Perturbing dimer interactions and allosteric communication modulates the immunosuppressive activity of human galectin-7.

The design of allosteric modulators to control protein function is a key objective in drug discovery programs. Altering functionally essential allosteric residue networks provides unique protein family subtype specificity, minimizes unwanted off-target effects, and helps avert resistance acquisition typically plaguing drugs that target orthosteric sites. In this work, we used protein engineering and dimer interface mutations to positively and negatively modulate the immunosuppressive activity of the proapoptotic human galectin-7 (GAL-7). Using the PoPMuSiC and BeAtMuSiC algorithms, mutational sites and residue identity were computationally probed and predicted to either alter or stabilize the GAL-7 dimer interface. By designing a covalent disulfide bridge between protomers to control homodimer strength and stability, we demonstrate the importance of dimer interface perturbations on the allosteric network bridging the two opposite glycan-binding sites on GAL-7, resulting in control of induced apoptosis in Jurkat T cells. Molecular investigation of G16X GAL-7 variants using X-ray crystallography, biophysical, and computational characterization illuminates residues involved in dimer stability and allosteric communication, along with discrete long-range dynamic behaviors involving loops 1, 3, and 5. We show that perturbing the protein-protein interface between GAL-7 protomers can modulate its biological function, even when the overall structure and ligand-binding affinity remains unaltered. This study highlights new avenues for the design of galectin-specific modulators influencing both glycan-dependent and glycan-independent interactions.

Prevalence and mechanisms of azole resistance in clinical isolates of Aspergillus section Fumigati species in a Canadian tertiary care centre, 2000 to 2013.

OBJECTIVES: Azole resistance among Aspergillus fumigatus isolates is a growing concern worldwide. Induction of mutations during azole therapy, environment-acquired mutations caused by azole fungicides and intrinsic resistance of cryptic Fumigati species all contribute to the burden of resistance. However, there is a lack of data in Canada on this emerging threat. METHODS: To gain insights into the magnitude and mechanisms of resistance, a 14 year collection of Aspergillus section Fumigati comprising 999 isolates from 807 patients at a Montreal hospital was screened for azole resistance, and resistance mechanisms were investigated with the combined use of genome sequencing, 3D modelling and phenotypic efflux pump assays. RESULTS: Overall azole resistance was low (4/807 patients; 0.5%). A single azole-resistant A. fumigatus sensu stricto strain, isolated from a patient with pulmonary aspergillosis, displayed efflux-pump-mediated resistance. Three patients were colonized or infected with azole-resistant cryptic Fumigati species (one Aspergillus thermomutatus, one Aspergillus lentulus and one Aspergillus turcosus). Evidence is presented that azole resistance is efflux-pump-mediated in the A. turcosus isolate, but not in the A. lentulus and A. thermomutatus isolates. CONCLUSIONS: Azole resistance is rare in our geographic area and currently driven by cryptic Fumigati species. Continued surveillance of emergence of resistance is warranted.

Photoreleasable ligands to study intracrine angiotensin II signalling.

KEY POINTS: The renin-angiotensin system plays a key role in cardiovascular physiology and its overactivation has been implicated in the pathogenesis of several major cardiovascular diseases. There is growing evidence that angiotensin II (Ang-II) may function as an intracellular peptide to activate intracellular/nuclear receptors and their downstream signalling effectors independently of cell surface receptors. Current methods used to study intracrine Ang-II signalling are limited to indirect approaches because of a lack of selective intracellularly-acting probes. Here, we present novel photoreleasable Ang-II analogues used to probe intracellular actions with spatial and temporal precision. The photorelease of intracellular Ang-II causes nuclear and cytosolic calcium mobilization and initiates the de novo synthesis of RNA in cardiac cells, demonstrating the application of the method. ABSTRACT: Several lines of evidence suggest that intracellular angiotensin II (Ang-II) contributes to the regulation of cardiac contractility, renal salt reabsorption, vascular tone and metabolism; however, work on intracrine Ang-II signalling has been limited to indirect approaches because of a lack of selective intracellularly-acting probes. Here, we aimed to synthesize and characterize cell-permeant Ang-II analogues that are inactive without uncaging, but release active Ang-II upon exposure to a flash of UV-light, and act as novel tools for use in the study of intracrine Ang-II physiology. We prepared three novel caged Ang-II analogues, [Tyr(DMNB)(4)]Ang-II, Ang-II-ODMNB and [Tyr(DMNB)(4)]Ang-II-ODMNB, based upon the incorporation of the photolabile moiety 4,5-dimethoxy-2-nitrobenzyl (DMNB). Compared to Ang-II, the caged Ang-II analogues showed 2-3 orders of magnitude reduced affinity toward both angiotensin type-1 (AT1R) and type-2 (AT2R) receptors in competition binding assays, and greatly-reduced potency in contraction assays of rat thoracic aorta. After receiving UV-irradiation, all three caged Ang-II analogues released Ang-II and potently induced the contraction of rat thoracic aorta. [Tyr(DMNB)(4)]Ang-II showed the most rapid photolysis upon UV-irradiation and was the focus of subsequent characterization. Whereas Ang-II and photolysed [Tyr(DMNB)(4)]Ang-II increased ERK1/2 phosphorylation (via AT1R) and cGMP production (AT2R), caged [Tyr(DMNB)(4)]Ang-II did not. Cellular uptake of [Tyr(DMNB)(4)]Ang-II was 4-fold greater than that of Ang-II and significantly greater than uptake driven by the positive-control HIV TAT(48-60) peptide. Intracellular photolysis of [Tyr(DMNB)(4)]Ang-II induced an increase in nucleoplasmic Ca(2+) ([Ca(2+)]n), and initiated 18S rRNA and nuclear factor kappa B mRNA synthesis in adult cardiac cells. We conclude that caged Ang-II analogues represent powerful new tools for use in the selective study of intracrine signalling via Ang-II.

Design of a truncated cardiotoxin-I analogue with potent insulinotropic activity.

Insulin secretion by pancreatic ß-cells in response to glucose or other secretagogues is tightly coupled to membrane potential. Various studies have highlighted the prospect of enhancing insulin secretion in a glucose-dependent manner by blocking voltage-gated potassium channels (K(v)) and calcium-activated potassium channels (K(Ca)). Such strategy is expected to present a lower risk for hypoglycemic events compared to KATP channel blockers. Our group recently reported the discovery of a new insulinotropic agent, cardiotoxin-I (CTX-I), from the Naja kaouthia snake venom. In the present study, we report the design and synthesis of [Lys(52)]CTX-I(41-60) via structure-guided modification, a truncated, equipotent analogue of CTX-I, and demonstrate, using various pharmacological inhibitors, that this derivative probably exerts its action through Kv channels. This new analogue could represent a useful pharmacological tool to study ß-cell physiology or even open a new therapeutic avenue for the treatment of type 2 diabetes.

Development and pharmacological characterization of conformationally constrained urotensin II-related peptide agonists.

Urotensin II (UII) and its paralog peptide, urotensin II-related peptide (URP), exert not only common but also divergent actions through the activation of UT, a specific membrane-bound receptor that belongs to the 1A G protein-coupled receptor subclass. In this study, we have designed and synthesized new URP analogues in which the intracyclic Trp residue was replaced with natural, unnatural, and constrained amino acids to determine important physicochemical features for receptor binding and activation. The biological data, highlighting the potent agonistic behavior of [Tiq(4)]URP and [Tpi(4)]URP, also suggest that the Trp residue, and more specifically the indole ring, is not critical for receptor interaction and could in fact be involved in the intramolecular stabilization of the bioactive conformation of URP. Finally, these analogues, which are intracyclic constrained URP-based agonists, could represent useful pharmacological tools for the study of the urotensinergic system.

Systematic mutational analysis of the putative hydrolase PqsE: toward a deeper molecular understanding of virulence acquisition in Pseudomonas aeruginosa.

Pseudomonas aeruginosa is an important opportunistic human pathogen that can establish bacterial communication by synchronizing the behavior of individual cells in a molecular phenomenon known as "quorum sensing". Through an elusive mechanism involving gene products of the pqs operon, the PqsE enzyme is absolutely required for the synthesis of extracellular phenazines, including the toxic blue pigment pyocyanin, effectively allowing cells to achieve full-fledged virulence. Despite several functional and structural attempts at deciphering the role of this relevant enzymatic drug target, no molecular function has yet been ascribed to PqsE. In the present study, we report a series of alanine scanning experiments aimed at altering the biological function of PqsE, allowing us to uncover key amino acid positions involved in the molecular function of this enzyme. We use sequence analysis and structural overlays with members of homologous folds to pinpoint critical positions located in the vicinity of the ligand binding cleft and surrounding environment, revealing the importance of a unique C-terminal α-helical motif in the molecular function of PqsE. Our results suggest that the active site of the enzyme involves residues that extend further into the hydrophobic core of the protein, advocating for a lid-like movement of the two terminal helices. This information should help design virtual libraries of PqsE inhibitors, providing means to counter P. aeruginosa virulence acquisition and helping to reduce nosocomial infections.

Avian lipocalin expression in chickens following Escherichia coli infection and inhibition of avian pathogenic Escherichia coli growth by Ex-FABP.

Avian pathogenic Escherichia coli (APEC) causes respiratory disease and sepsis in poultry. To persist in its host, E. coli requires essential nutrients including iron. Since iron is limited in extra-intestinal tissues, E. coli produces siderophores, small molecules with high affinity for ferric iron, to sequester this essential nutrient. To counter bacterial siderophore systems, mammalian hosts secrete siderocalin (also called lipocalin 2 or NGAL), which binds ferric-siderophore complexes rendering them unavailable to bacteria. In humans and mice, siderocalin is known to play a role in primary defense against bacterial infections. In poultry, 4 proteins display homology to the human NGAL (CALß, CALγ, Ggal-C8GC and Ex-FABP). The function and expression of the genes coding for these 4 proteins during infection by APEC is still unknown. Expression levels of these genes were determined by quantitative RT-PCR using RNA extracted from lungs, livers and spleens of healthy 3-week-old chickens and chickens infected with APEC. The gene coding for Ex-FABP was overexpressed in all organs tested. It was significantly more overexpressed in the lungs and liver than in the spleen (37.3 and 27.3 times versus 11.5 times, respectively). The genes coding for Calß and Calγ were also found significantly overexpressed in the liver (27 and 8.2 times, respectively). To confirm the function of Ex-FABP as a siderocalin, the gene coding for this protein was cloned in an expression vector and the protein was purified. In vitro growth inhibition of E. coli strains by Ex-FABP was assayed in parallel with growth inhibition caused by human siderocalin. Purified Ex-FABP inhibited growth of E. coli K-12, which only produces the siderophore enterobactin. However, E. coli strains producing pathogen-associated siderophores including salmochelins (glucosylated enterobactin), aerobactin and yersiniabactin grew normally in the presence of Ex-FABP. These results indicate that Ex-FABP is an avian siderocalin with a siderophore-binding activity similar to that of human siderocalin and that pathogen-specific siderophores are required by APEC to overcome this innate defense protein in poultry.

Design and characterization of novel cell-penetrating peptides from pituitary adenylate cyclase-activating polypeptide.

The discovery of cell-penetrating peptide opened up new promising avenues for the non-invasive delivery of non-permeable biomolecules within the intracellular compartment. However, some setbacks such as possible toxic effects or unexpected immunological responses have limited their use in clinic. To overcome these obstacles, we investigated the use of novel cell-penetrating peptides (CPPs) derived from the endogenous neuropeptide Pituitary adenylate cyclase-activating polypeptide (PACAP). First, we demonstrated the propensity of native PACAP isoforms (PACAP27 and PACAP38) to efficiently deliver a large and non-permeable molecule, i.e. streptavidin, into cells. An inactive modified fragment of PACAP38, i.e. [Arg(17)]PACAP(11-38), with preserved cell-penetrating physico-chemical properties, was also synthesized and successfully use for the intracellular delivery of various cargoes such as small molecules, peptides, proteins, and polynucleotides. Especially, its effectiveness as a transfection agent was comparable to Lipofectamine 2000 while being non-toxic for cells. Uptake mechanism studies demonstrated that direct translocation, caveolae-dependent endocytosis and macropinocytosis were involved in the internalization of [Arg(17)]PACAP(11-38). This study not only opened up a new aspect in the usefulness of PACAP and its derivatives for therapeutic application but also contributed to the identification of new members of the CPP family. As such, inactive PACAP-related analogs could represent excellent vectors for in vitro and in vivo applications.

Cardiotoxin-I: an unexpectedly potent insulinotropic agent.

Insulin secretion from pancreatic ß-cells is a complex process, involving the integration and interaction of multiple external and internal stimuli, in which glucose plays a major role. Understanding the physiology leading to insulin release is a crucial step toward the identification of new targets. In this study, we evaluated the presence of insulinotropic metabolites in Naja kaouthia snake venom. Only one fraction, identified as cardiotoxin-I (CTX-I) was able to induce insulin secretion from INS-1E cells without affecting cell viability and integrity, as assessed by MTT and LDH assays. Interestingly, CTX-I was also able to stimulate insulin secretion from INS-1E cells even in the absence of glucose. Although cardiotoxins have been characterized as potent hemolytic agents and vasoconstrictors, CTX-I was unable to induce direct hemolysis of human erythrocytes or to induce potent vasoconstriction. As such, this newly identified insulin-releasing toxin will surely enrich the pool of existing tools to study ß-cell physiology or even open a new therapeutic avenue.

Synthesis and studies of water-soluble Prussian Blue-type nanoparticles into chitosan beads.

A new approach to the synthesis of highly stable aqueous colloids of coordination polymer nanoparticles was developed by using water-soluble chitosan beads as template and as stabilizing agent. The method consists in the synthesis of nanocomposite beads containing cyano-bridged coordination polymer nanoparticles via step-by-step coordination of the metal ions and the hexacyanometallate precursors into the chitosan pores and then water solubilization of these as-obtained nanocomposite beads. We obtain a large range of M(2+)/[M'(CN)(6)](3-)/chitosan (where M(2+) = Ni(2+), Cu(2+), Fe(2+), Co(2+), Mn(2+) and M' = Fe(3+) and Cr(3+)) nanocomposite beads and their respective aqueous colloids containing coordination polymer core/chitosan shell nanoparticles. The nanocomposite beads and the corresponding aqueous colloids were studied by Infrared (IR) and UV-Vis spectroscopy, nitrogen sorption (BET), Transmission Electron Microscopy (TEM), High Resolution Transmission Electron Microscopy (HRTEM) and magnetic analyses, which reveal the presence of homogeneously dispersed uniformly-sized cyano-bridged coordination polymer nanoparticles. The detailed studies of the static and dynamic magnetic properties of these nanoparticles show the occurrence of a spin-glass like behavior presumably produced by intra-particle spin disorder due to the low spin exchange energy characterizing these materials.

Thermo- and mesostabilizing protein interactions identified by temperature-dependent statistical potentials.

The goal of controlling protein thermostability is tackled here through establishing, by in silico analyses, the relative weight of residue-residue interactions in proteins as a function of temperature. We have designed for that purpose a (melting-) temperature-dependent, statistical distance potential, where the interresidue distances are computed between the side-chain geometric centers or their functional centers. Their separate derivation from proteins of either high or low thermal resistance reveals the interactions that contribute most to stability in different temperature ranges. Thermostabilizing interactions include salt bridges and cation-pi interactions (especially those involving arginine), aromatic interactions, and H-bonds between negatively charged and some aromatic residues. In contrast, H-bonds between two polar noncharged residues or between a polar noncharged residue and a negatively charged residue are relatively less stabilizing at high temperatures. An important observation is that it is necessary to consider both repulsive and attractive interactions in overall thermostabilization, as the degree of repulsion may also vary with temperature. These temperature-dependent potentials are not only useful for the identification of meso- and thermostabilizing pair interactions, but also exhibit predictive power, as illustrated by their ability to predict the melting temperature of a protein based on the melting temperature of homologous proteins.

Fast and accurate predictions of protein stability changes upon mutations using statistical potentials and neural networks: PoPMuSiC-2.0.

MOTIVATION: The rational design of proteins with modified properties, through amino acid substitutions, is of crucial importance in a large variety of applications. Given the huge number of possible substitutions, every protein engineering project would benefit strongly from the guidance of in silico methods able to predict rapidly, and with reasonable accuracy, the stability changes resulting from all possible mutations in a protein. RESULTS: We exploit newly developed statistical potentials, based on a formalism that highlights the coupling between four protein sequence and structure descriptors, and take into account the amino acid volume variation upon mutation. The stability change is expressed as a linear combination of these energy functions, whose proportionality coefficients vary with the solvent accessibility of the mutated residue and are identified with the help of a neural network. A correlation coefficient of R = 0.63 and a root mean square error of sigma(c) = 1.15 kcal/mol between measured and predicted stability changes are obtained upon cross-validation. These scores reach R = 0.79, and sigma(c) = 0.86 kcal/mol after exclusion of 10% outliers. The predictive power of our method is shown to be significantly higher than that of other programs described in the literature. AVAILABILITY: http://babylone.ulb.ac.be/popmusic

Revisiting the correlation between proteins' thermoresistance and organisms' thermophilicity.

The possibility to rationally design protein mutants that remain structured and active at high temperatures strongly depends on a better understanding of the mechanisms of protein thermostability. Studies devoted to this issue often rely on the living temperature (T(env)) of the host organism rather than on the melting temperature (T(m)) of the analyzed protein. To investigate the scale of this approximation, we probed the relationship between T(m) and T(env) on a dataset of 127 proteins, and found a much weaker correlation than previously expected: the correlation coefficient is equal to 0.59 and the regression line is T(m) approximately 42.9 degrees C + 0.62T(env). To illustrate the effect of using T(env) rather than T(m) to analyze protein thermoresistance, we derive statistical distance potentials, describing Glu-Arg and Asp-Arg salt bridges, from protein structure sets with high or low T(m) or T(env). The results show that the more favorable nature of salt bridges, relative to other interactions, at high temperatures is more clear-cut when defining thermoresistance in terms of T(m). The T(env)-based sets nevertheless remain informative.

Thermostability of salt bridges versus hydrophobic interactions in proteins probed by statistical potentials.

The temperature dependence of the interactions that stabilize protein structures is a long-standing issue, the elucidation of which would enable the prediction and the rational modification of the thermostability of a target protein. It is tackled here by deriving distance-dependent amino acid pair potentials from four datasets of proteins with increasing melting temperatures (Tm). The temperature dependence of the interactions is determined from the differences in the shape of the potentials derived from the four datasets. Note that, here, we use an unusual dataset definition, which is based on the Tm values, rather than on the living temperature of the host organisms. Our results show that the stabilizing weight of hydrophobic interactions (between Ile, Leu, and Val) remains constant as the temperature increases, compared to the other interactions. In contrast, the two minima of the Arg--Glu and Arg--Asp salt bridge potentials show a significant Tm dependence. These two minima correspond to two geometries: the fork--fork geometry, where the side chains point toward each other, and the fork--stick geometry, which involves the N(epsilon) side chain atom of Arg. These two types of salt bridges were determined to be significantly more stabilizing at high temperature. Moreover, a preference for more-compact salt bridges is noticeable in heat-resistant proteins, especially for the fork--fork geometry. The Tm-dependent potentials that have been defined here should be useful for predicting thermal stability changes upon mutation.

Magnetic water-soluble cyano-bridged metal coordination nano-polymers.

Magnetic water-soluble cyano-bridged metallic coordination polymer nanoparticles of controlled size were prepared by using water-soluble chitosan beads.