Showing papers on "Cooperativity published in 2013"

Modulation of allostery by protein intrinsic disorder

Abstract: Allostery is an intrinsic property of many globular proteins and enzymes that is indispensable for cellular regulatory and feedback mechanisms. Recent theoretical and empirical observations indicate that allostery is also manifest in intrinsically disordered proteins, which account for a substantial proportion of the proteome. Many intrinsically disordered proteins are promiscuous binders that interact with multiple partners and frequently function as molecular hubs in protein interaction networks. The adenovirus early region 1A (E1A) oncoprotein is a prime example of a molecular hub intrinsically disordered protein. E1A can induce marked epigenetic reprogramming of the cell within hours after infection, through interactions with a diverse set of partners that include key host regulators such as the general transcriptional coactivator CREB binding protein (CBP), its paralogue p300, and the retinoblastoma protein (pRb; also called RB1). Little is known about the allosteric effects at play in E1A-CBP-pRb interactions, or more generally in hub intrinsically disordered protein interaction networks. Here we used single-molecule fluorescence resonance energy transfer (smFRET) to study coupled binding and folding processes in the ternary E1A system. The low concentrations used in these high-sensitivity experiments proved to be essential for these studies, which are challenging owing to a combination of E1A aggregation propensity and high-affinity binding interactions. Our data revealed that E1A-CBP-pRb interactions have either positive or negative cooperativity, depending on the available E1A interaction sites. This striking cooperativity switch enables fine-tuning of the thermodynamic accessibility of the ternary versus binary E1A complexes, and may permit a context-specific tuning of associated downstream signalling outputs. Such a modulation of allosteric interactions is probably a common mechanism in molecular hub intrinsically disordered protein function.

Base Metal Catalysts for Photochemical C–H Borylation That Utilize Metal–Metal Cooperativity

Abstract: Heterobimetallic Cu–Fe and Zn–Fe complexes catalyze C–H borylation, a transformation that previously required noble metal catalysts. The optimal catalyst, (IPr)Cu-FeCp(CO)2, exhibits efficient activity at 5 mol% loading under photochemical conditions, shows only minimal decrease in activity upon reuse, and is able to catalyze borylation of a variety of arene substrates. Stoichiometric reactivity studies are consistent with a proposed mechanism that exploits metal–metal cooperativity and showcases bimetallic versions of the classical organometallic processes, oxidative addition and reductive elimination.

Activation of Water, Ammonia, and Other Small Molecules by PCcarbeneP Nickel Pincer Complexes

Abstract: Nickel complexes of a PC(carbene)P pincer ligand framework are described. Dehydrobromination of the precursor (PC(sp)(3)P)NiBr in the presence of a donor (PPh3 or NC(t)Bu) leads to the title complexes, which feature a rare nickel-carbene linkage as the pincer ligand anchor point. This strongly donating, nucleophilic carbene center engages in a variety of E-H bond activations (E = H, C, N, O), some of which are reversible. This represents a new mode of bond activation by ligand cooperativity in nickel pincer complexes.

Stepwise protein folding at near amino acid resolution by hydrogen exchange and mass spectrometry

Abstract: The kinetic folding of ribonuclease H was studied by hydrogen exchange (HX) pulse labeling with analysis by an advanced fragment separation mass spectrometry technology. The results show that folding proceeds through distinct intermediates in a stepwise pathway that sequentially incorporates cooperative native-like structural elements to build the native protein. Each step is seen as a concerted transition of one or more segments from an HX-unprotected to an HX-protected state. Deconvolution of the data to near amino acid resolution shows that each step corresponds to the folding of a secondary structural element of the native protein, termed a “foldon.” Each folded segment is retained through subsequent steps of foldon addition, revealing a stepwise buildup of the native structure via a single dominant pathway. Analysis of the pertinent literature suggests that this model is consistent with experimental results for many proteins and some current theoretical results. Two biophysical principles appear to dictate this behavior. The principle of cooperativity determines the central role of native-like foldon units. An interaction principle termed “sequential stabilization” based on native-like interfoldon interactions orders the pathway.

Cooperative Binding

Abstract: Molecular binding is an interaction between molecules that results in a stable association between those molecules. Cooperative binding occurs if the number of binding sites of a macromolecule that are occupied by a specific type of ligand is a nonlinear function of this ligand's concentration. This can be due, for instance, to an affinity for the ligand that depends on the amount of ligand bound. Cooperativity can be positive (supralinear) or negative (infralinear). Cooperative binding is most often observed in proteins, but nucleic acids can also exhibit cooperative binding, for instance of transcription factors. Cooperative binding has been shown to be the mechanism underlying a large range of biochemical and physiological processes.

Allosteric mechanisms can be distinguished using structural mass spectrometry

Abstract: The activity of many proteins, including metabolic enzymes, molecular machines, and ion channels, is often regulated by conformational changes that are induced or stabilized by ligand binding. In cases of multimeric proteins, such allosteric regulation has often been described by the concerted Monod–Wyman–Changeux and sequential Koshland–Nemethy–Filmer classic models of cooperativity. Despite the important functional implications of the mechanism of cooperativity, it has been impossible in many cases to distinguish between these various allosteric models using ensemble measurements of ligand binding in bulk protein solutions. Here, we demonstrate that structural MS offers a way to break this impasse by providing the full distribution of ligand-bound states of a protein complex. Given this distribution, it is possible to determine all the binding constants of a ligand to a highly multimeric cooperative system, and thereby infer its allosteric mechanism. Our approach to the dissection of allosteric mechanisms relies on advances in MS—which provide the required resolution of ligand-bound states—and in data analysis. We validated our approach using the well-characterized Escherichia coli chaperone GroEL, a double-heptameric ring containing 14 ATP binding sites, which has become a paradigm for molecular machines. The values of the 14 binding constants of ATP to GroEL were determined, and the ATP-loading pathway of the chaperone was characterized. The methodology and analyses presented here are directly applicable to numerous other cooperative systems and are therefore expected to promote further research on allosteric systems.

Transmembrane Halogen-Bonding Cascades

Abstract: Halogen bonds have recently been introduced as ideal to transport anions across lipid bilayer membranes. However, activities obtained with small transporters were not impressive, and cyclic arrays of strong halogen-bond donors above a calix[4]arene scaffold gave even weaker activities. Here, we report that their linear alignment for anion hopping along transmembrane rigid-rod scaffolds gives excellent activities with an unprecedented cooperativity coefficient m = 3.37.

Artificial allosteric receptors.

Abstract: Cooperative effects in the binding of two or more substrates to different binding sites of a receptor that are a result of a conformational change caused by the binding of the first substrate--also referred to as the effector--are called allosteric effects. In biological systems, allosteric regulation is a widely used mechanism to control the function of proteins and enzymes in cellular metabolism. Inspired by this a lot of efforts have been made in supramolecular chemistry to implement this concept into artificial systems to control functions as molecular recognition, signal amplification, or even reactivity and catalysis. This review gives an up-to-date overview over the different approaches that have been reported ever since the first examples from the late 1970s/early 1980s. It covers both homo- and heterotropic examples and is divided according to the nature of the effector--cationic, anionic, or neutral--effectors and systems that use combinations of those.

Characterization of the p53 cistrome--DNA binding cooperativity dissects p53's tumor suppressor functions.

Abstract: p53 protects us from cancer by transcriptionally regulating tumor suppressive programs designed to either prevent the development or clonal expansion of malignant cells. How p53 selects target genes in the genome in a context- and tissue-specific manner remains largely obscure. There is growing evidence that the ability of p53 to bind DNA in a cooperative manner prominently influences target gene selection with activation of the apoptosis program being completely dependent on DNA binding cooperativity. Here, we used ChIP-seq to comprehensively profile the cistrome of p53 mutants with reduced or increased cooperativity. The analysis highlighted a particular relevance of cooperativity for extending the p53 cistrome to non-canonical binding sequences characterized by deletions, spacer insertions and base mismatches. Furthermore, it revealed a striking functional separation of the cistrome on the basis of cooperativity; with low cooperativity genes being significantly enriched for cell cycle and high cooperativity genes for apoptotic functions. Importantly, expression of high but not low cooperativity genes was correlated with superior survival in breast cancer patients. Interestingly, in contrast to most p53-activated genes, p53-repressed genes did not commonly contain p53 binding elements. Nevertheless, both the degree of gene activation and repression were cooperativity-dependent, suggesting that p53-mediated gene repression is largely indirect and mediated by cooperativity-dependently transactivated gene products such as CDKN1A, E2F7 and non-coding RNAs. Since both activation of apoptosis genes with non-canonical response elements and repression of pro-survival genes are crucial for p53's apoptotic activity, the cistrome analysis comprehensively explains why p53-induced apoptosis, but not cell cycle arrest, strongly depends on the intermolecular cooperation of p53 molecules as a possible safeguard mechanism protecting from accidental cell killing.

Modulation of global low-frequency motions underlies allosteric regulation : demonstration in CRP/FNR family transcription factors.

Abstract: Allostery is a fundamental process by which ligand binding to a protein alters its activity at a distinct site. There is growing evidence that allosteric cooperativity can be communicated by modulation of protein dynamics without conformational change. The mechanisms, however, for communicating dynamic fluctuations between sites are debated. We provide a foundational theory for how allostery can occur as a function of low-frequency dynamics without a change in structure. We have generated coarse-grained models that describe the protein backbone motions of the CRP/FNR family transcription factors, CAP of Escherichia coli and GlxR of Corynebacterium glutamicum. The latter we demonstrate as a new exemplar for allostery without conformation change. We observe that binding the first molecule of cAMP ligand is correlated with modulation of the global normal modes and negative cooperativity for binding the second cAMP ligand without a change in mean structure. The theory makes key experimental predictions that are tested through an analysis of variant proteins by structural biology and isothermal calorimetry. Quantifying allostery as a free energy landscape revealed a protein “design space” that identified the inter- and intramolecular regulatory parameters that frame CRP/FNR family allostery. Furthermore, through analyzing CAP variants from diverse species, we demonstrate an evolutionary selection pressure to conserve residues crucial for allosteric control. This finding provides a link between the position of CRP/FNR transcription factors within the allosteric free energy landscapes and evolutionary selection pressures. Our study therefore reveals significant features of the mechanistic basis for allostery. Changes in low-frequency dynamics correlate with allosteric effects on ligand binding without the requirement for a defined spatial pathway. In addition to evolving suitable three-dimensional structures, CRP/FNR family transcription factors have been selected to occupy a dynamic space that fine-tunes biological activity and thus establishes the means to engineer allosteric mechanisms driven by low-frequency dynamics.

Probing the Metabotropic Glutamate Receptor 5 (mGlu5) Positive Allosteric Modulator (PAM) Binding Pocket: Discovery of Point Mutations That Engender a “Molecular Switch” in PAM Pharmacology

Abstract: Positive allosteric modulation of metabotropic glutamate receptor subtype 5 (mGlu5) is a promising novel approach for the treatment of schizophrenia and cognitive disorders. Allosteric binding sites are topographically distinct from the endogenous ligand (orthosteric) binding site, allowing for co-occupation of a single receptor with the endogenous ligand and an allosteric modulator. Negative allosteric modulators (NAMs) inhibit and positive allosteric modulators (PAMs) enhance the affinity and/or efficacy of the orthosteric agonist. The molecular determinants that govern mGlu5 modulator affinity versus cooperativity are not well understood. Focusing on the modulators based on the acetylene scaffold, we sought to determine the molecular interactions that contribute to PAM versus NAM pharmacology. Generation of a comparative model of the transmembrane-spanning region of mGlu5 served as a tool to predict and interpret the impact of mutations in this region. Application of an operational model of allosterism allowed for determination of PAM and NAM affinity estimates at receptor constructs that possessed no detectable radioligand binding as well as delineation of effects on affinity versus cooperativity. Novel mutations within the transmembrane domain (TM) regions were identified that had differential effects on acetylene PAMs versus 2-methyl-6-(phenylethynyl)-pyridine, a prototypical NAM. Three conserved amino acids (Y658, T780, and S808) and two nonconserved residues (P654 and A809) were identified as key determinants of PAM activity. Interestingly, we identified two point mutations in TMs 6 and 7 that, when mutated, engender a mode switch in the pharmacology of certain PAMs.

Conditional Cooperativity of Toxin - Antitoxin Regulation Can Mediate Bistability between Growth and Dormancy

Abstract: Many toxin-antitoxin operons are regulated by the toxin/antitoxin ratio by mechanisms collectively coined "conditional cooperativity". Toxin and antitoxin form heteromers with different stoichiometric ratios, and the complex with the intermediate ratio works best as a transcription repressor. This allows transcription at low toxin level, strong repression at intermediate toxin level, and then again transcription at high toxin level. Such regulation has two interesting features; firstly, it provides a non-monotonous response to the concentration of one of the proteins, and secondly, it opens for ultra-sensitivity mediated by the sequestration of the functioning heteromers. We explore possible functions of conditional regulation in simple feedback motifs, and show that it can provide bistability for a wide range of parameters. We then demonstrate that the conditional cooperativity in toxin-antitoxin systems combined with the growth-inhibition activity of free toxin can mediate bistability between a growing state and a dormant state.

Combined Model of Intrinsic and Extrinsic Variability for Computational Network Design with Application to Synthetic Biology

Abstract: Biological systems are inherently variable, with their dynamics influenced by intrinsic and extrinsic sources. These systems are often only partially characterized, with large uncertainties about specific sources of extrinsic variability and biochemical properties. Moreover, it is not yet well understood how different sources of variability combine and affect biological systems in concert. To successfully design biomedical therapies or synthetic circuits with robust performance, it is crucial to account for uncertainty and effects of variability. Here we introduce an efficient modeling and simulation framework to study systems that are simultaneously subject to multiple sources of variability, and apply it to make design decisions on small genetic networks that play a role of basic design elements of synthetic circuits. Specifically, the framework was used to explore the effect of transcriptional and post-transcriptional autoregulation on fluctuations in protein expression in simple genetic networks. We found that autoregulation could either suppress or increase the output variability, depending on specific noise sources and network parameters. We showed that transcriptional autoregulation was more successful than post-transcriptional in suppressing variability across a wide range of intrinsic and extrinsic magnitudes and sources. We derived the following design principles to guide the design of circuits that best suppress variability: (i) high protein cooperativity and low miRNA cooperativity, (ii) imperfect complementarity between miRNA and mRNA was preferred to perfect complementarity, and (iii) correlated expression of mRNA and miRNA – for example, on the same transcript – was best for suppression of protein variability. Results further showed that correlations in kinetic parameters between cells affected the ability to suppress variability, and that variability in transient states did not necessarily follow the same principles as variability in the steady state. Our model and findings provide a general framework to guide design principles in synthetic biology.

Phosphorus as a simultaneous electron-pair acceptor in intermolecular P···N pnicogen bonds and electron-pair donor to Lewis acids.

Abstract: Ab initio MP2/aug’-cc-pVTZ calculations have been performed to investigate the structures and energies of binary complexes LA:PH2F and LA:PH3 and of ternary complexes LA:H2FP:NFH2 and LA:H3P:NH3 in which the pnicogen-bonded P atom also acts as an electron-pair donor to a Lewis acid (LA), for LA = BH3, NCH, ClH, FH, FCl, and HLi. Hydrogen bonds, halogen bonds, and dative covalent bonds are found at P in some cases, depending on the nature of the Lewis acid. HLi forms a lithium bond with P only in the binary complex HLi:PH3. The binding energies of ternary complexes exhibit a classical synergistic effect, although the computed cooperativity may be overestimated due to neglect of the interaction of the Lewis acid with NH2F or NH3 in some cases. The hydrogen-bonding Lewis acids appear to have little effect on the strength of the P···N bond, while the remaining Lewis acids strengthen the pnicogen bond. 31P absolute chemical shieldings increase in LA:H2FP:NFH2 complexes relative to the corresponding LA:PH2F com...

Structural basis for cooperativity of CRM1 export complex formation

Abstract: In eukaryotes, the nucleocytoplasmic transport of macromolecules is mainly mediated by soluble nuclear transport receptors of the karyopherin-β superfamily termed importins and exportins. The highly versatile exportin chromosome region maintenance 1 (CRM1) is essential for nuclear depletion of numerous structurally and functionally unrelated protein and ribonucleoprotein cargoes. CRM1 has been shown to adopt a toroidal structure in several functional transport complexes and was thought to maintain this conformation throughout the entire nucleocytoplasmic transport cycle. We solved crystal structures of free CRM1 from the thermophilic eukaryote Chaetomium thermophilum. Surprisingly, unbound CRM1 exhibits an overall extended and pitched superhelical conformation. The two regulatory regions, namely the acidic loop and the C-terminal α-helix, are dramatically repositioned in free CRM1 in comparison with the ternary CRM1–Ran–Snurportin1 export complex. Single-particle EM analysis demonstrates that, in a noncrystalline environment, free CRM1 exists in equilibrium between extended, superhelical and compact, ring-like conformations. Molecular dynamics simulations show that the C-terminal helix plays an important role in regulating the transition from an extended to a compact conformation and reveal how the binding site for nuclear export signals of cargoes is modulated by different CRM1 conformations. Combining these results, we propose a model for the cooperativity of CRM1 export complex assembly involving the long-range allosteric communication between the distant binding sites of GTP-bound Ran and cargo.

A General Model for Toxin-Antitoxin Module Dynamics Can Explain Persister Cell Formation in E. coli

Abstract: Toxin-Antitoxin modules are small operons involved in stress response and persister cell formation that encode a “toxin” and its corresponding neutralizing “antitoxin”. Regulation of these modules involves a complex mechanism known as conditional cooperativity, which is supposed to prevent unwanted toxin activation. Here we develop mathematical models for their regulation, based on published molecular and structural data, and parameterized using experimental data for F-plasmid ccdAB, bacteriophage P1 phd/doc and E. coli relBE. We show that the level of free toxin in the cell is mainly controlled through toxin sequestration in toxin-antitoxin complexes of various stoichiometry rather than by gene regulation. If the toxin translation rate exceeds twice the antitoxin translation rate, toxins accumulate in all cells. Conditional cooperativity and increasing the number of binding sites on the operator serves to reduce the metabolic burden of the cell by reducing the total amounts of proteins produced. Combining conditional cooperativity and bridging of antitoxins by toxins when bound to their operator sites allows creation of persister cells through rare, extreme stochastic spikes in the free toxin level. The amplitude of these spikes determines the duration of the persister state. Finally, increases in the antitoxin degradation rate and decreases in the bacterial growth rate cause a rise in the amount of persisters during nutritional stress.

Cooperativity of hydrogen and halogen bond interactions

Abstract: The cooperativity effects in the Cl−···HCCH···HF, Cl−···ClCCH···HF and F−···ClCCH···HF complexes are analyzed here. The results show that the formation of the hydrogen and halogen bonds is ruled by the same mechanisms and that the cooperativity enhances these interactions. The MP2(full)/6-311 ++G(d,p) calculations were performed for the above triads and the corresponding sub-units; dyads linked by the hydrogen or halogen bonds and monomers. The NEDA scheme of the decomposition of the interaction energy was applied here. It was found that for the halogen bonded systems, the most important is the polarization term of the energy of interaction while for the hydrogen bonds the charge transfer interaction energy and next the electrostatic contribution. The interaction between orbitals is also analyzed here in terms of the Natural Bond Orbitals method.

Cooperativity and Regulation in Biochemical Processes

Abstract: 1. Introducing the Fundamental Concept. 2. The Binding Isotherm (BI). 3. Adsorption on a Single Polymer with Conformation Changes Induced by the Binding Process. 4. Two-site Systems Direct and Indirect Cooperativity. 5. Three-site Systems Non-additivity and Long Range Correlations. 6. 7. Large Linear Systems of Binding Sites. 8. Regulatory Enzymes. 9. Solvent Effects on Cooperativity. 10. Appendices. Appendix A: Pair and triple correlations between events. Appendix B: Localization of the adsorbent molecules, and its effect on the binding isotherm. Appendix C: Transition from microstates to macrostates. Appendix D: First order correction to non-ideality of the ligand's reservoir. Appendix E: Relative slopes of the equilibrated and 'frozen in' BI's in a multi macrostate system. Appendix F: Spurious cooperativity in single-site systems. Appendix G: The relation between the binding isotherm and the titration curves for two-site systems. Appendix H: Synthetic data. Appendix I: A comment on nomenclature. Appendix J: Average binding constants and correlation functions. Appendix K: Utility function in binding systems.

Binding Affinities and Thermodynamics of Noncovalent Functionalization of Carbon Nanotubes with Surfactants

Abstract: Binding affinity and thermodynamic understanding between a surfactant and carbon nanotube is essential to develop various carbon nanotube applications. Flavin mononucleotide-wrapped carbon nanotubes showing a large redshift in optical signature were utilized to determine the binding affinity and related thermodynamic parameters of 12 different nanotube chiralities upon exchange with other surfactants. Determined from the midpoint of sigmoidal transition, the equilibrium constant (K), which is inversely proportional to the binding affinity of the initial surfactant-carbon nanotube, provided quantitative binding strengths of surfactants as SDBS > SC ≈ FMN > SDS, irrespective of electronic types of SWNTs. Binding affinity of metallic tubes is weaker than that of semiconducting tubes. The complex K patterns from semiconducting tubes show preference to certain SWNT chiralities and surfactant-specific cooperativity according to nanotube chirality. Controlling temperature was effective to modulate K values by 30...

Ligand binding and self-association cooperativity of β-lactoglobulin.

Abstract: Unlike most small globular proteins, lipocalins lack a compact hydrophobic core. Instead, they present a large central cavity that functions as the primary binding site for hydrophobic molecules. Not surprisingly, these proteins typically exhibit complex structural dynamics in solution, which is intricately modified by intermolecular recognition events. Although many lipocalins are monomeric, an increasing number of them have been proven to form oligomers. The coupling effects between self-association and ligand binding in these proteins are largely unknown. To address this issue, we have calorimetrically characterized the recognition of dodecyl sulfate by bovine β-lactoglobulin, which forms weak homodimers at neutral pH. A thermodynamic analysis based on coupled-equilibria revealed that dimerization exerts disparate effects on the ligand-binding capacity of β-lactoglobulin. Protein dimerization decreases ligand affinity (or, reciprocally, ligand binding promotes dimer dissociation). The two subunits in the dimer exhibit a positive, entropically driven cooperativity. To investigate the structural determinants of the interaction, the crystal structure of β-lactoglobulin bound to dodecyl sulfate was solved at 1.64 A resolution.

Side pockets provide the basis for a new mechanism of Kv channel–specific inhibition

Abstract: Most known small-molecule inhibitors of voltage-gated ion channels have poor subtype specificity because they interact with a highly conserved binding site in the central cavity. Using alanine-scanning mutagenesis, electrophysiological recordings and molecular modeling, we have identified a new drug-binding site in Kv1.x channels. We report that Psora-4 can discriminate between related Kv channel subtypes because, in addition to binding the central pore cavity, it binds a second, less conserved site located in side pockets formed by the backsides of S5 and S6, the S4-S5 linker, part of the voltage sensor and the pore helix. Simultaneous drug occupation of both binding sites results in an extremely stable nonconducting state that confers high affinity, cooperativity, use-dependence and selectivity to Psora-4 inhibition of Kv1.x channels. This new mechanism of inhibition represents a molecular basis for the development of a new class of allosteric and selective voltage-gated channel inhibitors.

Solution-Phase vs Surface-Phase Aptamer-Protein Affinity from a Label-Free Kinetic Biosensor

Abstract: Aptamers are selected DNA ligands that target biomolecules such as proteins. In recent years, they are showing an increasing interest as potential therapeutic agents or recognition elements in biosensor applications. In both cases, the need for characterizing the mating between the target and the aptamer either in solution or immobilized on a surface, is pressing. In this context, we have developed a kinetic biosensor made of micro-arrayed anti-thrombin aptamers to assess the kinetic parameters of this interaction. The binding of label-free thrombin on the biosensor was monitored in real-time by Surface Plasmon Resonance imaging. Remarkable performances were obtained for the quantification of thrombin without amplification (sub-nanomolar limit of detection and linear range of quantification to two orders of magnitude). The independent determinations of both the solution- and surface-phase affinities, respectively KDSol and KDSurf, revealed distinct values illustrating the importance of probes, targets or surface interactions in biosensors. Interestingly, KDSurf values depend on the aptamer grafting density and linearly extrapolate towards KDSol for highly diluted probes. This suggests a lesser impact of the surface compared to the probe or target cooperativity interactions since the latter decrease with a reduced grafting density.

SOD1 exhibits allosteric frustration to facilitate metal binding affinity

Abstract: Superoxide dismutase–1 (SOD1) is a ubiquitous, Cu and Zn binding, free-radical defense enzyme whose misfolding and aggregation play a potential key role in amyotrophic lateral sclerosis, an invariably fatal neurodegenerative disease Over 150 mutations in SOD1 have been identified with a familial form of the disease, but it is presently not clear what unifying features, if any, these mutants share to make them pathogenic Here, we develop several unique computational assays for probing the thermo-mechanical properties of both ALS-associated and rationally designed SOD1 variants Allosteric interaction-free energies between residues and metals are calculated, and a series of atomic force microscopy experiments are simulated with variable tether positions to quantify mechanical rigidity “fingerprints” for SOD1 variants Mechanical fingerprinting studies of a series of C-terminally truncated mutants, along with an analysis of equilibrium dynamic fluctuations while varying native constraints, potential energy change upon mutation, frustratometer analysis, and analysis of the coupling between local frustration and metal binding interactions for a glycine scan of 90 residues together, reveal that the apo protein is internally frustrated, that these internal stresses are partially relieved by mutation but at the expense of metal-binding affinity, and that the frustration of a residue is directly related to its role in binding metals This evidence points to apo SOD1 as a strained intermediate with “self-allostery” for high metal-binding affinity Thus, the prerequisites for the function of SOD1 as an antioxidant compete with apo state thermo-mechanical stability, increasing the susceptibility of the protein to misfold in the apo state

SERCA mutant E309Q binds two Ca(2+) ions but adopts a catalytically incompetent conformation.

Abstract: The sarco(endo)plasmic reticulum Ca 2+ ‐ATPase (SERCA) couples ATP hydrolysis to transport of Ca 2+ . This directed energy transfer requires cross‐talk between the two Ca 2+ sites and the phosphorylation site over 50 A distance. We have addressed the mechano‐structural basis for this intramolecular signal by analysing the structure and the functional properties of SERCA mutant E309Q. Glu 309 contributes to Ca 2+ coordination at site II, and a consensus has been that E309Q only binds Ca 2+ at site I. The crystal structure of E309Q in the presence of Ca 2+ and an ATP analogue, however, reveals two occupied Ca 2+ sites of a non‐catalytic Ca 2 E 1 state. Ca 2+ is bound with micromolar affinity by both Ca 2+ sites in E309Q, but without cooperativity. The Ca 2+ ‐bound mutant does phosphorylate from ATP, but at a very low maximal rate. Phosphorylation depends on the correct positioning of the A‐domain, requiring a shift of transmembrane segment M1 into an ‘up and kinked position’. This transition is impaired in the E309Q mutant, most likely due to a lack of charge neutralization and altered hydrogen binding capacities at Ca 2+ site II.