Structural and functional characterization of A-B toxins: diphtheria toxin and clostridial neurotoxins

I performed my doctorate research activity studying three important human pathogens that are A-B toxins: Diphtheria Toxin (DT), Tetanus Neurotoxin (TeNT) and Botulinum neurotoxins (BoNTs), the etiologic agents of diphtheria, tetanus and botulism respectively. In terms of structural organization these toxins consist of three domains, which are termed L chain (the N-terminal catalytic domain), HN (the transmembrane domain), and HC (the C-terminal binding domain). These domains are closely related to the common four step mechanism of action: membrane binding mediated by HC, endocytosis, membrane translocation mediated by HN and L-chain mediated substrate modification. I studied the conformational change of diphtheria toxin at acidic pH. DT includes a T domain which is known to mediate the pH-dependent membrane translocation, by forming a channel through which the catalytic domain crosses the endocytic vesicle membrane. To date no structural data are available about the pore/channel formed by the T domain, nor is known if it is monomeric or oligomeric. I have performed biochemical and structural studies to characterize the T domain of DT. The T domain is also considered a prospective anti-cancer agent for the targeted delivery of cytotoxic therapy to cancer cells. I obtained the crystal structure of DT in the presence of lipid bicelles (which simulate the endocytic vesicle membrane) and grown at pH 5.5, pH that mimics the acidic environment where translocation takes place. The reported structure throws lights on the initial event of this process, the destabilization of the three α-helices present at the bottom of the toxin (Leka et al., 2014). I then worked on a project which aimed to unravel the three dimensional structure of tetanus neurotoxin by crystallization studies. Because TeNT is considered “uncrystallizable” I focused on the use of antibody fragments (Fabs) as crystallization chaperons to aid the structural determination. Native gel analysis and size exclusion chromatography showed the formation of a stable complex in vitro between TeNT and the relative Fabs. Several crystallization experiments were carried out by high throughput crystallization screens. Further, I performed functional analysis on the trafficking of botulinum neurotoxin at the neuromuscular junction (NMJ). I expressed the binding domains of different BoNT serotypes, which are both necessary and sufficient for binding to the neuronal surface and internalization. The two step purifications, chromatography and gel filtration, were sufficient to yield purifications of each binding domain to >90% purity. Using cerebellum granular neurons (CGNs), I tested their functionality and specificity. I performed also in vivo assays in order to analyze their distribution along the NMJ. The data from fluorescence analysis show high specificity of these binding domains at the NMJ, and a different staining between different BoNT serotypes, reflecting their different time of intoxication, and perhaps a different pathway of vesicular trafficking

The first non Clostridial botulinum-like toxin cleaves VAMP within the juxtamembrane domain

The genome of Weissella oryzae SG25T was recently sequenced and a botulinum neurotoxin (BoNT) like gene was identified by bioinformatics methods. The typical three-domains organization of BoNTs with a N-terminal metalloprotease domain, a translocation and a cell binding domains could be identified. The BoNT family of neurotoxins is rapidly growing, but this was the first indication of the possible expression of a BoNT toxin outside the Clostridium genus. We performed molecular modeling and dynamics simulations showing that the 50 kDa N-terminal domain folds very similarly to the metalloprotease domain of BoNT/B, whilst the binding part is different. However, neither the recombinant metalloprotease nor the binding domains showed cross-reactivity with the standard antisera that define the seven serotypes of BoNTs. We found that the purified Weissella metalloprotease cleaves VAMP at a single site untouched by the other VAMP-specific BoNTs. This site is a unique Trp-Trp peptide bond located within the juxtamembrane segment of VAMP which is essential for neurotransmitter release. Therefore, the present study identifies the first non-Clostridial BoNT-like metalloprotease that cleaves VAMP at a novel and relevant site and we propose to label it BoNT/Wo

A novel inhibitor prevents the peripheral neuroparalysis of Botulinum neurotoxins

Botulinum neurotoxins (BoNTs) form a large class of potent and deadly neurotoxins. Given their growing number, it is of paramount importance to discover novel inhibitors targeting common steps of their intoxication process. Recently, EGA was shown to inhibit the action of bacterial toxins and viruses exhibiting a pH-dependent translocation step in mammalian cells, by interfering with their entry route. As BoNTs act in the cytosol of nerve terminals, the entry into an appropriate compartment wherefrom they translocate the catalytic moiety is essential for toxicity. Herein we propose an optimized procedure to synthesize EGA and we show that, in vitro, it prevents the neurotoxicity of different BoNT serotypes by interfering with their trafficking. Furthermore, in mice, EGA mitigates botulism symptoms induced by BoNT/A and significantly decreases the lethality of BoNT/B and BoNT/D. This opens the possibility of using EGA as a lead compound to develop novel inhibitors of botulinum neurotoxins

Structural and functional characterization of A-B toxins: diphtheria toxin and clostridial neurotoxins

I performed my doctorate research activity studying three important human pathogens that are A-B toxins: Diphtheria Toxin (DT), Tetanus Neurotoxin (TeNT) and Botulinum neurotoxins (BoNTs), the etiologic agents of diphtheria, tetanus and botulism respectively. In terms of structural organization these toxins consist of three domains, which are termed L chain (the N-terminal catalytic domain), HN (the transmembrane domain), and HC (the C-terminal binding domain). These domains are closely related to the common four step mechanism of action: membrane binding mediated by HC, endocytosis, membrane translocation mediated by HN and L-chain mediated substrate modification. I studied the conformational change of diphtheria toxin at acidic pH. DT includes a T domain which is known to mediate the pH-dependent membrane translocation, by forming a channel through which the catalytic domain crosses the endocytic vesicle membrane. To date no structural data are available about the pore/channel formed by the T domain, nor is known if it is monomeric or oligomeric. I have performed biochemical and structural studies to characterize the T domain of DT. The T domain is also considered a prospective anti-cancer agent for the targeted delivery of cytotoxic therapy to cancer cells. I obtained the crystal structure of DT in the presence of lipid bicelles (which simulate the endocytic vesicle membrane) and grown at pH 5.5, pH that mimics the acidic environment where translocation takes place. The reported structure throws lights on the initial event of this process, the destabilization of the three α-helices present at the bottom of the toxin (Leka et al., 2014). I then worked on a project which aimed to unravel the three dimensional structure of tetanus neurotoxin by crystallization studies. Because TeNT is considered “uncrystallizable” I focused on the use of antibody fragments (Fabs) as crystallization chaperons to aid the structural determination. Native gel analysis and size exclusion chromatography showed the formation of a stable complex in vitro between TeNT and the relative Fabs. Several crystallization experiments were carried out by high throughput crystallization screens. Further, I performed functional analysis on the trafficking of botulinum neurotoxin at the neuromuscular junction (NMJ). I expressed the binding domains of different BoNT serotypes, which are both necessary and sufficient for binding to the neuronal surface and internalization. The two step purifications, chromatography and gel filtration, were sufficient to yield purifications of each binding domain to >90% purity. Using cerebellum granular neurons (CGNs), I tested their functionality and specificity. I performed also in vivo assays in order to analyze their distribution along the NMJ. The data from fluorescence analysis show high specificity of these binding domains at the NMJ, and a different staining between different BoNT serotypes, reflecting their different time of intoxication, and perhaps a different pathway of vesicular trafficking.Ho effettuato la mia attività di ricerca studiando tre importanti patogeni umani, che sono tossine di tipo A-B: la tossina difterica (DT), la neurotossina tetanica (TeNT) e le neurotossine botuliniche (BoNTs), gli agenti eziologici di difterite, tetano e botulismo, rispettivamente. In termini di organizzazione strutturale queste tossine sono costituite da tre domini: il dominio catalitico (LH), il dominio di translocazione (HN) e il dominio di legame (HC). Questa organizzazione dei domini è strettamente correlata al loro comune meccanismo d’azione che comprende: il legame alla membrane cellulare mediato dal HC, la traslocazione del dominio catalitico nel citoplasma mediata dal canale di permeazione formato dal HN. Ho studiato il cambiamento conformazionale della tossina difterica a pH acido. DT include un dominio di translocazione (dominio T), che forma il canale attraverso il quale il dominio catalitico attraversa la membrana della vescicola endosomica. Fino ad oggi non ci sono dati strutturali che riguardano il canale formato dal dominio T, non si sa neanche se è un monomero o oligomero. Ho eseguito studi biochimici e strutturali per caratterizzare il dominio T di DT. Il dominio T è anche considerato un agente anti-cancro nelle terapie mirate contro le cellule tumorali. Ho ottenuto la struttura tridimensionale della tossina difterica in presenza di doppi strati lipidici (che simulano la membrana della vescicola endosomica) ed in condizioni di pH 5,5 (pH corrispondente all'ambiente acido in cui avviene la il processo di traslocazione). La struttura riportata getta luci sull'evento iniziale di questo processo, la destabilizzazione di tre alfa-eliche presenti nella parte inferiore della tossina (Leka et al., 2014). Ho poi lavorato su un progetto che mirava a caratterizzare la struttura tridimensionale della tosssina tetanica. Poiché la cristallizzazione di questa tossina risulta d’essere molto difficile, mi sono concentrata sull'utilizzo di frammenti di anticorpi (Fab) come tools per aiutare la determinazione strutturale. Analisi da gel nativo e da cromatografia ad esclusione mostrano la formazione di un complesso stabile in vitro tra la tossina ed i relativi Fab. Diversi esperimenti di cristallizzazione sono stati eseguiti, e per il momento non abbiamo ancora informazioni strutturali sulla tossina. Inoltre, ho studiato anche la localizzazione ed il processo di internalizzazione delle tossine botuliniche a livello della giunzione neuromuscolare (NMJ). Ho espresso i domini di legame di diversi sierotipi di tossine botuliniche, domini che sono necessari e sufficienti per il legame alla superficie dei neuroni. I domini di legame sono stati purificati utilizzando cromatografia di affinità e per esclusione, ottendo alla fine una purezza > 90% . Utilizzando i neuroni granulari di cervelletto (CGN), ho testato la loro funzionalità e specificità. Questi domini sono stati iniettati in vivo al fine di analizzare la loro localizzazione a livello della giunzione neuromuscolare. I dati ottenuti con analisi di microscopia confocale ed a fluorescenza mostrano che questi domini si localizzano proprio a livello della giunzione muscolare. Nelle marcature si osserva anche una colorazione diversa tra i diversi sierotipi BoNT, e questo risultato riflette il diverso tempo di intossicazione tra i vari serotipi di tossine botuliniche, e forse anche una diversa localizzazione in diverse vescicole endosomiche

Diphtheria Toxin conformational switching at acidic pH

Diphtheria toxin (DT), the etiological agent of the homonymous disease, like other bacterial toxins, has to undergo a dramatic structural change in order to be internalized into the cytosol, where it finally performs its function. The molecular mechanism of toxin transit across the membrane is not well known, but the available experimental evidence indicates that one of the three domains of the toxin, called the central alpha-helical domain, inserts into the lipid bilayer, so favoring the translocation of the catalytic domain. This process is driven by the acidic pH of the endosomal lumen. Here, we describe the crystal structure of DT grown at acidic pH in the presence of bicelles. We were unable to freeze the moment of DT insertion into the lipid bilayer, but our crystal structure indicates that the low pH causes the unfolding of the TH2, TH3 and TH4 alpha-helices. This event gives rise to the exposure of a hydrophobic surface that includes the TH5 and TH8 alpha-helices, and the loop region connecting the TH8 and TH9 alpha-helices. Their exposure is probably favored by the presence of lipid bilayers in the crystallization solution, and they appear to be ready to insert into the membrane

A coiled-coil-based design strategy for the thermostabilization of G-protein-coupled receptors

Abstract Structure elucidation of inactive-state GPCRs still mostly relies on X-ray crystallography. The major goal of our work was to create a new GPCR tool that would provide receptor stability and additional soluble surface for crystallization. Towards this aim, we selected the two-stranded antiparallel coiled coil as a domain fold that satisfies both criteria. A selection of antiparallel coiled coils was used for structure-guided substitution of intracellular loop 3 of the β3 adrenergic receptor. Unexpectedly, only the two GPCR variants containing thermostable coiled coils were expressed. We showed that one GPCR chimera is stable upon purification in detergent, retains ligand-binding properties, and can be crystallized. However, the quality of the crystals was not suitable for structure determination. By using two other examples, 5HTR2C and α2BAR, we demonstrate that our approach is generally suitable for the stabilization of GPCRs. To provide additional surface for promoting crystal contacts, we replaced in a structure-based approach the loop connecting the antiparallel coiled coil by T4L. We found that the engineered GPCR is even more stable than the coiled-coil variant. Negative-staining TEM revealed a homogeneous distribution of particles, indicating that coiled-coil-T4L receptor variants might also be promising candidate proteins for structure elucidation by cryo-EM. Our approach should be of interest for applications that benefit from stable GPCRs

A DARPin promotes faster onset of botulinum neurotoxin A1 action

In this study, we characterize Designed Ankyrin Repeat Proteins (DARPins) as investigative tools to probe botulinum neurotoxin A1 (BoNT/A1) structure and function. We identify DARPin-F5 that completely blocks SNAP25 substrate cleavage by BoNT/A1 in vitro. X-ray crystallography reveals that DARPin-F5 inhibits BoNT/A1 activity by interacting with a substrate-binding region between the α- and β-exosite. This DARPin does not block substrate cleavage of BoNT/A3, indicating that DARPin-F5 is a subtype-specific inhibitor. BoNT/A1 Glu-171 plays a critical role in the interaction with DARPin-F5 and its mutation to Asp, the residue found in BoNT/A3, results in a loss of inhibition of substrate cleavage. In contrast to the in vitro results, DARPin-F5 promotes faster substrate cleavage of BoNT/A1 in primary neurons and muscle tissue by increasing toxin translocation. Our findings could have important implications for the application of BoNT/A1 in therapeutic areas requiring faster onset of toxin action combined with long persistence

A DARPin promotes faster onset of botulinum neurotoxin A1 action

Abstract In this study, we characterize Designed Ankyrin Repeat Proteins (DARPins) as investigative tools to probe botulinum neurotoxin A1 (BoNT/A1) structure and function. We identify DARPin-F5 that completely blocks SNAP25 substrate cleavage by BoNT/A1 in vitro. X-ray crystallography reveals that DARPin-F5 inhibits BoNT/A1 activity by interacting with a substrate-binding region between the α- and β-exosite. This DARPin does not block substrate cleavage of BoNT/A3, indicating that DARPin-F5 is a subtype-specific inhibitor. BoNT/A1 Glu-171 plays a critical role in the interaction with DARPin-F5 and its mutation to Asp, the residue found in BoNT/A3, results in a loss of inhibition of substrate cleavage. In contrast to the in vitro results, DARPin-F5 promotes faster substrate cleavage of BoNT/A1 in primary neurons and muscle tissue by increasing toxin translocation. Our findings could have important implications for the application of BoNT/A1 in therapeutic areas requiring faster onset of toxin action combined with long persistence