on the intracellular C terminus of the P2X2 receptors. Coexpression of α6β4 nAChRs with P2X3 receptors shifts the ATP dose-response relation to the right, even in the absence of acetylcholine (ACh). Moreover, currents become nonadditive when ACh and ATP are coapplied, as previously reported for other Cys-loop receptors interacting with P2X receptors, and this crosstalk is dependent on the presence of the P2X3 C-terminal domain. P2X2 receptors also functionally interact with α6β4β3 but through a different mechanism from α6β4. The interaction with P2X3 receptors is less pronounced for the α6β4β3 nAChR than the α6β4 nAChR. We also measured a functional interaction between the α6β4 nAChRs and the heteromeric P2X2/3 receptor. Experiments with the nAChR channel blocker mecamylamine on P2X2-α6β4 oocytes point to the loss of P2X2 channel activity during the crosstalk, whereas the ion channel pores of the P2X receptors were fully functional and unaltered by the receptor interaction for P2X2-α6β4β3, P2X2/3-α6β4, and P2X2/3-α6β4β3. These results may be relevant to dorsal root ganglion cells and to other neurons that coexpress these receptor subunits.

The ensemble nature of allostery

Allostery is the process by which biological macromolecules (mostly proteins) transmit the effect of binding at one site to another, often distal, functional site, allowing for regulation of activity. Recent experimental observations demonstrating that allostery can be facilitated by dynamic and intrinsically disordered proteins have resulted in a new paradigm for understanding allosteric mechanisms, which focuses on the conformational ensemble and the statistical nature of the interactions responsible for the transmission of information. Analysis of allosteric ensembles reveals a rich spectrum of regulatory strategies, as well as a framework to unify the description of allosteric mechanisms from different systems.

Precision sensing by two opposing gradient sensors: how does Escherichia coli find its preferred pH level?

It is essential for bacteria to find optimal conditions for their growth and survival. The optimal levels of certain environmental factors (such as pH and temperature) often correspond to some intermediate points of the respective gradients. This requires the ability of bacteria to navigate from both directions toward the optimum location and is distinct from the conventional unidirectional chemotactic strategy. Remarkably, Escherichia coli cells can perform such a precision sensing task in pH taxis by using the same chemotaxis machinery, but with opposite pH responses from two different chemoreceptors (Tar and Tsr). To understand bacterial pH sensing, we developed an Ising-type model for a mixed cluster of opposing receptors based on the push-pull mechanism. Our model can quantitatively explain experimental observations in pH taxis for various mutants and wild-type cells. We show how the preferred pH level depends on the relative abundance of the competing sensors and how the sensory activity regulates the behavioral response. Our model allows us to make quantitative predictions on signal integration of pH and chemoattractant stimuli. Our study reveals two general conditions and a robust push-pull scheme for precision sensing, which should be applicable in other adaptive sensory systems with opposing gradient sensors.

S6 peptide derived from KvAP channel shows cooperativity in gating on bilayer lipid membrane

Collective behavior of S6 peptide channels derived from KvAP (a bacterial potassium channel) incorporated in lipid bilayer membrane, has been investigated at various applied potentials through multi-channel electrophysiological experiments. The current versus time traces at any particular membrane potential show clear steps for sequential opening of the multi-channels. The minimum current (representing one-channel current) was found out from the amplitude histograms. Accordingly, the number of open channels corresponding to a particular open state was calculated. It was observed that the above-mentioned one channel current is higher than the corresponding single-channel current at most of the applied membrane potentials. Moreover, the difference between the single and one channel conductances is a nonlinear function of the membrane potential. We conclude that the S6 multi-channels show co-operative gating. Voltage relaxation studies support the above-mentioned conclusion.

Combined genetic and pharmacological inhibition of TRPV1 and P2X3 attenuates colorectal hypersensitivity and afferent sensitization

The ligand-gated channels transient receptor potential vanilloid 1 (TRPV1) and P2X3 have been reported to facilitate colorectal afferent neuron sensitization, thus contributing to organ hypersensitivity and pain. In the present study, we hypothesized that TRPV1 and P2X3 cooperate to modulate colorectal nociception and afferent sensitivity. To test this hypothesis, we employed TRPV1-P2X3 double knockout (TPDKO) mice and channel-selective pharmacological antagonists and evaluated combined channel contributions to behavioral responses to colorectal distension (CRD) and afferent fiber responses to colorectal stretch. Baseline responses to CRD were unexpectedly greater in TPDKO compared with control mice, but zymosan-produced CRD hypersensitivity was absent in TPDKO mice. Relative to control mice, proportions of mechanosensitive and -insensitive pelvic nerve afferent classes were not different in TPDKO mice. Responses of mucosal and serosal class afferents to mechanical probing were unaffected, whereas responses of muscular (but not muscular/mucosal) afferents to stretch were significantly attenuated in TPDKO mice; sensitization of both muscular and muscular/mucosal afferents by inflammatory soup was also significantly attenuated. In pharmacological studies, the TRPV1 antagonist A889425 and P2X3 antagonist TNP-ATP, alone and in combination, applied onto stretch-sensitive afferent endings attenuated responses to stretch; combined antagonism produced greater attenuation. In the aggregate, these observations suggest that 1) genetic manipulation of TRPV1 and P2X3 leads to reduction in colorectal mechanosensation peripherally and compensatory changes and/or disinhibition of other channels centrally, 2) combined pharmacological antagonism produces more robust attenuation of mechanosensation peripherally than does antagonism of either channel alone, and 3) the relative importance of these channels appears to be enhanced in colorectal hypersensitivity.

Structure, function, and on-off switching of a core unit contact between CheA kinase and CheW adaptor protein in the bacterial chemosensory array: A disulfide mapping and mutagenesis study

The ultrasensitive, ultrastable bacterial chemosensory array of Escherichia coli and Salmonella typhimurium is representative of the large, conserved family of sensory arrays that control the cellular chemotaxis of motile bacteria and Archaea. The core framework of the membrane-bound array is a lattice assembled from three components: a transmembrane receptor, a cytoplasmic His kinase (CheA), and a cytoplasmic adaptor protein (CheW). Structural studies in the field have revealed the global architecture of the array and complexes between specific components, but much remains to be learned about the essential protein-protein interfaces that define array structure and transmit signals between components. This study has focused on the structure, function, and on-off switching of a key contact between the kinase and adaptor proteins in the working, membrane-bound array. Specifically, the study addressed interface 1 in the putative kinase-adaptor ring where subdomain 1 of the kinase regulatory domain contacts subdomain 2 of the adaptor protein. Two independent approaches, disulfide mapping and site-directed Trp and Ala mutagenesis, were employed (i) to test the structural model of interface 1 and (ii) to investigate its functional roles in both stable kinase incorporation and receptor-regulated kinase on-off switching. Studies were conducted in functional, membrane-bound arrays or in live cells. The findings reveal that crystal structures of binary and ternary complexes accurately depict the native interface in its kinase-activating on state. Furthermore, the findings indicate that at least part of the interface becomes less closely packed in its kinase-inhibiting off state. Together, the evidence shows the interface has a dual structural and signaling function that is crucial for incorporation of the stable kinase into the array, for kinase activation in the array on state, and likely for attractant-triggered kinase on-off switching. A model is presented that describes the concerted transmission of a conformational signal among the receptor, the kinase regulatory domain, and the adaptor protein. In principle, this signal could spread out into the surrounding array via the kinase-adaptor ring, employing a series of alternating frozen-dynamic transitions that transmit low-energy attractant signals long distances.

The Mediator complex and transcription regulation

The Mediator complex is a multi-subunit assembly that appears to be required for regulating expression of most RNA polymerase II (pol II) transcripts, which include protein-coding and most non-coding RNA genes. Mediator and pol II function within the pre-initiation complex (PIC), which consists of Mediator, pol II, TFIIA, TFIIB, TFIID, TFIIE, TFIIF and TFIIH and is approximately 4.0 MDa in size. Mediator serves as a central scaffold within the PIC and helps regulate pol II activity in ways that remain poorly understood. Mediator is also generally targeted by sequence-specific, DNA-binding transcription factors (TFs) that work to control gene expression programs in response to developmental or environmental cues. At a basic level, Mediator functions by relaying signals from TFs directly to the pol II enzyme, thereby facilitating TF-dependent regulation of gene expression. Thus, Mediator is essential for converting biological inputs (communicated by TFs) to physiological responses (via changes in gene expression). In this review, we summarize an expansive body of research on the Mediator complex, with an emphasis on yeast and mammalian complexes. We focus on the basics that underlie Mediator function, such as its structure and subunit composition, and describe its broad regulatory influence on gene expression, ranging from chromatin architecture to transcription initiation and elongation, to mRNA processing. We also describe factors that influence Mediator structure and activity, including TFs, non-coding RNAs and the CDK8 module.