1
|
Santander EA, Bravo G, Chang-Halabi Y, Olguín-Orellana GJ, Naulin PA, Barrera MJ, Montenegro FA, Barrera NP. The Adsorption of P2X2 Receptors Interacting with IgG Antibodies Revealed by Combined AFM Imaging and Mechanical Simulation. Int J Mol Sci 2023; 25:336. [PMID: 38203505 PMCID: PMC10778698 DOI: 10.3390/ijms25010336] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2023] [Revised: 12/16/2023] [Accepted: 12/19/2023] [Indexed: 01/12/2024] Open
Abstract
The adsorption of proteins onto surfaces significantly impacts biomaterials, medical devices, and biological processes. This study aims to provide insights into the irreversible adsorption process of multiprotein complexes, particularly focusing on the interaction between anti-His6 IgG antibodies and the His6-tagged P2X2 receptor. Traditional approaches to understanding protein adsorption have centered around kinetic and thermodynamic models, often examining individual proteins and surface coverage, typically through Molecular Dynamics (MD) simulations. In this research, we introduce a computational approach employing Autodesk Maya 3D software for the investigation of multiprotein complexes' adsorption behavior. Utilizing Atomic Force Microscopy (AFM) imaging and Maya 3D-based mechanical simulations, our study yields real-time structural and kinetic observations. Our combined experimental and computational findings reveal that the P2X2 receptor-IgG antibody complex likely undergoes absorption in an 'extended' configuration. Whereas the P2X2 receptor is less adsorbed once is complexed to the IgG antibody compared to its individual state, the opposite is observed for the antibody. This insight enhances our understanding of the role of protein-protein interactions in the process of protein adsorption.
Collapse
Affiliation(s)
- Eduardo A. Santander
- Laboratory of Nanophysiology and Structural Biology, Faculty of Biological Sciences, Pontificia Universidad Católica de Chile, Alameda 340, Santiago 8331150, Chile; (E.A.S.); (G.B.); (G.J.O.-O.)
| | - Graciela Bravo
- Laboratory of Nanophysiology and Structural Biology, Faculty of Biological Sciences, Pontificia Universidad Católica de Chile, Alameda 340, Santiago 8331150, Chile; (E.A.S.); (G.B.); (G.J.O.-O.)
- Department of Chemical and Bioprocess Engineering, School of Engineering, Pontificia Universidad Católica de Chile, Santiago 7820436, Chile
| | - Yuan Chang-Halabi
- Laboratory of Nanophysiology and Structural Biology, Faculty of Biological Sciences, Pontificia Universidad Católica de Chile, Alameda 340, Santiago 8331150, Chile; (E.A.S.); (G.B.); (G.J.O.-O.)
| | - Gabriel J. Olguín-Orellana
- Laboratory of Nanophysiology and Structural Biology, Faculty of Biological Sciences, Pontificia Universidad Católica de Chile, Alameda 340, Santiago 8331150, Chile; (E.A.S.); (G.B.); (G.J.O.-O.)
| | - Pamela A. Naulin
- Laboratory of Nanophysiology and Structural Biology, Faculty of Biological Sciences, Pontificia Universidad Católica de Chile, Alameda 340, Santiago 8331150, Chile; (E.A.S.); (G.B.); (G.J.O.-O.)
| | - Mario J. Barrera
- Laboratory of Nanophysiology and Structural Biology, Faculty of Biological Sciences, Pontificia Universidad Católica de Chile, Alameda 340, Santiago 8331150, Chile; (E.A.S.); (G.B.); (G.J.O.-O.)
| | - Felipe A. Montenegro
- Laboratory of Nanophysiology and Structural Biology, Faculty of Biological Sciences, Pontificia Universidad Católica de Chile, Alameda 340, Santiago 8331150, Chile; (E.A.S.); (G.B.); (G.J.O.-O.)
| | - Nelson P. Barrera
- Laboratory of Nanophysiology and Structural Biology, Faculty of Biological Sciences, Pontificia Universidad Católica de Chile, Alameda 340, Santiago 8331150, Chile; (E.A.S.); (G.B.); (G.J.O.-O.)
| |
Collapse
|
2
|
Leiva-Sabadini C, Tiozzo-Lyon P, Hidalgo-Galleguillos L, Rivas L, Robles AI, Fierro A, Barrera NP, Bozec L, Schuh CMAP, Aguayo S. Nanoscale Dynamics of Streptococcal Adhesion to AGE-Modified Collagen. J Dent Res 2023:220345231166294. [PMID: 37203151 DOI: 10.1177/00220345231166294] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/20/2023] Open
Abstract
The adhesion of initial colonizers such as Streptococcus mutans to collagen is critical for dentinal and root caries progression. One of the most described pathological and aging-associated changes in collagen-including dentinal collagen-is the generation of advanced glycation end-products (AGEs) such as methylglyoxal (MGO)-derived AGEs. Despite previous reports suggesting that AGEs alter bacterial adhesion to collagen, the biophysics driving oral streptococcal attachment to MGO-modified collagen remains largely understudied. Thus, the aim of this work was to unravel the dynamics of the initial adhesion of S. mutans to type I collagen in the presence and absence of MGO-derived AGEs by employing bacterial cell force spectroscopy with atomic force microscopy (AFM). Type I collagen gels were treated with 10 mM MGO to induce AGE formation, which was characterized with microscopy and enzyme-linked immunosorbent assay. Subsequently, AFM cantilevers were functionalized with living S. mutans UA 159 or Streptococcus sanguinis SK 36 cells and probed against collagen surfaces to obtain force curves displaying bacterial attachment in real time, from which the adhesion force, number of events, Poisson analysis, and contour and rupture lengths for each individual detachment event were computed. Furthermore, in silico computer simulation docking studies between the relevant S. mutans UA 159 collagen-binding protein SpaP and collagen were computed, in the presence and absence of MGO. Overall, results showed that MGO modification increased both the number and adhesion force of single-unbinding events between S. mutans and collagen, without altering the contour or rupture lengths. Both experimental and in silico simulations suggest that this effect is due to increased specific and nonspecific forces and interactions between S. mutans UA 159 and MGO-modified collagen substrates. In summary, these results suggest that collagen alterations due to aging and glycation may play a role in early bacterial adherence to oral tissues, associated with conditions such as aging or chronic hyperglycemia, among others.
Collapse
Affiliation(s)
- C Leiva-Sabadini
- School of Dentistry, Faculty of Medicine, Pontificia Universidad Católica de Chile, Santiago, Chile
- Institute for Biological and Medical Engineering, Schools of Engineering, Medicine and Biological Sciences, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - P Tiozzo-Lyon
- School of Dentistry, Faculty of Medicine, Pontificia Universidad Católica de Chile, Santiago, Chile
- Institute for Biological and Medical Engineering, Schools of Engineering, Medicine and Biological Sciences, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - L Hidalgo-Galleguillos
- School of Dentistry, Faculty of Medicine, Pontificia Universidad Católica de Chile, Santiago, Chile
- Institute for Biological and Medical Engineering, Schools of Engineering, Medicine and Biological Sciences, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - L Rivas
- Genomics & Resistant Microbes group (GeRM), Instituto de Ciencias e Innovación en Medicina (ICIM), Facultad de Medicina, Clínica Alemana, Universidad del Desarrollo, Concepción, Chile
- Millennium Initiative for Collaborative Research on Bacterial Resistance (MICROB-R)
| | - A I Robles
- Departamento de Química Orgánica, Escuela de Química, Facultad de Química y de Farmacia, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - A Fierro
- Departamento de Química Orgánica, Escuela de Química, Facultad de Química y de Farmacia, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - N P Barrera
- Department of Physiology, Faculty of Biological Sciences, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - L Bozec
- Faculty of Dentistry, University of Toronto, Toronto, Ontario, Canada
| | - C M A P Schuh
- Centro de Medicina Regenerativa, Facultad de Medicina, Clínica Alemana-Universidad del Desarrollo, Santiago, Chile
| | - S Aguayo
- School of Dentistry, Faculty of Medicine, Pontificia Universidad Católica de Chile, Santiago, Chile
- Institute for Biological and Medical Engineering, Schools of Engineering, Medicine and Biological Sciences, Pontificia Universidad Católica de Chile, Santiago, Chile
| |
Collapse
|
3
|
Chang-Halabi Y, Cordero J, Sarabia X, Villalobos D, Barrera NP. Crosstalking interactions between P2X4 and 5-HT 3A receptors. Neuropharmacology 2023; 236:109574. [PMID: 37156336 DOI: 10.1016/j.neuropharm.2023.109574] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2022] [Revised: 05/01/2023] [Accepted: 05/06/2023] [Indexed: 05/10/2023]
Abstract
Ionotropic receptors are ligand-gated ion channels triggering fast neurotransmitter responses. Among them, P2X and 5-HT3 receptors have been shown to physically interact each other and functionally inducing cross inhibitory responses. Nevertheless, despite the importance of P2X4 and 5-HT3A receptors that mediate for example neuropathic pain and psychosis respectively, complementary evidence has recently started to move forward in the understanding of this interaction. In this review, we discuss current evidence supporting the mechanism of crosstalking between both receptors, from the structural to the transduction pathway level. We expect this work may guide the design of further experiments to obtain a comprehensive view for the neuropharmacological role of these interacting receptors.
Collapse
Affiliation(s)
- Yuan Chang-Halabi
- Faculty of Biological Sciences, Pontificia Universidad Católica de Chile, Alameda 340, Santiago, Chile
| | - José Cordero
- Faculty of Biological Sciences, Pontificia Universidad Católica de Chile, Alameda 340, Santiago, Chile
| | - Xander Sarabia
- Faculty of Biological Sciences, Pontificia Universidad Católica de Chile, Alameda 340, Santiago, Chile
| | - Daniela Villalobos
- Faculty of Biological Sciences, Pontificia Universidad Católica de Chile, Alameda 340, Santiago, Chile
| | - Nelson P Barrera
- Faculty of Biological Sciences, Pontificia Universidad Católica de Chile, Alameda 340, Santiago, Chile.
| |
Collapse
|
4
|
Guffick C, Hsieh PY, Ali A, Shi W, Howard J, Chinthapalli DK, Kong AC, Salaa I, Crouch LI, Ansbro MR, Isaacson SC, Singh H, Barrera NP, Nair AV, Robinson CV, Deery MJ, van Veen HW. Drug-dependent inhibition of nucleotide hydrolysis in the heterodimeric ABC multidrug transporter PatAB from Streptococcus pneumoniae. FEBS J 2022; 289:3770-3788. [PMID: 35066976 PMCID: PMC9541285 DOI: 10.1111/febs.16366] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2021] [Revised: 12/07/2021] [Accepted: 01/20/2022] [Indexed: 02/02/2023]
Abstract
The bacterial heterodimeric ATP‐binding cassette (ABC) multidrug exporter PatAB has a critical role in conferring antibiotic resistance in multidrug‐resistant infections by Streptococcus pneumoniae. As with other heterodimeric ABC exporters, PatAB contains two transmembrane domains that form a drug translocation pathway for efflux and two nucleotide‐binding domains that bind ATP, one of which is hydrolysed during transport. The structural and functional elements in heterodimeric ABC multidrug exporters that determine interactions with drugs and couple drug binding to nucleotide hydrolysis are not fully understood. Here, we used mass spectrometry techniques to determine the subunit stoichiometry in PatAB in our lactococcal expression system and investigate locations of drug binding using the fluorescent drug‐mimetic azido‐ethidium. Surprisingly, our analyses of azido‐ethidium‐labelled PatAB peptides point to ethidium binding in the PatA nucleotide‐binding domain, with the azido moiety crosslinked to residue Q521 in the H‐like loop of the degenerate nucleotide‐binding site. Investigation into this compound and residue’s role in nucleotide hydrolysis pointed to a reduction in the activity for a Q521A mutant and ethidium‐dependent inhibition in both mutant and wild type. Most transported drugs did not stimulate or inhibit nucleotide hydrolysis of PatAB in detergent solution or lipidic nanodiscs. However, further examples for ethidium‐like inhibition were found with propidium, novobiocin and coumermycin A1, which all inhibit nucleotide hydrolysis by a non‐competitive mechanism. These data cast light on potential mechanisms by which drugs can regulate nucleotide hydrolysis by PatAB, which might involve a novel drug binding site near the nucleotide‐binding domains.
Collapse
Affiliation(s)
| | - Pei-Yu Hsieh
- Department of Pharmacology, University of Cambridge, UK
| | - Anam Ali
- Department of Pharmacology, University of Cambridge, UK
| | - Wilma Shi
- Department of Pharmacology, University of Cambridge, UK
| | - Julie Howard
- Cambridge Centre for Proteomics, Department of Biochemistry, University of Cambridge, UK
| | | | - Alex C Kong
- Department of Pharmacology, University of Cambridge, UK
| | - Ihsene Salaa
- Department of Pharmacology, University of Cambridge, UK
| | - Lucy I Crouch
- Department of Pharmacology, University of Cambridge, UK
| | | | | | | | - Nelson P Barrera
- Department of Physiology, Faculty of Biological Sciences, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Asha V Nair
- Department of Pharmacology, University of Cambridge, UK
| | | | - Michael J Deery
- Cambridge Centre for Proteomics, Department of Biochemistry, University of Cambridge, UK
| | | |
Collapse
|
5
|
Leiva-Sabadini C, Schuh CM, Barrera NP, Aguayo S. Ultrastructural characterisation of young and aged dental enamel by atomic force microscopy. J Microsc 2022; 288:185-192. [PMID: 35621144 DOI: 10.1111/jmi.13126] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2022] [Revised: 04/28/2022] [Accepted: 05/19/2022] [Indexed: 11/28/2022]
Abstract
Recent advances in atomic force microscopy (AFM) have allowed the characterisation of dental-associated biomaterials and biological surfaces with high-resolution. In this context, the topography of dental enamel - the hardest mineralised tissue in the body - has been explored with AFM-based approaches at the micro-scale. With age, teeth are known to suffer changes that can impact their structural stability and function; however, changes in enamel structure because of ageing have not yet been explored with nanoscale resolution. Therefore, the aim of this exploratory work was to optimise an approach to characterise the ultrastructure of dental enamel and determine potential differences in topography, hydroxyapatite (HA) crystal size, and surface roughness at the nanoscale associated to ageing. For this, a total of six teeth were collected from human donors from which enamel specimens were prepared. By employing intermittent contact (AC mode) imaging, HA crystals were characterised in both transversal and longitudinal orientation (respect to surface plane) with high-resolution in environmental conditions. The external enamel surface displayed the presence of a pellicle-like coating on its surface, that was not observable on cleaned specimens. Acid-etching exposed crystals that were imaged and morphologically characterised in high-resolution at the nanoscale in both the external and internal regions of enamel in older and younger specimens. Our results demonstrated important individual variations in HA crystal width and roughness parameters across the analysed specimens; however, an increase in surface roughness and decrease in HA width was observed for the pooled older external enamel group compared to younger specimens. Overall, high-resolution AFM was an effective approach for the qualitative and quantitative characterisation of human dental enamel ultrastructure. Future work should focus on exploring the ageing of dental enamel with increased sample sizes to compensate for individual differences as well as other potential confounding factors such as behavioural habits and mechanical forces. Lay abstract: Currently, advanced microscopy techniques such as atomic force microscopy (AFM) can be used to characterise surfaces relevant to dentistry with great detail. Among these surfaces of interest, dental enamel - the hardest mineralised tissue in the body- is important as it protects the deeper areas of the tooth from harmful stimuli such as sudden temperature changes, bacterial penetration, and chemical attack. Also, dental enamel is an important surface for the adhesion of some types of dental restorations; thus, its structure and organisation is highly relevant for both dental scientists and clinicians. With age, teeth are known to suffer changes that can impact their structural stability and function; however, changes in enamel structure as a result of ageing have not yet been explored with nanoscale resolution. It is necessary to develop and optimise AFM-based techniques in order to process specimens from dental samples across different age groups for ageing-associated nanoscale studies in the future. Therefore, the aim of this investigation was to optimise an approach to characterise the ultrastructure of dental enamel and determine potential differences in enamel topography, hydroxyapatite (HA) crystal size, and surface roughness at the nanoscale associated to ageing. For this, human enamel specimens obtained from a total of six teeth were collected and analysed with AFM, and HA crystals were characterised in both transversal and longitudinal orientation with high-resolution in environmental conditions. Upon AFM observation, sound superficial enamel displayed the presence of a pellicle-like coating on its surface, that was not observable after specimens were cleaned. Furthermore, acid-etching exposed HA crystals that were imaged and morphologically characterised in high-resolution at the nanoscale across different regions of enamel in older and younger specimens. We observed important individual variations in HA crystal width and roughness parameters across the analysed specimens and groups, suggesting individual as well as age-associated differences. Overall, high-resolution AFM was an effective approach for the qualitative and quantitative characterisation of human dental enamel ultrastructure at the nanometer range with minimal sample preparation. This proof-of-concept work can pave the way for future studies employing increased sample sizes to compensate for individual differences and population level factors. This article is protected by copyright. All rights reserved.
Collapse
Affiliation(s)
- Camila Leiva-Sabadini
- School of Dentistry, Faculty of Medicine, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Christina Map Schuh
- Centro de Medicina Regenerativa, Facultad de Medicina Clínica Alemana-Universidad del Desarrollo, Santiago, Chile
| | - Nelson P Barrera
- Department of Physiology, Faculty of Biological Sciences, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Sebastian Aguayo
- School of Dentistry, Faculty of Medicine, Pontificia Universidad Católica de Chile, Santiago, Chile.,Institute for Biological and Medical Engineering, Schools of Engineering, Medicine and Biological Sciences, Pontificia Universidad Católica de Chile, Santiago, Chile
| |
Collapse
|
6
|
Lozano B, Santibañez J, Severino N, Saldias C, Vera M, Retamal J, Torres S, Barrera NP. Hypothesis: How far are we from predicting multi-drug interactions during treatment for COVID-19 infection? Br J Pharmacol 2022; 179:3831-3838. [PMID: 35180811 DOI: 10.1111/bph.15819] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2021] [Revised: 01/04/2022] [Accepted: 01/28/2022] [Indexed: 11/27/2022] Open
Abstract
Seriously ill patients infected with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and hospitalized in intensive care units (ICUs) are commonly given a combination of drugs, a process known as multi-drug treatment. After extracting data on drug-drug interactions with clinical relevance from available online platforms, we hypothesize that an overall interaction map can be generated for all drugs administered. Furthermore, by combining this approach with simulations of cellular biochemical pathways, we may be able to explain the general clinical outcome. Finally, we postulate that by applying this strategy retrospectively to a cohort of patients hospitalized in ICU, a prediction of the timing of developing acute kidney injury (AKI) could be made. Whether or not this approach can be extended to other diseases is uncertain. Still, we believe it represents a valuable pharmacological insight to help improve clinical outcomes for severely ill patients.
Collapse
Affiliation(s)
- Benjamin Lozano
- Department of Physiology, Faculty of Biological Sciences, Pontificia Universidad Católica de, Chile
| | - Javier Santibañez
- Department of Mathematics Engineering, Faculty of Mathematical and Physical Sciences, Universidad de, Chile
| | - Nicolás Severino
- Department of Intensive Medicine, Faculty of Medicine, Pontificia Universidad Católica de, Chile
| | - Cristina Saldias
- School of Medicine, Faculty of Medicine, Universidad de Valparaíso
| | - Magdalena Vera
- Department of Intensive Medicine, Faculty of Medicine, Pontificia Universidad Católica de, Chile
| | - Jaime Retamal
- Department of Intensive Medicine, Faculty of Medicine, Pontificia Universidad Católica de, Chile
| | - Soledad Torres
- CIMFAV, Faculty of Engineering, Universidad de Valparaíso
| | - Nelson P Barrera
- Department of Physiology, Faculty of Biological Sciences, Pontificia Universidad Católica de, Chile
| |
Collapse
|
7
|
Schuh CMAP, Leiva-Sabadini C, Huang S, Barrera NP, Bozec L, Aguayo S. Nanomechanical and Molecular Characterization of Aging in Dentinal Collagen. J Dent Res 2022; 101:840-847. [PMID: 35130787 DOI: 10.1177/00220345211072484] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
Methylglyoxal (MGO) is an important molecule derived from glucose metabolism with the capacity of attaching to collagen and generating advanced glycation end products (AGEs), which accumulate in tissues over time and are associated with aging and diseases. However, the accumulation of MGO-derived AGEs in dentin and their effect on the nanomechanical properties of dentinal collagen remain unknown. Thus, the aim of the present study was to quantify MGO-based AGEs in the organic matrix of human dentin as a function of age and associate these changes with alterations in the nanomechanical and ultrastructural properties of dentinal collagen. For this, 12 healthy teeth from <26-y-old and >50-y-old patients were collected and prepared to obtain crown and root dentin discs. Following demineralization, MGO-derived AGEs were quantified with a competitive ELISA. In addition, atomic force microscopy nanoindentation was utilized to measure changes in elastic modulus in peritubular and intertubular collagen fibrils. Finally, principal component analysis was carried out to determine aging profiles for crown and root dentin. Results showed an increased presence of MGO AGEs in the organic matrix of dentin in the >50-y-old specimens as compared with the <26-y-old specimens in crown and root. Furthermore, an increase in peritubular and intertubular collagen elasticity was observed in the >50-y-old group associated with ultrastructural changes in the organic matrix as determined by atomic force microscopy analysis. Furthermore, principal component analysis loading plots suggested different "aging profiles" in crown and root dentin, which could have important therapeutic implications in restorative and adhesive dentistry approaches. Overall, these results demonstrate that the organic matrix of human dentin undergoes aging-related changes due to MGO-derived AGEs with important changes in the nanomechanical behavior of collagen that may affect diagnostic and restorative procedures in older people.
Collapse
Affiliation(s)
- C M A P Schuh
- Centro de Medicina Regenerativa, Facultad de Medicina Clínica Alemana-Universidad del Desarrollo, Santiago, Chile
| | - C Leiva-Sabadini
- Dentistry School, Faculty of Medicine, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - S Huang
- Faculty of Dentistry, University of Toronto, Toronto, Canada
| | - N P Barrera
- Department of Physiology, Faculty of Biological Sciences, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - L Bozec
- Faculty of Dentistry, University of Toronto, Toronto, Canada
| | - S Aguayo
- Dentistry School, Faculty of Medicine, Pontificia Universidad Católica de Chile, Santiago, Chile.,Institute for Biological and Medical Engineering, Schools of Engineering, Medicine and Biological Sciences, Pontificia Universidad Católica de Chile, Santiago, Chile
| |
Collapse
|
8
|
Leiva-Sabadini C, Alvarez S, Barrera NP, Schuh CMAP, Aguayo S. Antibacterial Effect of Honey-Derived Exosomes Containing Antimicrobial Peptides Against Oral Streptococci. Int J Nanomedicine 2021; 16:4891-4900. [PMID: 34321877 PMCID: PMC8312616 DOI: 10.2147/ijn.s315040] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2021] [Accepted: 06/17/2021] [Indexed: 12/13/2022] Open
Abstract
Purpose Recently, our group found exosome-like extracellular vesicles (EVs) in Apis mellifera honey displaying strong antibacterial effects; however, the underlying mechanism is still not understood. Thus, the aim of this investigation was to characterize the molecular and nanomechanical properties of A. mellifera honey-derived EVs in order to elucidate the mechanisms behind their antibacterial effect, as well as to determine differential antibiofilm properties against relevant oral streptococci. Methods A. mellifera honey-derived EVs (HEc-EVs) isolated via ultracentrifugation were characterized with Western Blot and ELISA to determine the presence of specific exosomal markers and antibacterial cargo, and atomic force microscopy (AFM) was utilized to explore their ultrastructural and nanomechanical properties via non-destructive immobilization onto poly-L-lysine substrates. Furthermore, the effect of HEc-EVs on growth and biofilm inhibition of S. mutans was explored with microplate assays and compared to S. sanguinis. AFM was utilized to describe ultrastructural and nanomechanical alterations such as cell wall elasticity changes following HEc-EV exposure. Results Molecular characterization of HEc-EVs identified for the first time important conserved exosome markers such as CD63 and syntenin, and the antibacterial molecules MRJP1, defensin-1 and jellein-3 were found as intravesicular cargo. Nanomechanical characterization revealed that honey-derived EVs were mostly <150nm, with elastic modulus values in the low MPa range, comparable to EVs from other biological sources. Furthermore, incubating oral streptococci with EVs confirmed their antibacterial and antibiofilm capacities, displaying an increased effect on S. mutans compared to S. sanguinis. AFM nanocharacterization showed topographical and nanomechanical alterations consistent with membrane damage on S. mutans. Conclusion Honey is a promising new source of highly active EVs with exosomal origin, containing a number of antibacterial peptides as cargo molecules. Furthermore, the differential effect of HEC-EVs on S. mutans and S. sanguinis may serve as a novel biofilm-modulating strategy in dental caries.
Collapse
Affiliation(s)
- Camila Leiva-Sabadini
- Dentistry School, Faculty of Medicine, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Simon Alvarez
- Centro de Medicina Regenerativa, Facultad de Medicina Clínica Alemana-Universidad del Desarrollo, Santiago, Chile
| | - Nelson P Barrera
- Department of Physiology, Faculty of Biological Sciences, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Christina M A P Schuh
- Centro de Medicina Regenerativa, Facultad de Medicina Clínica Alemana-Universidad del Desarrollo, Santiago, Chile
| | - Sebastian Aguayo
- Dentistry School, Faculty of Medicine, Pontificia Universidad Católica de Chile, Santiago, Chile.,Institute for Biological and Medical Engineering, Schools of Engineering, Medicine and Biological Sciences, Pontificia Universidad Católica de Chile, Santiago, Chile
| |
Collapse
|
9
|
Ramírez OJ, Alvarez S, Contreras-Kallens P, Barrera NP, Aguayo S, Schuh CMAP. Type I collagen hydrogels as a delivery matrix for royal jelly derived extracellular vesicles. Drug Deliv 2021; 27:1308-1318. [PMID: 32924637 PMCID: PMC7534280 DOI: 10.1080/10717544.2020.1818880] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Throughout the last decade, extracellular vesicles (EVs) have become increasingly popular
in several areas of regenerative medicine. Recently, Apis
mellifera royal jelly EVs (RJ EVs) were shown to display favorable wound
healing properties such as stimulation of mesenchymal stem cell migration and inhibition
of staphylococcal biofilms. However, the sustained and effective local delivery of EVs in
non-systemic approaches – such as patches for chronic cutaneous wounds – remains an
important challenge for the development of novel EV-based wound healing therapies.
Therefore, the present study aimed to assess the suitability of type I collagen -a
well-established biomaterial for wound healing – as a continuous delivery matrix. RJ EVs
were integrated into collagen gels at different concentrations, where gels containing
2 mg/ml collagen were found to display the most stable release kinetics. Functionality of
released RJ EVs was confirmed by assessing fibroblast EV uptake and migration in a wound
healing assay. We could demonstrate reliable EV uptake into fibroblasts with a sustained
pro-migratory effect for up to 7 d. Integrating fibroblasts into the RJ EV-containing
collagen gel increased the contractile capacity of these cells, confirming availability of
RJ EVs to fibroblasts within the collagen gel. Furthermore, EVs released from collagen
gels were found to inhibit Staphylococcus aureus ATCC 29213
biofilm formation. Overall, our results suggest that type I collagen could be utilized as
a reliable, reproducible release system to deliver functional RJ EVs for wound healing
therapies.
Collapse
Affiliation(s)
- Orlando J Ramírez
- Facultad de Medicina, Centro de Medicina Regenerativa, Clínica Alemana Universidad del Desarrollo, Santiago, Chile
| | - Simón Alvarez
- Facultad de Medicina, Centro de Medicina Regenerativa, Clínica Alemana Universidad del Desarrollo, Santiago, Chile
| | - Pamina Contreras-Kallens
- Facultad de Medicina, Centro de Medicina Regenerativa, Clínica Alemana Universidad del Desarrollo, Santiago, Chile
| | - Nelson P Barrera
- Faculty of Biological Sciences, Department of Physiology, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Sebastian Aguayo
- Faculty of Medicine, Dentistry School, Pontificia Universidad Católica de Chile, Santiago, Chile.,Institute for Biological and Medical Engineering, Schools of Engineering, Medicine and Biological Sciences, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Christina M A P Schuh
- Facultad de Medicina, Centro de Medicina Regenerativa, Clínica Alemana Universidad del Desarrollo, Santiago, Chile
| |
Collapse
|
10
|
Caro-Lara L, Ramos-Moore E, Vargas IT, Walczak M, Fuentes C, Gómez AV, Barrera NP, Castillo J, Pizarro G. Initial adhesion suppression of biofilm-forming and copper-tolerant bacterium Variovorax sp. on laser microtextured copper surfaces. Colloids Surf B Biointerfaces 2021; 202:111656. [PMID: 33735634 DOI: 10.1016/j.colsurfb.2021.111656] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2020] [Revised: 02/13/2021] [Accepted: 02/22/2021] [Indexed: 11/24/2022]
Abstract
The growth of detrimental biofilms on metal surfaces affects their structural performance and lifespan. Microtopographic texturization has emerged as an approach to suppress biofilm growth by preventing the initial stages of bacterial adhesion. This work studies the effects of linear pattern copper texturization on the initial adhesion steps of the biofilm-forming and copper-resistant bacterium Variovorax sp. Linear patterns with 4.7, 6.8, 14, and 18 μm periodicity were produced by direct laser interference patterning (DLIP) on copper coupons. Surface features were characterized by microscopic and spectroscopic techniques, and bacterial adhesion behavior was characterized by epifluorescence microscopy and functionalization of atomic force microscopy tips. We found a periodicity of 4.7 μm as the most efficient pattern to suppress Variovorax sp. initial adhesion by 31.1 % with respect to the nontextured surface. Preferential settlement in hummocks over hollows was observed for patterns with 14 and 18 μm periodicity, with adhesion events showing higher frequency in these topographies than patterns with periodicities of 4.7 and 6.8 μm. Our results highlight an understanding of the initial bacteria-copper adhesion and settlement behavior, thus contributing to the potential development of innocuous strategies for controlling biofilm growth on copper-based materials.
Collapse
Affiliation(s)
- Luis Caro-Lara
- Departamento de Ingeniería Hidráulica y Ambiental, Pontificia Universidad Católica de Chile, Santiago, Chile; Marine Energy Research & Innovation Center. Chile.
| | - Esteban Ramos-Moore
- Instituto de Física, Facultad de Física, Pontificia Universidad Católica de Chile Casilla 306, Av. Vicuña Mackenna 4860, Macul, Santiago, Chile; Centro de Investigación en Nanotecnología y Materiales Avanzados (CIEN-UC), Pontificia Universidad Católica de Chile, Av. Vicuña Mackenna 4860, Macul, Santiago, Chile.
| | - Ignacio T Vargas
- Departamento de Ingeniería Hidráulica y Ambiental, Pontificia Universidad Católica de Chile, Santiago, Chile; Marine Energy Research & Innovation Center. Chile
| | - Magdalena Walczak
- Marine Energy Research & Innovation Center. Chile; Departamento de Ingeniería Mecánica y Metalúrgica, Pontificia Universidad Católica de Chile, Av. Vicuña Mackenna 4860, Macul, Santiago, Chile
| | - Christian Fuentes
- Departamento de Fisiología, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Andrea V Gómez
- Departamento de Fisiología, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Santiago, Chile; Centro de Biología Celular y Biomedicina (CEBICEM), Facultad de Medicina y Ciencia, Universidad San Sebastián, Santiago, Chile
| | - Nelson P Barrera
- Departamento de Fisiología, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Javiera Castillo
- Departamento de Ingeniería Hidráulica y Ambiental, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Gonzalo Pizarro
- Departamento de Ingeniería Hidráulica y Ambiental, Pontificia Universidad Católica de Chile, Santiago, Chile; Marine Energy Research & Innovation Center. Chile
| |
Collapse
|
11
|
Naulin PA, Lozano B, Fuentes C, Liu Y, Schmidt C, Contreras JE, Barrera NP. Polydisperse molecular architecture of connexin 26/30 heteromeric hemichannels revealed by atomic force microscopy imaging. J Biol Chem 2020; 295:16499-16509. [PMID: 32887797 PMCID: PMC7864052 DOI: 10.1074/jbc.ra119.012128] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2019] [Revised: 08/31/2020] [Indexed: 11/06/2022] Open
Abstract
Connexin (Cx) protein forms hemichannels and gap junctional channels, which play diverse and profound roles in human physiology and diseases. Gap junctions are arrays of intercellular channels formed by the docking of two hemichannels from adjacent cells. Each hexameric hemichannel contains the same or different Cx isoform. Although homomeric Cxs forms have been largely described functionally and structurally, the stoichiometry and arrangement of heteromeric Cx channels remain unknown. The latter, however, are widely expressed in human tissues and variation might have important implications on channel function. Investigating properties of heteromeric Cx channels is challenging considering the high number of potential subunit arrangements and stoichiometries, even when only combining two Cx isoforms. To tackle this problem, we engineered an HA tag onto Cx26 or Cx30 subunits and imaged hemichannels that were liganded by Fab-epitope antibody fragments via atomic force microscopy. For Cx26-HA/Cx30 or Cx30-HA/Cx26 heteromeric channels, the Fab-HA binding distribution was binomial with a maximum of three Fab-HA bound. Furthermore, imaged Cx26/Cx30-HA triple liganded by Fab-HA showed multiple arrangements that can be derived from the law of total probabilities. Atomic force microscopy imaging of ringlike structures of Cx26/Cx30-HA hemichannels confirmed these findings and also detected a polydisperse distribution of stoichiometries. Our results indicate a dominant subunit stoichiometry of 3Cx26:3Cx30 with the most abundant subunit arrangement of Cx26-Cx26-Cx30-Cx26-Cx30-Cx30. To our knowledge, this is the first time that the molecular architecture of heteromeric Cx channels has been revealed, thus providing the basis to explore the functional effect of these channels in biology.
Collapse
Affiliation(s)
- Pamela A Naulin
- Department of Physiology, Faculty of Biological Sciences, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Benjamin Lozano
- Department of Physiology, Faculty of Biological Sciences, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Christian Fuentes
- Department of Physiology, Faculty of Biological Sciences, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Yu Liu
- Department of Pharmacology, Physiology and Neuroscience, New Jersey Medical School, Rutgers University, Newark, New Jersey, USA
| | - Carla Schmidt
- Department of Chemistry, University of Oxford, Oxford, United Kingdom
| | - Jorge E Contreras
- Department of Pharmacology, Physiology and Neuroscience, New Jersey Medical School, Rutgers University, Newark, New Jersey, USA
| | - Nelson P Barrera
- Department of Physiology, Faculty of Biological Sciences, Pontificia Universidad Católica de Chile, Santiago, Chile.
| |
Collapse
|
12
|
Bergler F, Fuentes C, Kadir MF, Navarrete C, Supple J, Barrera NP, Edwardson JM. Activation of P2X4 receptors induces an increase in the area of the extracellular region and a decrease in receptor mobility. FEBS Lett 2020; 594:4381-4389. [PMID: 32979222 DOI: 10.1002/1873-3468.13942] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2020] [Accepted: 09/15/2020] [Indexed: 11/09/2022]
Abstract
The P2X4 receptor (P2X4R) is an ATP-gated cation channel. Here, we used fast-scan atomic force microscopy (AFM) to visualize changes in the structure and mobility of individual P2X4Rs in response to activation. P2X4Rs were purified from detergent extracts of transfected cells and integrated into lipid bilayers. Activation resulted in a rapid (2 s) and substantial (10-20 nm2 ) increase in the cross-sectional area of the extracellular region of the receptor and a corresponding decrease in receptor mobility. Both effects were blocked by the P2X4R antagonist 5-BDBD. Addition of cholesterol to the bilayer reduced receptor mobility, although the ATP-induced reduction in mobility was still observed. We suggest that the observed responses to activation may have functional consequences for purinergic signalling.
Collapse
Affiliation(s)
- Frederik Bergler
- Department of Pharmacology, University of Cambridge, Cambridge, UK
| | - Christian Fuentes
- Department of Pharmacology, University of Cambridge, Cambridge, UK.,Department of Physiology, Faculty of Biological Sciences, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Md Fahim Kadir
- Department of Pharmacology, University of Cambridge, Cambridge, UK
| | - Camilo Navarrete
- Department of Pharmacology, University of Cambridge, Cambridge, UK.,Department of Physiology, Faculty of Biological Sciences, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Jack Supple
- Department of Pharmacology, University of Cambridge, Cambridge, UK
| | - Nelson P Barrera
- Department of Physiology, Faculty of Biological Sciences, Pontificia Universidad Católica de Chile, Santiago, Chile
| | | |
Collapse
|
13
|
Abstract
Biofilm-mediated oral diseases such as dental caries and periodontal disease remain highly prevalent in populations worldwide. Biofilm formation initiates with the attachment of primary colonizers onto surfaces, and in the context of caries, the adhesion of oral streptococci to dentinal collagen is crucial for biofilm progression. It is known that dentinal collagen suffers from glucose-associated crosslinking as a function of aging or disease; however, the effect of collagen crosslinking on the early adhesion and subsequent biofilm formation of relevant oral streptococci remains unknown. Therefore, the aim of this work was to determine the impact of collagen glycation on the initial adhesion of primary colonizers such as Streptococcus mutans UA159 and Streptococcus sanguinis SK 36, as well as its effect on the early stages of streptococcal biofilm formation in vitro. Type I collagen matrices were crosslinked with either glucose or methylglyoxal. Atomic force microscopy nanocharacterization revealed morphologic and mechanical changes within the collagen matrix as a function of crosslinking, such as a significantly increased elastic modulus in crosslinked fibrils. Increased nanoadhesion forces were observed for S. mutans on crosslinked collagen surfaces as compared with the control, and retraction curves obtained for both streptococcal strains demonstrated nanoscale unbinding behavior consistent with bacterial adhesin-substrate coupling. Overall, glucose-crosslinked substrates specifically promoted the initial adhesion, biofilm formation, and insoluble extracellular polysaccharide production of S. mutans, while methylglyoxal treatment reduced biofilm formation for both strains. Changes in the adhesion behavior and biofilm formation of oral streptococci as a function of collagen glycation could help explain the biofilm dysbiosis seen in older people and patients with diabetes. Further studies are necessary to determine the influence of collagen crosslinking on the balance between acidogenic and nonacidogenic streptococci to aid in the development of novel preventive and therapeutic treatment against dental caries in these patients.
Collapse
Affiliation(s)
- C M A P Schuh
- Centro de Medicina Regenerativa, Facultad de Medicina Clínica Alemana-Universidad del Desarrollo, Santiago, Chile
| | - B Benso
- School of Dentistry, Faculty of Medicine, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - P A Naulin
- Department of Physiology, Faculty of Biological Sciences, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - N P Barrera
- Department of Physiology, Faculty of Biological Sciences, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - L Bozec
- Faculty of Dentistry, University of Toronto, Toronto, Canada
| | - S Aguayo
- School of Dentistry, Faculty of Medicine, Pontificia Universidad Católica de Chile, Santiago, Chile.,Institute for Biological and Medical Engineering, Schools of Engineering, Medicine and Biological Sciences, Pontificia Universidad Católica de Chile, Santiago, Chile
| |
Collapse
|
14
|
Braz JKFS, Martins GM, Morales N, Naulin P, Fuentes C, Barrera NP, O Vitoriano J, Rocha HAO, Oliveira MF, Alves C, Moura CEB. Live endothelial cells on plasma-nitrided and oxidized titanium: An approach for evaluating biocompatibility. Mater Sci Eng C Mater Biol Appl 2020; 113:111014. [PMID: 32487415 DOI: 10.1016/j.msec.2020.111014] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/27/2019] [Revised: 03/18/2020] [Accepted: 04/22/2020] [Indexed: 02/03/2023]
Abstract
We evaluated the effects of titanium plasma nitriding and oxidation on live endothelial cell viscoelasticity. For this, mechanically polished titanium surfaces and two surfaces treated by planar cathode discharge in nitriding (36N2 and 24H2) and oxidant (36O2 and 24H2). Surfaces were characterized regarding wettability, roughness and chemical composition. Rabbit aortic endothelial cells (RAECs) were cultured on the titanium surfaces. Cell morphology, viability and viscoelasticity were evaluated by scanning electron microscopy (SEM), methyl thiazolyl tetrazolium (MTT) assay and atomic force microscopy (AFM), respectively. Grazing Incidence X-ray Diffraction confirmed the presence of TiN0,26 on the surface (grazing angle theta 1°) of the nitrided samples, decreasing with depth. On the oxidized surface had the formation of TiO3 on the material surface (Theta 1°) and in the deeper layers was noted, with a marked presence of Ti (Theta 3°). Both plasma treatments increased surface roughness and they are hydrophilic (angle <90°). However, oxidation led to a more hydrophilic titanium surface (66.59° ± 3.65 vs. 76.88° ± 2.68; p = 0.001) due to titanium oxide films in their stoichiometric varieties (Ti3O, TiO2, Ti6O), especially Ti3O. Despite focal adhesion on the surfaces, viability was different after 24 h, as cell viability on the oxidized surface was higher than on the nitrided surface (9.1 × 103 vs. 4.5 × 103cells; p < 0.05). This can be explained by analyzing the viscoelastic property of the cellular cytoskeleton (nuclear and peripheral) by AFM. Surface oxidation significantly increased RAECs viscoelasticity at cell periphery, in comparison to the nucleus (2.36 ± 0.3 vs. 1.5 ± 0.4; p < 0.05), and to the RAECs periphery in contact with nitrided surfaces (1.36 ± 0.7; p < 0.05) and polished surfaces (1.55 ± 0.6; p < 0.05). Taken together, our results have shown that titanium plasma treatment directly increased cell viscoelasticity via surface oxidation, and this mechanobiological property subsequently increased biocompatibility.
Collapse
Affiliation(s)
- Janine Karla F S Braz
- Department of Animal Science, Universidade Federal Rural do Semi-Árido, Mossoró, Brazil; Escola Multicampi de Ciências Médicas do Rio Grande do Norte, Universidade Federal do Rio Grande do Norte, Brazil.
| | - Gabriel Moura Martins
- Department of Animal Science, Universidade Federal Rural do Semi-Árido, Mossoró, Brazil
| | - Nicole Morales
- Department of Physiology, Faculty of Biological Sciences, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Pamela Naulin
- Department of Physiology, Faculty of Biological Sciences, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Christian Fuentes
- Department of Physiology, Faculty of Biological Sciences, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Nelson P Barrera
- Department of Physiology, Faculty of Biological Sciences, Pontificia Universidad Católica de Chile, Santiago, Chile.
| | - Jussier O Vitoriano
- Laboratório de Plasma Aplicado a Agricultura, Saúde e Meio Ambiente, Universidade Federal do Rio Grande do Norte, Brazil
| | - Hugo A O Rocha
- Department of Biochemistry, Universidade Federal do Rio Grande do Norte, Natal, Brazil.
| | - Moacir F Oliveira
- Department of Animal Science, Universidade Federal Rural do Semi-Árido, Mossoró, Brazil.
| | - Clodomiro Alves
- Laboratório de Plasma Aplicado a Agricultura, Saúde e Meio Ambiente, Universidade Federal do Rio Grande do Norte, Brazil.
| | - Carlos Eduardo B Moura
- Department of Animal Science, Universidade Federal Rural do Semi-Árido, Mossoró, Brazil.
| |
Collapse
|
15
|
Casanova-Morales N, Figueroa NL, Alfaro K, Montenegro F, Barrera NP, Maze JR, Wilson CAM, Conejeros P. Structural characterization of the saxitoxin-targeting APTSTX1 aptamer using optical tweezers and molecular dynamics simulations. PLoS One 2019; 14:e0222468. [PMID: 31697710 PMCID: PMC6837747 DOI: 10.1371/journal.pone.0222468] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2019] [Accepted: 08/30/2019] [Indexed: 02/07/2023] Open
Abstract
Optical tweezers have enabled the exploration of picoNewton forces and dynamics in single-molecule systems such as DNA and molecular motors. In this work, we used optical tweezers to study the folding/unfolding dynamics of the APTSTX1-aptamer, a single-stranded DNA molecule with high affinity for saxitoxin (STX), a lethal neurotoxin. By measuring the transition force during (un)folding processes, we were able to characterize and distinguish the conformational changes of this aptamer in the presence of magnesium ions and toxin. This work was supported by molecular dynamics (MD) simulations to propose an unfolding mechanism of the aptamer-Mg+2 complex. Our results are a step towards the development of new aptamer-based STX sensors that are potentially cheaper and more sensitive than current alternatives.
Collapse
Affiliation(s)
- Nathalie Casanova-Morales
- Instituto de Física, Pontificia Universidad Católica de Chile, Santiago, Chile
- Departamento de Bioquímica y Biología Molecular, Facultad de Ciencias Químicas y Farmacéuticas, Universidad de Chile, Santiago, Chile
- Facultad de Artes Liberales, Universidad Adolfo Ibáñez, Santiago, Chile
| | | | - Karol Alfaro
- CIGREN. Instituto de Biología. Facultad de Ciencias. Universidad de Valparaíso, Valparaíso, Chile
| | - Felipe Montenegro
- Department of Physiology, Faculty of Biological Sciences, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Nelson P. Barrera
- Department of Physiology, Faculty of Biological Sciences, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - J. R. Maze
- Instituto de Física, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Christian A. M. Wilson
- Departamento de Bioquímica y Biología Molecular, Facultad de Ciencias Químicas y Farmacéuticas, Universidad de Chile, Santiago, Chile
| | - Pablo Conejeros
- CIGREN. Instituto de Biología. Facultad de Ciencias. Universidad de Valparaíso, Valparaíso, Chile
| |
Collapse
|
16
|
Dawe GB, Kadir MF, Venskutonytė R, Perozzo AM, Yan Y, Alexander RP, Navarrete C, Santander EA, Arsenault M, Fuentes C, Aurousseau MR, Frydenvang K, Barrera NP, Kastrup JS, Edwardson JM, Bowie D. Nanoscale Mobility of the Apo State and TARP Stoichiometry Dictate the Gating Behavior of Alternatively Spliced AMPA Receptors. Neuron 2019; 102:976-992.e5. [DOI: 10.1016/j.neuron.2019.03.046] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2018] [Revised: 03/08/2019] [Accepted: 03/28/2019] [Indexed: 12/19/2022]
|
17
|
Latapiat V, Rodríguez FE, Godoy F, Montenegro FA, Barrera NP, Huidobro-Toro JP. P2X4 Receptor in Silico and Electrophysiological Approaches Reveal Insights of Ivermectin and Zinc Allosteric Modulation. Front Pharmacol 2017; 8:918. [PMID: 29326590 PMCID: PMC5737101 DOI: 10.3389/fphar.2017.00918] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2017] [Accepted: 12/01/2017] [Indexed: 12/21/2022] Open
Abstract
Protein allosteric modulation is a pillar of metabolic regulatory mechanisms; this concept has been extended to include ion channel regulation. P2XRs are ligand-gated channels activated by extracellular ATP, sensitive to trace metals and other chemicals. By combining in silico calculations with electrophysiological recordings, we investigated the molecular basis of P2X4R modulation by Zn(II) and ivermectin, an antiparasite drug currently used in veterinary medicine. To this aim, docking studies, molecular dynamics simulations and non-bonded energy calculations for the P2X4R in the apo and holo states or in the presence of ivermectin and/or Zn(II) were accomplished. Based on the crystallized Danio rerio P2X4R, the rat P2X4R, P2X2R, and P2X7R structures were modeled, to determine ivermectin binding localization. Calculations revealed that its allosteric site is restricted to transmembrane domains of the P2X4R; the role of Y42 and W46 plus S341 and non-polar residues were revealed as essential, and are not present in the homologous P2X2R or P2X7R transmembrane domains. This finding was confirmed by preferential binding conformations and electrophysiological data, revealing P2X4R modulator specificity. Zn(II) acts in the P2X4R extracellular domain neighboring the SS3 bridge. Molecular dynamics in the different P2X4R states revealed allosterism-induced stability. Pore and lateral fenestration measurements of the P2X4R showed conformational changes in the presence of both modulators compatible with a larger opening of the extracellular vestibule. Electrophysiological studies demonstrated additive effects in the ATP-gated currents by joint applications of ivermectin plus Zn(II). The C132A P2X4R mutant was insensitive to Zn(II); but IVM caused a 4.9 ± 0.7-fold increase in the ATP-evoked currents. Likewise, the simultaneous application of both modulators elicited a 7.1 ± 1.7-fold increase in the ATP-gated current. Moreover, the C126A P2X4R mutant evoked similar ATP-gated currents comparable to those of wild-type P2X4R. Finally, a P2X4/2R chimera did not respond to IVM but Zn(II) elicited a 2.7 ± 0.6-fold increase in the ATP-gated current. The application of IVM plus Zn(II) evoked a 2.7 ± 0.9-fold increase in the ATP-gated currents. In summary, allosteric modulators caused additive ATP-gated currents; consistent with lateral fenestration enlargement. Energy calculations demonstrated a favorable transition of the holo receptor state following both allosteric modulators binding, as expected for allosteric interactions.
Collapse
Affiliation(s)
- Verónica Latapiat
- Laboratorio de Farmacología de Nucleótidos, Departamento de Biología, Facultad de Química y Biología, Estación Central, Universidad de Santiago de Chile, Santiago, Chile
| | - Felipe E Rodríguez
- Laboratorio de Farmacología de Nucleótidos, Departamento de Biología, Facultad de Química y Biología, Estación Central, Universidad de Santiago de Chile, Santiago, Chile
| | - Francisca Godoy
- Departamento de Fisiología, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Felipe A Montenegro
- Departamento de Fisiología, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Nelson P Barrera
- Departamento de Fisiología, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Juan P Huidobro-Toro
- Laboratorio de Farmacología de Nucleótidos, Departamento de Biología, Facultad de Química y Biología, Estación Central, Universidad de Santiago de Chile, Santiago, Chile.,Centro Desarrollo de Nanociencia y Nanotecnología, CEDENNA, Estación Central, Universidad de Santiago de Chile, Santiago, Chile
| |
Collapse
|
18
|
Montenegro FA, Cantero JR, Barrera NP. Combining Mass Spectrometry and X-Ray Crystallography for Analyzing Native-Like Membrane Protein Lipid Complexes. Front Physiol 2017; 8:892. [PMID: 29170643 PMCID: PMC5684187 DOI: 10.3389/fphys.2017.00892] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2017] [Accepted: 10/24/2017] [Indexed: 01/22/2023] Open
Abstract
Membrane proteins represent a challenging family of macromolecules, particularly related to the methodology aimed at characterizing their three-dimensional structure. This is mostly due to their amphipathic nature as well as requirements of ligand bindings to stabilize or control their function. Recently, Mass Spectrometry (MS) has become an important tool to identify the overall stoichiometry of native-like membrane proteins complexed to ligand bindings as well as to provide insights into the transport mechanism across the membrane, with complementary information coming from X-ray crystallography. This perspective article emphasizes MS findings coupled with X-ray crystallography in several membrane protein lipid complexes, in particular transporters, ion channels and molecular machines, with an overview of techniques that allows a more thorough structural interpretation of the results, which can help us to unravel hidden mysteries on the membrane protein function.
Collapse
Affiliation(s)
- Felipe A Montenegro
- Laboratory of Nanophysiology and Structural Biology, Department of Physiology, Faculty of Biological Sciences, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Jorge R Cantero
- Laboratory of Nanophysiology and Structural Biology, Department of Physiology, Faculty of Biological Sciences, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Nelson P Barrera
- Laboratory of Nanophysiology and Structural Biology, Department of Physiology, Faculty of Biological Sciences, Pontificia Universidad Católica de Chile, Santiago, Chile
| |
Collapse
|
19
|
Droguett K, Rios M, Carreño DV, Navarrete C, Fuentes C, Villalón M, Barrera NP. An autocrine ATP release mechanism regulates basal ciliary activity in airway epithelium. J Physiol 2017; 595:4755-4767. [PMID: 28422293 PMCID: PMC5509870 DOI: 10.1113/jp273996] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2016] [Accepted: 04/10/2017] [Indexed: 01/07/2023] Open
Abstract
KEY POINTS Extracellular ATP, in association with [Ca2+ ]i regulation, is required to maintain basal ciliary beat frequency. Increasing extracellular ATP levels increases ciliary beating in airway epithelial cells, maintaining a sustained response by inducing the release of additional ATP. Extracellular ATP levels in the millimolar range, previously associated with pathophysiological conditions of the airway epithelium, produce a transient arrest of ciliary activity. The regulation of ciliary beat frequency is dependent on ATP release by hemichannels (connexin/pannexin) and P2X receptor activation, the blockage of which may even stop ciliary movement. The force exerted by cilia, measured by atomic force microscopy, is reduced following extracellular ATP hydrolysis. This result complements the current understanding of the ciliary beating regulatory mechanism, with special relevance to inflammatory diseases of the airway epithelium that affect mucociliary clearance. ABSTRACT Extracellular nucleotides, including ATP, are locally released by the airway epithelium and stimulate ciliary activity in a [Ca2+ ]i -dependent manner after mechanical stimulation of ciliated cells. However, it is unclear whether the ATP released is involved in regulating basal ciliary activity and mediating changes in ciliary activity in response to chemical stimulation. In the present study, we evaluated ciliary beat frequency (CBF) and ciliary beating forces in primary cultures from mouse tracheal epithelium, using videomicroscopy and atomic force microscopy (AFM), respectively. Extracellular ATP levels and [Ca2+ ]i were measured by luminometric and fluorimetric assays, respectively. Uptake of ethidium bromide was measured to evaluate hemichannel functionality. We show that hydrolysis of constitutive extracellular ATP levels with apyrase (50 U ml-1 ) reduced basal CBF by 45% and ciliary force by 67%. The apyrase effect on CBF was potentiated by carbenoxolone, a hemichannel inhibitor, and oxidized ATP, an antagonist used to block P2X7 receptors, which reduced basal CBF by 85%. Additionally, increasing extracellular ATP levels (0.1-100 μm) increased CBF, maintaining a sustained response that was suppressed in the presence of carbenoxolone. We also show that high levels of ATP (1 mm), associated with inflammatory conditions, lowered basal CBF by reducing [Ca2+ ]i and hemichannel functionality. In summary, we provide evidence indicating that airway epithelium ATP release is the molecular autocrine mechanism regulating basal ciliary activity and is also the mediator of the ciliary response to chemical stimulation.
Collapse
Affiliation(s)
- Karla Droguett
- Department of Physiology, Faculty of Biological SciencesPontificia Universidad Católica de ChileSantiagoChile
| | - Mariana Rios
- Department of Physiology, Faculty of Biological SciencesPontificia Universidad Católica de ChileSantiagoChile
| | - Daniela V. Carreño
- Department of Physiology, Faculty of Biological SciencesPontificia Universidad Católica de ChileSantiagoChile
| | - Camilo Navarrete
- Department of Physiology, Faculty of Biological SciencesPontificia Universidad Católica de ChileSantiagoChile
| | - Christian Fuentes
- Department of Physiology, Faculty of Biological SciencesPontificia Universidad Católica de ChileSantiagoChile
| | - Manuel Villalón
- Department of Physiology, Faculty of Biological SciencesPontificia Universidad Católica de ChileSantiagoChile
| | - Nelson P. Barrera
- Department of Physiology, Faculty of Biological SciencesPontificia Universidad Católica de ChileSantiagoChile
| |
Collapse
|
20
|
Navarrete LC, Barrera NP, Huidobro-Toro JP. Vas deferens neuro-effector junction: from kymographic tracings to structural biology principles. Auton Neurosci 2014; 185:8-28. [PMID: 24956963 DOI: 10.1016/j.autneu.2014.05.010] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2013] [Revised: 05/14/2014] [Accepted: 05/20/2014] [Indexed: 11/29/2022]
Abstract
The vas deferens is a simple bioassay widely used to study the physiology of sympathetic neurotransmission and the pharmacodynamics of adrenergic drugs. The role of ATP as a sympathetic co-transmitter has gained increasing attention and furthered our understanding of its role in sympathetic reflexes. In addition, new information has emerged on the mechanisms underlying the storage and release of ATP. Both noradrenaline and ATP concur to elicit the tissue smooth muscle contractions following sympathetic reflexes or electrical field stimulation of the sympathetic nerve terminals. ATP and adenosine (its metabolic byproduct) are powerful presynaptic regulators of co-transmitter actions. In addition, neuropeptide Y, the third member of the sympathetic triad, is an endogenous modulator. The peptide plus ATP and/or adenosine play a significant role as sympathetic modulators of transmitter's release. This review focuses on the physiological principles that govern sympathetic co-transmitter activity, with special interest in defining the motor role of ATP. In addition, we intended to review the recent structural biology findings related to the topology of the P2X1R based on the crystallized P2X4 receptor from Danio rerio, or the crystallized adenosine A2A receptor as a member of the G protein coupled family of receptors as prototype neuro modulators. This review also covers structural elements of ectonucleotidases, since some members are found in the vas deferens neuro-effector junction. The allosteric principles that apply to purinoceptors are also reviewed highlighting concepts derived from receptor theory at the light of the current available structural elements. Finally, we discuss clinical applications of these concepts.
Collapse
Affiliation(s)
- L Camilo Navarrete
- Laboratorio de Estructura de Proteínas de Membrana y Señalización, Núcleo Milenio de Biología Estructural, NuBEs, Facultad de Ciencias Biológicas, P. Universidad Católica de Chile, Chile
| | - Nelson P Barrera
- Laboratorio de Estructura de Proteínas de Membrana y Señalización, Núcleo Milenio de Biología Estructural, NuBEs, Facultad de Ciencias Biológicas, P. Universidad Católica de Chile, Chile
| | - J Pablo Huidobro-Toro
- Laboratorio de Nucleótidos, Departamento de Biología, Facultad de Química y Biología, Universidad de Santiago de Chile, Chile.
| |
Collapse
|
21
|
Naulin PA, Liu Y, Harris A, Contreras JE, Barrera NP. Structural Studies of Heteromeric Connexin26/30 Hemichannels via Atomic Force Microscopy Imaging. Biophys J 2014. [DOI: 10.1016/j.bpj.2013.11.1558] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
|
22
|
Naulin PA, Alveal NA, Barrera NP. Toward atomic force microscopy and mass spectrometry to visualize and identify lipid rafts in plasmodesmata. Front Plant Sci 2014; 5:234. [PMID: 24910637 PMCID: PMC4038920 DOI: 10.3389/fpls.2014.00234] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/08/2013] [Accepted: 05/11/2014] [Indexed: 05/08/2023]
Abstract
Plant cell-to-cell communication is mediated by nanopores called plasmodesmata (PDs) which are complex structures comprising plasma membrane (PM), highly packed endoplasmic reticulum and numerous membrane proteins. Although recent advances on proteomics have led to insights into mechanisms of transport, there is still an inadequate characterization of the lipidic composition of the PM where membrane proteins are inserted. It has been postulated that PDs could be formed by lipid rafts, however no structural evidence has shown to visualize and analyse their lipid components. In this perspective article, we discuss proposed experiments to characterize lipid rafts and proteins in the PDs. By using atomic force microscopy (AFM) and mass spectrometry (MS) of purified PD vesicles it is possible to determine the presence of lipid rafts, specific bound proteins and the lipidomic profile of the PD under physiological conditions and after changing transport permeability. In addition, MS can determine the stoichiometry of intact membrane proteins inserted in lipid rafts. This will give novel insights into the role of membrane proteins and lipid rafts on the PD structure.
Collapse
Affiliation(s)
| | | | - Nelson P. Barrera
- *Correspondence: Nelson P. Barrera, Department of Physiology, Faculty of Biological Sciences, Pontificia Universidad Católica de Chile, Alameda 340, Santiago 8331150, Chile e-mail:
| |
Collapse
|
23
|
Balasuriya D, Goetze TA, Barrera NP, Stewart AP, Suzuki Y, Edwardson JM. α-Amino-3-hydroxy-5-methyl-4-isoxazole propionic acid (AMPA) and N-methyl-D-aspartate (NMDA) receptors adopt different subunit arrangements. J Biol Chem 2013; 288:21987-98. [PMID: 23760273 PMCID: PMC3724652 DOI: 10.1074/jbc.m113.469205] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
Ionotropic glutamate receptors are widely distributed in the central nervous system and play a major role in excitatory synaptic transmission. All three ionotropic glutamate subfamilies (i.e. AMPA-type, kainate-type, and NMDA-type) assemble as tetramers of four homologous subunits. There is good evidence that both heteromeric AMPA and kainate receptors have a 2:2 subunit stoichiometry and an alternating subunit arrangement. Recent studies based on presumed structural homology have indicated that NMDA receptors adopt the same arrangement. Here, we use atomic force microscopy imaging of receptor-antibody complexes to show that whereas the GluA1/GluA2 AMPA receptor assembles with an alternating (i.e. 1/2/1/2) subunit arrangement, the GluN1/GluN2A NMDA receptor adopts an adjacent (i.e. 1/1/2/2) arrangement. We conclude that the two types of ionotropic glutamate receptor are built in different ways from their constituent subunits. This surprising finding necessitates a reassessment of the assembly of these important receptors.
Collapse
Affiliation(s)
- Dilshan Balasuriya
- Department of Pharmacology, University of Cambridge, Tennis Court Road, Cambridge CB2 1PD, United Kingdom
| | | | | | | | | | | |
Collapse
|
24
|
Montenegro F, Barrera M, Alveal N, Cantero J, Brugues G, Barrera NP. Combined Mass Spectrometry and Molecular Dynamics to Study Membrane Protein Stability in Gas Phase. Biophys J 2013. [DOI: 10.1016/j.bpj.2012.11.1863] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022] Open
|
25
|
Morgner N, Montenegro F, Barrera NP, Robinson CV. Mass spectrometry--from peripheral proteins to membrane motors. J Mol Biol 2012; 423:1-13. [PMID: 22750574 PMCID: PMC4058634 DOI: 10.1016/j.jmb.2012.06.033] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2012] [Revised: 06/18/2012] [Accepted: 06/20/2012] [Indexed: 10/28/2022]
Abstract
That membrane protein complexes could survive in the gas phase had always seemed impossible. The lack of chargeable residues, high hydrophobicity, and poor solubility and the vast excess of detergent contributed to the view that it would not be possible to obtain mass spectra of intact membrane complexes. With the recent success in recording mass spectra of these complexes, first from recombinant sources and later from the cellular environment, many surprising properties of these gas phase membrane complexes have been revealed. The first of these was that the interactions between membrane and soluble subunits could survive in vacuum, without detergent molecules adhering to the complex. The second unexpected feature was that their hydrophobicity and, consequently, lower charge state did not preclude ionization. The final surprising finding was that these gas phase membrane complexes carry with them lipids, bound specifically in subunit interfaces. This provides us with an opportunity to distinguish annular lipids that surround the membrane complexes, from structural lipids that have a role in maintaining structure and subunit interactions. In this perspective, we track these developments and suggest explanations for the various discoveries made during this research.
Collapse
Affiliation(s)
- Nina Morgner
- Department of Chemistry, University of Oxford, South Parks Road, Oxford, OX1 5QY, UK
| | | | | | | |
Collapse
|
26
|
Barrera NP, Zhou M, Robinson CV. The role of lipids in defining membrane protein interactions: insights from mass spectrometry. Trends Cell Biol 2012; 23:1-8. [PMID: 22980035 DOI: 10.1016/j.tcb.2012.08.007] [Citation(s) in RCA: 115] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2012] [Revised: 08/14/2012] [Accepted: 08/14/2012] [Indexed: 12/19/2022]
Abstract
Cellular membranes comprise hundreds of lipids in which protein complexes, such as ion channels, receptors, and scaffolding complexes, are embedded. These protein assemblies act as signalling and trafficking platforms for processes fundamental to life. Much effort in recent years has focused on identifying the protein components of these complexes after their extraction from the lipid membrane in detergent micelles. Spectacular advances have been made using X-ray crystallography, providing in some cases detailed information about the mechanism of pumping and channel gating. These structural studies are leading to a growing realisation that, to understand their function, it is not only the structures of the protein components that are important but also knowledge of the protein-lipid interactions. This review highlights recent insights gained from this knowledge, surveys methods being developed for probing these interactions, and focuses specifically on the potential of mass spectrometry in this growing area of research.
Collapse
Affiliation(s)
- Nelson P Barrera
- Department of Physiology, Pontificia Universidad Católica de Chile, Alameda 340, Santiago, 8331150, Chile.
| | | | | |
Collapse
|
27
|
Barrera NP. Single Molecule Cross-Talk Transferred from a Molecular Event to an Organ Function. Biophys J 2012. [DOI: 10.1016/j.bpj.2011.11.874] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/14/2022] Open
|
28
|
Zhou M, Morgner N, Barrera NP, Politis A, Isaacson SC, Matak-Vinković D, Murata T, Bernal RA, Stock D, Robinson CV. Mass spectrometry of intact V-type ATPases reveals bound lipids and the effects of nucleotide binding. Science 2011; 334:380-385. [PMID: 22021858 PMCID: PMC3927129 DOI: 10.1126/science.1210148] [Citation(s) in RCA: 222] [Impact Index Per Article: 17.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
The ability of electrospray to propel large viruses into a mass spectrometer is established and is rationalized by analogy to the atmospheric transmission of the common cold. Much less clear is the fate of membrane-embedded molecular machines in the gas phase. Here we show that rotary adenosine triphosphatases (ATPases)/synthases from Thermus thermophilus and Enterococcus hirae can be maintained intact with membrane and soluble subunit interactions preserved in vacuum. Mass spectra reveal subunit stoichiometries and the identity of tightly bound lipids within the membrane rotors. Moreover, subcomplexes formed in solution and gas phases reveal the regulatory effects of nucleotide binding on both ATP hydrolysis and proton translocation. Consequently, we can link specific lipid and nucleotide binding with distinct regulatory roles.
Collapse
Affiliation(s)
- Min Zhou
- Department of Chemistry, Physical and Theoretical Chemistry Laboratory, University of Oxford, Oxford OX1 3QZ
| | - Nina Morgner
- Department of Chemistry, Physical and Theoretical Chemistry Laboratory, University of Oxford, Oxford OX1 3QZ
| | - Nelson P Barrera
- Department of Chemistry, Lensfield Road, University of Cambridge CB2 1EW
- Department of Physiology, Pontificia Universidad Católica de Chile, Alameda 340, Santiago, Chile
| | - Argyris Politis
- Department of Chemistry, Physical and Theoretical Chemistry Laboratory, University of Oxford, Oxford OX1 3QZ
| | - Shoshanna C Isaacson
- Department of Chemistry, Physical and Theoretical Chemistry Laboratory, University of Oxford, Oxford OX1 3QZ
| | | | - Takeshi Murata
- Department of Chemistry, Graduate School of Science, Chiba University, 1-33 Yayoi-cho, Inage, Chiba 263-8522, Japan
| | - Ricardo A Bernal
- Department of Chemistry, University of Texas at El Paso, El Paso, Texas 79968, USA
| | - Daniela Stock
- The Victor Chang Cardiac Research Institute, Lowy Packer Building, 405 Liverpool Street, Darlinghurst NSW 2010
- Faculty of Medicine, University of New South Wales, Sydney 2052, Australia
| | - Carol V Robinson
- Department of Chemistry, Physical and Theoretical Chemistry Laboratory, University of Oxford, Oxford OX1 3QZ
| |
Collapse
|
29
|
Abstract
Rapid advances in structural genomics and in large-scale proteomic projects have yielded vast amounts of data on soluble proteins and their complexes. Despite these advances, progress in studying membrane proteins using mass spectrometry (MS) has been slow. This is due in part to the inherent solubility and dynamic properties of these proteins, but also to their low abundance and the absence of polar side chains in amino acid residues. Considerable progress in overcoming these challenges is, however, now being made for all levels of structural characterization. This progress includes MS studies of the primary structure of membrane proteins, wherein sophisticated enrichment and trapping procedures are allowing multiple posttranslational modifications to be defined through to the secondary structure level in which proteins and peptides have been probed using hydrogen exchange, covalent, or radiolytic labeling methods. Exciting possibilities now exist to go beyond primary and secondary structure to reveal the tertiary and quaternary interactions of soluble and membrane subunits within intact assemblies of more than 700 kDa.
Collapse
Affiliation(s)
- Nelson P Barrera
- Department of Physiology, Pontificia Universidad Católica de Chile, Santiago 8331150, Chile.
| | | |
Collapse
|
30
|
Janganan TK, Bavro VN, Zhang L, Matak-Vinkovic D, Barrera NP, Venien-Bryan C, Robinson CV, Borges-Walmsley MI, Walmsley AR. Evidence for the assembly of a bacterial tripartite multidrug pump with a stoichiometry of 3:6:3. J Biol Chem 2011; 286:26900-12. [PMID: 21610073 PMCID: PMC3143649 DOI: 10.1074/jbc.m111.246595] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022] Open
Abstract
The multiple transferable resistance (mTR) pump from Neisseria gonorrhoeae MtrCDE multidrug pump is assembled from the inner and outer membrane proteins MtrD and MtrE and the periplasmic membrane fusion protein MtrC. Previously we established that while there is a weak interaction of MtrD and MtrE, MtrC binds with relatively high affinity to both MtrD and MtrE. MtrD conferred antibiotic resistance only when it was expressed with MtrE and MtrC, suggesting that these proteins form a functional tripartite complex in which MtrC bridges MtrD and MtrE. Furthermore, we demonstrated that MtrC interacts with an intraprotomer groove on the surface of MtrE, inducing channel opening. However, a second groove is apparent at the interface of the MtrE subunits, which might also be capable of engaging MtrC. We have now established that MtrC can be cross-linked to cysteines placed in this interprotomer groove and that mutation of residues in the groove impair the ability of the pump to confer antibiotic resistance by locking MtrE in the closed channel conformation. Moreover, MtrE K390C forms an intermolecular disulfide bond with MtrC E149C locking MtrE in the open channel conformation, suggesting that a functional salt bridge forms between these residues during the transition from closed to open channel conformations. MtrC forms dimers that assemble into hexamers, and electron microscopy studies of single particles revealed that these hexamers are arranged into ring-like structures with an internal aperture sufficiently large to accommodate the MtrE trimer. Cross-linking of single cysteine mutants of MtrC to stabilize the dimer interface in the presence of MtrE, trapped an MtrC-MtrE complex with a molecular mass consistent with a stoichiometry of 3:6 (MtrE3MtrC6), suggesting that dimers of MtrC interact with MtrE, presumably by binding to the two grooves. As both MtrE and MtrD are trimeric, our studies suggest that the functional pump is assembled with a stoichiometry of 3:6:3.
Collapse
Affiliation(s)
- Thamarai K Janganan
- School of Biological and Biomedical Sciences, Durham University, South Road, Durham DH1 3LE, United Kingdom
| | | | | | | | | | | | | | | | | |
Collapse
|
31
|
Carnally SM, Edwardson JM, Barrera NP. Imaging the spatial orientation of subunits within membrane receptors by atomic force microscopy. Methods Mol Biol 2011; 736:47-60. [PMID: 21660720 DOI: 10.1007/978-1-61779-105-5_4] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
Our experimental approach is based on the atomic force microscope (AFM) imaging of epitope-tagged subunits within membrane protein complexes purified in small amounts and decorated by anti-tag antibodies. Furthermore, we can produce simultaneous decoration of protein complexes using Fab fragments and IgG antibodies, which, combined with chemical modification of the substrate, allows us to determine the protein orientation across the cell membrane. Here, we describe a detailed protocol for membrane protein purification, AFM data collection, analysis, and interpretation of results. The protocol also covers basic AFM instrument settings and best practices for both observation of membrane protein complexes by AFM and automatic detection of the structures by an in-house algorithm. Once a sufficient number of membrane protein complexes have been visualized by AFM, data acquisition and processing can be completed in approximately 10 min using a scanning surface of 1 μm(2).
Collapse
Affiliation(s)
- Stewart M Carnally
- Department of Physiology, Pontificia Universidad Católica de Chile, Santiago, Chile
| | | | | |
Collapse
|
32
|
Janganan TK, Zhang L, Bavro VN, Matak-Vinkovic D, Barrera NP, Burton MF, Steel PG, Robinson CV, Borges-Walmsley MI, Walmsley AR. Opening of the outer membrane protein channel in tripartite efflux pumps is induced by interaction with the membrane fusion partner. J Biol Chem 2010; 286:5484-93. [PMID: 21115481 PMCID: PMC3037662 DOI: 10.1074/jbc.m110.187658] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Abstract
The multiple transferable resistance (MTR) pump, from Neisseria gonorrhoeae, is typical of the specialized machinery used to translocate drugs across the inner and outer membranes of Gram-negative bacteria. It consists of a tripartite complex composed of an inner-membrane transporter, MtrD, a periplasmic membrane fusion protein, MtrC, and an outer-membrane channel, MtrE. We have expressed the components of the pump in Escherichia coli and used the antibiotic vancomycin, which is too large to cross the outer-membrane by passive diffusion, to test for opening of the MtrE channel. Cells expressing MtrCDE are not susceptible to vancomycin, indicating that the channel is closed; but become susceptible to vancomycin in the presence of transported substrates, consistent with drug-induced opening of the MtrE channel. A mutational analysis identified residues Asn-198, Glu-434, and Gln-441, lining an intraprotomer groove on the surface of MtrE, to be important for pump function; mutation of these residues yielded cells that were sensitive to vancomycin. Pull-down assays and micro-calorimetry measurements indicated that this functional impairment is not due to the inability of MtrC to interact with the MtrE mutants; nor was it due to the MtrE mutants adopting an open conformation, because cells expressing these MtrE mutants alone are relatively insensitive to vancomycin. However, cells expressing the MtrE mutants with MtrC are sensitive to vancomycin, indicating that residues lining the intra-protomer groove control opening of the MtrE channel in response to binding of MtrC.
Collapse
Affiliation(s)
- Thamarai K Janganan
- School of Biological and Biomedical Sciences, Durham University, Durham DH1 3LE, United Kingdom
| | | | | | | | | | | | | | | | | | | |
Collapse
|
33
|
Benesch JLP, Ruotolo BT, Simmons DA, Barrera NP, Morgner N, Wang L, Saibil HR, Robinson CV. Separating and visualising protein assemblies by means of preparative mass spectrometry and microscopy. J Struct Biol 2010; 172:161-8. [PMID: 20227505 DOI: 10.1016/j.jsb.2010.03.004] [Citation(s) in RCA: 52] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2009] [Revised: 03/03/2010] [Accepted: 03/04/2010] [Indexed: 10/19/2022]
Abstract
Many multi-protein assemblies exhibit characteristics which hamper their structural and dynamical characterization. These impediments include low copy number, heterogeneity, polydispersity, hydrophobicity, and intrinsic disorder. It is becoming increasingly apparent that both novel and hybrid structural biology approaches need to be developed to tackle the most challenging targets. Nanoelectrospray mass spectrometry has matured over the last decade to enable the elucidation of connectivity and composition of large protein assemblies. Moreover, comparing mass spectrometry data with transmission electron microscopy images has enabled the mapping of subunits within topological models. Here we describe a preparative form of mass spectrometry designed to isolate specific protein complexes from within a heterogeneous ensemble, and to 'soft-land' these target complexes for ex situ imaging. By building a retractable probe incorporating a versatile target holder, and modifying the ion optics of a commercial mass spectrometer, we show that we can steer the macromolecular ion beam onto a target for imaging by means of transmission electron microscopy and atomic force microscopy. Our data for the tetradecameric chaperonin GroEL show that not only are the molecular volumes of the landed particles consistent with the overall dimensions of the complex, but also that their gross topological features can be maintained.
Collapse
Affiliation(s)
- Justin L P Benesch
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, UK
| | | | | | | | | | | | | | | |
Collapse
|
34
|
Wang SC, Politis A, Di Bartolo N, Bavro VN, Tucker SJ, Booth PJ, Barrera NP, Robinson CV. Ion Mobility Mass Spectrometry of Two Tetrameric Membrane Protein Complexes Reveals Compact Structures and Differences in Stability and Packing. J Am Chem Soc 2010; 132:15468-70. [DOI: 10.1021/ja104312e] [Citation(s) in RCA: 68] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Sheila C. Wang
- Department of Chemistry, University of Oxford, Oxford OX1 3TA, U.K., Department of Biochemistry, University of Bristol, Bristol BS8 1TD, U.K., Department of Physics, University of Oxford, Clarendon Laboratory, Oxford OX1 3PU, U.K., and Department of Physiology, Pontificia Universidad Católica de Chile, Alameda 340, Santiago, Chile
| | - Argyris Politis
- Department of Chemistry, University of Oxford, Oxford OX1 3TA, U.K., Department of Biochemistry, University of Bristol, Bristol BS8 1TD, U.K., Department of Physics, University of Oxford, Clarendon Laboratory, Oxford OX1 3PU, U.K., and Department of Physiology, Pontificia Universidad Católica de Chile, Alameda 340, Santiago, Chile
| | - Natalie Di Bartolo
- Department of Chemistry, University of Oxford, Oxford OX1 3TA, U.K., Department of Biochemistry, University of Bristol, Bristol BS8 1TD, U.K., Department of Physics, University of Oxford, Clarendon Laboratory, Oxford OX1 3PU, U.K., and Department of Physiology, Pontificia Universidad Católica de Chile, Alameda 340, Santiago, Chile
| | - Vassiliy N. Bavro
- Department of Chemistry, University of Oxford, Oxford OX1 3TA, U.K., Department of Biochemistry, University of Bristol, Bristol BS8 1TD, U.K., Department of Physics, University of Oxford, Clarendon Laboratory, Oxford OX1 3PU, U.K., and Department of Physiology, Pontificia Universidad Católica de Chile, Alameda 340, Santiago, Chile
| | - Stephen J. Tucker
- Department of Chemistry, University of Oxford, Oxford OX1 3TA, U.K., Department of Biochemistry, University of Bristol, Bristol BS8 1TD, U.K., Department of Physics, University of Oxford, Clarendon Laboratory, Oxford OX1 3PU, U.K., and Department of Physiology, Pontificia Universidad Católica de Chile, Alameda 340, Santiago, Chile
| | - Paula J. Booth
- Department of Chemistry, University of Oxford, Oxford OX1 3TA, U.K., Department of Biochemistry, University of Bristol, Bristol BS8 1TD, U.K., Department of Physics, University of Oxford, Clarendon Laboratory, Oxford OX1 3PU, U.K., and Department of Physiology, Pontificia Universidad Católica de Chile, Alameda 340, Santiago, Chile
| | - Nelson P. Barrera
- Department of Chemistry, University of Oxford, Oxford OX1 3TA, U.K., Department of Biochemistry, University of Bristol, Bristol BS8 1TD, U.K., Department of Physics, University of Oxford, Clarendon Laboratory, Oxford OX1 3PU, U.K., and Department of Physiology, Pontificia Universidad Católica de Chile, Alameda 340, Santiago, Chile
| | - Carol V. Robinson
- Department of Chemistry, University of Oxford, Oxford OX1 3TA, U.K., Department of Biochemistry, University of Bristol, Bristol BS8 1TD, U.K., Department of Physics, University of Oxford, Clarendon Laboratory, Oxford OX1 3PU, U.K., and Department of Physiology, Pontificia Universidad Católica de Chile, Alameda 340, Santiago, Chile
| |
Collapse
|
35
|
Velamakanni S, Lau CHF, Gutmann DAP, Venter H, Barrera NP, Seeger MA, Woebking B, Matak-Vinkovic D, Balakrishnan L, Yao Y, U ECY, Shilling RA, Robinson CV, Thorn P, van Veen HW. A multidrug ABC transporter with a taste for salt. PLoS One 2009; 4:e6137. [PMID: 19593434 PMCID: PMC2704374 DOI: 10.1371/journal.pone.0006137] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2009] [Accepted: 05/22/2009] [Indexed: 11/30/2022] Open
Abstract
BACKGROUND LmrA is a multidrug ATP-binding cassette (ABC) transporter from Lactococcus lactis with no known physiological substrate, which can transport a wide range of chemotherapeutic agents and toxins from the cell. The protein can functionally replace the human homologue ABCB1 (also termed multidrug resistance P-glycoprotein MDR1) in lung fibroblast cells. Even though LmrA mediates ATP-dependent transport, it can use the proton-motive force to transport substrates, such as ethidium bromide, across the membrane by a reversible, H(+)-dependent, secondary-active transport reaction. The mechanism and physiological context of this reaction are not known. METHODOLOGY/PRINCIPAL FINDINGS We examined ion transport by LmrA in electrophysiological experiments and in transport studies using radioactive ions and fluorescent ion-selective probes. Here we show that LmrA itself can transport NaCl by a similar secondary-active mechanism as observed for ethidium bromide, by mediating apparent H(+)-Na(+)-Cl(-) symport. Remarkably, LmrA activity significantly enhances survival of high-salt adapted lactococcal cells during ionic downshift. CONCLUSIONS/SIGNIFICANCE The observations on H(+)-Na(+)-Cl(-) co-transport substantiate earlier suggestions of H(+)-coupled transport by LmrA, and indicate a novel link between the activity of LmrA and salt stress. Our findings demonstrate the relevance of investigations into the bioenergetics of substrate translocation by ABC transporters for our understanding of fundamental mechanisms in this superfamily. This study represents the first use of electrophysiological techniques to analyze substrate transport by a purified multidrug transporter.
Collapse
Affiliation(s)
- Saroj Velamakanni
- Department of Pharmacology, University of Cambridge, Cambridge, United Kingdom
| | - Calvin H. F. Lau
- Department of Pharmacology, University of Cambridge, Cambridge, United Kingdom
| | | | - Henrietta Venter
- Department of Pharmacology, University of Cambridge, Cambridge, United Kingdom
| | - Nelson P. Barrera
- Department of Chemistry, University of Cambridge, Cambridge, United Kingdom
| | - Markus A. Seeger
- Department of Pharmacology, University of Cambridge, Cambridge, United Kingdom
| | - Barbara Woebking
- Department of Pharmacology, University of Cambridge, Cambridge, United Kingdom
| | | | | | - Yao Yao
- Department of Pharmacology, University of Cambridge, Cambridge, United Kingdom
| | - Edmond C. Y. U
- Department of Pharmacology, University of Cambridge, Cambridge, United Kingdom
| | - Richard A. Shilling
- Department of Pharmacology, University of Cambridge, Cambridge, United Kingdom
| | - Carol V. Robinson
- Department of Chemistry, University of Cambridge, Cambridge, United Kingdom
| | - Peter Thorn
- Department of Pharmacology, University of Cambridge, Cambridge, United Kingdom
| | - Hendrik W. van Veen
- Department of Pharmacology, University of Cambridge, Cambridge, United Kingdom
| |
Collapse
|
36
|
Barrera NP, Isaacson SC, Zhou M, Bavro VN, Welch A, Schaedler TA, Seeger MA, Miguel RN, Korkhov VM, van Veen HW, Venter H, Walmsley AR, Tate CG, Robinson CV. Mass spectrometry of membrane transporters reveals subunit stoichiometry and interactions. Nat Methods 2009; 6:585-7. [PMID: 19578383 DOI: 10.1038/nmeth.1347] [Citation(s) in RCA: 150] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2009] [Accepted: 05/18/2009] [Indexed: 11/09/2022]
Abstract
We describe a general mass spectrometry approach to determine subunit stoichiometry and lipid binding in intact membrane protein complexes. By exploring conditions for preserving interactions during transmission into the gas phase and for optimally stripping away detergent, by subjecting the complex to multiple collisions, we released the intact complex largely devoid of detergent. This enabled us to characterize both subunit stoichiometry and lipid binding in 4 membrane protein complexes.
Collapse
|
37
|
Lin HT, Bavro VN, Barrera NP, Frankish HM, Velamakanni S, van Veen HW, Robinson CV, Borges-Walmsley MI, Walmsley AR. MacB ABC transporter is a dimer whose ATPase activity and macrolide-binding capacity are regulated by the membrane fusion protein MacA. J Biol Chem 2008; 284:1145-54. [PMID: 18955484 PMCID: PMC2613632 DOI: 10.1074/jbc.m806964200] [Citation(s) in RCA: 77] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
Gram-negative bacteria utilize specialized machinery to translocate drugs
and protein toxins across the inner and outer membranes, consisting of a
tripartite complex composed of an inner membrane secondary or primary active
transporter (IMP), a periplasmic membrane fusion protein, and an outer
membrane channel. We have investigated the assembly and function of the
MacAB/TolC system that confers resistance to macrolides in Escherichia
coli. The membrane fusion protein MacA not only stabilizes the tripartite
assembly by interacting with both the inner membrane protein MacB and the
outer membrane protein TolC, but also has a role in regulating the function of
MacB, apparently increasing its affinity for both erythromycin and ATP.
Analysis of the kinetic behavior of ATP hydrolysis indicated that MacA
promotes and stabilizes the ATP-binding form of the MacB transporter. For the
first time, we have established unambiguously the dimeric nature of a
noncanonic ABC transporter, MacB that has an N-terminal nucleotide binding
domain, by means of nondissociating mass spectrometry, analytical
ultracentrifugation, and atomic force microscopy. Structural studies of ABC
transporters indicate that ATP is bound between a pair of nucleotide binding
domains to stabilize a conformation in which the substrate-binding site is
outward-facing. Consequently, our data suggest that in the presence of ATP the
same conformation of MacB is promoted and stabilized by MacA. Thus, MacA would
facilitate the delivery of drugs by MacB to TolC by enhancing the binding of
drugs to it and inducing a conformation of MacB that is primed and competent
for binding TolC. Our structural studies are an important first step in
understanding how the tripartite complex is assembled.
Collapse
Affiliation(s)
- Hong Ting Lin
- School of Biological and Biomedical Sciences, Durham University, South Road, Durham DH1 3LE, UK
| | | | | | | | | | | | | | | | | |
Collapse
|
38
|
Barrera NP, Edwardson JM. The subunit arrangement and assembly of ionotropic receptors. Trends Neurosci 2008; 31:569-76. [PMID: 18774187 DOI: 10.1016/j.tins.2008.08.001] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2008] [Revised: 08/05/2008] [Accepted: 08/05/2008] [Indexed: 11/17/2022]
Abstract
Ionotropic receptors mediate rapid communication between neurons. These receptors are oligomers and are usually assembled from multiple subunit types. Receptors built from different subunit combinations have distinct functional properties, such as single-channel conductances, rates of desensitization and sensitivities to activators and inactivators; they can also have different intracellular locations. Methods are now available for determining not only the subunit stoichiometry but also the subunit arrangement within ionotropic receptors. This information will inform experiments designed to understand the molecular basis of receptor assembly and function. It will also permit the modelling of potential ligand-binding sites at the interfaces between the subunits and should lead to a more rational approach to drug development.
Collapse
Affiliation(s)
- Nelson P Barrera
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, UK
| | | |
Collapse
|
39
|
Abstract
The ability to maintain interactions between soluble protein subunits in the gas phase of a mass spectrometer gives critical insight into the stoichiometry and interaction networks of protein complexes. Conversely, for membrane protein complexes in micelles, the transition into the gas phase usually leads to the disruption of interactions, particularly between cytoplasmic and membrane subunits, and a mass spectrum dominated by large aggregates of detergent molecules. We show that by applying nanoelectrospray to a micellar solution of a membrane protein complex, the heteromeric adenosine 5'-triphosphate (ATP)-binding cassette transporter BtuC2D2, we can maintain the complex intact in the gas phase of a mass spectrometer. Dissociation of either transmembrane (BtuC) or cytoplasmic (BtuD) subunits uncovers modifications to the transmembrane subunits and cooperative binding of ATP. By protecting a membrane protein complex within a n-dodecyl-beta-d-maltoside micelle, we demonstrated a powerful strategy that will enable the subunit stoichiometry and ligand-binding properties of membrane complexes to be determined directly, by precise determination of the masses of intact complexes and dissociated subunits.
Collapse
Affiliation(s)
- Nelson P Barrera
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB21EW, UK
| | | | | | | |
Collapse
|
40
|
Barrera NP, Ge H, Henderson RM, Fitzgerald WJ, Edwardson JM. Automated analysis of the architecture of receptors, imaged by atomic force microscopy. Micron 2008; 39:101-10. [PMID: 17296302 DOI: 10.1016/j.micron.2006.12.006] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2006] [Accepted: 12/19/2006] [Indexed: 10/23/2022]
Abstract
Fast neurotransmission involves the operation of ionotropic receptors, which are multi-subunit proteins that respond to activation by opening an integral ion channel. Examples of such channels include the GABA(A) receptor, the 5-HT(3) receptor and the P2X receptor for ATP. These receptors contain more than one type of subunit, although the exact subunit stoichiometry and arrangement around the receptor rosette is often unknown. We are using atomic force microscopy (AFM) of purified receptors to address these issues. Measurement of the molecular volume of the receptor permits the determination of the number of subunits that it contains. Furthermore, analysis of the geometry of complexes between receptors and subunit-specific antibodies reveals the subunit arrangement. Our AFM-based approach has so far been dependent on manual data processing, which is both time-consuming and prone to operator bias. In this study, we set out to develop a novel method capable of automatic segmentation and quantitative analysis of both single receptor particles and receptor-antibody complexes. The method was validated using images of wild type and mutant forms of the P2X(6) receptor. We suggest that the automated method will greatly facilitate further progress in the use of AFM for the determination of receptor and multi-protein architecture.
Collapse
Affiliation(s)
- Nelson P Barrera
- Department of Pharmacology, University of Cambridge, Tennis Court Road, Cambridge CB2 1PD, UK.
| | | | | | | | | |
Collapse
|
41
|
Barrera NP, Morales B, Villalon M. ATP and adenosine trigger the interaction of plasma membrane IP3 receptors with protein kinase A in oviductal ciliated cells. Biochem Biophys Res Commun 2008; 364:815-21. [PMID: 18163243 DOI: 10.1016/j.bbrc.2007.10.104] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
We have demonstrated that adenosine did not produce any change of intracellular free Ca2+ concentration ([Ca2+]i) in oviductal ciliated cells; however, it increased the ATP-induced Ca2+ influx through the activation of protein kinase A (PKA). Uncaging of IP3 and cAMP triggered a larger Ca2+ influx than did IP3 alone. Furthermore, the IP3 effect was abolished by Xestospongin C, an IP3 receptor blocker. Whole-cell recordings demonstrated the presence of an ATP-induced Ca2+ current, and the addition of adenosine increased the peak of this current. This effect was not observed in the presence of H-89, a PKA inhibitor. Using excised macro-patches of plasma membrane, IP3 generated a current, which was higher in the presence of the catalytic PKA subunit and this current was blocked by Xestospongin C. We show here that activation of plasma membrane IP3 receptors directly triggers Ca2+ influx in response to ATP and that these receptors are modulated by adenosine-activated PKA.
Collapse
Affiliation(s)
- Nelson P Barrera
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 IEW, United Kingdom.
| | | | | |
Collapse
|
42
|
Shahin V, Barrera NP. Providing Unique Insight into Cell Biology via Atomic Force Microscopy. International Review of Cytology 2008; 265:227-52. [DOI: 10.1016/s0074-7696(07)65006-2] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
|
43
|
Barrera NP, Betts J, You H, Henderson RM, Martin IL, Dunn SMJ, Edwardson JM. Atomic force microscopy reveals the stoichiometry and subunit arrangement of the alpha4beta3delta GABA(A) receptor. Mol Pharmacol 2007; 73:960-7. [PMID: 18079275 DOI: 10.1124/mol.107.042481] [Citation(s) in RCA: 71] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
The GABA(A) receptor is a chloride-selective ligand-gated ion channel of the Cys-loop superfamily. The receptor consists of five subunits arranged pseudosymmetrically around a central pore. The predominant form of the receptor in the brain contains alpha(1)-, beta(2)-, and gamma(2)-subunits in the arrangement alphabetaalphagammabeta, counter-clockwise around the pore. GABA(A) receptors containing delta-instead of gamma-subunits, although a minor component of the total receptor population, have interesting properties, such as an extrasynaptic location, high sensitivity to GABA, and potential association with conditions such as epilepsy. They are therefore attractive targets for drug development. Here we addressed the subunit arrangement within the alpha(4)beta(3)delta form of the receptor. Different epitope tags were engineered onto the three subunits, and complexes between receptors and anti-epitope antibodies were imaged by atomic force microscopy. Determination of the numbers of receptors doubly decorated by each of the three antibodies revealed a subunit stoichiometry of 2alpha:2beta:1delta. The distributions of angles between pairs of antibodies against the alpha- and beta-subunits both had peaks at around 144 degrees , indicating that these pairs of subunits were nonadjacent. Decoration of the receptor with ligands that bind to the extracellular domain (i.e., the lectin concanavalin A and an antibody that recognizes the beta-subunit N-terminal sequence) showed that the receptor preferentially binds to the mica extracellular face down. Given this orientation, the geometry of complexes of receptors with both an antibody against the delta-subunit and Fab fragments against the alpha-subunits indicates a predominant subunit arrangement of alphabetaalphadeltabeta, counter-clockwise around the pore when viewed from the extracellular space.
Collapse
Affiliation(s)
- Nelson P Barrera
- Department of Pharmacology, University of Cambridge, Tennis Court Road, Cambridge CB2 1PD, United Kingdom
| | | | | | | | | | | | | |
Collapse
|
44
|
Barrera NP, Shaifta Y, McFadzean I, Ward JPT, Henderson RM, Edwardson JM. AFM imaging reveals the tetrameric structure of the TRPC1 channel. Biochem Biophys Res Commun 2007; 358:1086-90. [PMID: 17517368 DOI: 10.1016/j.bbrc.2007.05.039] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2007] [Accepted: 05/08/2007] [Indexed: 11/16/2022]
Abstract
We have determined the subunit stoichiometry of the transient receptor potential C1 (TRPC1) channel by imaging isolated channels using atomic force microscopy (AFM). A frequency distribution of the molecular volumes of individual channel particles had two peaks, at 170 and 720 nm(3), corresponding with the expected sizes of TRPC1 monomers and tetramers, respectively. Complexes were formed between TRPC1 channels and antibodies against a V5 epitope tag present on each subunit. The frequency distribution of angles between pairs of bound antibodies had two peaks, at 88 degrees and 178 degrees. This result again indicates that the channel assembles as a tetramer.
Collapse
Affiliation(s)
- Nelson P Barrera
- Department of Pharmacology, University of Cambridge, Tennis Court Road, Cambridge CB2 1PD, UK
| | | | | | | | | | | |
Collapse
|
45
|
Barrera NP, Henderson RM, Murrell-Lagnado RD, Edwardson JM. The stoichiometry of P2X2/6 receptor heteromers depends on relative subunit expression levels. Biophys J 2007; 93:505-12. [PMID: 17449665 PMCID: PMC1896263 DOI: 10.1529/biophysj.106.101048] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Abstract
Fast synaptic transmission involves the operation of ionotropic receptors, which are often composed of at least two types of subunit. We have developed a method, based on atomic force microscopy imaging to determine the stoichiometry and subunit arrangement within ionotropic receptors. We showed recently that the P2X(2) receptor for ATP is expressed as a trimer but that the P2X(6) subunit is unable to oligomerize. In this study we addressed the subunit stoichiometry of heteromers containing both P2X(2) and P2X(6) subunits. We transfected tsA 201 cells with both P2X(2) and P2X(6) subunits, bearing different epitope tags. We manipulated the transfection conditions so that either P2X(2) or P2X(6) was the predominant subunit expressed. By atomic force microscopy imaging of isolated receptors decorated with antiepitope antibodies, we demonstrate that when expression of the P2X(2) subunit predominates, the receptors contain primarily 2 x P2X(2) subunits and 1 x P2X(6) subunit. In contrast, when the P2X(6) subunit predominates, the subunit stoichiometry of the receptors is reversed. Our results show that the composition of P2X receptor heteromers is plastic and dependent on the relative subunit expression levels. We suggest that this property of receptor assembly might introduce an additional layer of subtlety into P2X receptor signaling.
Collapse
Affiliation(s)
- Nelson P Barrera
- Department of Pharmacology, University of Cambridge, Cambridge CB2 1PD, United Kingdom
| | | | | | | |
Collapse
|
46
|
|
47
|
Ormond SJ, Barrera NP, Qureshi OS, Henderson RM, Edwardson JM, Murrell-Lagnado RD. An Uncharged Region within the N Terminus of the P2X6 Receptor Inhibits Its Assembly and Exit from the Endoplasmic Reticulum. Mol Pharmacol 2006; 69:1692-700. [PMID: 16452399 DOI: 10.1124/mol.105.020404] [Citation(s) in RCA: 50] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
ATP-gated P2X receptors are trimeric complexes formed by the homomeric or heteromeric assembly of seven different subunits. We have shown previously that, unlike all of the other P2X subunits, the P2X6 subunit cannot form homomeric receptors and when expressed alone is retained in the endoplasmic reticulum (ER) in monomeric form (J Biol Chem 280: 107591-10765, 2005). However, other studies have shown that P2X6 can form functional heteromeric receptors with P2X2 and P2X4 subunits. In this study, we used a combination of immunocytochemistry, surface biotinylation, and atomic force microscopy to investigate the assembly and trafficking of the P2X6 subunit, both alone and as part of a heteromer. We show that as a heteromer, it exits the ER and is either stably expressed at the cell surface or constitutively internalized, depending on its partner. Through the use of targeted mutation, we demonstrate that an uncharged region at the N terminus of P2X6 exerts an inhibitory effect on its assembly and export from the ER. When this region is removed, or when charge is added to it, P2X6 forms homotrimeric assemblies, undergoes complex glycosylation and is delivered to the plasma membrane, albeit less efficiently than the P2X2 receptor. The N-terminal mutants were, however, nonfunctional. Substituting the uncharged 14-amino acid N-terminal region for the equivalent region of P2X2 increased ER retention but was not sufficient to prevent the formation of functional homomeric receptors. We propose that the N terminus of the P2X6 subunit contributes to a mechanism that prevents the inappropriate export and plasma membrane expression of nonfunctional P2X receptors.
Collapse
Affiliation(s)
- Susan J Ormond
- Department of Pharmacology, University of Cambridge, Tennis Court Road, Cambridge CB2 1PD, United Kingdom
| | | | | | | | | | | |
Collapse
|
48
|
Barrera NP, Morales B, Torres S, Villalón M. Principles: mechanisms and modeling of synergism in cellular responses. Trends Pharmacol Sci 2005; 26:526-32. [PMID: 16125797 DOI: 10.1016/j.tips.2005.08.003] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2005] [Revised: 07/20/2005] [Accepted: 08/11/2005] [Indexed: 10/25/2022]
Abstract
Cells can be considered as integrators of simultaneous stimuli, in which cross-talk between transduction pathways can eventually produce responses that are significantly different from simply additive responses. Synergism represents an efficient means of increasing the amplitude of cellular responses induced by low levels of stimulation. Recently, several kinetic and physicochemical models have been developed to describe and predict synergistic responses. In this article, the mechanisms that control the magnitude and timing of cellular synergism are discussed. We suggest that the analysis of theoretical models could enable a general prediction of synergism despite the presence of signal-specific synergistic responses. In addition, application of the proposed concepts should aid understanding of the wide occurrence of synergism induced by interacting transduction pathways in multi-drug clinical treatment.
Collapse
Affiliation(s)
- Nelson P Barrera
- Department of Pharmacology, University of Cambridge, Tennis Court Road, Cambridge CB2 1PD, UK.
| | | | | | | |
Collapse
|
49
|
Barrera NP, Herbert P, Henderson RM, Martin IL, Edwardson JM. Atomic force microscopy reveals the stoichiometry and subunit arrangement of 5-HT3 receptors. Proc Natl Acad Sci U S A 2005; 102:12595-600. [PMID: 16116092 PMCID: PMC1194916 DOI: 10.1073/pnas.0503253102] [Citation(s) in RCA: 97] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023] Open
Abstract
The 5-HT3 receptor is a cation-selective ligand-gated ion channel of the Cys-loop superfamily. The receptor is an important therapeutic target, with receptor antagonists being widely used as antiemetics in cancer therapy. The two known receptor subunits, A and B, form homomeric 5-HT 3A receptors and heteromeric 5-HT 3A/B receptors. The heteromeric receptor has the higher single-channel conductance and more closely mimics the properties of the native receptor. We have used atomic force microscopy to study the architecture of 5-HT 3A and 5-HT 3A/B receptors. We engineered different epitope tags onto the A- and B-subunits and imaged receptors that were doubly liganded by anti-epitope antibodies. We found that, for the 5-HT 3A/B receptor, the distribution of angles between antibodies against the A-subunit had a single peak at approximately 144 degrees , whereas the distribution for antibodies against the B-subunit had two peaks at approximately 72 degrees and 144 degrees . Our results indicate that the subunit stoichiometry is 2A:3B and that the subunit arrangement around the receptor rosette is B-B-A-B-A. This arrangement may account for the difference between the agonist Hill coefficients and the single-channel conductances for the two types of receptor.
Collapse
Affiliation(s)
- Nelson P Barrera
- Department of Pharmacology, University of Cambridge, Tennis Court Road, Cambridge CB2 1PD, United Kingdom
| | | | | | | | | |
Collapse
|
50
|
Barrera NP, Ormond SJ, Henderson RM, Murrell-Lagnado RD, Edwardson JM. Atomic Force Microscopy Imaging Demonstrates that P2X2 Receptors Are Trimers but That P2X6 Receptor Subunits Do Not Oligomerize. J Biol Chem 2005; 280:10759-65. [PMID: 15657042 DOI: 10.1074/jbc.m412265200] [Citation(s) in RCA: 154] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
P2X receptors are cation-selective channels activated by extracellular ATP. The architecture of these receptors is still not completely clear. Here we have addressed this issue by both chemical cross-linking and direct imaging of individual receptors by atomic force microscopy (AFM). Cross-linking of the P2X(2) receptor produced higher order adducts, consistent with the presence of trimers. The mean molecular volume of the receptor determined by AFM (409 nm(3)) also points to a trimeric structure. P2X(2) receptors bearing His(6) epitope tags were incubated with anti-His(6) antibodies, and the resultant complexes were imaged by AFM. For receptors with two bound antibodies, the mean angle between the antibodies was 123 degrees , again indicating that the receptor is a trimer. In contrast, cross-linking of the P2X(6) receptor did not produce higher order adducts, and the mean molecular volume of the receptor was 145 nm(3). We conclude that P2X(2) receptors are trimers, whereas the P2X(6) receptor subunits do not form stable oligomers.
Collapse
Affiliation(s)
- Nelson P Barrera
- Department of Pharmacology, University of Cambridge, Tennis Court Road, Cambridge CB2 1PD, UK
| | | | | | | | | |
Collapse
|