Showing papers on "Cooperativity published in 2018"

Cooperativity Principles in Self-Assembled Nanomedicine

Abstract: Nanomedicine is a discipline that applies nanoscience and nanotechnology principles to the prevention, diagnosis, and treatment of human diseases. Self-assembly of molecular components is becoming a common strategy in the design and syntheses of nanomaterials for biomedical applications. In both natural and synthetic self-assembled nanostructures, molecular cooperativity is emerging as an important hallmark. In many cases, interplay of many types of noncovalent interactions leads to dynamic nanosystems with emergent properties where the whole is bigger than the sum of the parts. In this review, we provide a comprehensive analysis of the cooperativity principles in multiple self-assembled nanostructures. We discuss the molecular origin and quantitative modeling of cooperative behaviors. In selected systems, we describe the examples on how to leverage molecular cooperativity to design nanomedicine with improved diagnostic precision and therapeutic efficacy in medicine.

A supramolecular lanthanide separation approach based on multivalent cooperative enhancement of metal ion selectivity.

Abstract: Multivalent cooperativity plays an important role in the supramolecular self-assembly process. Herein, we report a remarkable cooperative enhancement of both structural integrity and metal ion selectivity on metal-organic M4L4 tetrahedral cages self-assembled from a tris-tridentate ligand (L1) with a variety of metal ions spanning across the periodic table, including alkaline earth (CaII), transition (CdII), and all the lanthanide (LnIII) metal ions. All these M4L14 cages are stable to excess metal ions and ligands, which is in sharp contrast with the tridentate (L2) ligand and bis-tridentate (L3) ligand bearing the same coordination motif as L1. Moreover, high-precision metal ion self-sorting is observed during the mixed-metal self-assembly of tetrahedral M4L4 cages, but not on the M2L3 counterparts. Based on the strong cooperative metal ion self-recognition behavior of M4L4 cages, a supramolecular approach to lanthanide separation is demonstrated, offering a new design principle of next-generation extractants for highly efficient lanthanide separation.

Increasing spin crossover cooperativity in 2D Hofmann-type materials with guest molecule removal

Abstract: Molecule-based spin state switching materials that display ambient temperature transitions with accompanying wide thermal hysteresis offer an opportunity for electronic switching, data storage, and optical technologies but are rare in existence. Here, we present the first 2D Hofmann-type materials to exhibit the elusive combination of ambient temperature spin crossover with wide thermal hysteresis (ΔT = 50 and 65 K). Combined structural, magnetic, spectroscopic, and theoretical analyses show that the highly cooperative transition behaviours of these layered materials arise due to strong host–host interactions in their interdigitated lattices, which optimises long-range communication pathways. With the presence of water molecules in the interlayer pore space in the hydrated phases, competing host–host and host–guest interactions occur, whilst water removal dramatically increases the framework cooperativity, thus affording systematic insight into the structural features that favour optimal spin crossover properties.

Exploiting correlated molecular-dynamics networks to counteract enzyme activity-stability trade-off.

Abstract: The directed evolution of enzymes for improved activity or substrate specificity commonly leads to a trade-off in stability. We have identified an activity-stability trade-off and a loss in unfolding cooperativity for a variant (3M) of Escherichia coli transketolase (TK) engineered to accept aromatic substrates. Molecular dynamics simulations of 3M revealed increased flexibility in several interconnected active-site regions that also form part of the dimer interface. Mutating the newly flexible active-site residues to regain stability risked losing the new activity. We hypothesized that stabilizing mutations could be targeted to residues outside of the active site, whose dynamics were correlated with the newly flexible active-site residues. We previously stabilized WT TK by targeting mutations to highly flexible regions. These regions were much less flexible in 3M and would not have been selected a priori as targets using the same strategy based on flexibility alone. However, their dynamics were highly correlated with the newly flexible active-site regions of 3M. Introducing the previous mutations into 3M reestablished the WT level of stability and unfolding cooperativity, giving a 10.8-fold improved half-life at 55 °C, and increased midpoint and aggregation onset temperatures by 3 °C and 4.3 °C, respectively. Even the activity toward aromatic aldehydes increased up to threefold. Molecular dynamics simulations confirmed that the mutations rigidified the active-site via the correlated network. This work provides insights into the impact of rigidifying mutations within highly correlated dynamic networks that could also be useful for developing improved computational protein engineering strategies.

Achieving Strong Positive Cooperativity through Activating Weak Non‐Covalent Interactions

Abstract: Positive cooperativity achieved through activating weak non-covalent interactions is common in biological assemblies but is rarely observed in synthetic complexes. Two new molecular tubes have been synthesized and the syn isomer binds DABCO-based organic cations with high orientational selectivity. Surprisingly, the ternary complex with two hosts and one guest shows a high cooperativity factor (α=580), which is the highest reported for synthetic systems without involving ion-pairing interactions. The X-ray single-crystal structure revealed that the strong positive cooperativity likely originates from eight C-H⋅⋅⋅O hydrogen bonds between the two head-to-head-arranged syn tube molecules. These relatively weak hydrogen bonds were not observed in the free hosts and only emerged in the complex. Furthermore, this complex was used as a basic motif to construct a robust [2+2] cyclic assembly, thus demonstrating its potential in molecular self-assembly.

Nature of bonding and cooperativity in linear DMSO clusters: A DFT, AIM and NCI analysis.

Abstract: This study aims to cast light on the nature of interactions and cooperativity that exists in linear dimethyl sulfoxide (DMSO) clusters using dispersion corrected density functional theory. In the linear DMSO, DMSO molecules in the middle of the clusters are bound strongly than at the terminal. The plot of the total binding energy of the clusters vs the cluster size and mean polarizabilities vs cluster size shows an excellent linearity demonstrating the presence of cooperativity effect. The computed incremental binding energy of the clusters remains nearly constant, implying that DMSO addition at the terminal site can happen to form an infinite chain. In the linear clusters, two σ-hole at the terminal DMSO molecules were found and the value on it was found to increase with the increase in cluster size. The quantum theory of atoms in molecules topography shows the existence of hydrogen and SO⋯S type in linear tetramer and larger clusters. In the dimer and trimer SO⋯OS type of interaction exists. In 2D non-covalent interactions plot, additional peaks in the regions which contribute to the stabilization of the clusters were observed and it splits in the trimer and intensifies in the larger clusters. In the trimer and larger clusters in addition to the blue patches due to hydrogen bonds, additional, light blue patches were seen between the hydrogen atom of the methyl groups and the sulphur atom of the nearby DMSO molecule. Thus, in addition to the strong H-bonds, strong electrostatic interactions between the sulphur atom and methyl hydrogens exists in the linear clusters.

Membrane fluctuations and acidosis regulate cooperative binding of 'marker of self' protein CD47 with the macrophage checkpoint receptor SIRPα.

Abstract: Cell-cell interactions that result from membrane proteins binding weakly in trans can cause accumulations in cis that suggest cooperativity and thereby an acute sensitivity to environmental factors. The ubiquitous 'marker of self' protein CD47 binds weakly to SIRPα on macrophages, which leads to accumulation of SIRPα (also known as SHPS-1, CD172A and SIRPA) at phagocytic synapses and ultimately to inhibition of engulfment of 'self' cells - including cancer cells. We reconstituted this macrophage checkpoint with GFP-tagged CD47 on giant vesicles generated from plasma membranes and then imaged vesicles adhering to SIRPα immobilized on a surface. CD47 diffusion is impeded near the surface, and the binding-unbinding events reveal cooperative interactions as a concentration-dependent two-dimensional affinity. Membrane fluctuations out-of-plane link cooperativity to membrane flexibility with suppressed fluctuations in the vicinity of bound complexes. Slight acidity (pH 6) stiffens membranes, diminishes cooperative interactions and also reduces 'self' signaling of cancer cells in phagocytosis. Sensitivity of cell-cell interactions to microenvironmental factors - such as the acidity of tumors and other diseased or inflamed sites - can thus arise from the collective cooperative properties of flexible membranes.This article has an associated First Person interview with the first author of the paper.

Structural basis for reactivating the mutant TERT promoter by cooperative binding of p52 and ETS1

Abstract: Transcriptional factors ETS1/2 and p52 synergize downstream of non-canonical NF-κB signaling to drive reactivation of the -146C>T mutant TERT promoter in multiple cancer types, but the mechanism underlying this cooperativity remains unknown. Here we report the crystal structure of a ternary p52/ETS1/-146C>T TERT promoter complex. While p52 needs to associate with consensus κB sites on the DNA to function during non-canonical NF-κB signaling, we show that p52 can activate the -146C>T TERT promoter without binding DNA. Instead, p52 interacts with ETS1 to form a heterotetramer, counteracting autoinhibition of ETS1. Analogous to observations with the GABPA/GABPB heterotetramer, the native flanking ETS motifs are required for sustained activation of the -146C>T TERT promoter by the p52/ETS1 heterotetramer. These observations provide a unifying mechanism for transcriptional activation by GABP and ETS1, and suggest that genome-wide targets of non-canonical NF-κB signaling are not limited to those driven by consensus κB sequences.

Sequence and Surface Confinement Direct Cooperativity in Catalytic Precision Oligomers.

Abstract: Confinement and cooperativity are important design principles used by Nature to optimize catalytic activity in enzymes. In these biological systems, the precise sequence of the protein encodes for specific chain folding to preorganize critical amino acid side chains within defined binding pockets, allowing synergistic catalytic activation pathways to be expressed and triggered. Here we show that short synthetic precision oligomers with the optimal sequence of catalytic units, spatially arranged by dense surface grafting to form confined cooperative “pockets”, display an up to 5-fold activity improvement compared to a “mismatched” sequence or free oligomers using the (pyta)Cu/TEMPO/NMI-catalyzed aerobic selective oxidation of alcohols as a model reaction. We thus demonstrate that, in analogy with enzymes, sequence definition combined with surface grafting induce the optimized distribution, both radially (interchain) and axially (intrachain), of a catalytic triad, and that the impressive improvement of cata...

Multiple Binding Sites Contribute to the Mechanism of Mixed Agonistic and Positive Allosteric Modulators of the Cannabinoid CB1 Receptor.

Abstract: The cannabinoid CB1 receptor (CB1R) is an abundant metabotropic G-protein-coupled receptor that has been difficult to address therapeutically because of CNS side effects exerted by orthosteric drug candidates. Recent efforts have focused on developing allosteric modulators that target CB1R. Compounds from the recently discovered class of mixed agonistic and positive allosteric modulators (Ago-PAMs) based on 2-phenylindoles have shown promising functional and binding properties as CB1R ligands. Here, we identify binding modes of both the CP 55,940 agonist and GAT228, a 2-phenylindole allosteric modulator, by using our metadynamics simulation protocol, and quantify their affinity and cooperativity by atomistic simulations. We demonstrate the involvement of multiple adjunct binding sites in the Ago-PAM characteristics of the 2-phenylindole modulators and explain their ability to compete with orthosteric agonists at higher concentrations. We validate these results experimentally by showing the contribution of multiple sites on the allosteric binding of ZCZ011, another homologous member of the class, together with the orthosteric agonist.

A Copper-Peptoid as a Highly Stable, Efficient, and Reusable Homogeneous Water Oxidation Electrocatalyst

Abstract: Water electrolysis is among the simplest methods to generate hydrogen, which can be used as a clean and renewable energy source. Within this process, the oxidation of water into molecular oxygen is considered as the bottleneck reaction because it involves the transfer of four electrons toward the oxidation of a highly stable small molecule. Challenges in this area include the development of stable and effective electro- and photocatalysts that utilize readily available metal ions. Herein we report a copper–peptidomimetic complex as an electrocatalyst for water oxidation, which is both highly stable and efficient. Inspired by enzymatic catalysis, which is largely based on intramolecular cooperativity between a metal center and functional organic molecules located on one scaffold, we have designed and synthesized a peptoid trimer bearing a 2,2′-bipyridine (bipy) ligand, an −OH group, and a benzyl group. Both experimental and computational data reveal that binding of CuII to this peptoid in aqueous medium oc...

Membrane-Mediated Cooperativity of Proteins

Abstract: Besides direct protein–protein interactions, indirect interactions mediated by membranes play an important role for the assembly and cooperative function of proteins in membrane shaping and adhesion. The intricate shapes of biological membranes are generated by proteins that locally induce membrane curvature. Indirect curvature-mediated interactions between these proteins arise because the proteins jointly affect the bending energy of the membranes. These curvature-mediated interactions are attractive for crescent-shaped proteins and are a driving force in the assembly of the proteins during membrane tubulation. Membrane adhesion results from the binding of receptor and ligand proteins that are anchored in the apposing membranes. The binding of these proteins strongly depends on nanoscale shape fluctuations of the membranes, leading to a fluctuation-mediated binding cooperativity. A length mismatch between receptor–ligand complexes in membrane adhesion zones causes repulsive curvature-mediated interaction...

Quantification and origin of cooperativity: insights from density functional reactivity theory.

Abstract: Cooperativity is a widely used chemical concept whose existence is ubiquitous in chemical and biological systems but whose quantification is still controversial and origin much less appreciated. In this work, using the interaction energy of a molecular system, which is composed of multiple copies of a building block, we propose a quantitative measurement to evaluate the cooperativity effect. This quantification approach is then applied to six molecular systems, i.e., water cluster, argon cluster, protonated water cluster, zinc atom cluster, water cluster on top of a graphene sheet, and alpha helix of glycine amino acids, each with up to 20 copies of the building block. Cooperativity is seen in all these systems. Both positive and negative cooperativity effects are observed. Employing the two energy partition schemes in density functional theory and the information-theoretic quantities such as Shannon entropy, Fisher information, information gain, etc., we then examine the origin of the cooperativity effect for these systems. Strong linear correlations between the cooperativity measure and some of these theoretical quantities have been unveiled. With these correlations, we are able to quantitatively account for their origin of cooperativity. Our results show that the interactions governing the existence and validity of the cooperativity effect are complicated. An opposite mechanism in enthalpy–entropy compensation for positive and negative cooperativity has been unveiled. These results should provide new insights and understandings from a different viewpoint about the nature and origin of cooperativity to appreciate this vastly important chemical concept.

Elastically Collective Nonlinear Langevin Equation Theory of Glass-Forming Liquids: Transient Localization, Thermodynamic Mapping, and Cooperativity.

Abstract: We analyze multiple new issues concerning activated relaxation in glassy hard sphere fluids and molecular and polymer liquids based on the elastically collective nonlinear Langevin equation (ECNLE) theory. By invoking a high-temperature reference state, a near universality of the apparent dynamic localization length scale is predicted for liquids of widely varying fragility, a result that is relevant to recent simulation studies and quasi-elastic neutron-scattering measurements. In contrast, in the same format, a strongly nonuniversal behavior is found for the activation barrier that controls long-time relaxation. Two measures of cooperativity in the ECNLE theory are analyzed. A particle-level total displacement associated with the alpha relaxation event is found to be only of order 1–2 particle diameters and weakly increases with cooling. In contrast, an alternative cooperativity length is defined as the spatial scale required to essentially recover the full barrier and bulk alpha time. This length scale...

Molecular Basis of Aquaporin-7 Permeability Regulation by pH.

Abstract: The aquaglyceroporin AQP7, a family member of aquaporin membrane channels, facilitates the permeation of water and glycerol through cell membranes and is crucial for body lipid and energy homeostasis. Regulation of glycerol permeability via AQP7 is considered a promising therapeutic strategy towards fat-related metabolic complications. Here, we used a yeast aqy-null strain for heterologous expression and functional analysis of human AQP7 and investigated its regulation by pH. Using a combination of in vitro and in silico approaches, we found that AQP7 changes from fully permeable to virtually closed at acidic pH, and that Tyr135 and His165 facing the extracellular environment are crucial residues for channel permeability. Moreover, instead of reducing the pore size, the protonation of key residues changes AQP7’s protein surface electrostatic charges, which, in turn, may decrease glycerol’s binding affinity to the pore, resulting in decreased permeability. In addition, since some pH-sensitive residues are located at the monomer-monomer interface, decreased permeability may result from cooperativity between AQP7’s monomers. Considering the importance of glycerol permeation via AQP7 in multiple pathophysiological conditions, this mechanism of hAQP7 pH-regulation may help the design of selective modulators targeting aquaglyceroporin-related disorders.

Unravelling the mechanistic details of metal binding to mammalian metallothioneins from stoichiometric, kinetic, and binding affinity data

Abstract: Metallothioneins (MTs) are small, cysteine-rich proteins, found throughout Nature Their ability to bind a number of different metals with a range of stoichiometric ratios means that this protein family is critically important for essential metal (Zn2+ and Cu+) homeostasis, metal storage, metal donation to nascent metalloenzymes as well as heavy metal detoxification With its 20 cysteines, metallothionein is also considered to protect cells against oxidative stress MT has been studied by a large number of researchers over the last 6 decades using a variety of spectroscopic techniques The lack of distinguishing chromophores for the multitude of binding sites has made the evaluation of stoichiometric properties for different metals challenging Initially, only 113Cd-NMR spectroscopy could provide strong evidence for the proposed cluster formation of Cd-MT The extraordinary development of electrospray ionization mass spectrometry (ESI-MS), where all coexisting species in solution are observed, revolutionized MT research Prior to the use of ESI-MS data, a range of “magic numbers” representing metal-to-MT molar ratios were reported from optical spectroscopic studies The availability of ESI mass spectral data led to (i) the confirmation of cluster formation, (ii) a conceptual understanding of the cooperativity involved in multiple metal binding events, (iii) the presence of domain specificity between regions of the protein and (iv) mechanistic details involving both binding affinities and rate constants The kinetic experiments identified the presence of multiple individual binding sites, each with a unique rate constant and an analogous binding affinity The almost linear trend in rate constants as a function of bound As3+ provided a unique insight that became a critical step in the complete understanding of the mechanistic details of the metalation of MT To fully define the biological function of this sulfur-rich protein it is necessary to determine kinetic rate constants and binding affinities for the essential metals Recently, Zn2+ competition experiments between both of the isolated fragments (α and β) and the full-length protein (βα-MT 1a) as well as Zn2+ competition between βα-MT 1a and carbonic anhydrase were reported From these data, the trend in binding affinities and the values of the Kf of the 7 bimolecular reactions involved in metalation were determined From the analysis of ESI-MS data for Cu+ binding to βα-MT 1a at different pH-values, a trend in the 20 binding affinities for the complete metalation mechanism was reported This review details a personal view of the historical development of the determination of stoichiometry for metal binding, the structure of the binding sites, the rates of the metalation reactions and the underlying binding affinities for each metalation step We have attempted to summarize the experimental developments that led to the publication in May 2017 of the experimental determination of the 20 binding constants for the 20 sequential bimolecular reactions for Cu+ binding to the 20 Cys of apoMT as a function of pH that show the appearance and disappearance of clusters We report both published data and in a series of tables an assembly of stoichiometries, and equilibrium constants for Zn2+ and Cu+ for many different metallothioneins

Chalcogen bonding interactions in organic selenocyanates: from cooperativity to chelation

Abstract: Intermolecular chalcogen bonding interactions are identified in crystalline organic selenocyanates where a linear Se⋯NC interaction takes place, leading to the recurrent formation of chain-like motifs ⋯Se(R)–CN⋯Se(R)–CN⋯, stabilized by cooperativity. Analysis of 15 reported structures of such selenocyanates is complemented by the structural determinations of three other novel polytopic selenocyanates, namely 1,3,5-tris(selenocyanatomethyl)benzene (1a), 1,3,5-tris(selenocyanatomethyl)-2,4,6-trimethylbenzene (1b) and 1,2,4,5-tetrakis(selenocyanatomethyl)benzene (2). While the recurrent chain-like motifs with short and linear Se⋯N contacts are indeed observed in the pure compounds, solvates with DMF and AcOEt also demonstrate that the nitrile N atom can be easily displaced from the chalcogen bond by stronger Lewis bases such as carbonyl oxygen atoms, leading in the case of (2)·(DMF)2 to a chelating motif where two neighboring CH2–SeCN groups link to the same oxygen atom through Se⋯O interactions.

Spatial Coordination of Cooperativity in Silica-Supported Cu/TEMPO/Imidazole Catalytic Triad

Abstract: Multifunctional catalysts obtained by the covalent immobilization of discrete molecular species on porous supports represent a unique approach to emulate some of the design principle and performances of enzymes. However, it is decisive in such systems to control the stoichiometry, spatial distribution, and proximity between the grafted catalytic centers to satisfy the chemical and geometrical requirements for cooperativity. Here, we present strategies to optimize the activity of a catalytic triad on mesoporous silica particles in the representative aerobic oxidation of benzyl alcohol and show that, in contrast with the more-traditional mixed-monolayer approach, activity can be amplified by tuning the spatial distribution of the co-catalysts to maximize the probability of full synergistic pairings.

Switching from Negative-Cooperativity to No-Cooperativity in the Binding of Ion-Pair Dimers by a Bis(calix[4]pyrrole) Macrocycle

Abstract: We report the synthesis of a macrocyclic receptor containing two di-meso-phenylcalix[4]pyrrole units linked by two triazole spacers. The 1,4-substitution of the 1,2,3-triazole spacers conveys different binding affinities to the two heteroditopic binding sites. These features make the receptor an ideal candidate to investigate allosteric cooperativity in the binding of ion-pair dimers. We probed the interaction of tetraalkylammonium salts (TBA·Cl, TBA·OCN, and MTOA·Cl) with the tetra-heterotopic macrocyclic receptor in chloroform solution using 1H NMR spectroscopic titration experiments. The results obtained show that, at millimolar concentration, the addition of 2 equiv of the salt to the receptor’s solution induced the quantitative pairwise binding of the ion-pairs. The 2:1 (ion-pair:receptor) complexes feature different binding geometries and binding cooperativities depending on the nature of the alkylammonium cation. The binding geometries assigned to the complexes of the ion-pair dimers in solution ar...

A window of opportunity for cooperativity in the T cell receptor

Abstract: The T-cell antigen receptor (TCR) is pre-organised in oligomers, known as nanoclusters. Nanoclusters could provide a framework for inter-TCR cooperativity upon peptide antigen-major histocompatibility complex (pMHC) binding. Here we have used soluble pMHC oligomers in search for cooperativity effects along the plasma membrane plane. We find that initial binding events favour subsequent pMHC binding to additional TCRs, during a narrow temporal window. This behaviour can be explained by a 3-state model of TCR transition from Resting to Active, to a final Inhibited state. By disrupting nanoclusters and hampering the Active conformation, we show that TCR cooperativity is consistent with TCR nanoclusters adopting the Active state in a coordinated manner. Preferential binding of pMHC to the Active TCR at the immunological synapse suggests that there is a transient time frame for signal amplification in the TCR, allowing the T cells to keep track of antigen quantity and binding time.

Weak IgG self- and hetero-association characterized by fluorescence analytical ultracentrifugation.

Abstract: Weak protein–protein interactions may be important to binding cooperativity. A panel of seven fluorescently labeled tracer monoclonal IgG antibodies, differing in variable (V) and constant (C) region sequences, were sedimented in increasing concentrations of unlabeled IgGs of identical, similar, and different backgrounds. Weak IgG::IgG attractive interactions were detected and characterized by global analysis of the hydrodynamic nonideality coefficient, k s. The effects of salt concentration and temperature on k s suggest the interactions are predominantly enthalpic in origin. The interactions were found to be variable in strength, affected by both the variable and constant regions, but indiscriminate with respect to IgG subclass. Furthermore, weak attractive interactions were observed for all the mAbs with freshly purified human poly‐IgG. The universality of the weak interactions suggest that they may contribute to effector function cooperativity in the normal immune response, and we postulate that the generality of the interactions allows for a broader range of epitope spacing for complement activation. These studies demonstrate the utility of analytical ultracentrifuge fluorescence detection in measuring weak protein–protein interactions. It also shows the strength of global analysis of sedimentation velocity data by SEDANAL to extract hydrodynamic nonideality k s to characterize weak macromolecular interactions.