G-protein-coupled receptors (GPCRs) represent a ubiquitous membrane protein family and are important drug targets. Their diverse signaling pathways are driven by complex pharmacology arising from a ...conformational ensemble rarely captured by structural methods. Here, fluorine nuclear magnetic resonance spectroscopy (19F NMR) is used to delineate key functional states of the adenosine A2A receptor (A2AR) complexed with heterotrimeric G protein (Gαsβ1γ2) in a phospholipid membrane milieu. Analysis of A2AR spectra as a function of ligand, G protein, and nucleotide identifies an ensemble represented by inactive states, a G-protein-bound activation intermediate, and distinct nucleotide-free states associated with either partial- or full-agonist-driven activation. The Gβγ subunit is found to be critical in facilitating ligand-dependent allosteric transmission, as shown by 19F NMR, biochemical, and computational studies. The results provide a mechanistic basis for understanding basal signaling, efficacy, precoupling, and allostery in GPCRs.
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•19F NMR of the A2A receptor reveals a conformational ensemble in lipid bilayers•Binding of G protein stabilizes a precoupled activation intermediate•Two distinct active states facilitate nucleotide exchange by full or partial agonist•Gβγ is key in facilitating allosteric signal transmission within the ternary complex
Monitoring conformational ensembles of a GPCR along the entire activation pathway in lipid bilayer captures key receptor states associated with G protein coupling and uncovers the role of Gβγ in facilitating ligand-dependent allosteric signal transmission.
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GEOZS, IJS, IMTLJ, KILJ, KISLJ, NLZOH, NUK, OILJ, PNG, SAZU, SBCE, SBJE, UILJ, UL, UM, UPCLJ, UPUK, ZAGLJ, ZRSKP
Mapping the constellation of structural and dynamic changes concurrent with allosteric inhibitor binding to caspase‐7, also known as allosteric structure–activity relationships (ASARs), reveals the ...nexus between the active site and the remote allosteric pocket. These ASARs also elucidate the link between structure and catalytic power for caspase‐7. Our insights from exploration of caspase‐7 allostery offer a new path for navigating allosteric drug discovery. More information can be found in the Research Article by M. A. Spies and co‐workers (DOI: 10.1002/chem.202300872).
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BFBNIB, FZAB, GIS, IJS, KILJ, NLZOH, NUK, OILJ, SBCE, SBMB, UL, UM, UPUK
The protein NLRP3 and its complexes are associated with an array of inflammatory pathologies, among which neurodegenerative, autoimmune, and metabolic diseases. Targeting the NLRP3 inflammasome ...represents a promising strategy for easing the symptoms of pathologic neuroinflammation. When the inflammasome is activated, NLRP3 undergoes a conformational change triggering the production of pro-inflammatory cytokines IL-1β and IL-18, as well as cell death by pyroptosis. NLRP3 nucleotide-binding and oligomerization (NACHT) domain plays a crucial role in this function by binding and hydrolysing ATP and is primarily responsible, together with conformational transitions involving the PYD domain, for the complex-assembly process. Allosteric ligands proved able to induce NLRP3 inhibition.
Herein, we examine the origins of allosteric inhibition of NLRP3. Through the use of molecular dynamics (MD) simulations and advanced analysis methods, we provide molecular-level insights into how allosteric binding affects protein structure and dynamics, remodelling of the conformational ensembles populated by the protein, with key reverberations on how NLRP3 is preorganized for assembly and ultimately function. The data are used to develop a Machine Learning model to define the protein as Active or Inactive, only based on the analysis of its internal dynamics. We propose this model as a novel tool to select allosteric ligands.
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GEOZS, IJS, IMTLJ, KILJ, KISLJ, NLZOH, NUK, OILJ, PNG, SAZU, SBCE, SBJE, UILJ, UL, UM, UPCLJ, UPUK, ZAGLJ, ZRSKP
Protein–protein interactions often regulate the activity of protein kinases by allosterically modulating the conformation of the ATP-binding site. Bidirectional allostery implies that reverse ...modulation (i.e., from the ATP-binding site to the interaction and regulatory sites) must also be possible. Here, we review both the allosteric regulation of protein kinases and recent work describing how compounds binding at the ATP-binding site can promote or inhibit protein kinase interactions at regulatory sites via the reverse mechanism. Notably, the pharmaceutical industry has been developing compounds that bind to the ATP-binding site of protein kinases and potently disrupt protein–protein interactions between target protein kinases and their regulatory interacting partners. Learning to modulate allosteric processes will facilitate the development of protein–protein interaction modulators.
Allostery is widespread in protein kinases.Allostery is defined as bidirectional communication between the regulatory site and the active site in protein kinases.Compounds binding at the ATP-binding site of protein kinases can enhance or disrupt protein–protein interactions.Metabolites can bind to the ATP-binding site and can potentially modulate physiological protein kinase interactions.Understanding allostery at the molecular level will enable the rational design of drugs with the desired allosteric effects.
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GEOZS, IJS, IMTLJ, KILJ, KISLJ, NLZOH, NUK, OILJ, PNG, SAZU, SBCE, SBJE, UILJ, UL, UM, UPCLJ, UPUK, ZAGLJ, ZRSKP
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•Omnipresence of allostery in folds and functions.•Protein folds reveal conserved patterns of structure-based allosteric communication.•Function-specific allosteric signalling emerges ...via sequence divergence.•Repertoire of structural platforms for allosterically regulated functions.•Evolutionary-driven design of allosteric regulation.
Hand-in-hand work of physics and evolution delivered protein universe with diversity of forms, sizes, and functions. Pervasiveness and advantageous traits of allostery made it an important component of the protein function regulation, calling for thorough investigation of its structural determinants and evolution. Learning directly from nature, we explored here allosteric communication in several major folds and repeat proteins, including α/β and β-barrels, β-propellers, Ig-like fold, ankyrin and α/β leucine-rich repeat proteins, which provide structural platforms for many different enzymatic and signalling functions. We obtained a picture of conserved allosteric communication characteristic in different fold types, modifications of the structure-driven signalling patterns via sequence-determined divergence to specific functions, as well as emergence and potential diversification of allosteric regulation in multi-domain proteins and oligomeric assemblies. Our observations will be instrumental in facilitating the engineering and de novo design of proteins with allosterically regulated functions, including development of therapeutic biologics. In particular, results described here may guide the identification of the optimal structural platforms (e.g. fold type, size, and oligomerization states) and the types of diversifications/perturbations, such as mutations, effector binding, and order–disorder transition. The tunable allosteric linkage across distant regions can be used as a pivotal component in the design/engineering of modular biological systems beyond the traditional scaffolding function.
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GEOZS, IJS, IMTLJ, KILJ, KISLJ, NLZOH, NUK, OILJ, PNG, SAZU, SBCE, SBJE, UILJ, UL, UM, UPCLJ, UPUK, ZAGLJ, ZRSKP
The transcription factor CooA is a CRP/FNR (cAMP receptor protein/ fumarate and nitrate reductase) superfamily protein that uses heme to sense carbon monoxide (CO). Allosteric activation of CooA in ...response to CO binding is currently described as a series of discrete structural changes, without much consideration for the potential role of protein dynamics in the process of DNA binding. This work uses site-directed spin-label electron paramagnetic resonance spectroscopy (SDSL-EPR) to probe slow timescale (μs-ms) conformational dynamics of CooA with a redox-stable nitroxide spin label, and IR spectroscopy to probe the environment at the CO-bound heme. A series of cysteine substitution variants were created to selectively label CooA in key functional regions, the heme-binding domain, the 4/5-loop, the hinge region, and the DNA binding domain. The EPR spectra of labeled CooA variants are compared across three functional states: Fe(III) “locked off”, Fe(II)-CO “on”, and Fe(II)-CO bound to DNA. We observe changes in the multicomponent EPR spectra at each location; most notably in the hinge region and DNA binding domain, broadening the description of the CooA allosteric mechanism to include the role of protein dynamics in DNA binding. DNA-dependent changes in IR vibrational frequency and band broadening further suggest that there is conformational heterogeneity in the active WT protein and that DNA binding alters the environment of the heme-bound CO.
Dynamic protein motions throughout the allosteric mechanism of transcription factor CooA are studied with site-directed spin label electron paramagnetic resonance spectroscopy via nitroxide probes and by monitoring the IR vibrational frequency at heme-bound carbon monoxide. Display omitted
•Allosteric transcription factor CooA uses heme to sense CO.•Slow timescale conformational dynamics of CooA are monitored with two complimentary methods.•CooA variants show changes in protein dynamics in all regions of the protein, notably in the hinge.•Upon DNA binding, key functional regions of CooA experience changes in protein dynamics.•The conformational environment around heme-bound CO is altered upon DNA binding.
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GEOZS, IJS, IMTLJ, KILJ, KISLJ, NLZOH, NUK, OILJ, PNG, SAZU, SBCE, SBJE, UILJ, UL, UM, UPCLJ, UPUK, ZAGLJ, ZRSKP
9.
Periodic training of creeping solids Hexner, Daniel; Liu, Andrea J.; Nagel, Sidney R.
Proceedings of the National Academy of Sciences - PNAS,
11/2020, Volume:
117, Issue:
50
Journal Article
Peer reviewed
Significance
It is well appreciated that many disordered materials deform their shape irreversibly (plastically) under an external load (e.g., memory foam). Here, we show that this plasticity can be ...exploited to train materials to develop novel elastic responses by straining them periodically. By applying different periodic strains to a common viscoelastic material, we are able to design a number of different responses. These include a maximally negative Poisson’s ratio, bistable behavior, and nonlocal bond-specific responses. In contrast to computer-aided design, we rely on plasticity to self-organize the system in response to local stresses. This approach shows promise to achieve an unprecedented control over behavior at large strains well beyond the linear-response regime.
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BFBNIB, NMLJ, NUK, PNG, SAZU, UL, UM, UPUK
Universality of allosteric signaling in proteins, molecular machines, and receptors complemented by the great advantages of prospected allosteric drugs in the highly specific, non-competitive, and ...modulatory nature of their actions calls for deeper theoretical understanding of allosteric communication. We present a computational model that makes it possible to tackle the problem of modulating the energetics of protein allosteric communication. In the context of the energy landscape paradigm, allosteric signaling is always a result of perturbations, such as ligand binding, mutations, and intermolecular interactions. The calculation of local partition functions in the protein harmonic model with perturbations allows us to evaluate the energetics of allosteric communication at the single-residue level. In this framework, Allosteric Signaling Maps are proposed as a tool to exhaustively describe allosteric communication in the protein, to tune already existing signaling, and to design new elements of regulation for taking the protein activity under allosteric control.
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•Structure-based statistical mechanical model of allostery (SBSMMA)•Perturbations by allosteric ligands and mutations allow control of protein activity•The allosteric modulation range is a generic descriptor of the allosteric signaling•Allosteric signaling map gives exhaustive description of allosteric communication
Guarnera and Berezovsky propose a theoretical framework for achieving the comprehensive allosteric control over protein activity. They introduce the allosteric signaling maps, which exhaustively describe the protein allosteric communication at per-residue resolution, allowing the tuning of already existing signaling and the design of new elements of regulation.
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GEOZS, IJS, IMTLJ, KILJ, KISLJ, NLZOH, NUK, OILJ, PNG, SAZU, SBCE, SBJE, UILJ, UL, UM, UPCLJ, UPUK, ZAGLJ, ZRSKP
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