1
|
Lucignano R, Sanità G, Esposito E, Russo Krauss I, D'Ursi AM, Buonocore M, Picone D. Human ferritin nanocarriers for drug-delivery: A molecular view of the disassembly process. Int J Biol Macromol 2024; 277:134373. [PMID: 39094874 DOI: 10.1016/j.ijbiomac.2024.134373] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2024] [Revised: 07/20/2024] [Accepted: 07/30/2024] [Indexed: 08/04/2024]
Abstract
Ferritins are natural proteins which spontaneously self-assemble forming hollow nanocages physiologically deputed to iron storage and homeostasis. Thanks to their high stability and easy production in vitro, ferritins represent an intriguing system for nanobiotechnology. Here we investigated the mechanism of disassembly and reassembly of a human recombinant ferritin constituted by the heavy chain (hHFt) exploiting a new procedure which involves the use of minimal amounts of sodium dodecyl sulfate (SDS) and assessed its effectiveness in comparison with two commonly used protocols based on pH shift at highly acidic and alkaline values. The interest in this ferritin as drug nanocarrier is related to the strong affinity of the human H-chain for the transferrin receptor TfR-1, overexpressed in several tumoral cell lines. Using different techniques, like NMR, TEM and DLS, we demonstrated that the small concentrations of SDS can eliminate the nanocage architecture without detaching the monomers from each other, which instead remain strongly associated. Following this procedure, we encapsulated into the nanocage a small ruthenium complex with a remarkable improvement with respect to previous protocols in terms of yield, structural integrity of the recovered protein and encapsulation efficiency. In our opinion, the extensive network of interchain interactions preserved during the SDS-based disassembly procedure represents the key for a complete and correct hHFt reassembly.
Collapse
Affiliation(s)
- Rosanna Lucignano
- Department of Chemical Sciences, University of Naples "Federico II", University of Napoli Federico II Complesso Universitario Monte Sant'Angelo, Via Cintia, 80126 Naples, Italy
| | - Gennaro Sanità
- Institute of Applied Sciences and Intelligent Systems (ISASI), Naples Cryo Electron Microscopy Laboratory - EYE LAB, National Research Council (CNR), Via Pietro Castellino 111, 80131 Naples, Italy
| | - Emanuela Esposito
- Institute of Applied Sciences and Intelligent Systems (ISASI), Naples Cryo Electron Microscopy Laboratory - EYE LAB, National Research Council (CNR), Via Pietro Castellino 111, 80131 Naples, Italy
| | - Irene Russo Krauss
- Department of Chemical Sciences, University of Naples "Federico II", University of Napoli Federico II Complesso Universitario Monte Sant'Angelo, Via Cintia, 80126 Naples, Italy; CSGI (Consorzio per lo Sviluppo dei Sistemi a Grande Interfase), I-50019 Florence, Italy
| | - Anna Maria D'Ursi
- Department of Pharmacy, University of Salerno, Via Giovanni Paolo II, 132, 84084 Fisciano, Salerno, Italy
| | - Michela Buonocore
- Department of Chemical Sciences, University of Naples "Federico II", University of Napoli Federico II Complesso Universitario Monte Sant'Angelo, Via Cintia, 80126 Naples, Italy.
| | - Delia Picone
- Department of Chemical Sciences, University of Naples "Federico II", University of Napoli Federico II Complesso Universitario Monte Sant'Angelo, Via Cintia, 80126 Naples, Italy.
| |
Collapse
|
2
|
Wang X, Lu Y, Lin X. Heterogeneous cryo-EM projection image classification using a two-stage spectral clustering based on novel distance measures. Brief Bioinform 2022; 23:6543485. [PMID: 35255494 DOI: 10.1093/bib/bbac032] [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: 12/22/2021] [Revised: 01/17/2022] [Accepted: 01/23/2022] [Indexed: 11/13/2022] Open
Abstract
Single-particle cryo-electron microscopy (cryo-EM) has become one of the mainstream technologies in the field of structural biology to determine the three-dimensional (3D) structures of biological macromolecules. Heterogeneous cryo-EM projection image classification is an effective way to discover conformational heterogeneity of biological macromolecules in different functional states. However, due to the low signal-to-noise ratio of the projection images, the classification of heterogeneous cryo-EM projection images is a very challenging task. In this paper, two novel distance measures between projection images integrating the reliability of common lines, pixel intensity and class averages are designed, and then a two-stage spectral clustering algorithm based on the two distance measures is proposed for heterogeneous cryo-EM projection image classification. In the first stage, the novel distance measure integrating common lines and pixel intensities of projection images is used to obtain preliminary classification results through spectral clustering. In the second stage, another novel distance measure integrating the first novel distance measure and class averages generated from each group of projection images is used to obtain the final classification results through spectral clustering. The proposed two-stage spectral clustering algorithm is applied on a simulated and a real cryo-EM dataset for heterogeneous reconstruction. Results show that the two novel distance measures can be used to improve the classification performance of spectral clustering, and using the proposed two-stage spectral clustering algorithm can achieve higher classification and reconstruction accuracy than using RELION and XMIPP.
Collapse
Affiliation(s)
- Xiangwen Wang
- School of Information Science and Engineering, Lanzhou University, 730000, Lanzhou, China.,College of Computer Science and Engineering, Northwest Normal University, 730070, Lanzhou, China
| | - Yonggang Lu
- School of Information Science and Engineering, Lanzhou University, 730000, Lanzhou, China
| | - Xianghong Lin
- College of Computer Science and Engineering, Northwest Normal University, 730070, Lanzhou, China
| |
Collapse
|
3
|
A Fast Image Alignment Approach for 2D Classification of Cryo-EM Images Using Spectral Clustering. Curr Issues Mol Biol 2021; 43:1652-1668. [PMID: 34698131 PMCID: PMC8928942 DOI: 10.3390/cimb43030117] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2021] [Revised: 10/14/2021] [Accepted: 10/14/2021] [Indexed: 01/22/2023] Open
Abstract
Three-dimensional (3D) reconstruction in single-particle cryo-electron microscopy (cryo-EM) is a significant technique for recovering the 3D structure of proteins or other biological macromolecules from their two-dimensional (2D) noisy projection images taken from unknown random directions. Class averaging in single-particle cryo-EM is an important procedure for producing high-quality initial 3D structures, where image alignment is a fundamental step. In this paper, an efficient image alignment algorithm using 2D interpolation in the frequency domain of images is proposed to improve the estimation accuracy of alignment parameters of rotation angles and translational shifts between the two projection images, which can obtain subpixel and subangle accuracy. The proposed algorithm firstly uses the Fourier transform of two projection images to calculate a discrete cross-correlation matrix and then performs the 2D interpolation around the maximum value in the cross-correlation matrix. The alignment parameters are directly determined according to the position of the maximum value in the cross-correlation matrix after interpolation. Furthermore, the proposed image alignment algorithm and a spectral clustering algorithm are used to compute class averages for single-particle 3D reconstruction. The proposed image alignment algorithm is firstly tested on a Lena image and two cryo-EM datasets. Results show that the proposed image alignment algorithm can estimate the alignment parameters accurately and efficiently. The proposed method is also used to reconstruct preliminary 3D structures from a simulated cryo-EM dataset and a real cryo-EM dataset and to compare them with RELION. Experimental results show that the proposed method can obtain more high-quality class averages than RELION and can obtain higher reconstruction resolution than RELION even without iteration.
Collapse
|
4
|
Ramlaul K, Palmer CM, Nakane T, Aylett CHS. Mitigating local over-fitting during single particle reconstruction with SIDESPLITTER. J Struct Biol 2020; 211:107545. [PMID: 32534144 PMCID: PMC7369633 DOI: 10.1016/j.jsb.2020.107545] [Citation(s) in RCA: 52] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2020] [Revised: 05/28/2020] [Accepted: 06/02/2020] [Indexed: 01/31/2023]
Abstract
Single particle analysis has become a key structural biology technique. Experimental images are extremely noisy, and during iterative refinement it is possible to stably incorporate noise into the reconstruction. Such "over-fitting" can lead to misinterpretation of the structure and flawed biological results. Several strategies are routinely used to prevent over-fitting, the most common being independent refinement of two sides of a split dataset. In this study, we show that over-fitting remains an issue within regions of low local signal-to-noise, despite independent refinement of half datasets. We propose a modification of the refinement process through the application of a local signal-to-noise filter: SIDESPLITTER. We show that our approach can reduce over-fitting for both idealised and experimental data while maintaining independence between the two sides of a split refinement. SIDESPLITTER refinement leads to improved density, and can also lead to improvement of the final resolution in extreme cases where datasets are prone to severe over-fitting, such as small membrane proteins.
Collapse
Affiliation(s)
- Kailash Ramlaul
- Section for Structural and Synthetic Biology, Department of Infectious Disease, Faculty of Medicine, Imperial College Road, South Kensington, London SW7 2BB, United Kingdom
| | - Colin M Palmer
- Scientific Computing Department, Science and Technology Facilities Council, Research Complex at Harwell, Didcot OX11 0FA, United Kingdom
| | - Takanori Nakane
- Medical Research Council Laboratory of Molecular Biology, Cambridge CB2 0QH, United Kingdom
| | - Christopher H S Aylett
- Section for Structural and Synthetic Biology, Department of Infectious Disease, Faculty of Medicine, Imperial College Road, South Kensington, London SW7 2BB, United Kingdom.
| |
Collapse
|
5
|
Zehni M, Donati L, Soubies E, Zhao ZJ, Unser M. Joint Angular Refinement and Reconstruction for Single-Particle Cryo-EM. IEEE TRANSACTIONS ON IMAGE PROCESSING : A PUBLICATION OF THE IEEE SIGNAL PROCESSING SOCIETY 2020; 29:6151-6163. [PMID: 32248108 DOI: 10.1109/tip.2020.2984313] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Single-particle cryo-electron microscopy (cryo-EM) reconstructs the three-dimensional (3D) structure of biomolecules from a large set of 2D projection images with random and unknown orientations. A crucial step in the single-particle cryo-EM pipeline is 3D refinement, which resolves a highresolution 3D structure from an initial approximate volume by refining the estimation of the orientation of each projection. In this work, we propose a new approach that refines the projection angles on the continuum. We formulate the optimization problem over the density map and the orientations jointly. The density map is updated using the efficient alternating-direction method of multipliers, while the orientations are updated through a semicoordinate- wise gradient descent for which we provide an explicit derivation of the gradient. Our method eliminates the requirement for a fine discretization of the orientation space and does away with the classical but computationally expensive templatematching step. Numerical results demonstrate the feasibility and performance of our approach compared to several baselines.
Collapse
|
6
|
Donati L, Nilchian M, Sorzano COS, Unser M. Fast multiscale reconstruction for Cryo-EM. J Struct Biol 2018; 204:543-554. [PMID: 30261282 PMCID: PMC7343242 DOI: 10.1016/j.jsb.2018.09.008] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2018] [Revised: 09/13/2018] [Accepted: 09/20/2018] [Indexed: 12/01/2022]
Abstract
We present a multiscale reconstruction framework for single-particle analysis (SPA). The representation of three-dimensional (3D) objects with scaled basis functions permits the reconstruction of volumes at any desired scale in the real-space. This multiscale approach generates interesting opportunities in SPA for the stabilization of the initial volume problem or the 3D iterative refinement procedure. In particular, we show that reconstructions performed at coarse scale are more robust to angular errors and permit gains in computational speed. A key component of the proposed iterative scheme is its fast implementation. The costly step of reconstruction, which was previously hindering the use of advanced iterative methods in SPA, is formulated as a discrete convolution with a cost that does not depend on the number of projection directions. The inclusion of the contrast transfer function inside the imaging matrix is also done at no extra computational cost. By permitting full 3D regularization, the framework is by itself a robust alternative to direct methods for performing reconstruction in adverse imaging conditions (e.g., heavy noise, large angular misassignments, low number of projections). We present reconstructions obtained at different scales from a dataset of the 2015/2016 EMDataBank Map Challenge. The algorithm has been implemented in the Scipion package.
Collapse
Affiliation(s)
- Laurène Donati
- Biomedical Imaging Group, École polytechnique fédérale de Lausanne (EPFL), Station 17, CH-1015 Lausanne, Switzerland.
| | - Masih Nilchian
- Biomedical Imaging Group, École polytechnique fédérale de Lausanne (EPFL), Station 17, CH-1015 Lausanne, Switzerland
| | - Carlos Oscar S Sorzano
- National Center of Biotechnology (CSIC), c/Darwin, 3, Campus Univ. Autonoma de Madrid, 28049 Cantoblanco, Madrid, Spain.
| | - Michael Unser
- Biomedical Imaging Group, École polytechnique fédérale de Lausanne (EPFL), Station 17, CH-1015 Lausanne, Switzerland.
| |
Collapse
|
7
|
Fortun D, Guichard P, Hamel V, Sorzano COS, Banterle N, Gonczy P, Unser M. Reconstruction From Multiple Particles for 3D Isotropic Resolution in Fluorescence Microscopy. IEEE TRANSACTIONS ON MEDICAL IMAGING 2018; 37:1235-1246. [PMID: 29727286 DOI: 10.1109/tmi.2018.2795464] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
The imaging of proteins within macromolecular complexes has been limited by the low axial resolution of optical microscopes. To overcome this problem, we propose a novel computational reconstruction method that yields isotropic resolution in fluorescence imaging. The guiding principle is to reconstruct a single volume from the observations of multiple rotated particles. Our new operational framework detects particles, estimates their orientation, and reconstructs the final volume. The main challenge comes from the absence of initial template and a priori knowledge about the orientations. We formulate the estimation as a blind inverse problem, and propose a block-coordinate stochastic approach to solve the associated non-convex optimization problem. The reconstruction is performed jointly in multiple channels. We demonstrate that our method is able to reconstruct volumes with 3D isotropic resolution on simulated data. We also perform isotropic reconstructions from real experimental data of doubly labeled purified human centrioles. Our approach revealed the precise localization of the centriolar protein Cep63 around the centriole microtubule barrel. Overall, our method offers new perspectives for applications in biology that require the isotropic mapping of proteins within macromolecular assemblies.
Collapse
|
8
|
A Survey of the Use of Iterative Reconstruction Algorithms in Electron Microscopy. BIOMED RESEARCH INTERNATIONAL 2017; 2017:6482567. [PMID: 29312997 PMCID: PMC5623807 DOI: 10.1155/2017/6482567] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 09/16/2016] [Accepted: 03/09/2017] [Indexed: 11/18/2022]
Abstract
One of the key steps in Electron Microscopy is the tomographic reconstruction of a three-dimensional (3D) map of the specimen being studied from a set of two-dimensional (2D) projections acquired at the microscope. This tomographic reconstruction may be performed with different reconstruction algorithms that can be grouped into several large families: direct Fourier inversion methods, back-projection methods, Radon methods, or iterative algorithms. In this review, we focus on the latter family of algorithms, explaining the mathematical rationale behind the different algorithms in this family as they have been introduced in the field of Electron Microscopy. We cover their use in Single Particle Analysis (SPA) as well as in Electron Tomography (ET).
Collapse
|
9
|
Zhou Q, Zhou N, Wang HW. Particle segmentation algorithm for flexible single particle reconstruction. BIOPHYSICS REPORTS 2017; 3:43-55. [PMID: 28782000 PMCID: PMC5515998 DOI: 10.1007/s41048-017-0038-7] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2017] [Accepted: 03/15/2017] [Indexed: 12/12/2022] Open
Abstract
As single particle cryo-electron microscopy has evolved to a new era of atomic resolution, sample heterogeneity still imposes a major limit to the resolution of many macromolecular complexes, especially those with continuous conformational flexibility. Here, we describe a particle segmentation algorithm towards solving structures of molecules composed of several parts that are relatively flexible with each other. In this algorithm, the different parts of a target molecule are segmented from raw images according to their alignment information obtained from a preliminary 3D reconstruction and are subjected to single particle processing in an iterative manner. This algorithm was tested on both simulated and experimental data and showed improvement of 3D reconstruction resolution of each segmented part of the molecule than that of the entire molecule.
Collapse
Affiliation(s)
- Qiang Zhou
- State Key Laboratory of Biomembrane and Membrane Biotechnology, Center for Structural Biology, School of Life Sciences, Tsinghua University, Beijing, 100084 China.,Ministry of Education Key Laboratory of Protein Science, Tsinghua-Peking Joint Center for Life Sciences, Center for Structural Biology, School of Life Sciences, Tsinghua University, Beijing, 100084 China
| | - Niyun Zhou
- Ministry of Education Key Laboratory of Protein Science, Tsinghua-Peking Joint Center for Life Sciences, Center for Structural Biology, School of Life Sciences, Tsinghua University, Beijing, 100084 China
| | - Hong-Wei Wang
- Ministry of Education Key Laboratory of Protein Science, Tsinghua-Peking Joint Center for Life Sciences, Center for Structural Biology, School of Life Sciences, Tsinghua University, Beijing, 100084 China
| |
Collapse
|
10
|
Wadell C, Inagaki S, Nakamura T, Shi J, Nakamura Y, Sannomiya T. Nanocuvette: A Functional Ultrathin Liquid Container for Transmission Electron Microscopy. ACS NANO 2017; 11:1264-1272. [PMID: 28135067 DOI: 10.1021/acsnano.6b05007] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Advances in TEM techniques have spurred a renewed interest in a wide variety of research fields. A rather recent track within these endeavors is the use of TEM for in situ imaging in liquids. In this article, we show the fabrication of a liquid cell for TEM observations which we call the nanocuvette. The structure consists of a nanohole film sandwiched by carbon films, sealing liquid in the holes. The hole film can be produced using a variety of materials, tailored for the desired application. Since the fabrication is based on self-assembly, it is both cheap and straightforward. Compared to previously reported liquid cells, this structure allows for thinner liquid layers with better controlled cell structures, making it possible to achieve a high resolution even at lower acceleration voltages and electron doses. We demonstrate a resolution corresponding to an information transfer up to ∼2 nm at 100 kV for molecular imaging. Apart from the advantages arising from the thin liquid layer, the nanocuvette also enables the possibility to study liquid-solid interfaces at the side walls of the nanoholes. We illustrate the possibilities of the nanocuvette by studying several model systems: electron beam induced growth dynamics of silver nanoparticles in salt solution, polymer deposition from solution, and imaging of nonstained antibodies in solution. Finally, we show how the inclusion of a plasmonically active gold layer in the nanocuvette structure enables optical confirmation of successful liquid encapsulation prior to TEM studies. The nanocuvette provides an easily fabricated and flexible platform which can help further the understanding of reactions, processes, and conformation of molecules and atoms in liquid environments.
Collapse
Affiliation(s)
- Carl Wadell
- Department of Materials Science and Engineering, School of Materials and Chemical Technologies, Tokyo Institute of Technology , 4259 Nagatsuta, Midoriku, Yokohama 226-8503 Japan
| | - Satoshi Inagaki
- Department of Materials Science and Engineering, School of Materials and Chemical Technologies, Tokyo Institute of Technology , 4259 Nagatsuta, Midoriku, Yokohama 226-8503 Japan
| | - Tomiro Nakamura
- Department of Materials Science and Engineering, School of Materials and Chemical Technologies, Tokyo Institute of Technology , 4259 Nagatsuta, Midoriku, Yokohama 226-8503 Japan
| | - Ji Shi
- Department of Materials Science and Engineering, School of Materials and Chemical Technologies, Tokyo Institute of Technology , 4259 Nagatsuta, Midoriku, Yokohama 226-8503 Japan
| | - Yoshio Nakamura
- Department of Materials Science and Engineering, School of Materials and Chemical Technologies, Tokyo Institute of Technology , 4259 Nagatsuta, Midoriku, Yokohama 226-8503 Japan
| | - Takumi Sannomiya
- Department of Materials Science and Engineering, School of Materials and Chemical Technologies, Tokyo Institute of Technology , 4259 Nagatsuta, Midoriku, Yokohama 226-8503 Japan
| |
Collapse
|
11
|
Orlov I, Myasnikov AG, Andronov L, Natchiar SK, Khatter H, Beinsteiner B, Ménétret JF, Hazemann I, Mohideen K, Tazibt K, Tabaroni R, Kratzat H, Djabeur N, Bruxelles T, Raivoniaina F, Pompeo LD, Torchy M, Billas I, Urzhumtsev A, Klaholz BP. The integrative role of cryo electron microscopy in molecular and cellular structural biology. Biol Cell 2016; 109:81-93. [PMID: 27730650 DOI: 10.1111/boc.201600042] [Citation(s) in RCA: 44] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2016] [Revised: 10/04/2016] [Accepted: 10/05/2016] [Indexed: 01/10/2023]
Abstract
After gradually moving away from preparation methods prone to artefacts such as plastic embedding and negative staining for cell sections and single particles, the field of cryo electron microscopy (cryo-EM) is now heading off at unprecedented speed towards high-resolution analysis of biological objects of various sizes. This 'revolution in resolution' is happening largely thanks to new developments of new-generation cameras used for recording the images in the cryo electron microscope which have much increased sensitivity being based on complementary metal oxide semiconductor devices. Combined with advanced image processing and 3D reconstruction, the cryo-EM analysis of nucleoprotein complexes can provide unprecedented insights at molecular and atomic levels and address regulatory mechanisms in the cell. These advances reinforce the integrative role of cryo-EM in synergy with other methods such as X-ray crystallography, fluorescence imaging or focussed-ion beam milling as exemplified here by some recent studies from our laboratory on ribosomes, viruses, chromatin and nuclear receptors. Such multi-scale and multi-resolution approaches allow integrating molecular and cellular levels when applied to purified or in situ macromolecular complexes, thus illustrating the trend of the field towards cellular structural biology.
Collapse
Affiliation(s)
- Igor Orlov
- Centre for Integrative Biology (CBI), Department of Integrated Structural Biology, IGBMC (Institute of Genetics and of Molecular and Cellular Biology), Illkirch, France.,Centre National de la Recherche Scientifique (CNRS) UMR 7104, Illkirch, France.,Institut National de la Santé et de la Recherche Médicale (INSERM) U964, Illkirch, France.,Université de Strasbourg, Strasbourg, France
| | - Alexander G Myasnikov
- Centre for Integrative Biology (CBI), Department of Integrated Structural Biology, IGBMC (Institute of Genetics and of Molecular and Cellular Biology), Illkirch, France.,Centre National de la Recherche Scientifique (CNRS) UMR 7104, Illkirch, France.,Institut National de la Santé et de la Recherche Médicale (INSERM) U964, Illkirch, France.,Université de Strasbourg, Strasbourg, France
| | - Leonid Andronov
- Centre for Integrative Biology (CBI), Department of Integrated Structural Biology, IGBMC (Institute of Genetics and of Molecular and Cellular Biology), Illkirch, France.,Centre National de la Recherche Scientifique (CNRS) UMR 7104, Illkirch, France.,Institut National de la Santé et de la Recherche Médicale (INSERM) U964, Illkirch, France.,Université de Strasbourg, Strasbourg, France
| | - S Kundhavai Natchiar
- Centre for Integrative Biology (CBI), Department of Integrated Structural Biology, IGBMC (Institute of Genetics and of Molecular and Cellular Biology), Illkirch, France.,Centre National de la Recherche Scientifique (CNRS) UMR 7104, Illkirch, France.,Institut National de la Santé et de la Recherche Médicale (INSERM) U964, Illkirch, France.,Université de Strasbourg, Strasbourg, France
| | - Heena Khatter
- Centre for Integrative Biology (CBI), Department of Integrated Structural Biology, IGBMC (Institute of Genetics and of Molecular and Cellular Biology), Illkirch, France.,Centre National de la Recherche Scientifique (CNRS) UMR 7104, Illkirch, France.,Institut National de la Santé et de la Recherche Médicale (INSERM) U964, Illkirch, France.,Université de Strasbourg, Strasbourg, France
| | - Brice Beinsteiner
- Centre for Integrative Biology (CBI), Department of Integrated Structural Biology, IGBMC (Institute of Genetics and of Molecular and Cellular Biology), Illkirch, France.,Centre National de la Recherche Scientifique (CNRS) UMR 7104, Illkirch, France.,Institut National de la Santé et de la Recherche Médicale (INSERM) U964, Illkirch, France.,Université de Strasbourg, Strasbourg, France
| | - Jean-François Ménétret
- Centre for Integrative Biology (CBI), Department of Integrated Structural Biology, IGBMC (Institute of Genetics and of Molecular and Cellular Biology), Illkirch, France.,Centre National de la Recherche Scientifique (CNRS) UMR 7104, Illkirch, France.,Institut National de la Santé et de la Recherche Médicale (INSERM) U964, Illkirch, France.,Université de Strasbourg, Strasbourg, France
| | - Isabelle Hazemann
- Centre for Integrative Biology (CBI), Department of Integrated Structural Biology, IGBMC (Institute of Genetics and of Molecular and Cellular Biology), Illkirch, France.,Centre National de la Recherche Scientifique (CNRS) UMR 7104, Illkirch, France.,Institut National de la Santé et de la Recherche Médicale (INSERM) U964, Illkirch, France.,Université de Strasbourg, Strasbourg, France
| | - Kareem Mohideen
- Centre for Integrative Biology (CBI), Department of Integrated Structural Biology, IGBMC (Institute of Genetics and of Molecular and Cellular Biology), Illkirch, France.,Centre National de la Recherche Scientifique (CNRS) UMR 7104, Illkirch, France.,Institut National de la Santé et de la Recherche Médicale (INSERM) U964, Illkirch, France.,Université de Strasbourg, Strasbourg, France
| | - Karima Tazibt
- Centre for Integrative Biology (CBI), Department of Integrated Structural Biology, IGBMC (Institute of Genetics and of Molecular and Cellular Biology), Illkirch, France.,Centre National de la Recherche Scientifique (CNRS) UMR 7104, Illkirch, France.,Institut National de la Santé et de la Recherche Médicale (INSERM) U964, Illkirch, France.,Université de Strasbourg, Strasbourg, France
| | - Rachel Tabaroni
- Centre for Integrative Biology (CBI), Department of Integrated Structural Biology, IGBMC (Institute of Genetics and of Molecular and Cellular Biology), Illkirch, France.,Centre National de la Recherche Scientifique (CNRS) UMR 7104, Illkirch, France.,Institut National de la Santé et de la Recherche Médicale (INSERM) U964, Illkirch, France.,Université de Strasbourg, Strasbourg, France
| | - Hanna Kratzat
- Centre for Integrative Biology (CBI), Department of Integrated Structural Biology, IGBMC (Institute of Genetics and of Molecular and Cellular Biology), Illkirch, France.,Centre National de la Recherche Scientifique (CNRS) UMR 7104, Illkirch, France.,Institut National de la Santé et de la Recherche Médicale (INSERM) U964, Illkirch, France.,Université de Strasbourg, Strasbourg, France
| | - Nadia Djabeur
- Centre for Integrative Biology (CBI), Department of Integrated Structural Biology, IGBMC (Institute of Genetics and of Molecular and Cellular Biology), Illkirch, France.,Centre National de la Recherche Scientifique (CNRS) UMR 7104, Illkirch, France.,Institut National de la Santé et de la Recherche Médicale (INSERM) U964, Illkirch, France.,Université de Strasbourg, Strasbourg, France
| | - Tatiana Bruxelles
- Centre for Integrative Biology (CBI), Department of Integrated Structural Biology, IGBMC (Institute of Genetics and of Molecular and Cellular Biology), Illkirch, France.,Centre National de la Recherche Scientifique (CNRS) UMR 7104, Illkirch, France.,Institut National de la Santé et de la Recherche Médicale (INSERM) U964, Illkirch, France.,Université de Strasbourg, Strasbourg, France
| | - Finaritra Raivoniaina
- Centre for Integrative Biology (CBI), Department of Integrated Structural Biology, IGBMC (Institute of Genetics and of Molecular and Cellular Biology), Illkirch, France.,Centre National de la Recherche Scientifique (CNRS) UMR 7104, Illkirch, France.,Institut National de la Santé et de la Recherche Médicale (INSERM) U964, Illkirch, France.,Université de Strasbourg, Strasbourg, France
| | - Lorenza di Pompeo
- Centre for Integrative Biology (CBI), Department of Integrated Structural Biology, IGBMC (Institute of Genetics and of Molecular and Cellular Biology), Illkirch, France.,Centre National de la Recherche Scientifique (CNRS) UMR 7104, Illkirch, France.,Institut National de la Santé et de la Recherche Médicale (INSERM) U964, Illkirch, France.,Université de Strasbourg, Strasbourg, France
| | - Morgan Torchy
- Centre for Integrative Biology (CBI), Department of Integrated Structural Biology, IGBMC (Institute of Genetics and of Molecular and Cellular Biology), Illkirch, France.,Centre National de la Recherche Scientifique (CNRS) UMR 7104, Illkirch, France.,Institut National de la Santé et de la Recherche Médicale (INSERM) U964, Illkirch, France.,Université de Strasbourg, Strasbourg, France
| | - Isabelle Billas
- Centre for Integrative Biology (CBI), Department of Integrated Structural Biology, IGBMC (Institute of Genetics and of Molecular and Cellular Biology), Illkirch, France.,Centre National de la Recherche Scientifique (CNRS) UMR 7104, Illkirch, France.,Institut National de la Santé et de la Recherche Médicale (INSERM) U964, Illkirch, France.,Université de Strasbourg, Strasbourg, France
| | - Alexandre Urzhumtsev
- Centre for Integrative Biology (CBI), Department of Integrated Structural Biology, IGBMC (Institute of Genetics and of Molecular and Cellular Biology), Illkirch, France.,Centre National de la Recherche Scientifique (CNRS) UMR 7104, Illkirch, France.,Institut National de la Santé et de la Recherche Médicale (INSERM) U964, Illkirch, France.,Université de Strasbourg, Strasbourg, France
| | - Bruno P Klaholz
- Centre for Integrative Biology (CBI), Department of Integrated Structural Biology, IGBMC (Institute of Genetics and of Molecular and Cellular Biology), Illkirch, France.,Centre National de la Recherche Scientifique (CNRS) UMR 7104, Illkirch, France.,Institut National de la Santé et de la Recherche Médicale (INSERM) U964, Illkirch, France.,Université de Strasbourg, Strasbourg, France
| |
Collapse
|
12
|
Liao LX, Zhao MB, Dong X, Jiang Y, Zeng KW, Tu PF. TDB protects vascular endothelial cells against oxygen-glucose deprivation/reperfusion-induced injury by targeting miR-34a to increase Bcl-2 expression. Sci Rep 2016; 6:37959. [PMID: 27885275 PMCID: PMC5122842 DOI: 10.1038/srep37959] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2016] [Accepted: 11/03/2016] [Indexed: 12/30/2022] Open
Abstract
Prolonged ischemia can result in apoptotic death of vascular endothelial cells and lead to ischemic vascular diseases including vascular dementia, arteriosclerosis and brain oedema. Finding protective strategies to prevent this is therefore an urgent mission. Recent studies have shown that dysregulation of microRNAs (miRNAs) can lead to imbalance of Bcl-2 family proteins and mitochondrial dysfunction, leading to further damage of vascular cells under ischemic conditions. However, whether miRNAs can be used as a drug target for treating vascular diseases is not fully understood. In this study, we observed that the natural product 2,4,5-trihydroxybenzaldehyde (TDB) could effectively inhibit vascular cell apoptosis following oxygen-glucose deprivation/reperfusion (OGD/R) by maintaining mitochondrial membrane potential (MMP) and suppressing activation of the mitochondria-dependent caspase-9/3 apoptosis pathway. Furthermore, we identified miR-34a, a crucial negative regulator of Bcl-2, as a target for the protective effect of TDB on vascular cells. TDB-induced suppression of miR-34a resulted in a significant upregulation of Bcl-2 protein, MMP maintenance, and the survival of vascular cells following OGD/R. Our findings suggest that targeting miR-34a with the natural product TDB may provide a novel strategy for the treatment of ischemic vascular injuries, and demonstrate the therapeutic potential in targeting miRNAs using appropriate small molecules.
Collapse
Affiliation(s)
- Li-Xi Liao
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing 100191, China
| | - Ming-Bo Zhao
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing 100191, China
| | - Xin Dong
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing 100191, China
| | - Yong Jiang
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing 100191, China
| | - Ke-Wu Zeng
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing 100191, China
| | - Peng-Fei Tu
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing 100191, China
| |
Collapse
|
13
|
Carroni M, Saibil HR. Cryo electron microscopy to determine the structure of macromolecular complexes. Methods 2015; 95:78-85. [PMID: 26638773 PMCID: PMC5405050 DOI: 10.1016/j.ymeth.2015.11.023] [Citation(s) in RCA: 63] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2015] [Revised: 11/14/2015] [Accepted: 11/26/2015] [Indexed: 01/28/2023] Open
Abstract
Structural biology. Cryo electron microscopy. Macromolecular complexes. Single particle analysis.
Cryo-electron microscopy (cryo-EM) is a structural molecular and cellular biology technique that has experienced major advances in recent years. Technological developments in image recording as well as in processing software make it possible to obtain three-dimensional reconstructions of macromolecular assemblies at near-atomic resolution that were formerly obtained only by X-ray crystallography or NMR spectroscopy. In parallel, cryo-electron tomography has also benefitted from these technological advances, so that visualization of irregular complexes, organelles or whole cells with their molecular machines in situ has reached subnanometre resolution. Cryo-EM can therefore address a broad range of biological questions. The aim of this review is to provide a brief overview of the principles and current state of the cryo-EM field.
Collapse
Affiliation(s)
- Marta Carroni
- ISMB, Birkbeck College, Malet St, London WC1E 7HX, UK
| | | |
Collapse
|
14
|
Lawson CL, Patwardhan A, Baker ML, Hryc C, Garcia ES, Hudson BP, Lagerstedt I, Ludtke SJ, Pintilie G, Sala R, Westbrook JD, Berman HM, Kleywegt GJ, Chiu W. EMDataBank unified data resource for 3DEM. Nucleic Acids Res 2015; 44:D396-403. [PMID: 26578576 PMCID: PMC4702818 DOI: 10.1093/nar/gkv1126] [Citation(s) in RCA: 190] [Impact Index Per Article: 21.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2015] [Accepted: 10/15/2015] [Indexed: 01/10/2023] Open
Abstract
Three-dimensional Electron Microscopy (3DEM) has become a key experimental method in structural biology for a broad spectrum of biological specimens from molecules to cells. The EMDataBank project provides a unified portal for deposition, retrieval and analysis of 3DEM density maps, atomic models and associated metadata (emdatabank.org). We provide here an overview of the rapidly growing 3DEM structural data archives, which include maps in EM Data Bank and map-derived models in the Protein Data Bank. In addition, we describe progress and approaches toward development of validation protocols and methods, working with the scientific community, in order to create a validation pipeline for 3DEM data.
Collapse
Affiliation(s)
- Catherine L Lawson
- Department of Chemistry and Chemical Biology and Research Collaboratory for Structural Bioinformatics, Rutgers, The State University of New Jersey, 610 Taylor Road Piscataway, NJ 08854, USA
| | - Ardan Patwardhan
- Protein Data Bank in Europe, European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Matthew L Baker
- Verna and Marrs McLean Department of Biochemistry & Molecular Biology, National Center for Macromolecular Imaging, Baylor College of Medicine, 1 Baylor Plaza, Houston, TX 70030, USA
| | - Corey Hryc
- Verna and Marrs McLean Department of Biochemistry & Molecular Biology, National Center for Macromolecular Imaging, Baylor College of Medicine, 1 Baylor Plaza, Houston, TX 70030, USA
| | - Eduardo Sanz Garcia
- Protein Data Bank in Europe, European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Brian P Hudson
- Department of Chemistry and Chemical Biology and Research Collaboratory for Structural Bioinformatics, Rutgers, The State University of New Jersey, 610 Taylor Road Piscataway, NJ 08854, USA
| | - Ingvar Lagerstedt
- Protein Data Bank in Europe, European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Steven J Ludtke
- Verna and Marrs McLean Department of Biochemistry & Molecular Biology, National Center for Macromolecular Imaging, Baylor College of Medicine, 1 Baylor Plaza, Houston, TX 70030, USA
| | - Grigore Pintilie
- Verna and Marrs McLean Department of Biochemistry & Molecular Biology, National Center for Macromolecular Imaging, Baylor College of Medicine, 1 Baylor Plaza, Houston, TX 70030, USA
| | - Raul Sala
- Department of Chemistry and Chemical Biology and Research Collaboratory for Structural Bioinformatics, Rutgers, The State University of New Jersey, 610 Taylor Road Piscataway, NJ 08854, USA
| | - John D Westbrook
- Department of Chemistry and Chemical Biology and Research Collaboratory for Structural Bioinformatics, Rutgers, The State University of New Jersey, 610 Taylor Road Piscataway, NJ 08854, USA
| | - Helen M Berman
- Department of Chemistry and Chemical Biology and Research Collaboratory for Structural Bioinformatics, Rutgers, The State University of New Jersey, 610 Taylor Road Piscataway, NJ 08854, USA
| | - Gerard J Kleywegt
- Protein Data Bank in Europe, European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Wah Chiu
- Verna and Marrs McLean Department of Biochemistry & Molecular Biology, National Center for Macromolecular Imaging, Baylor College of Medicine, 1 Baylor Plaza, Houston, TX 70030, USA
| |
Collapse
|
15
|
Valpuesta JM, Carrascosa JL. Electron microscopy: the coming of age of a structural biology technique. Arch Biochem Biophys 2015; 581:1-2. [DOI: 10.1016/j.abb.2015.06.018] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
|