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Dong C, Ren J. Resonance Light-Scattering Correlation Spectroscopy and Its Application in Analytical Chemistry for Life Science. Acc Chem Res 2023; 56:2582-2594. [PMID: 37706459 DOI: 10.1021/acs.accounts.3c00306] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/15/2023]
Abstract
Resonance light-scattering correlation spectroscopy (RLSCS) is a new single-particle detection method with its working principle being like fluorescence correlation spectroscopy (FCS). RLSCS is obtained by autocorrelation function analysis on the measured fluctuation of the resonance light scattering (RLS) intensity occurring within a subfemtoliter volume when a single nanoparticle (such as gold nanoparticles (NPs) or silver (SNPs)) freely diffuses through the volume. The RLSCS technique can detect such parameters as concentration, diffusion coefficient (translation and rotation), etc. Compared with the FCS technique, the correlated fluorescence intensity signal in RLSCS is replaced with the RLS signal of the nanoparticles, overcoming some limits of the fluorescent probes such as photobleaching under high-intensity or long-term illumination. In this Account, we showcase RLSCS methods, theoretical models at different optical configurations, and some key applications. First, the RLSCS optical detection system was constructed based on the confocal optics, its theoretical model was proposed, and the diffusion behaviors of the nanoparticles in the solution were studied including the rotational and translational diffusion. And, methods were developed to measure the concentration, size, aspect ratio, and size distribution of the NPs. Second, based on the RLSCS methods, some detection strategies were developed for homogeneous DNA detection, immunoassay, apoptosis assay, self-thermophoresis of the nanomotor, and quantitative assay in single living cells. Meanwhile, a new fluorescence/scattering cross-correlation spectroscopy (FSCCS) method was proposed for monitoring the molecule-particle interaction. This method enriched the conventional fluorescence/fluorescence cross-correlation spectroscopy (FCCS) method. Third, using the EMCCD with high sensitivity and rapid response as an optical detector, two temporospatially resolved scattering correlation spectroscopy methods and their theoretical models were developed: total internal reflection (TIR) configuration-based spatially resolved scattering correlation spectroscopy (SRSCS) and dark-field illumination-based scattering correlation spectroscopy (DFSCS). These methods extended single-spot confocal RLSCS to imaging RLSCS, which makes RLSCS have the ability for multiple channel detection with temporospatial resolution. The method was successfully used for investigating the dynamic behaviors of gold NPs in live cells and obtained its temporospatial concentration distribution and diffusion behaviors. The final section of this Account outlines future directions in the development of RLSCS.
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Affiliation(s)
- Chaoqing Dong
- School of Chemistry and Chemical Engineering, Frontiers Science Centre for Transformative Molecules, State Key Laboratory of Metal Matrix Composites, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai 200240, China
| | - Jicun Ren
- School of Chemistry and Chemical Engineering, Frontiers Science Centre for Transformative Molecules, State Key Laboratory of Metal Matrix Composites, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai 200240, China
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2
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Anaya EU, Amin AE, Wester MJ, Danielson ME, Michel KS, Neumann AK. Dectin-1 multimerization and signaling depends on fungal β-glucan structure and exposure. Biophys J 2023; 122:3749-3767. [PMID: 37515324 PMCID: PMC10541497 DOI: 10.1016/j.bpj.2023.07.021] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2023] [Revised: 06/30/2023] [Accepted: 07/25/2023] [Indexed: 07/30/2023] Open
Abstract
Dectin-1A is a C-type lectin innate immunoreceptor that recognizes β-(1,3;1,6)-glucan, a structural component of Candida species cell walls. β-Glucans can adopt solution structures ranging from random coil to insoluble fiber due to tertiary (helical) and quaternary structure. Fungal β-glucans of medium and high molecular weight are highly structured, but low molecular weight glucan is much less structured. Despite similar affinity for Dectin-1, the ability of glucans to induce Dectin-1A-mediated signaling correlates with degree of structure. Glucan denaturation experiments showed that glucan structure determines agonistic potential, but not receptor binding affinity. We explored the impact of glucan structure on molecular aggregation of Dectin-1A. Stimulation with glucan signaling decreased Dectin-1A diffusion coefficient. Fluorescence measurements provided direct evidence of ligation-induced Dectin-1A aggregation, which positively correlated with increasing glucan structure content. In contrast, Dectin-1A is predominantly in a low aggregation state in resting cells. Molecular aggregates formed during interaction with highly structured, agonistic glucans did not exceed relatively small (<15 nm) clusters of a few engaged receptors. Finally, we observed increased molecular aggregation of Dectin-1A at fungal particle contact sites in a manner that positively correlated with the degree of exposed glucan on the particle surface. These results indicate that Dectin-1A senses the solution conformation of β-glucans through their varying ability to drive receptor dimer/oligomer formation and activation of membrane proximal signaling events.
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Affiliation(s)
- Eduardo U Anaya
- Department of Pathology, University of New Mexico, School of Medicine, Albuquerque, New Mexico
| | - Akram Etemadi Amin
- Department of Pathology, University of New Mexico, School of Medicine, Albuquerque, New Mexico; Department of Physics and Astronomy, University of New Mexico, Albuquerque, New Mexico
| | - Michael J Wester
- Department of Mathematics and Statistics, University of New Mexico, Albuquerque, New Mexico
| | | | | | - Aaron K Neumann
- Department of Pathology, University of New Mexico, School of Medicine, Albuquerque, New Mexico.
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3
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Leong SK, Hsiao JC, Shie JJ. A Multiscale Molecular Dynamic Analysis Reveals the Effect of Sialylation on EGFR Clustering in a CRISPR/Cas9-Derived Model. Int J Mol Sci 2022; 23:ijms23158754. [PMID: 35955894 PMCID: PMC9368999 DOI: 10.3390/ijms23158754] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2022] [Revised: 07/28/2022] [Accepted: 08/03/2022] [Indexed: 11/16/2022] Open
Abstract
Bacterial and viral pathogens can modulate the glycosylation of key host proteins to facilitate pathogenesis by using various glycosidases, particularly sialidases. Epidermal growth factor receptor (EGFR) signaling is activated by ligand-induced receptor dimerization and oligomerization. Ligand binding induces conformational changes in EGFR, leading to clusters and aggregation. However, information on the relevance of EGFR clustering in the pattern of glycosylation during bacterial and viral invasion remains unclear. In this study, (1) we established CRISPR/Cas9-mediated GFP knock-in (EGFP-KI) HeLa cells expressing fluorescently tagged EGFR at close to endogenous levels to study EGF-induced EGFR clustering and molecular dynamics; (2) We studied the effect of sialylation on EGF-induced EGFR clustering and localization in live cells using a high content analysis platform and raster image correlation spectroscopy (RICS) coupled with a number and brightness (N&B) analysis; (3) Our data reveal that the removal of cell surface sialic acids by sialidase treatment significantly decreases EGF receptor clustering with reduced fluorescence intensity, number, and area of EGFR-GFP clusters per cell upon EGF stimulation. Sialylation appears to mediate EGF-induced EGFR clustering as demonstrated by the change of EGFR-GFP clusters in the diffusion coefficient and molecular brightness, providing new insights into the role of sialylation in EGF-induced EGFR activation; and (4) We envision that the combination of CRISPR/Cas9-mediated fluorescent tagging of endogenous proteins and fluorescence imaging techniques can be the method of choice for studying the molecular dynamics and interactions of proteins in live cells.
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Affiliation(s)
- Shwee Khuan Leong
- Institute of Chemistry, Academia Sinica, Taipei 11529, Taiwan
- Taiwan International Graduate Program (TIGP), Sustainable Chemical Science & Technology (SCST), Academia Sinica, Taipei 11529, Taiwan
- Department of Applied Chemistry, National Yang Ming Chiao Tung University (NYCU), Hsinchu 30050, Taiwan
| | - Jye-Chian Hsiao
- Institute of Chemistry, Academia Sinica, Taipei 11529, Taiwan
| | - Jiun-Jie Shie
- Institute of Chemistry, Academia Sinica, Taipei 11529, Taiwan
- Correspondence:
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4
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The use of fluorescence correlation spectroscopy to characterise the molecular mobility of G protein-coupled receptors in membrane microdomains: an update. Biochem Soc Trans 2021; 49:1547-1554. [PMID: 34436556 DOI: 10.1042/bst20201001] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2021] [Revised: 07/26/2021] [Accepted: 07/28/2021] [Indexed: 12/24/2022]
Abstract
It has become increasingly apparent that some G protein-coupled receptors (GPCRs) are not homogeneously expressed within the plasma membrane but may instead be organised within distinct signalling microdomains. These microdomains localise GPCRs in close proximity with other membrane proteins and intracellular signalling partners and could have profound implications for the spatial and temporal control of downstream signalling. In order to probe the molecular mechanisms that govern GPCR pharmacology within these domains, fluorescence techniques with effective single receptor sensitivity are required. Of these, fluorescence correlation spectroscopy (FCS) is a technique that meets this sensitivity threshold. This short review will provide an update of the recent uses of FCS based techniques in conjunction with GPCR subtype selective fluorescent ligands to characterise dynamic ligand-receptor interactions in whole cells and using purified GPCRs.
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Nederveen-Schippers LM, Pathak P, Keizer-Gunnink I, Westphal AH, van Haastert PJM, Borst JW, Kortholt A, Skakun V. Combined FCS and PCH Analysis to Quantify Protein Dimerization in Living Cells. Int J Mol Sci 2021; 22:ijms22147300. [PMID: 34298920 PMCID: PMC8307594 DOI: 10.3390/ijms22147300] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2021] [Revised: 06/25/2021] [Accepted: 07/01/2021] [Indexed: 11/29/2022] Open
Abstract
Protein dimerization plays a crucial role in the regulation of numerous biological processes. However, detecting protein dimers in a cellular environment is still a challenge. Here we present a methodology to measure the extent of dimerization of GFP-tagged proteins in living cells, using a combination of fluorescence correlation spectroscopy (FCS) and photon counting histogram (PCH) analysis of single-color fluorescence fluctuation data. We named this analysis method brightness and diffusion global analysis (BDGA) and adapted it for biological purposes. Using cell lysates containing different ratios of GFP and tandem-dimer GFP (diGFP), we show that the average brightness per particle is proportional to the fraction of dimer present. We further adapted this methodology for its application in living cells, and we were able to distinguish GFP, diGFP, as well as ligand-induced dimerization of FKBP12 (FK506 binding protein 12)-GFP. While other analysis methods have only sporadically been used to study dimerization in living cells and may be prone to errors, this paper provides a robust approach for the investigation of any cytosolic protein using single-color fluorescence fluctuation spectroscopy.
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Affiliation(s)
- Laura M. Nederveen-Schippers
- Department of Cell Biochemistry, University of Groningen, 9747 AG Groningen, The Netherlands; (L.M.N.-S.); (P.P.); (I.K.-G.); (P.J.M.v.H.)
| | - Pragya Pathak
- Department of Cell Biochemistry, University of Groningen, 9747 AG Groningen, The Netherlands; (L.M.N.-S.); (P.P.); (I.K.-G.); (P.J.M.v.H.)
| | - Ineke Keizer-Gunnink
- Department of Cell Biochemistry, University of Groningen, 9747 AG Groningen, The Netherlands; (L.M.N.-S.); (P.P.); (I.K.-G.); (P.J.M.v.H.)
| | - Adrie H. Westphal
- Laboratory of Biochemistry, Wageningen University & Research, 6708 WE Wageningen, The Netherlands; (A.H.W.); (J.W.B.)
| | - Peter J. M. van Haastert
- Department of Cell Biochemistry, University of Groningen, 9747 AG Groningen, The Netherlands; (L.M.N.-S.); (P.P.); (I.K.-G.); (P.J.M.v.H.)
| | - Jan Willem Borst
- Laboratory of Biochemistry, Wageningen University & Research, 6708 WE Wageningen, The Netherlands; (A.H.W.); (J.W.B.)
| | - Arjan Kortholt
- Department of Cell Biochemistry, University of Groningen, 9747 AG Groningen, The Netherlands; (L.M.N.-S.); (P.P.); (I.K.-G.); (P.J.M.v.H.)
- Correspondence: (A.K.); (V.S.)
| | - Victor Skakun
- Department of Systems Analysis and Computer Simulation, Belarusian State University, 220030 Minsk, Belarus
- Correspondence: (A.K.); (V.S.)
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6
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Bernabé-Rubio M, Bosch-Fortea M, Alonso MA, Bernardino de la Serna J. Multi-dimensional and spatiotemporal correlative imaging at the plasma membrane of live cells to determine the continuum nano-to-micro scale lipid adaptation and collective motion. Methods 2021; 193:136-147. [PMID: 34126167 DOI: 10.1016/j.ymeth.2021.06.007] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2021] [Revised: 06/07/2021] [Accepted: 06/09/2021] [Indexed: 12/25/2022] Open
Abstract
The primary cilium is a specialized plasma membrane protrusion with important receptors for signalling pathways. In polarized epithelial cells, the primary cilium assembles after the midbody remnant (MBR) encounters the centrosome at the apical surface. The membrane surrounding the MBR, namely remnant-associated membrane patch (RAMP), once situated next to the centrosome, releases some of its lipid components to form a centrosome-associated membrane patch (CAMP) from which the ciliary membrane stems. The RAMP undergoes a spatiotemporal membrane refinement during the formation of the CAMP, which becomes highly enriched in condensed membranes with low lateral mobility. To better understand this process, we have developed a correlative imaging approach that yields quantitative information about the lipid lateral packing, its mobility and collective assembly at the plasma membrane at different spatial scales over time. Our work paves the way towards a quantitative understanding of the spatiotemporal lipid collective assembly at the plasma membrane as a functional determinant in cell biology and its direct correlation with the membrane physicochemical state. These findings allowed us to gain a deeper insight into the mechanisms behind the biogenesis of the ciliary membrane of polarized epithelial cells.
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Affiliation(s)
- Miguel Bernabé-Rubio
- Department of Cell Biology and Immunology, Centro de Biología Molecular Severo Ochoa, Consejo Superior de Investigaciones Científicas and Universidad Autónoma de Madrid, Madrid 28049, Spain; King's College London Centre for Stem Cells and Regenerative Medicine, 28th Floor, Tower Wing, Guy's Campus, Great Maze Pond, London SE1 9RT, UK
| | - Minerva Bosch-Fortea
- Department of Cell Biology and Immunology, Centro de Biología Molecular Severo Ochoa, Consejo Superior de Investigaciones Científicas and Universidad Autónoma de Madrid, Madrid 28049, Spain; Institute of Bioengineering and School of Engineering and Materials Science, Queen Mary, University of London, Mile End Road, London E1 4NS, UK
| | - Miguel A Alonso
- Department of Cell Biology and Immunology, Centro de Biología Molecular Severo Ochoa, Consejo Superior de Investigaciones Científicas and Universidad Autónoma de Madrid, Madrid 28049, Spain
| | - Jorge Bernardino de la Serna
- Central Laser Facility, Rutherford Appleton Laboratory, MRC-Research Complex at Harwell, Science and Technology Facilities Council, Harwell OX11 0QX, UK; National Heart and Lung Institute, Imperial College London, Sir Alexander Fleming Building, London SW7 2AZ, UK; NIHR Imperial Biomedical Research Centre, London SW7 2AZ, UK.
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7
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Fukushima R, Yamamoto J, Kinjo M. Empirical Bayes method using surrounding pixel information for number and brightness analysis. Biophys J 2021; 120:2156-2171. [PMID: 33812845 PMCID: PMC8390835 DOI: 10.1016/j.bpj.2021.03.033] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2020] [Revised: 03/13/2021] [Accepted: 03/23/2021] [Indexed: 11/26/2022] Open
Abstract
Number and brightness (N&B) analysis is useful for monitoring the spatial distribution of the concentration and oligomeric state of fluorescently labeled proteins in cells. N&B analysis is based on the statistical analysis of fluorescence images by using the method of moments (MoM). Furthermore, N&B analysis can determine the particle number and particle brightness, which indicate the concentration and oligomeric state, respectively. However, the statistical accuracy and precision are limited in actual experiments with fluorescent proteins, owing to low excitation and the limited number of images. In this study, we applied maximum likelihood (ML) estimation and maximum a posteriori (MAP) estimation coupled with the empirical Bayes (EB) method (referred to as EB-MAP). In EB-MAP, we constructed a simple prior distribution for a pixel to utilize the information of the surrounding pixels. To evaluate the accuracy and precision of our method, we conducted simulations and experiments and compared the results of MoM, ML, and EB-MAP. The results showed that MoM estimated the particle number with many outliers. The outliers hampered the visibility of the spatial distribution and cellular structure. In contrast, EB-MAP suppressed the number of outliers and improved the visibility notably. The precision of EB-MAP was better by an order of magnitude in terms of particle number and 1.5 times better in terms of particle brightness compared with those of MoM. The proposed method (EB-MAP-N&B) is applicable to studies on fluorescence imaging and would aid in accurately recognizing changes in the concentration and oligomeric state in cells. Our results hold significant importance because quantifying the concentration and oligomeric state would contribute to the understanding of dynamic processes in molecular mechanism in cells.
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Affiliation(s)
- Ryosuke Fukushima
- Laboratory of Molecular Cell Dynamics, Graduate School of Life Science, Hokkaido University, Sapporo, Japan
| | - Johtaro Yamamoto
- Health and Medical Research Institute, National Institute of Advanced Industrial Science and Technology, Tsukuba, Japan; Laboratory of Molecular Cell Dynamics, Faculty of Advanced Life Science, Hokkaido University, Sapporo, Japan
| | - Masataka Kinjo
- Laboratory of Molecular Cell Dynamics, Faculty of Advanced Life Science, Hokkaido University, Sapporo, Japan.
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8
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Amiar S, Husby ML, Wijesinghe KJ, Angel S, Bhattarai N, Gerstman BS, Chapagain PP, Li S, Stahelin RV. Lipid-specific oligomerization of the Marburg virus matrix protein VP40 is regulated by two distinct interfaces for virion assembly. J Biol Chem 2021; 296:100796. [PMID: 34019871 PMCID: PMC8191294 DOI: 10.1016/j.jbc.2021.100796] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2021] [Revised: 05/12/2021] [Accepted: 05/14/2021] [Indexed: 02/03/2023] Open
Abstract
Marburg virus (MARV) is a lipid-enveloped virus harboring a negative-sense RNA genome, which has caused sporadic outbreaks of viral hemorrhagic fever in sub-Saharan Africa. MARV assembles and buds from the host cell plasma membrane where MARV matrix protein (mVP40) dimers associate with anionic lipids at the plasma membrane inner leaflet and undergo a dynamic and extensive self-oligomerization into the structural matrix layer. The MARV matrix layer confers the virion filamentous shape and stability but how host lipids modulate mVP40 oligomerization is mostly unknown. Using in vitro and cellular techniques, we present a mVP40 assembly model highlighting two distinct oligomerization interfaces: the (N-terminal domain [NTD] and C-terminal domain [CTD]) in mVP40. Cellular studies of NTD and CTD oligomerization interface mutants demonstrate the importance of each interface in matrix assembly. The assembly steps include protein trafficking to the plasma membrane, homo-multimerization that induced protein enrichment, plasma membrane fluidity changes, and elongations at the plasma membrane. An ascorbate peroxidase derivative (APEX)-transmission electron microscopy method was employed to closely assess the ultrastructural localization and formation of viral particles for wildtype mVP40 and NTD and CTD oligomerization interface mutants. Taken together, these studies present a mechanistic model of mVP40 oligomerization and assembly at the plasma membrane during virion assembly that requires interactions with phosphatidylserine for NTD–NTD interactions and phosphatidylinositol-4,5-bisphosphate for proper CTD–CTD interactions. These findings have broader implications in understanding budding of lipid-enveloped viruses from the host cell plasma membrane and potential strategies to target protein–protein or lipid–protein interactions to inhibit virus budding.
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Affiliation(s)
- Souad Amiar
- Department of Medicinal Chemistry & Molecular Pharmacology, Purdue University, West Lafayette, Indiana, USA
| | - Monica L Husby
- Department of Medicinal Chemistry & Molecular Pharmacology, Purdue University, West Lafayette, Indiana, USA
| | - Kaveesha J Wijesinghe
- Department of Medicinal Chemistry & Molecular Pharmacology, Purdue University, West Lafayette, Indiana, USA; Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana, USA
| | - Stephanie Angel
- Department of Medicinal Chemistry & Molecular Pharmacology, Purdue University, West Lafayette, Indiana, USA
| | - Nisha Bhattarai
- Department of Physics, Florida International University, Miami, Florida, USA
| | - Bernard S Gerstman
- Department of Physics, Florida International University, Miami, Florida, USA; Biomolecular Sciences Institute, Florida International University, Miami, Florida, USA
| | - Prem P Chapagain
- Department of Physics, Florida International University, Miami, Florida, USA; Biomolecular Sciences Institute, Florida International University, Miami, Florida, USA
| | - Sheng Li
- Department of Medicine, University of California San Diego, La Jolla, California, USA
| | - Robert V Stahelin
- Department of Medicinal Chemistry & Molecular Pharmacology, Purdue University, West Lafayette, Indiana, USA.
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9
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Montecinos-Franjola F, Bauer BL, Mears JA, Ramachandran R. GFP fluorescence tagging alters dynamin-related protein 1 oligomerization dynamics and creates disassembly-refractory puncta to mediate mitochondrial fission. Sci Rep 2020; 10:14777. [PMID: 32901052 PMCID: PMC7479153 DOI: 10.1038/s41598-020-71655-x] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2020] [Accepted: 08/19/2020] [Indexed: 01/22/2023] Open
Abstract
Green fluorescent protein (GFP)-tagging is the prevalent strategy to monitor protein dynamics in living cells. However, the consequences of appending the bulky GFP moiety to the protein of interest are rarely investigated. Here, using a powerful combination of quantitative fluorescence spectroscopic and imaging techniques, we have examined the oligomerization dynamics of the GFP-tagged mitochondrial fission GTPase dynamin-related protein 1 (Drp1) both in vitro and in vivo. We find that GFP-tagged Drp1 exhibits impaired oligomerization equilibria in solution that corresponds to a greatly diminished cooperative GTPase activity in comparison to native Drp1. Consequently, GFP-tagged Drp1 constitutes aberrantly stable, GTP-resistant supramolecular assemblies both in vitro and in vivo, neither of which reflects a more dynamic native Drp1 oligomerization state. Indeed, GFP-tagged Drp1 is detected more frequently per unit length over mitochondria in Drp1-null mouse embryonic fibroblasts (MEFs) compared to wild-type (wt) MEFs, indicating that the drastically reduced GTP turnover restricts oligomer disassembly from the mitochondrial surface relative to mixed oligomers comprising native and GFP-tagged Drp1. Yet, GFP-tagged Drp1 retains the capacity to mediate membrane constriction in vitro and mitochondrial division in vivo. These findings suggest that instead of robust assembly-disassembly dynamics, persistent Drp1 higher-order oligomerization over membranes is sufficient for mitochondrial fission.
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Affiliation(s)
- Felipe Montecinos-Franjola
- Department of Physiology and Biophysics, Case Western Reserve University School of Medicine, Cleveland, OH, 44106, USA
| | - Brianna L Bauer
- Department of Pharmacology, Case Western Reserve University School of Medicine, Cleveland, OH, 44106, USA
| | - Jason A Mears
- Department of Pharmacology, Case Western Reserve University School of Medicine, Cleveland, OH, 44106, USA.,Center for Mitochondrial Diseases, Case Western Reserve University School of Medicine, Cleveland, OH, 44106, USA.,Cleveland Center for Membrane and Structural Biology, Case Western Reserve University School of Medicine, Cleveland, OH, 44106, USA
| | - Rajesh Ramachandran
- Department of Physiology and Biophysics, Case Western Reserve University School of Medicine, Cleveland, OH, 44106, USA. .,Cleveland Center for Membrane and Structural Biology, Case Western Reserve University School of Medicine, Cleveland, OH, 44106, USA.
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10
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Determination of oligomerization state of Drp1 protein in living cells at nanomolar concentrations. Sci Rep 2019; 9:5906. [PMID: 30976093 PMCID: PMC6459820 DOI: 10.1038/s41598-019-42418-0] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2018] [Accepted: 03/11/2019] [Indexed: 12/15/2022] Open
Abstract
Biochemistry in living cells is an emerging field of science. Current quantitative bioassays are performed ex vivo, thus equilibrium constants and reaction rates of reactions occurring in human cells are still unknown. To address this issue, we present a non-invasive method to quantitatively characterize interactions (equilibrium constants, KD) directly within the cytosol of living cells. We reveal that cytosolic hydrodynamic drag depends exponentially on a probe's size, and provide a model for its determination for different protein sizes (1-70 nm). We analysed oligomerization of dynamin-related protein 1 (Drp1, wild type and mutants: K668E, G363D, C505A) in HeLa cells. We detected the coexistence of wt-Drp1 dimers and tetramers in cytosol, and determined that KD for tetramers was 0.7 ± 0.5 μM. Drp1 kinetics was modelled by independent simulations, giving computational results which matched experimental data. This robust method can be applied to in vivo determination of KD for other protein-protein complexes, or drug-target interactions.
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11
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Gupta A, Sankaran J, Wohland T. Fluorescence correlation spectroscopy: The technique and its applications in soft matter. PHYSICAL SCIENCES REVIEWS 2019. [DOI: 10.1515/psr-2017-0104] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Abstract
Fluorescence correlation spectroscopy (FCS) is a well-established single-molecule method used for the quantitative spatiotemporal analysis of dynamic processes in a wide range of samples. It possesses single-molecule sensitivity but provides ensemble averaged molecular parameters such as mobility, concentration, chemical reaction kinetics, photophysical properties and interaction properties. These parameters have been utilized to characterize a variety of soft matter systems. This review provides an overview of the basic principles of various FCS modalities, their instrumentation, data analysis, and the applications of FCS to soft matter systems.
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12
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Cutrale F, Rodriguez D, Hortigüela V, Chiu CL, Otterstrom J, Mieruszynski S, Seriola A, Larrañaga E, Raya A, Lakadamyali M, Fraser SE, Martinez E, Ojosnegros S. Using enhanced number and brightness to measure protein oligomerization dynamics in live cells. Nat Protoc 2019; 14:616-638. [DOI: 10.1038/s41596-018-0111-9] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
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13
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Chong S, Dugast-Darzacq C, Liu Z, Dong P, Dailey GM, Cattoglio C, Heckert A, Banala S, Lavis L, Darzacq X, Tjian R. Imaging dynamic and selective low-complexity domain interactions that control gene transcription. Science 2018; 361:eaar2555. [PMID: 29930090 PMCID: PMC6961784 DOI: 10.1126/science.aar2555] [Citation(s) in RCA: 596] [Impact Index Per Article: 99.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2017] [Revised: 03/12/2018] [Accepted: 06/13/2018] [Indexed: 12/18/2022]
Abstract
Many eukaryotic transcription factors (TFs) contain intrinsically disordered low-complexity sequence domains (LCDs), but how these LCDs drive transactivation remains unclear. We used live-cell single-molecule imaging to reveal that TF LCDs form local high-concentration interaction hubs at synthetic and endogenous genomic loci. TF LCD hubs stabilize DNA binding, recruit RNA polymerase II (RNA Pol II), and activate transcription. LCD-LCD interactions within hubs are highly dynamic, display selectivity with binding partners, and are differentially sensitive to disruption by hexanediols. Under physiological conditions, rapid and reversible LCD-LCD interactions occur between TFs and the RNA Pol II machinery without detectable phase separation. Our findings reveal fundamental mechanisms underpinning transcriptional control and suggest a framework for developing single-molecule imaging screens for drugs targeting gene regulatory interactions implicated in disease.
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Affiliation(s)
- Shasha Chong
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA
- Howard Hughes Medical Institute, University of California, Berkeley, CA, USA
| | - Claire Dugast-Darzacq
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA
- CIRM Center of Excellence, University of California, Berkeley, CA, USA
| | - Zhe Liu
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, USA
| | - Peng Dong
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, USA
| | - Gina M Dailey
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA
| | - Claudia Cattoglio
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA
- Howard Hughes Medical Institute, University of California, Berkeley, CA, USA
| | - Alec Heckert
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA
| | - Sambashiva Banala
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, USA
| | - Luke Lavis
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, USA
| | - Xavier Darzacq
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA
- CIRM Center of Excellence, University of California, Berkeley, CA, USA
| | - Robert Tjian
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA.
- Howard Hughes Medical Institute, University of California, Berkeley, CA, USA
- CIRM Center of Excellence, University of California, Berkeley, CA, USA
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14
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Garcia E, Bernardino de la Serna J. Dissecting single-cell molecular spatiotemporal mobility and clustering at focal adhesions in polarised cells by fluorescence fluctuation spectroscopy methods. Methods 2018; 140-141:85-96. [PMID: 29605734 DOI: 10.1016/j.ymeth.2018.03.008] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2017] [Revised: 03/20/2018] [Accepted: 03/22/2018] [Indexed: 11/21/2022] Open
Abstract
Quantitative fluorescence fluctuation spectroscopy from optical microscopy datasets is a very powerful tool to resolve multiple spatiotemporal cellular and subcellular processes at the molecular level. In particular, raster image correlation spectroscopy (RICS) and number and brightness analyses (N&B) yield molecular mobility and clustering dynamic information extracted from real-time cellular processes. This quantitative information can be inferred in a highly flexible and detailed manner, i.e. 1) at the localisation level: from full-frame datasets and multiple regions of interest within; and 2) at the temporal level: not only from full-frame and multiple regions, but also intermediate temporal events. Here we build on previous research in deciphering the molecular dynamics of paxillin, a main component of focal adhesions. Cells use focal adhesions to attach to the extracellular matrix and interact with their local environment. Through focal adhesions and other adhesion structures, cells sense their local environment and respond accordingly; due to this continuous communication, these structures can be highly dynamic depending on the extracellular characteristics. By using a previously well-characterised model like paxillin, we examine the powerful sensitivity and some limitations of RICS and N&B analyses. We show that cells upon contact to different surfaces show differential self-assembly dynamics in terms of molecular diffusion and oligomerisation. In addition, single-cell studies show that these dynamics change gradually following an antero-posterior gradient.
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Affiliation(s)
- Esther Garcia
- Central Laser Facility, Science and Technology Facilities Council, Rutherford Appleton Laboratory, Research Complex at Harwell, Harwell-Oxford, UK
| | - Jorge Bernardino de la Serna
- Central Laser Facility, Science and Technology Facilities Council, Rutherford Appleton Laboratory, Research Complex at Harwell, Harwell-Oxford, UK; Department of Physics, King's College London, London, UK.
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15
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Friend JE, Sayyad WA, Arasada R, McCormick CD, Heuser JE, Pollard TD. Fission yeast Myo2: Molecular organization and diffusion in the cytoplasm. Cytoskeleton (Hoboken) 2017; 75:164-173. [PMID: 29205883 DOI: 10.1002/cm.21425] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2017] [Revised: 11/22/2017] [Accepted: 11/27/2017] [Indexed: 12/20/2022]
Abstract
Myosin-II is required for the assembly and constriction of cytokinetic contractile rings in fungi and animals. We used electron microscopy, fluorescence recovery after photobleaching (FRAP), and fluorescence correlation spectroscopy (FCS) to characterize the physical properties of Myo2 from fission yeast Schizosaccharomyces pombe. By electron microscopy, Myo2 has two heads and a coiled-coiled tail like myosin-II from other species. The first 65 nm of the tail is a stiff rod, followed by a flexible, less-ordered region up to 30 nm long. Myo2 sediments as a 7 S molecule in high salt, but aggregates rather than forming minifilaments at lower salt concentrations; this is unaffected by heavy chain phosphorylation. We used FRAP and FCS to observe the dynamics of Myo2 in live S. pombe cells and in cell extracts at different salt concentrations; both show that Myo2 with an N-terminal mEGFP tag has a diffusion coefficient of ∼ 3 µm2 s-1 in the cytoplasm of live cells during interphase and mitosis. Photon counting histogram analysis of the FCS data confirmed that Myo2 diffuses as doubled-headed molecules in the cytoplasm. FCS measurements on diluted cell extracts showed that mEGFP-Myo2 has a diffusion coefficient of ∼ 30 µm2 s-1 in 50 to 400 mM KCl concentrations.
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Affiliation(s)
- Janice E Friend
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, Connecticut 06520-8103
| | - Wasim A Sayyad
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, Connecticut 06520-8103
| | - Rajesh Arasada
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, Connecticut 06520-8103
| | - Chad D McCormick
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut 06520-8103.,Section on Integrative Biophysics, Eunice Kennedy Shriver National Institute of Child Health and Human Development, NIH, Bethesda, Maryland 20892-1855
| | - John E Heuser
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut 06520-8103
| | - Thomas D Pollard
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, Connecticut 06520-8103.,Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut 06520-8103.,Department of Cell Biology, Yale University, New Haven, Connecticut 06520-8103
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16
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Friedrich EE, Washburn NR. Transport patterns of anti-TNF-α in burn wounds: Therapeutic implications of hyaluronic acid conjugation. Biomaterials 2016; 114:10-22. [PMID: 27837681 DOI: 10.1016/j.biomaterials.2016.11.003] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2016] [Revised: 11/02/2016] [Accepted: 11/03/2016] [Indexed: 12/16/2022]
Abstract
A central complication in burn injuries is progression of the zone of necrosis, which is associated with intense inflammatory responses. Conjugation of monoclonal antibodies against tumor necrosis factor-α (TNF-α), a central mediator of inflammation, to high molecular weight hyaluronic acid (HA) has been shown to be an effective treatment in reducing secondary necrosis in rodent models of deep partial-thickness burns. Here the transport of conjugated and non-conjugated antibodies in burn injuries was investigated to explore the effects of antibody tethering on the spatiotemporal distribution of anti-TNF-α. Diffusion constants were measured in solution and in type I collagen gels in vitro using fluorescence correlation spectroscopy to provide quantitative comparisons of the effects of conjugation. It is shown that the HA significantly increased the antibody residence time in the superficial region at 24 h in burn injuries, which strongly correlated with the pattern of inflammatory cell infiltrate in the tissue. A transport model was used to fit the results of antibody distribution in the tissue based on fluorescence correlation spectroscopy measurements, resulting in estimates for effective diffusion constants that demonstrate the effects of HA conjugation on the biodistribution of therapeutic proteins. These results demonstrate that tuning residence time of therapeutic proteins can be an effective strategy in regulating the inflammatory response associated with acute injuries.
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Affiliation(s)
- Emily E Friedrich
- Carnegie Mellon University, Department of Biomedical Engineering, USA.
| | - Newell R Washburn
- Carnegie Mellon University, Department of Biomedical Engineering, USA; Carnegie Mellon University, Department of Chemistry, USA.
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17
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Sahoo B, Arduini I, Drombosky KW, Kodali R, Sanders LH, Greenamyre JT, Wetzel R. Folding Landscape of Mutant Huntingtin Exon1: Diffusible Multimers, Oligomers and Fibrils, and No Detectable Monomer. PLoS One 2016; 11:e0155747. [PMID: 27271685 PMCID: PMC4894636 DOI: 10.1371/journal.pone.0155747] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2015] [Accepted: 05/03/2016] [Indexed: 12/19/2022] Open
Abstract
Expansion of the polyglutamine (polyQ) track of the Huntingtin (HTT) protein above 36 is associated with a sharply enhanced risk of Huntington’s disease (HD). Although there is general agreement that HTT toxicity resides primarily in N-terminal fragments such as the HTT exon1 protein, there is no consensus on the nature of the physical states of HTT exon1 that are induced by polyQ expansion, nor on which of these states might be responsible for toxicity. One hypothesis is that polyQ expansion induces an alternative, toxic conformation in the HTT exon1 monomer. Alternative hypotheses posit that the toxic species is one of several possible aggregated states. Defining the nature of the toxic species is particularly challenging because of facile interconversion between physical states as well as challenges to identifying these states, especially in vivo. Here we describe the use of fluorescence correlation spectroscopy (FCS) to characterize the detailed time and repeat length dependent self-association of HTT exon1-like fragments both with chemically synthesized peptides in vitro and with cell-produced proteins in extracts and in living cells. We find that, in vitro, mutant HTT exon1 peptides engage in polyQ repeat length dependent dimer and tetramer formation, followed by time dependent formation of diffusible spherical and fibrillar oligomers and finally by larger, sedimentable amyloid fibrils. For expanded polyQ HTT exon1 expressed in PC12 cells, monomers are absent, with tetramers being the smallest molecular form detected, followed in the incubation time course by small, diffusible aggregates at 6–9 hours and larger, sedimentable aggregates that begin to build up at 12 hrs. In these cell cultures, significant nuclear DNA damage appears by 6 hours, followed at later times by caspase 3 induction, mitochondrial dysfunction, and cell death. Our data thus defines limits on the sizes and concentrations of different physical states of HTT exon1 along the reaction profile in the context of emerging cellular distress. The data provide some new candidates for the toxic species and some new reservations about more well-established candidates. Compared to other known markers of HTT toxicity, nuclear DNA damage appears to be a relatively early pathological event.
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Affiliation(s)
- Bankanidhi Sahoo
- Department of Structural Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA, 15260, United States of America
- Pittsburgh Institute for Neurodegenerative Diseases, University of Pittsburgh School of Medicine, Pittsburgh, PA, 15260, United States of America
| | - Irene Arduini
- Department of Structural Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA, 15260, United States of America
- Pittsburgh Institute for Neurodegenerative Diseases, University of Pittsburgh School of Medicine, Pittsburgh, PA, 15260, United States of America
| | - Kenneth W. Drombosky
- Department of Structural Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA, 15260, United States of America
- Pittsburgh Institute for Neurodegenerative Diseases, University of Pittsburgh School of Medicine, Pittsburgh, PA, 15260, United States of America
| | - Ravindra Kodali
- Department of Structural Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA, 15260, United States of America
- Pittsburgh Institute for Neurodegenerative Diseases, University of Pittsburgh School of Medicine, Pittsburgh, PA, 15260, United States of America
| | - Laurie H. Sanders
- Pittsburgh Institute for Neurodegenerative Diseases, University of Pittsburgh School of Medicine, Pittsburgh, PA, 15260, United States of America
- Department of Neurology, University of Pittsburgh School of Medicine, Pittsburgh, PA, 15260, United States of America
| | - J. Timothy Greenamyre
- Pittsburgh Institute for Neurodegenerative Diseases, University of Pittsburgh School of Medicine, Pittsburgh, PA, 15260, United States of America
- Department of Neurology, University of Pittsburgh School of Medicine, Pittsburgh, PA, 15260, United States of America
| | - Ronald Wetzel
- Department of Structural Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA, 15260, United States of America
- Pittsburgh Institute for Neurodegenerative Diseases, University of Pittsburgh School of Medicine, Pittsburgh, PA, 15260, United States of America
- * E-mail:
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18
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Sahoo B, Drombosky KW, Wetzel R. Fluorescence Correlation Spectroscopy: A Tool to Study Protein Oligomerization and Aggregation In Vitro and In Vivo. Methods Mol Biol 2016; 1345:67-87. [PMID: 26453206 DOI: 10.1007/978-1-4939-2978-8_5] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
Fluorescence correlation spectroscopy (FCS) is a highly sensitive analytical technique used to measure dynamic molecular parameters, such as diffusion time (from which particle size can be calculated), conformation, and concentration of fluorescent molecules. It has been particularly powerful in characterizing size distributions in molecular associations (e.g., dimer/multimer formation) both in well-behaved thermodynamically equilibrated systems in vitro as well as in more complex environments in vivo. Protein aggregation reactions like amyloid formation, in contrast, are complex, often involving a series of uniquely structured aggregation intermediates appearing at different time scales. Nonetheless, FCS can be used in appropriate cases to characterize the early stages of some aggregation reactions. Here are described step-by-step protocols and experimental procedures for the study of molecular complex formation in aggregation systems as observed in simple buffer systems, cell extracts, and living cells. The methods described are illustrated with examples from studies of the self-assembly of huntingtin fragments, but in principle can be adapted for any aggregating system.
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Affiliation(s)
- Bankanidhi Sahoo
- Department of Structural Biology and Pittsburgh Institute for Neurodegenerative Diseases, University of Pittsburgh School of Medicine, Biomedical Science Tower 3, 3501 5th Avenue, Pittsburgh, PA, 15260, USA
| | - Kenneth W Drombosky
- Department of Structural Biology and Pittsburgh Institute for Neurodegenerative Diseases, University of Pittsburgh School of Medicine, Biomedical Science Tower 3, 3501 5th Avenue, Pittsburgh, PA, 15260, USA
| | - Ronald Wetzel
- Department of Structural Biology and Pittsburgh Institute for Neurodegenerative Diseases, University of Pittsburgh School of Medicine, Biomedical Science Tower 3, 3501 5th Avenue, Pittsburgh, PA, 15260, USA.
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19
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Ward RJ, Pediani JD, Godin AG, Milligan G. Regulation of oligomeric organization of the serotonin 5-hydroxytryptamine 2C (5-HT2C) receptor observed by spatial intensity distribution analysis. J Biol Chem 2015; 290:12844-57. [PMID: 25825490 PMCID: PMC4432300 DOI: 10.1074/jbc.m115.644724] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2015] [Indexed: 12/19/2022] Open
Abstract
The questions of whether G protein-coupled receptors exist as monomers, dimers, and/or oligomers and if these species interconvert in a ligand-dependent manner are among the most contentious current issues in biology. When employing spatial intensity distribution analysis to laser scanning confocal microscope images of cells stably expressing either a plasma membrane-associated form of monomeric enhanced green fluorescent protein (eGFP) or a tandem version of this fluorophore, the eGFP tandem was identified as a dimer. Similar studies on cells stably expressing an eGFP-tagged form of the epidermal growth factor receptor demonstrated that, although largely a monomer in the basal state, this receptor rapidly became predominantly dimeric upon the addition of its ligand epidermal growth factor. In cells induced to express an eGFP-tagged form of the serotonin 5-hydroxytryptamine 2C (5-HT2C) receptor, global analysis of construct quantal brightness was consistent with the predominant form of the receptor being dimeric. However, detailed spatial intensity distribution analysis demonstrated the presence of multiple forms ranging from monomers to higher-order oligomers. Furthermore, treatment with chemically distinct 5-HT2C receptor antagonists resulted in a time-dependent change in the quaternary organization to one in which there was a preponderance of receptor monomers. This antagonist-mediated effect was reversible, because washout of the ligand resulted in the regeneration of many of the oligomeric forms of the receptor.
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Affiliation(s)
- Richard J Ward
- From the Institute of Molecular, Cell and Systems Biology, University of Glasgow, Glasgow G12 8QQ, Scotland, United Kingdom
| | - John D Pediani
- From the Institute of Molecular, Cell and Systems Biology, University of Glasgow, Glasgow G12 8QQ, Scotland, United Kingdom
| | - Antoine G Godin
- the University of Bordeaux, LP2N, UMR 5298, F-33405 Talence, France, and the Institut d'Optique Graduate School and CNRS, LP2N, UMR 5298, F-33405 Talence, France
| | - Graeme Milligan
- From the Institute of Molecular, Cell and Systems Biology, University of Glasgow, Glasgow G12 8QQ, Scotland, United Kingdom,
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