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Peacock H, Blum SA. Single-Micelle and Single-Zinc-Particle Imaging Provides Insights into the Physical Processes Underpinning Organozinc Reactions in Water. J Am Chem Soc 2022; 144:3285-3296. [PMID: 35156815 DOI: 10.1021/jacs.2c00421] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Micelles on the surfaces of individual metallic zinc particles are imaged by fluorescence microscopy with sensitivity up to single micelles. These micelles are made fluorescent to enable imaging, through the incorporation of boron dipyrromethene fluorophores as representative organic molecular "cargo". Highlighting an advantage of this in situ and sensitive fluorescence technique, the same micelles are not visible by ex situ scanning electron microscopy/energy dispersive X-ray spectroscopy analysis. Examination of micellar solutions with zinc reveals an aging process: micelles do not immediately adhere to the zinc surfaces upon mixing but rather build up over time. Furthermore, at longer times, smaller zinc particles become fully encased in micelle "shells". Once adhered, micelles remain in the local regions of the zinc surface for the duration of the imaging experiments (>2 h). Single micelles are imaged in solution, and their molecular contents are characterized. Two-color fluorescence crossover experiments show that micelles adhered to the surface of the zinc exchange molecular contents with micelles in solution, achieving molecular exchange equilibrium in ∼2.5 h. Unique (non-ensemble averaged) exchange kinetics are displayed by micelles at different locations on the zinc surface, consistent with exchange kinetics of single micelles or small local clusters of micelles. The aging of the micellar solutions and the rate of exchange while on the surface of the zinc suggest that micelle mass transport processes may contribute to overall reaction barriers in sustainable organozinc cross-coupling reactions in micellar water. The observed aging of the system suggests routes for improvement of preparative, bench-scale synthetic reactions involving micellar preparations of organozinc compounds.
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Affiliation(s)
- Hannah Peacock
- Department of Chemistry, University of California, Irvine, Irvine, California 92697-2025, United States
| | - Suzanne A Blum
- Department of Chemistry, University of California, Irvine, Irvine, California 92697-2025, United States
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2
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Sanches K, Wai DCC, Norton RS. Conformational dynamics in peptide toxins: Implications for receptor interactions and molecular design. Toxicon 2021; 201:127-140. [PMID: 34454969 DOI: 10.1016/j.toxicon.2021.08.020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2021] [Revised: 08/19/2021] [Accepted: 08/23/2021] [Indexed: 10/20/2022]
Abstract
Peptide toxins are potent and often exquisitely selective probes of the structure and function of ion channels and receptors, and are therefore of significant interest to the pharmaceutical and biotech industries as both pharmacological tools and therapeutic leads. The three-dimensional structures of peptide toxins are essential as a basis for understanding their structure-activity relationships and their binding to target receptors, as well as in guiding the design of analogues with modified potency and/or selectivity for key targets. NMR spectroscopy has played a key role in elucidating the structures of peptide toxins and probing their structure-function relationships. In this article, we highlight the additional important contribution of NMR to characterising the dynamics of peptide toxins. We also compare the information available from NMR measurements with that afforded by molecular dynamics simulations. We describe several examples of the importance of dynamics measurements over a range of timescales for understanding the structure-function relationships of peptide toxins and their receptor engagement. Peptide toxins that inhibit the voltage-gated potassium channel KV1.3 with pM affinities display different degrees of conformational flexibility, even though they contain multiple disulfide bonds, and this flexibility can affect the relative orientation of residues that have been shown to be critical for channel binding. Information on the dynamic properties of peptide toxins is important in the design of analogues or mimetics where receptor-bound structures are not available.
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Affiliation(s)
- Karoline Sanches
- Medicinal Chemistry, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Victoria, 3052, Australia; ARC Centre for Fragment-Based Design, Monash University, Parkville, Victoria, 3052, Australia
| | - Dorothy C C Wai
- Medicinal Chemistry, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Victoria, 3052, Australia
| | - Raymond S Norton
- Medicinal Chemistry, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Victoria, 3052, Australia; ARC Centre for Fragment-Based Design, Monash University, Parkville, Victoria, 3052, Australia.
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3
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Ghosh A, Chizhik AI, Karedla N, Enderlein J. Graphene- and metal-induced energy transfer for single-molecule imaging and live-cell nanoscopy with (sub)-nanometer axial resolution. Nat Protoc 2021; 16:3695-3715. [PMID: 34099942 DOI: 10.1038/s41596-021-00558-6] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2020] [Accepted: 04/19/2021] [Indexed: 02/05/2023]
Abstract
Super-resolution fluorescence imaging that surpasses the classical optical resolution limit is widely utilized for resolving the spatial organization of biological structures at molecular length scales. In one example, single-molecule localization microscopy, the lateral positions of single molecules can be determined more precisely than the diffraction limit if the camera collects individual photons separately. Using several schemes that introduce engineered optical aberrations in the imaging optics, super-resolution along the optical axis (perpendicular to the sample plane) has been achieved, and single-molecule localization microscopy has been successfully applied for the study of 3D biological structures. Nonetheless, the achievable axial localization accuracy is typically three to five times worse than the lateral localization accuracy. Only a few exceptional methods based on interferometry exist that reach nanometer 3D super-resolution, but they involve enormous technical complexity and restricted sample preparations that inhibit their widespread application. We developed metal-induced energy transfer imaging for localizing fluorophores along the axial direction with nanometer accuracy, using only a conventional fluorescence lifetime imaging microscope. In metal-induced energy transfer, experimentally measured fluorescence lifetime values increase linearly with axial distance in the range of 0-100 nm, making it possible to calculate their axial position using a theoretical model. If graphene is used instead of the metal (graphene-induced energy transfer), the same range of lifetime values occurs over a shorter axial distance (~25 nm), meaning that it is possible to get very accurate axial information at the scale of a membrane bilayer or a molecular complex in a membrane. Here, we provide a step-by-step protocol for metal- and graphene-induced energy transfer imaging in single molecules, supported lipid bilayer and live-cell membranes. Depending on the sample preparation time, the complete duration of the protocol is 1-3 d.
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Affiliation(s)
- Arindam Ghosh
- Third Institute of Physics-Biophysics, Georg August University, Göttingen, Germany
| | - Alexey I Chizhik
- Third Institute of Physics-Biophysics, Georg August University, Göttingen, Germany
| | - Narain Karedla
- Rosalind Franklin Institute, Didcot, UK.,Kennedy Institute for Rheumatology, University of Oxford, Oxford, UK
| | - Jörg Enderlein
- Third Institute of Physics-Biophysics, Georg August University, Göttingen, Germany. .,Cluster of Excellence 'Multiscale Bioimaging: from Molecular Machines to Networks of Excitable Cells' (MBExC), Georg August University, Göttingen, Germany.
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4
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Gomez MV, Ruiz-Castañeda M, Nitschke P, Gschwind RM, Jiménez MA. Insights Into the Micelle-Induced β-Hairpin-to-α-Helix Transition of a LytA-Derived Peptide by Photo-CIDNP Spectroscopy. Int J Mol Sci 2021; 22:ijms22136666. [PMID: 34206372 PMCID: PMC8268221 DOI: 10.3390/ijms22136666] [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: 04/29/2021] [Revised: 06/07/2021] [Accepted: 06/16/2021] [Indexed: 11/16/2022] Open
Abstract
A choline-binding module from pneumococcal LytA autolysin, LytA239–252, was reported to have a highly stable nativelike β-hairpin in aqueous solution, which turns into a stable amphipathic α-helix in the presence of micelles. Here, we aim to obtain insights into this DPC-micelle triggered β-hairpin-to-α-helix conformational transition using photo-CIDNP NMR experiments. Our results illustrate the dependency between photo-CIDNP phenomena and the light intensity in the sample volume, showing that the use of smaller-diameter (2.5 mm) NMR tubes instead of the conventional 5 mm ones enables more efficient illumination for our laser-diode light setup. Photo-CIDNP experiments reveal different solvent accessibility for the two tyrosine residues, Y249 and Y250, the latter being less accessible to the solvent. The cross-polarization effects of these two tyrosine residues of LytA239–252 allow for deeper insights and evidence their different behavior, showing that the Y250 aromatic side chain is involved in a stronger interaction with DPC micelles than Y249 is. These results can be interpreted in terms of the DPC micelle disrupting the aromatic stacking between W241 and Y250 present in the nativelike β-hairpin, hence initiating conversion towards the α-helix structure. Our photo-CIDNP methodology represents a powerful tool for observing residue-level information in switch peptides that is difficult to obtain by other spectroscopic techniques.
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Affiliation(s)
- M. Victoria Gomez
- IRICA, Department of Inorganic, Organic and Biochemistry, Faculty of Chemical Sciences and Technologies, Universidad de Castilla-La Mancha (UCLM), Av. Camilo José Cela 10, 13071 Ciudad Real, Spain;
- Correspondence: (M.V.G.); (M.A.J.)
| | - Margarita Ruiz-Castañeda
- IRICA, Department of Inorganic, Organic and Biochemistry, Faculty of Chemical Sciences and Technologies, Universidad de Castilla-La Mancha (UCLM), Av. Camilo José Cela 10, 13071 Ciudad Real, Spain;
| | - Philipp Nitschke
- Institute of Organic Chemistry, University of Regensburg, Universitätsstraße 31, 93053 Regensburg, Germany; (P.N.); (R.M.G.)
| | - Ruth M. Gschwind
- Institute of Organic Chemistry, University of Regensburg, Universitätsstraße 31, 93053 Regensburg, Germany; (P.N.); (R.M.G.)
| | - M. Angeles Jiménez
- Departamento de Química-Física Biológica, Instituto de Química Física Rocasolano (IQFR-CSIC), Serrano 119, 28006 Madrid, Spain
- Correspondence: (M.V.G.); (M.A.J.)
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5
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Hwang W, Seo J, Kim D, Lee CJ, Choi IH, Yoo KH, Kim DY. Large field-of-view nanometer-sectioning microscopy by using metal-induced energy transfer and biexponential lifetime analysis. Commun Biol 2021; 4:91. [PMID: 33469155 PMCID: PMC7815909 DOI: 10.1038/s42003-020-01628-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2020] [Accepted: 11/24/2020] [Indexed: 12/04/2022] Open
Abstract
Total internal reflection fluorescence (TIRF) microscopy, which has about 100-nm axial excitation depth, is the method of choice for nanometer-sectioning imaging for decades. Lately, several new imaging techniques, such as variable angle TIRF microscopy, supercritical-angle fluorescence microscopy, and metal-induced energy transfer imaging, have been proposed to enhance the axial resolution of TIRF. However, all of these methods use high numerical aperture (NA) objectives, and measured images inevitably have small field-of-views (FOVs). Small-FOV can be a serious limitation when multiple cells need to be observed. We propose large-FOV nanometer-sectioning microscopy, which breaks the complementary relations between the depth of focus and axial sectioning by using MIET. Large-FOV imaging is achieved with a low-magnification objective, while nanometer-sectioning is realized utilizing metal-induced energy transfer and biexponential fluorescence lifetime analysis. The feasibility of our proposed method was demonstrated by imaging nanometer-scale distances between the basal membrane of human aortic endothelial cells and a substrate. Hwang et al. demonstrate that a high axial resolution can be achieved even with low numerical aperture (NA) objectives. They show the nano-profile of a basal cell membrane using metal-induced energy transfer and biexponential fluorescence lifetime analysis. The low-NA objective provides a larger field-of-view (FOV), thereby overcoming the limitations of a small FOV of the usually used high-NA objectives.
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Affiliation(s)
- Wonsang Hwang
- Department of Physics, Yonsei University, Seoul, Republic of Korea
| | - Jinwon Seo
- Department of Microbiology, Institute for Immunology and Immunological Diseases, College of Medicine, Yonsei University, Seoul, Republic of Korea
| | - DongEun Kim
- Department of Physics, Yonsei University, Seoul, Republic of Korea
| | - Chang Jun Lee
- Department of Physics, Yonsei University, Seoul, Republic of Korea
| | - In-Hong Choi
- Department of Microbiology, Institute for Immunology and Immunological Diseases, College of Medicine, Yonsei University, Seoul, Republic of Korea
| | - Kyung-Hwa Yoo
- Department of Physics, Yonsei University, Seoul, Republic of Korea
| | - Dug Young Kim
- Department of Physics, Yonsei University, Seoul, Republic of Korea.
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6
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Vaippully R, Ramanujan V, Gopalakrishnan M, Bajpai S, Roy B. Detection of sub-degree angular fluctuations of the local cell membrane slope using optical tweezers. SOFT MATTER 2020; 16:7606-7612. [PMID: 32724976 DOI: 10.1039/d0sm00566e] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Normal thermal fluctuations of the cell membrane have been studied extensively using high resolution microscopy and focused light, particularly at the peripheral regions of a cell. We use a single probe particle attached non-specifically to the cell-membrane to determine that the power spectral density is proportional to (frequency)-5/3 in the range of 5 Hz to 1 kHz. We also use a new technique to simultaneously ascertain the slope fluctuations of the membrane by relying upon the determination of pitch motion of the birefringent probe particle trapped in linearly polarized optical tweezers. In the process, we also develop the technique to identify pitch rotation to a high resolution using optical tweezers. We find that the power spectrum of slope fluctuations is proportional to (frequency)-1, which we also explain theoretically. We find that we can extract parameters like bending rigidity directly from the coefficient of the power spectrum particularly at high frequencies, instead of being convoluted with other parameters, thereby improving the accuracy of estimation. We anticipate this technique for determination of the pitch angle in spherical particles to high resolution as a starting point for many interesting studies using the optical tweezers.
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Affiliation(s)
- Rahul Vaippully
- Department of Physics, Indian Institute of Technology Madras, Chennai, 600036, India.
| | - Vaibavi Ramanujan
- Department of Applied Mechanics, Indian Institute of Technology Madras, Chennai, 600036, India
| | - Manoj Gopalakrishnan
- Department of Physics, Indian Institute of Technology Madras, Chennai, 600036, India.
| | - Saumendra Bajpai
- Department of Applied Mechanics, Indian Institute of Technology Madras, Chennai, 600036, India
| | - Basudev Roy
- Department of Physics, Indian Institute of Technology Madras, Chennai, 600036, India.
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7
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Munusamy S, Conde R, Bertrand B, Munoz-Garay C. Biophysical approaches for exploring lipopeptide-lipid interactions. Biochimie 2020; 170:173-202. [PMID: 31978418 PMCID: PMC7116911 DOI: 10.1016/j.biochi.2020.01.009] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2019] [Accepted: 01/19/2020] [Indexed: 02/07/2023]
Abstract
In recent years, lipopeptides (LPs) have attracted a lot of attention in the pharmaceutical industry due to their broad-spectrum of antimicrobial activity against a variety of pathogens and their unique mode of action. This class of compounds has enormous potential for application as an alternative to conventional antibiotics and for pest control. Understanding how LPs work from a structural and biophysical standpoint through investigating their interaction with cell membranes is crucial for the rational design of these biomolecules. Various analytical techniques have been developed for studying intramolecular interactions with high resolution. However, these tools have been barely exploited in lipopeptide-lipid interactions studies. These biophysical approaches would give precise insight on these interactions. Here, we reviewed these state-of-the-art analytical techniques. Knowledge at this level is indispensable for understanding LPs activity and particularly their potential specificity, which is relevant information for safe application. Additionally, the principle of each analytical technique is presented and the information acquired is discussed. The key challenges, such as the selection of the membrane model are also been briefly reviewed. A brief overview of topics to understand the generalities of lipopeptide (LP) science. Main analytical techniques used to reveal the interaction and the distorting effect of LP on artificial membranes. Guidelines for selecting of the most adequate membrane models for the given analytical technique.
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Affiliation(s)
- Sathishkumar Munusamy
- Instituto de Ciencias Físicas, Universidad Nacional Autónoma de México, Av. Universidad 2001, Col. Chamilpa, 62210, Cuernavaca, Mexico
| | - Renaud Conde
- Centro de Investigación Sobre Enfermedades Infecciosas, Instituto Nacional de Salud Pública, Cuernavaca, Morelos, Mexico
| | - Brandt Bertrand
- Instituto de Ciencias Físicas, Universidad Nacional Autónoma de México, Av. Universidad 2001, Col. Chamilpa, 62210, Cuernavaca, Mexico
| | - Carlos Munoz-Garay
- Instituto de Ciencias Físicas, Universidad Nacional Autónoma de México, Av. Universidad 2001, Col. Chamilpa, 62210, Cuernavaca, Mexico.
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8
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Bozelli JC, Salay LC, Arcisio-Miranda M, Procopio J, Riciluca KCT, Silva Junior PI, Nakaie CR, Schreier S. A comparison of activity, toxicity, and conformation of tritrpticin and two TOAC-labeled analogues. Effects on the mechanism of action. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2019; 1862:183110. [PMID: 31672543 DOI: 10.1016/j.bbamem.2019.183110] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/13/2019] [Revised: 09/19/2019] [Accepted: 09/29/2019] [Indexed: 02/01/2023]
Abstract
A strategy that has been gaining increased application for the study of the conformation, dynamics, orientation, and physicochemical properties of peptides is labeling with the paramagnetic amino acid TOAC. This approach was used to gain a deeper understanding on the mechanism of action of the antimicrobial peptide tritrpticin (TRP3). TRP3 was labeled with TOAC at the N-terminus (prior to V1, TOAC0-TRP3) or internally (replacing P5, TOAC5-TRP3). Functional studies showed that labeling led to peptides with higher activity against Gram-positive bacteria and lower hemolytic activity with respect to TRP3. Peptide-induced model membranes permeabilization and ion channel-like activity studies corroborated the functional assays qualitatively, showing higher activity of the peptides against negatively charged membranes, which had the purpose of mimicking bacterial membranes. TOAC presented a greater freedom of motion at the N-terminus than at the internal position, as evinced by EPR spectra. EPR and fluorescence spectra reported on the peptides conformational properties, showing acquisition of a more packed conformation in the presence of the secondary structure-inducing solvent, TFE. CD studies showed that TOAC0-TRP3 acquires a conformation similar to that of TRP3, both in aqueous solution and in TFE, while TOAC5-TRP3 presents a different conformation in all environments. While the mechanism of action of TRP3 was impacted to some extent by TOAC labeling at the N-terminus, it did change upon replacement of P5 by TOAC. The results demonstrated that TOAC-labeling could be used to modulate TRP3 activity and mechanism of action and, more importantly, the critical role of P5 for TRP3 pore formation.
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Affiliation(s)
- José C Bozelli
- Department of Biochemistry, Institute of Chemistry, University of São Paulo, Avenida Professor Lineu Prestes, 748, São Paulo, SP 05508-000, Brazil; Department of Biochemistry and Biomedical Sciences, McMaster University, Health Sciences Centre, Hamilton, ON L8S 4K1, Canada.
| | - Luiz C Salay
- Department of Biochemistry, Institute of Chemistry, University of São Paulo, Avenida Professor Lineu Prestes, 748, São Paulo, SP 05508-000, Brazil; Department of Exact and Technological Sciences, State University of Santa Cruz-UESC, Ilhéus, BA 45662-900, Brazil
| | - Manoel Arcisio-Miranda
- Department of Physiology and Biophysics, Institute of Biomedical Sciences, University of São Paulo, Avenida Professor Lineu Prestes, 1524, São Paulo, SP 05508-000, Brazil
| | - Joaquim Procopio
- Department of Physiology and Biophysics, Institute of Biomedical Sciences, University of São Paulo, Avenida Professor Lineu Prestes, 1524, São Paulo, SP 05508-000, Brazil
| | - Katie C T Riciluca
- Laboratory for Applied Toxinology, Butantan Institute, São Paulo, SP 05503-900, Brazil
| | - Pedro I Silva Junior
- Laboratory for Applied Toxinology, Butantan Institute, São Paulo, SP 05503-900, Brazil
| | - Clovis R Nakaie
- Department of Biophysics, Federal University of São Paulo, São Paulo, SP 04044-020, Brazil
| | - Shirley Schreier
- Department of Biochemistry, Institute of Chemistry, University of São Paulo, Avenida Professor Lineu Prestes, 748, São Paulo, SP 05508-000, Brazil
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9
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Shruti SR, Rajasekaran R. Identification of therapeutic peptide scaffold from tritrpticin family for urinary tract infections using in silico techniques. J Biomol Struct Dyn 2019; 38:4407-4417. [DOI: 10.1080/07391102.2019.1680437] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Affiliation(s)
- S. R. Shruti
- Department of Biotechnology, School of Biosciences and Technology, VIT (Deemed to Be University), Vellore, India
| | - R. Rajasekaran
- Department of Biotechnology, School of Biosciences and Technology, VIT (Deemed to Be University), Vellore, India
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10
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Soubies E, Radwanska A, Grall D, Blanc-Féraud L, Van Obberghen-Schilling E, Schaub S. Nanometric axial resolution of fibronectin assembly units achieved with an efficient reconstruction approach for multi-angle-TIRF microscopy. Sci Rep 2019; 9:1926. [PMID: 30760745 PMCID: PMC6374485 DOI: 10.1038/s41598-018-36119-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2018] [Accepted: 11/08/2018] [Indexed: 02/01/2023] Open
Abstract
High resolution imaging of molecules at the cell-substrate interface is required for understanding key biological processes. Here we propose a complete pipeline for multi-angle total internal reflection fluorescence microscopy (MA-TIRF) going from instrument design and calibration procedures to numerical reconstruction. Our custom setup is endowed with a homogeneous field illumination and precise excitation beam angle. Given a set of MA-TIRF acquisitions, we deploy an efficient joint deconvolution/reconstruction algorithm based on a variational formulation of the inverse problem. This algorithm offers the possibility of using various regularizations and can run on graphics processing unit (GPU) for rapid reconstruction. Moreover, it can be easily used with other MA-TIRF devices and we provide it as an open-source software. This ensemble has enabled us to visualize and measure with unprecedented nanometric resolution, the depth of molecular components of the fibronectin assembly machinery at the basal surface of endothelial cells.
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Affiliation(s)
- Emmanuel Soubies
- Université Côte d'Azur, CNRS, Inria, I3S, France. .,Biomedical Imaging Group, EPFL, Lausanne, Switzerland.
| | | | | | | | | | - Sébastien Schaub
- Université Côte d'Azur, CNRS, Inria, I3S, France. .,Université Côte d'Azur, CNRS, Inserm, iBV, France.
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11
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Li J, Han W, Li Y, Chen Y, Shang Y, Chen Y, Gui Z. Inverse problem based on the fast alternating direction method of multipliers algorithm in multiangle total internal reflection fluorescence microscopy. APPLIED OPTICS 2018; 57:9828-9834. [PMID: 30462018 DOI: 10.1364/ao.57.009828] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/30/2018] [Accepted: 10/22/2018] [Indexed: 06/09/2023]
Abstract
Multiangle total internal reflection fluorescence microscopy (TIRFM) has become one of the most important techniques for achieving axial superresolution. The key process in this technique is solving the inverse problem. This paper applies an improved alternating direction method of multipliers algorithm to solve the inverse problem and validates the accuracy of the algorithm by reconstructing simulated microtubule structures in multiangle TIRFM images. The reconstruction times for different algorithms and the convergence speeds of the improved and original algorithms are compared. Experimental results show that the improved algorithm can achieve an axial resolution of 40 nm, reduce the influence of the penalty parameter on convergence, and improve the convergence speed of the iterative process while ensuring image reconstruction quality. Based on the algorithm, a three-dimensional image with the depth information of microtubules and mitochondria is reconstructed.
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12
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Chen Y, Liu W, Zhang Z, Zheng C, Huang Y, Cao R, Zhu D, Xu L, Zhang M, Zhang YH, Fan J, Jin L, Xu Y, Kuang C, Liu X. Multi-color live-cell super-resolution volume imaging with multi-angle interference microscopy. Nat Commun 2018; 9:4818. [PMID: 30446673 PMCID: PMC6240104 DOI: 10.1038/s41467-018-07244-4] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2018] [Accepted: 10/23/2018] [Indexed: 12/17/2022] Open
Abstract
Imaging and tracking of near-surface three-dimensional volumetric nanoscale dynamic processes of live cells remains a challenging problem. In this paper, we propose a multi-color live-cell near-surface-volume super-resolution microscopy method that combines total internal reflection fluorescence structured illumination microscopy with multi-angle evanescent light illumination. We demonstrate that our approach of multi-angle interference microscopy is perfectly adapted to studying subcellular dynamics of mitochondria and microtubule architectures during cell migration. 3D super-resolution imaging of dynamic processes in live cells is still challenging, especially in a large field of view. Here the authors combine SIM with multi-angle evanescent light illumination and achieve improved lateral and axial resolution, with stack acquisition time in the range of 1–2 s.
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Affiliation(s)
- Youhua Chen
- State Key Laboratory of Modern Optical Instrumentation, College of Optical Science and Engineering, Zhejiang University, Hangzhou, Zhejiang, 310027, China.,Shanxi Provincial Key Laboratory for Biomedical Imaging and Big Data, North University of China, Taiyuan, Shanxi, 030051, China
| | - Wenjie Liu
- State Key Laboratory of Modern Optical Instrumentation, College of Optical Science and Engineering, Zhejiang University, Hangzhou, Zhejiang, 310027, China
| | - Zhimin Zhang
- State Key Laboratory of Modern Optical Instrumentation, College of Optical Science and Engineering, Zhejiang University, Hangzhou, Zhejiang, 310027, China
| | - Cheng Zheng
- State Key Laboratory of Modern Optical Instrumentation, College of Optical Science and Engineering, Zhejiang University, Hangzhou, Zhejiang, 310027, China
| | - Yujia Huang
- State Key Laboratory of Modern Optical Instrumentation, College of Optical Science and Engineering, Zhejiang University, Hangzhou, Zhejiang, 310027, China
| | - Ruizhi Cao
- State Key Laboratory of Modern Optical Instrumentation, College of Optical Science and Engineering, Zhejiang University, Hangzhou, Zhejiang, 310027, China
| | - Dazhao Zhu
- State Key Laboratory of Modern Optical Instrumentation, College of Optical Science and Engineering, Zhejiang University, Hangzhou, Zhejiang, 310027, China
| | - Liang Xu
- State Key Laboratory of Modern Optical Instrumentation, College of Optical Science and Engineering, Zhejiang University, Hangzhou, Zhejiang, 310027, China
| | - Meng Zhang
- Britton Chance Center for Biomedical Photonics, Wuhan National Laboratory for Optoelectronics-Huazhong University of Science and Technology, Wuhan, Hubei, 430074, China
| | - Yu-Hui Zhang
- Britton Chance Center for Biomedical Photonics, Wuhan National Laboratory for Optoelectronics-Huazhong University of Science and Technology, Wuhan, Hubei, 430074, China
| | - Jiannan Fan
- Key Laboratory for Biomedical Engineering of Ministry of Education, Department of Biomedical Engineering, Zhejiang University, Hangzhou, 310027, China
| | - Luhong Jin
- Key Laboratory for Biomedical Engineering of Ministry of Education, Department of Biomedical Engineering, Zhejiang University, Hangzhou, 310027, China
| | - Yingke Xu
- Key Laboratory for Biomedical Engineering of Ministry of Education, Department of Biomedical Engineering, Zhejiang University, Hangzhou, 310027, China
| | - Cuifang Kuang
- State Key Laboratory of Modern Optical Instrumentation, College of Optical Science and Engineering, Zhejiang University, Hangzhou, Zhejiang, 310027, China. .,Collaborative Innovation Center of Extreme Optics, Shanxi University, Taiyuan, Shanxi, 030006, China.
| | - Xu Liu
- State Key Laboratory of Modern Optical Instrumentation, College of Optical Science and Engineering, Zhejiang University, Hangzhou, Zhejiang, 310027, China. .,Collaborative Innovation Center of Extreme Optics, Shanxi University, Taiyuan, Shanxi, 030006, China.
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Carretero GPB, Vicente EF, Cilli EM, Alvarez CM, Jenssen H, Schreier S. Dissecting the mechanism of action of actinoporins. Role of the N-terminal amphipathic α-helix in membrane binding and pore activity of sticholysins I and II. PLoS One 2018; 13:e0202981. [PMID: 30161192 PMCID: PMC6117003 DOI: 10.1371/journal.pone.0202981] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2018] [Accepted: 08/13/2018] [Indexed: 11/19/2022] Open
Abstract
Actinoporins sticholysin I and sticholysin II (St I, St II) are proposed to lyse model and biomembranes via toroidal pore formation by their N-terminal domain. Based on the hypothesis that peptide fragments can reproduce the structure and function of this domain, the behavior of peptides containing St I residues 12–31 (StI12-31), St II residues 11–30 (StII11-30), and its TOAC-labeled analogue (N-TOAC-StII11-30) was examined. Molecular modeling showed a good match with experimental structures, indicating amphipathic α-helices in the same regions as in the toxins. CD spectra revealed that the peptides were essentially unstructured in aqueous solution, acquiring α-helical conformation upon interaction with micelles and large unilamellar vesicles (LUV) of variable lipid composition. Fluorescence quenching studies with NBD-containing lipids indicated that N-TOAC-StII11-30’s nitroxide moiety is located in the membranes polar head group region. Pyrene-labeled phospholipid inter-leaflet redistribution suggested that the peptides form toroidal pores, according to the mechanism of action proposed for the toxins. Binding occurred only to negatively charged LUV, indicating the importance of electrostatic interactions; in contrast the peptides bound to both negatively charged and zwitterionic micelles, pointing to a lesser influence of these interactions. In addition, differences between bilayers and micelles in head group packing and in curvature led to differences in peptide-membrane interaction. We propose that the peptides topography in micelles resembles that of the toxins in the toroidal pore. The peptides mimicked the toxins permeabilizing activity, St II peptides being more effective than StI12-31. To our knowledge, this is the first demonstration that differences in the toxins N-terminal amphipathic α-helix play a role in the difference between St I and St II activities.
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Affiliation(s)
- Gustavo P. B. Carretero
- Department of Biochemistry, Institute of Chemistry, University of São Paulo, São Paulo, Brazil
- Department of Science and Environment, Roskilde University, Roskilde, Denmark
| | - Eduardo F. Vicente
- Faculty of Science and Engineering, State University of São Paulo, Tupã, Brazil
| | - Eduardo M. Cilli
- Institute of Chemistry, State University of São Paulo, Araraquara, Brazil
| | | | - Håvard Jenssen
- Department of Science and Environment, Roskilde University, Roskilde, Denmark
| | - Shirley Schreier
- Department of Biochemistry, Institute of Chemistry, University of São Paulo, São Paulo, Brazil
- * E-mail:
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de Paula VS, Valente AP. A Dynamic Overview of Antimicrobial Peptides and Their Complexes. Molecules 2018; 23:molecules23082040. [PMID: 30111717 PMCID: PMC6222744 DOI: 10.3390/molecules23082040] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2018] [Revised: 08/05/2018] [Accepted: 08/09/2018] [Indexed: 01/06/2023] Open
Abstract
In this narrative review, we comprehensively review the available information about the recognition, structure, and dynamics of antimicrobial peptides (AMPs). Their complex behaviors occur across a wide range of time scales and have been challenging to portray. Recent advances in nuclear magnetic resonance and molecular dynamics simulations have revealed the importance of the molecular plasticity of AMPs and their abilities to recognize targets. We also highlight experimental data obtained using nuclear magnetic resonance methodologies, showing that conformational selection is a major mechanism of target interaction in AMP families.
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Affiliation(s)
- Viviane Silva de Paula
- Department of Chemistry and Biochemistry, University of California Santa Cruz, Santa Cruz, CA 95064, USA.
| | - Ana Paula Valente
- Centro de Biologia Estrutural e Bioimagem, Instituto de Bioquímica Médica, Centro Nacional de Ressonância Magnética Nuclear Jiri Jonas, Universidade Federal do Rio de Janeiro, Rio de Janeiro 21941-902, Brazil.
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Satake H, Saito A, Sakata T. Elucidation of interfacial pH behaviour at the cell/substrate nanogap for in situ monitoring of cellular respiration. NANOSCALE 2018; 10:10130-10136. [PMID: 29781490 DOI: 10.1039/c8nr02950d] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
In situ monitoring of cellular metabolism is useful for elucidating dynamic functions of living cells. In our previous studies, cellular respiration was continuously monitored as a change in pH at the cell/electrode nanoscale interface (i.e., interfacial pH) using an ion-sensitive field-effect transistor (ISFET). However, such interfacial pH behaviour on the nanoscale has not been confirmed using other methods such as fluorescence imaging. In this study, we have clarified the interfacial pH behaviour at a cell/substrate nanogap using a laser scanning confocal fluorescence microscope. The phospholipid fluorescein used as a pH indicator was fixed to the plasma membrane on the external side of a cell by inserting its lipophilic alkyl chain into the membrane, and used to observe the change in interfacial pH. As a result, hydrogen ions generated by cellular respiration were gradually accumulated at the cell/substrate nanogap, resulting in a decrease in pH. Moreover, the interfacial pH between the plasma membrane and the substrate became lower than the pH near the surface of cells not in contact with the substrate. The data obtained in this study support the idea that potentiometric ion sensors such as ISFETs can detect a cellular-metabolism-induced change in pH at a cell/electrode nanogap in real time.
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Affiliation(s)
- Hiroto Satake
- Department of Materials Engineering, School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, Japan 113-8656.
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Okada M, Kajimoto S, Nakabayashi T. Embedding a Metal-Binding Motif for Copper Transporter into a Lipid Bilayer by Cu(I) Binding. J Phys Chem B 2018; 122:6364-6370. [DOI: 10.1021/acs.jpcb.8b03179] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Mariko Okada
- Graduate School of Pharmaceutical Sciences, Tohoku University, Aoba-ku, Sendai 980-8578, Japan
| | - Shinji Kajimoto
- Graduate School of Pharmaceutical Sciences, Tohoku University, Aoba-ku, Sendai 980-8578, Japan
| | - Takakazu Nakabayashi
- Graduate School of Pharmaceutical Sciences, Tohoku University, Aoba-ku, Sendai 980-8578, Japan
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Salay LC, Prazeres EA, Marín Huachaca NS, Lemos M, Piccoli JP, Sanches PRS, Cilli EM, Santos RS, Feitosa E. Molecular interactions between Pluronic F127 and the peptide tritrpticin in aqueous solution. Colloid Polym Sci 2018. [DOI: 10.1007/s00396-018-4304-0] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
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