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Pitard I, Malliavin TE. Structural Biology and Molecular Modeling to Analyze the Entry of Bacterial Toxins and Virulence Factors into Host Cells. Toxins (Basel) 2019; 11:toxins11060369. [PMID: 31238550 PMCID: PMC6628625 DOI: 10.3390/toxins11060369] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2019] [Revised: 06/17/2019] [Accepted: 06/18/2019] [Indexed: 12/26/2022] Open
Abstract
Understanding the functions and mechanisms of biological systems is an outstanding challenge. One way to overcome it is to combine together several approaches such as molecular modeling and experimental structural biology techniques. Indeed, the interplay between structural and dynamical properties of the system is crucial to unravel the function of molecular machinery’s. In this review, we focus on how molecular simulations along with structural information can aid in interpreting biological data. Here, we examine two different cases: (i) the endosomal translocation toxins (diphtheria, tetanus, botulinum toxins) and (ii) the activation of adenylyl cyclase inside the cytoplasm (edema factor, CyA, ExoY).
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Affiliation(s)
- Irène Pitard
- Unité de Bioinformatique Structurale, Institut Pasteur and CNRS UMR3528, 75015 Paris, France.
- Centre de Bioinformatique, Biostatistique et Biologie Intégrative, Institut Pasteur and CNRS USR3756, 75015 Paris, France.
- Sorbonne Université, Collège Doctoral, Ecole Doctorale Complexité du Vivant, 75005 Paris, France.
| | - Thérèse E Malliavin
- Unité de Bioinformatique Structurale, Institut Pasteur and CNRS UMR3528, 75015 Paris, France.
- Centre de Bioinformatique, Biostatistique et Biologie Intégrative, Institut Pasteur and CNRS USR3756, 75015 Paris, France.
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2
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Finley NL. Revealing how an adenylate cyclase toxin uses bait and switch tactics in its activation. PLoS Biol 2018; 16:e2005356. [PMID: 29485992 PMCID: PMC5844667 DOI: 10.1371/journal.pbio.2005356] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Revised: 03/09/2018] [Indexed: 01/16/2023] Open
Abstract
Dissecting how bacterial pathogens escape immune destruction and cause respiratory infections in humans is a work in progress. One tactic employed by microbes is to use bacterial adenylate cyclase toxins (ACTs) to disarm immune cells and disrupt cellular signaling in host cells, which facilitates the infection process. Several clinically significant pathogens, such as Bacillus anthracis and Bordetella pertussis, have ACTs that are stimulated by an activator protein in human cells. Research has shown that these bacterial ACTs have evolved distinct ways of controlling their activities, but our understanding of how the B. pertussis ACT does this is limited. In a recent study, O’Brien and colleagues provide new and exciting evidence demonstrating that the regulation of B. pertussis ACT involves conformational switching between flexible and rigid states, which is triggered upon binding the host activator protein. This study increases our knowledge of how bacterial ACTs are unique enzymes, representing a potentially novel class of drug targets that may open new pathways to combat reemerging infectious diseases.
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Affiliation(s)
- Natosha L. Finley
- Department of Microbiology, Miami University, Oxford, Ohio, United States of America
- Cell, Molecular, and Structural Biology Program, Miami University, Oxford, Ohio, United States of America
- * E-mail:
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3
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O’Brien DP, Durand D, Voegele A, Hourdel V, Davi M, Chamot-Rooke J, Vachette P, Brier S, Ladant D, Chenal A. Calmodulin fishing with a structurally disordered bait triggers CyaA catalysis. PLoS Biol 2017; 15:e2004486. [PMID: 29287065 PMCID: PMC5764468 DOI: 10.1371/journal.pbio.2004486] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2017] [Revised: 01/11/2018] [Accepted: 12/07/2017] [Indexed: 11/18/2022] Open
Abstract
Once translocated into the cytosol of target cells, the catalytic domain (AC) of the adenylate cyclase toxin (CyaA), a major virulence factor of Bordetella pertussis, is potently activated by binding calmodulin (CaM) to produce supraphysiological levels of cAMP, inducing cell death. Using a combination of small-angle X-ray scattering (SAXS), hydrogen/deuterium exchange mass spectrometry (HDX-MS), and synchrotron radiation circular dichroism (SR-CD), we show that, in the absence of CaM, AC exhibits significant structural disorder, and a 75-residue-long stretch within AC undergoes a disorder-to-order transition upon CaM binding. Beyond this local folding, CaM binding induces long-range allosteric effects that stabilize the distant catalytic site, whilst preserving catalytic loop flexibility. We propose that the high enzymatic activity of AC is due to a tight balance between the CaM-induced decrease of structural flexibility around the catalytic site and the preservation of catalytic loop flexibility, allowing for fast substrate binding and product release. The CaM-induced dampening of AC conformational disorder is likely relevant to other CaM-activated enzymes. Calmodulin is a widespread and highly conserved protein that interacts with a wide variety of eukaryotic proteins and enzymes, controlling their activities in response to calcium. The adenylate cyclase toxin (CyaA) of Bordetella pertussis, the causative agent of whooping cough, is one such calmodulin target. Once transported across the plasma membrane of eukaryotic cells, the catalytic domain (AC) of CyaA is activated by calmodulin, producing high levels of cAMP, which can induce cell death. We use an integrative structural biology approach combining several biophysical techniques to characterize the structural rearrangements in AC upon calmodulin binding and to elucidate their relationship to CyaA activation. We show that a disordered stretch of 75 amino acid residues in AC serves as a bait for calmodulin capture. Binding induces significant folding within this region, a prerequisite for CyaA activation. Calmodulin binding promotes the stabilization of the distant catalytic site, whilst maintaining its catalytic loop in a flexible and exposed state. Both phenomena contribute to the high enzymatic activity of AC, allowing for fast substrate binding and cAMP release. The calmodulin-induced reduction of AC conformational disorder is likely relevant to other calmodulin-activated enzymes.
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Affiliation(s)
- Darragh P. O’Brien
- Institut Pasteur, UMR CNRS 3528, Chemistry and Structural Biology Department, Paris, France
| | - Dominique Durand
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris-Sud, Université Paris-Saclay, Gif-sur-Yvette cedex, France
- * E-mail: (A.C.); (D.L.); (D.D.); (S.B.)
| | - Alexis Voegele
- Institut Pasteur, UMR CNRS 3528, Chemistry and Structural Biology Department, Paris, France
| | - Véronique Hourdel
- Institut Pasteur, USR CNRS 2000, Chemistry and Structural Biology Department, CITECH, Paris, France
| | - Marilyne Davi
- Institut Pasteur, UMR CNRS 3528, Chemistry and Structural Biology Department, Paris, France
| | - Julia Chamot-Rooke
- Institut Pasteur, USR CNRS 2000, Chemistry and Structural Biology Department, CITECH, Paris, France
| | - Patrice Vachette
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris-Sud, Université Paris-Saclay, Gif-sur-Yvette cedex, France
| | - Sébastien Brier
- Institut Pasteur, USR CNRS 2000, Chemistry and Structural Biology Department, CITECH, Paris, France
- * E-mail: (A.C.); (D.L.); (D.D.); (S.B.)
| | - Daniel Ladant
- Institut Pasteur, UMR CNRS 3528, Chemistry and Structural Biology Department, Paris, France
- * E-mail: (A.C.); (D.L.); (D.D.); (S.B.)
| | - Alexandre Chenal
- Institut Pasteur, UMR CNRS 3528, Chemistry and Structural Biology Department, Paris, France
- * E-mail: (A.C.); (D.L.); (D.D.); (S.B.)
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4
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Calcium-Dependent Interaction Occurs between Slow Skeletal Myosin Binding Protein C and Calmodulin. MAGNETOCHEMISTRY 2017. [DOI: 10.3390/magnetochemistry4010001] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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Johns CW, Finley NL. Site I Inactivation Impacts Calmodulin Calcium Binding and Activation of Bordetella pertussis Adenylate Cyclase Toxin. Toxins (Basel) 2017; 9:toxins9120389. [PMID: 29189743 PMCID: PMC5744109 DOI: 10.3390/toxins9120389] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2017] [Revised: 11/26/2017] [Accepted: 11/27/2017] [Indexed: 12/20/2022] Open
Abstract
Site I inactivation of calmodulin (CaM) was used to examine the importance of aspartic acid 22 at position 3 in CaM calcium binding, protein folding, and activation of the Bordetella pertussis adenylate cyclase toxin domain (CyaA-ACD). NMR calcium titration experiments showed that site I in the CaM mutant (D22A) remained largely unperturbed, while sites II, III, and IV exhibited calcium-induced conformational changes similar to wild-type CaM (CaMWt). Circular dichroism analyses revealed that D22A had comparable α-helical content to CaMWt, and only modest differences in α-helical composition were detected between CaMWt-CyaA-ACD and D22A-CyaA-ACD complexes. However, the thermal stability of the D22A-CyaA-ACD complex was reduced, as compared to the CaMWt-CyaA-ACD complex. Moreover, CaM-dependent activity of CyaA-ACD decreased 87% in the presence of D22A. Taken together, our findings provide evidence that D22A engages CyaA-ACD, likely through C-terminal mediated binding, and that site I inactivation exerts functional effects through the modification of stabilizing interactions that occur between N-terminal CaM and CyaA-ACD.
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Affiliation(s)
- Christian W Johns
- Cell, Molecular, and Structural Biology Program, Miami University, Oxford, OH 45056, USA.
| | - Natosha L Finley
- Cell, Molecular, and Structural Biology Program, Miami University, Oxford, OH 45056, USA.
- Department of Microbiology, Miami University, Oxford, OH 45056, USA.
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Structure-Function Relationships Underlying the Capacity of Bordetella Adenylate Cyclase Toxin to Disarm Host Phagocytes. Toxins (Basel) 2017; 9:toxins9100300. [PMID: 28946636 PMCID: PMC5666347 DOI: 10.3390/toxins9100300] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2017] [Revised: 09/19/2017] [Accepted: 09/21/2017] [Indexed: 01/18/2023] Open
Abstract
Bordetellae, pathogenic to mammals, produce an immunomodulatory adenylate cyclase toxin-hemolysin (CyaA, ACT or AC-Hly) that enables them to overcome the innate immune defense of the host. CyaA subverts host phagocytic cells by an orchestrated action of its functional domains, where an extremely catalytically active adenylyl cyclase enzyme is delivered into phagocyte cytosol by a pore-forming repeat-in-toxin (RTX) cytolysin moiety. By targeting sentinel cells expressing the complement receptor 3, known as the CD11b/CD18 (αMβ₂) integrin, CyaA compromises the bactericidal functions of host phagocytes and supports infection of host airways by Bordetellae. Here, we review the state of knowledge on structural and functional aspects of CyaA toxin action, placing particular emphasis on signaling mechanisms by which the toxin-produced 3',5'-cyclic adenosine monophosphate (cAMP) subverts the physiology of phagocytic cells.
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Molecular Modeling of the Catalytic Domain of CyaA Deepened the Knowledge of Its Functional Dynamics. Toxins (Basel) 2017; 9:toxins9070199. [PMID: 28672846 PMCID: PMC5535146 DOI: 10.3390/toxins9070199] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2017] [Revised: 06/21/2017] [Accepted: 06/22/2017] [Indexed: 12/16/2022] Open
Abstract
Although CyaA has been studied for over three decades and revealed itself to be a very good prototype for developing various biotechnological applications, only a little is known about its functional dynamics and about the conformational landscape of this protein. Molecular dynamics simulations helped to clarify the view on these points in the following way. First, the model of interaction between AC and calmodulin (CaM) has evolved from an interaction centered on the surface between C-CaM hydrophobic patch and the α helix H of AC, to a more balanced view, in which the C-terminal tail of AC along with the C-CaM Calcium loops play an important role. This role has been confirmed by the reduction of the affinity of AC for calmodulin in the presence of R338, D360 and N347 mutations. In addition, enhanced sampling studies have permitted to propose a representation of the conformational space for the isolated AC. It remains to refine this representation using structural low resolution information measured on the inactive state of AC. Finally, due to a virtual screening study on another adenyl cyclase from Bacillus anthracis, weak inhibitors of AC have been discovered.
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Springer TI, Emerson CC, Johns CW, Finley NL. Interaction with adenylate cyclase toxin from Bordetella pertussis affects the metal binding properties of calmodulin. FEBS Open Bio 2016; 7:25-34. [PMID: 28097085 PMCID: PMC5221433 DOI: 10.1002/2211-5463.12138] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2016] [Revised: 09/27/2016] [Accepted: 09/29/2016] [Indexed: 12/16/2022] Open
Abstract
Adenylate cyclase toxin domain (CyaA‐ACD) is a calmodulin (CaM)‐dependent adenylate cyclase involved in Bordetella pertussis pathogenesis. Calcium (Ca2+) and magnesium (Mg2+) concentrations impact CaM‐dependent CyaA‐ACD activation, but the structural mechanisms remain unclear. In this study, NMR, dynamic light scattering, and native PAGE were used to probe Mg2+‐induced transitions in CaM's conformation in the presence of CyaA‐ACD. Mg2+ binding was localized to sites I and II, while sites III and IV remained Ca2+ loaded when CaM was bound to CyaA‐ACD. 2Mg2+/2Ca2+‐loaded CaM/CyaA‐ACD was elongated, whereas mutation of site I altered global complex conformation. These data suggest that CyaA‐ACD interaction moderates CaM's Ca2+‐ and Mg2+‐binding capabilities, which may contribute to pathobiology.
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Affiliation(s)
| | - Corey C Emerson
- Department of Microbiology Miami University Oxford OH USA; Present address: Department of Pharmacology Cleveland Center for Membrane and Structural Biology Case Western Reserve University Cleveland OH 44106 USA
| | - Christian W Johns
- Cell, Molecular, and Structural Biology Program Miami University Oxford OH USA
| | - Natosha L Finley
- Department of Microbiology Miami University Oxford OH USA; Cell, Molecular, and Structural Biology Program Miami University Oxford OH USA
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Cortes-Ciriano I, Bouvier G, Nilges M, Maragliano L, Malliavin TE. Temperature Accelerated Molecular Dynamics with Soft-Ratcheting Criterion Orients Enhanced Sampling by Low-Resolution Information. J Chem Theory Comput 2015; 11:3446-54. [PMID: 26575778 DOI: 10.1021/acs.jctc.5b00153] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
Many proteins exhibit an equilibrium between multiple conformations, some of them being characterized only by low-resolution information. Visiting all conformations is a demanding task for computational techniques performing enhanced but unfocused exploration of collective variable (CV) space. Otherwise, pulling a structure toward a target condition biases the exploration in a way difficult to assess. To address this problem, we introduce here the soft-ratcheting temperature-accelerated molecular dynamics (sr-TAMD), where the exploration of CV space by TAMD is coupled to a soft-ratcheting algorithm that filters the evolving CV values according to a predefined criterion. Any low resolution or even qualitative information can be used to orient the exploration. We validate this technique by exploring the conformational space of the inactive state of the catalytic domain of the adenyl cyclase AC from Bordetella pertussis. The domain AC gets activated by association with calmodulin (CaM), and the available crystal structure shows that in the complex the protein has an elongated shape. High-resolution data are not available for the inactive, CaM-free protein state, but hydrodynamic measurements have shown that the inactive AC displays a more globular conformation. Here, using as CVs several geometric centers, we use sr-TAMD to enhance CV space sampling while filtering for CV values that correspond to centers moving close to each other, and we thus rapidly visit regions of conformational space that correspond to globular structures. The set of conformations sampled using sr-TAMD provides the most extensive description of the inactive state of AC up to now, consistent with available experimental information.
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Affiliation(s)
- Isidro Cortes-Ciriano
- Unité de Bioinformatique Structurale, CNRS UMR 3528, Structural Biology and Chemistry Department, Institut Pasteur , 25-28, rue Dr. Roux, 75 724 Paris, France
| | - Guillaume Bouvier
- Unité de Bioinformatique Structurale, CNRS UMR 3528, Structural Biology and Chemistry Department, Institut Pasteur , 25-28, rue Dr. Roux, 75 724 Paris, France
| | - Michael Nilges
- Unité de Bioinformatique Structurale, CNRS UMR 3528, Structural Biology and Chemistry Department, Institut Pasteur , 25-28, rue Dr. Roux, 75 724 Paris, France
| | - Luca Maragliano
- Department of Neuroscience and Brain Technologies, Istituto Italiano di Tecnologia , Genoa, Italy
| | - Thérèse E Malliavin
- Unité de Bioinformatique Structurale, CNRS UMR 3528, Structural Biology and Chemistry Department, Institut Pasteur , 25-28, rue Dr. Roux, 75 724 Paris, France
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