1
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Bochtler M. X-rays, electrons, and neutrons as probes of atomic matter. Structure 2024; 32:630-643.e6. [PMID: 38412856 DOI: 10.1016/j.str.2024.01.015] [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: 11/29/2022] [Revised: 03/21/2023] [Accepted: 01/31/2024] [Indexed: 02/29/2024]
Abstract
X-rays, electrons, and neutrons probe different properties of matter. X-rays feel electron density (ED). Electrons sense the electrostatic potential (ESP) of electrons and nuclei. Neutrons are sensitive to nuclear coherent scattering length (NCSL). While NCSL maps are widely understood to be different, ED and ESP maps are tacitly assumed to be similar. Here, I show that the belief in ED and ESP map equivalence is mistaken, but contains a grain of truth. Using density functional theory (DFT), the Bethe-Mott (BM) relation, and the Thomas-Fermi (TF) and Cromer-Mann (CM) atomic models, I show that ED and ESP maps are indeed more similar to each other than to NCSL maps. Nevertheless, peak and integrated map values depend differently on the atomic order number and on the contributions from electrons in the inner and outer CM shells. ED and ESP maps also differ in the sign and relative magnitude of excess charge effects.
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Affiliation(s)
- Matthias Bochtler
- IIMCB, Trojdena 4, 02-109 Warsaw, Poland; Polish Academy of Sciences, IBB, Pawinskiego 5a, 02-106 Warsaw, Poland.
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2
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Smith JW, Carnevale LN, Das A, Chen Q. Electron videography of a lipid-protein tango. SCIENCE ADVANCES 2024; 10:eadk0217. [PMID: 38630809 PMCID: PMC11023515 DOI: 10.1126/sciadv.adk0217] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/29/2023] [Accepted: 03/15/2024] [Indexed: 04/19/2024]
Abstract
Biological phenomena, from enzymatic catalysis to synaptic transmission, originate in the structural transformations of biomolecules and biomolecular assemblies in liquid water. However, directly imaging these nanoscopic dynamics without probes or labels has been a fundamental methodological challenge. Here, we developed an approach for "electron videography"-combining liquid phase electron microscopy with molecular modeling-with which we filmed the nanoscale structural fluctuations of individual, suspended, and unlabeled membrane protein nanodiscs in liquid. Systematic comparisons with biochemical data and simulation indicate the graphene encapsulation involved can afford sufficiently reduced effects of the illuminating electron beam for these observations to yield quantitative fingerprints of nanoscale lipid-protein interactions. Our results suggest that lipid-protein interactions delineate dynamically modified membrane domains across unexpectedly long ranges. Moreover, they contribute to the molecular mechanics of the nanodisc as a whole in a manner specific to the protein within. Overall, this work illustrates an experimental approach to film, quantify, and understand biomolecular dynamics at the nanometer scale.
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Affiliation(s)
- John W. Smith
- Department of Materials Science and Engineering, University of Illinois Urbana–Champaign, Urbana, IL 61801, USA
| | - Lauren N. Carnevale
- Department of Biochemistry, University of Illinois Urbana–Champaign, Urbana, IL 61801, USA
| | - Aditi Das
- School of Chemistry and Biochemistry, Parker H. Petit Institute for Bioengineering and Biosciences, Georgia Institute of Technology, Atlanta, GA 30332, USA
| | - Qian Chen
- Department of Materials Science and Engineering, University of Illinois Urbana–Champaign, Urbana, IL 61801, USA
- Beckman Institute for Advanced Science and Technology, University of Illinois Urbana–Champaign, Urbana, IL 61801, USA
- Department of Chemistry, University of Illinois Urbana–Champaign, Urbana, IL 61801, USA
- Materials Research Laboratory, University of Illinois Urbana–Champaign, Urbana, IL 61801, USA
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3
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Chung SC. Cryo-forum: A framework for orientation recovery with uncertainty measure with the application in cryo-EM image analysis. J Struct Biol 2024; 216:108058. [PMID: 38163450 DOI: 10.1016/j.jsb.2023.108058] [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: 08/09/2023] [Revised: 12/14/2023] [Accepted: 12/28/2023] [Indexed: 01/03/2024]
Abstract
In single-particle cryo-electron microscopy (cryo-EM), efficient determination of orientation parameters for particle images poses a significant challenge yet is crucial for reconstructing 3D structures. This task is complicated by the high noise levels in the datasets, which often include outliers, necessitating several time-consuming 2D clean-up processes. Recently, solutions based on deep learning have emerged, offering a more streamlined approach to the traditionally laborious task of orientation estimation. These solutions employ amortized inference, eliminating the need to estimate parameters individually for each image. However, these methods frequently overlook the presence of outliers and may not adequately concentrate on the components used within the network. This paper introduces a novel method using a 10-dimensional feature vector for orientation representation, extracting orientations as unit quaternions with an accompanying uncertainty metric. Furthermore, we propose a unique loss function that considers the pairwise distances between orientations, thereby enhancing the accuracy of our method. Finally, we also comprehensively evaluate the design choices in constructing the encoder network, a topic that has not received sufficient attention in the literature. Our numerical analysis demonstrates that our methodology effectively recovers orientations from 2D cryo-EM images in an end-to-end manner. Notably, the inclusion of uncertainty quantification allows for direct clean-up of the dataset at the 3D level. Lastly, we package our proposed methods into a user-friendly software suite named cryo-forum, designed for easy access by developers.
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Affiliation(s)
- Szu-Chi Chung
- Department of Applied Mathematics, National Sun Yat-sen University, No. 70, Lienhai Rd, Kaohsiung, Taiwan.
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4
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Wietfeldt H, Meana-Pañeda R, Machello C, Reboul CF, Van CTS, Kim S, Heo J, Kim BH, Kang S, Ercius P, Park J, Elmlund H. Small, solubilized platinum nanocrystals consist of an ordered core surrounded by mobile surface atoms. Commun Chem 2024; 7:4. [PMID: 38172567 PMCID: PMC10764312 DOI: 10.1038/s42004-023-01087-x] [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: 06/07/2023] [Accepted: 12/12/2023] [Indexed: 01/05/2024] Open
Abstract
In situ structures of Platinum (Pt) nanoparticles (NPs) can be determined with graphene liquid cell transmission electron microscopy. Atomic-scale three-dimensional structural information about their physiochemical properties in solution is critical for understanding their chemical function. We here analyze eight atomic-resolution maps of small (<3 nm) colloidal Pt NPs. Their structures are composed of an ordered crystalline core surrounded by surface atoms with comparatively high mobility. 3D reconstructions calculated from cumulative doses of 8500 and 17,000 electrons/pixel, respectively, are characterized in terms of loss of atomic densities and atomic displacements. Less than 5% of the total number of atoms are lost due to dissolution or knock-on damage in five of the structures analyzed, whereas 10-16% are lost in the remaining three. Less than 5% of the atomic positions are displaced due to the increased electron irradiation in all structures. The surface dynamics will play a critical role in the diverse catalytic function of Pt NPs and must be considered in efforts to model Pt NP function computationally.
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Affiliation(s)
- Henry Wietfeldt
- Center for Structural Biology, Center for Cancer Research, National Cancer Institute, Frederick, MD, 21702, USA
| | - Rubén Meana-Pañeda
- Center for Structural Biology, Center for Cancer Research, National Cancer Institute, Frederick, MD, 21702, USA
| | - Chiara Machello
- Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Melbourne, VIC, Australia
| | - Cyril F Reboul
- Center for Structural Biology, Center for Cancer Research, National Cancer Institute, Frederick, MD, 21702, USA
| | - Cong T S Van
- Center for Structural Biology, Center for Cancer Research, National Cancer Institute, Frederick, MD, 21702, USA
| | - Sungin Kim
- Center for Nanoparticle Research, Institute for Basic Science (IBS), Seoul, 08826, Republic of Korea
- School of Chemical and Biological Engineering, Institute of Chemical Process, Seoul National University, Seoul, 08826, Republic of Korea
| | - Junyoung Heo
- Center for Nanoparticle Research, Institute for Basic Science (IBS), Seoul, 08826, Republic of Korea
- School of Chemical and Biological Engineering, Institute of Chemical Process, Seoul National University, Seoul, 08826, Republic of Korea
| | - Byung Hyo Kim
- Department of Material Science and Engineering, Soongsil University, Seoul, 06978, Republic of Korea
| | - Sungsu Kang
- Center for Nanoparticle Research, Institute for Basic Science (IBS), Seoul, 08826, Republic of Korea
- School of Chemical and Biological Engineering, Institute of Chemical Process, Seoul National University, Seoul, 08826, Republic of Korea
| | - Peter Ercius
- National Center for Electron Microscopy, Molecular Foundry, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Jungwon Park
- Center for Nanoparticle Research, Institute for Basic Science (IBS), Seoul, 08826, Republic of Korea.
- School of Chemical and Biological Engineering, Institute of Chemical Process, Seoul National University, Seoul, 08826, Republic of Korea.
- Institute of Engineering Research, College of Engineering, Seoul National University, Seoul, 08826, Republic of Korea.
- Advanced Institute of Convergence Technology, Seoul National University, Suwon-si, Gyeonggi-do, 16229, Republic of Korea.
| | - Hans Elmlund
- Center for Structural Biology, Center for Cancer Research, National Cancer Institute, Frederick, MD, 21702, USA.
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5
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Norlén L. Molecular Organization of the Skin Barrier. Acta Derm Venereol 2023; 103:adv13356. [PMID: 37987626 PMCID: PMC10680981 DOI: 10.2340/actadv.v103.13356] [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: 05/22/2023] [Accepted: 10/19/2023] [Indexed: 11/22/2023] Open
Abstract
Cryo-electron microscopy of vitreous sections allows for investigation directly in situ of the molecular architecture of skin. Recently, this technique has contributed to the elucidation of the molecular organization of the skin's permeability barrier and its stepwise formation process. The aim of this review is to provide an overview of the procedure for cryo-electron microscopy of vitreous sections, its analysis using atomic detail molecular dynamics modelling and electron microscopy simulation, and its application in the investigation of the barrier structure and formation process of the skin.
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Affiliation(s)
- Lars Norlén
- Department of Cellular and Molecular Biology (CMB), Karolinska Institutet, Biomedicum, SE-171 77 Stockholm, Sweden.
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6
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Rice G, Wagner T, Stabrin M, Sitsel O, Prumbaum D, Raunser S. TomoTwin: generalized 3D localization of macromolecules in cryo-electron tomograms with structural data mining. Nat Methods 2023:10.1038/s41592-023-01878-z. [PMID: 37188953 DOI: 10.1038/s41592-023-01878-z] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2022] [Accepted: 04/12/2023] [Indexed: 05/17/2023]
Abstract
Cryogenic-electron tomography enables the visualization of cellular environments in extreme detail, however, tools to analyze the full amount of information contained within these densely packed volumes are still needed. Detailed analysis of macromolecules through subtomogram averaging requires particles to first be localized within the tomogram volume, a task complicated by several factors including a low signal to noise ratio and crowding of the cellular space. Available methods for this task suffer either from being error prone or requiring manual annotation of training data. To assist in this crucial particle picking step, we present TomoTwin: an open source general picking model for cryogenic-electron tomograms based on deep metric learning. By embedding tomograms in an information-rich, high-dimensional space that separates macromolecules according to their three-dimensional structure, TomoTwin allows users to identify proteins in tomograms de novo without manually creating training data or retraining the network to locate new proteins.
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Affiliation(s)
- Gavin Rice
- Department of Structural Biochemistry, Max Planck Institute of Molecular Physiology, Dortmund, Germany
| | - Thorsten Wagner
- Department of Structural Biochemistry, Max Planck Institute of Molecular Physiology, Dortmund, Germany
| | - Markus Stabrin
- Department of Structural Biochemistry, Max Planck Institute of Molecular Physiology, Dortmund, Germany
| | - Oleg Sitsel
- Department of Structural Biochemistry, Max Planck Institute of Molecular Physiology, Dortmund, Germany
| | - Daniel Prumbaum
- Department of Structural Biochemistry, Max Planck Institute of Molecular Physiology, Dortmund, Germany
| | - Stefan Raunser
- Department of Structural Biochemistry, Max Planck Institute of Molecular Physiology, Dortmund, Germany.
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7
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Zhang H, Li H, Zhang F, Zhu P. A strategy combining denoising and cryo-EM single particle analysis. Brief Bioinform 2023; 24:7140293. [PMID: 37096633 DOI: 10.1093/bib/bbad148] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2023] [Revised: 02/21/2023] [Accepted: 03/28/2023] [Indexed: 04/26/2023] Open
Abstract
In cryogenic electron microscopy (cryo-EM) single particle analysis (SPA), high-resolution three-dimensional structures of biological macromolecules are determined by iteratively aligning and averaging a large number of two-dimensional projections of molecules. Since the correlation measures are sensitive to the signal-to-noise ratio, various parameter estimation steps in SPA will be disturbed by the high-intensity noise in cryo-EM. However, denoising algorithms tend to damage high frequencies and suppress mid- and high-frequency contrast of micrographs, which exactly the precise parameter estimation relies on, therefore, limiting their application in SPA. In this study, we suggest combining a cryo-EM image processing pipeline with denoising and maximizing the signal's contribution in various parameter estimation steps. To solve the inherent flaws of denoising algorithms, we design an algorithm named MScale to correct the amplitude distortion caused by denoising and propose a new orientation determination strategy to compensate for the high-frequency loss. In the experiments on several real datasets, the denoised particles are successfully applied in the class assignment estimation and orientation determination tasks, ultimately enhancing the quality of biomacromolecule reconstruction. The case study on classification indicates that our strategy not only improves the resolution of difficult classes (up to 5 Å) but also resolves an additional class. In the case study on orientation determination, our strategy improves the resolution of the final reconstructed density map by 0.34 Å compared with conventional strategy. The code is available at https://github.com/zhanghui186/Mscale.
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Affiliation(s)
- Hui Zhang
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Hongjia Li
- University of Chinese Academy of Sciences, Beijing 100049, China
- High Performance Computer Research Center, Institute of Computing Technology, Chinese Academy of Sciences, Beijing 100190, China
| | - Fa Zhang
- School of Medical Technology, Beijing Institute of Technology, Beijing, 100081, China
| | - Ping Zhu
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
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8
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Rodríguez de Francisco B, Bezault A, Xu XP, Hanein D, Volkmann N. MEPSi: A tool for simulating tomograms of membrane-embedded proteins. J Struct Biol 2022; 214:107921. [PMID: 36372192 DOI: 10.1016/j.jsb.2022.107921] [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: 07/31/2022] [Revised: 10/27/2022] [Accepted: 11/05/2022] [Indexed: 11/11/2022]
Abstract
The throughput and fidelity of cryogenic cellular electron tomography (cryo-ET) is constantly increasing through advances in cryogenic electron microscope hardware, direct electron detection devices, and powerful image processing algorithms. However, the need for careful optimization of sample preparations and for access to expensive, high-end equipment, make cryo-ET a costly and time-consuming technique. Generally, only after the last step of the cryo-ET workflow, when reconstructed tomograms are available, it becomes clear whether the chosen imaging parameters were suitable for a specific type of sample in order to answer a specific biological question. Tools for a-priory assessment of the feasibility of samples to answer biological questions and how to optimize imaging parameters to do so would be a major advantage. Here we describe MEPSi (Membrane Embedded Protein Simulator), a simulation tool aimed at rapid and convenient evaluation and optimization of cryo-ET data acquisition parameters for studies of transmembrane proteins in their native environment. We demonstrate the utility of MEPSi by showing how to detangle the influence of different data collection parameters and different orientations in respect to tilt axis and electron beam for two examples: (1) simulated plasma membranes with embedded single-pass transmembrane αIIbβ3 integrin receptors and (2) simulated virus membranes with embedded SARS-CoV-2 spike proteins.
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Affiliation(s)
- Borja Rodríguez de Francisco
- Institut Pasteur, Université Paris Cité, CNRS UMR3528, Structural Studies of Macromolecular Machines in Cellulo Unit, Paris, France; Institut Pasteur, Université Paris Cité, CNRS UMR3528, Structural Image Analysis Unit, Paris, France
| | - Armel Bezault
- Institut Pasteur, Université Paris Cité, CNRS UMR3528, Structural Studies of Macromolecular Machines in Cellulo Unit, Paris, France; Institut Pasteur, Université Paris Cité, CNRS UMR3528, Structural Image Analysis Unit, Paris, France
| | | | - Dorit Hanein
- Institut Pasteur, Université Paris Cité, CNRS UMR3528, Structural Studies of Macromolecular Machines in Cellulo Unit, Paris, France; Scintillon Institute, San Diego, CA 92121, USA
| | - Niels Volkmann
- Institut Pasteur, Université Paris Cité, CNRS UMR3528, Structural Image Analysis Unit, Paris, France.
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9
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Lundborg M, Wennberg C, Lidmar J, Hess B, Lindahl E, Norlén L. Skin permeability prediction with MD simulation sampling spatial and alchemical reaction coordinates. Biophys J 2022; 121:3837-3849. [PMID: 36104960 PMCID: PMC9674988 DOI: 10.1016/j.bpj.2022.09.009] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2022] [Revised: 06/22/2022] [Accepted: 09/08/2022] [Indexed: 11/02/2022] Open
Abstract
A molecular-level understanding of skin permeation may rationalize and streamline product development, and improve quality and control, of transdermal and topical drug delivery systems. It may also facilitate toxicity and safety assessment of cosmetics and skin care products. Here, we present new molecular dynamics simulation approaches that make it possible to efficiently sample the free energy and local diffusion coefficient across the skin's barrier structure to predict skin permeability and the effects of chemical penetration enhancers. In particular, we introduce a new approach to use two-dimensional reaction coordinates in the accelerated weight histogram method, where we combine sampling along spatial coordinates with an alchemical perturbation virtual coordinate. We present predicted properties for 20 permeants, and demonstrate how our approach improves correlation with ex vivo/in vitro skin permeation data. For the compounds included in this study, the obtained log KPexp-calc mean square difference was 0.9 cm2 h-2.
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Affiliation(s)
| | | | - Jack Lidmar
- Department of Physics, KTH Royal Institute of Technology, Stockholm, Sweden
| | - Berk Hess
- Department of Applied Physics, Science for Life Laboratory, KTH Royal Institute of Technology, Solna, Sweden
| | - Erik Lindahl
- Department of Biophysics and Biochemistry, Science for Life Laboratory, Stockholm University, Solna, Sweden; Department of Physics, Swedish e-Science Research Center, KTH Royal Institute of Technology, Stockholm, Sweden
| | - Lars Norlén
- Department of Cell and Molecular Biology (CMB), Karolinska Institutet, Stockholm, Sweden; Dermatology Clinic, Karolinska University Hospital, Stockholm, Sweden.
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10
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Structural basis for the inhibition of IAPP fibril formation by the co-chaperonin prefoldin. Nat Commun 2022; 13:2363. [PMID: 35501361 PMCID: PMC9061850 DOI: 10.1038/s41467-022-30042-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2021] [Accepted: 04/13/2022] [Indexed: 01/16/2023] Open
Abstract
Chaperones, as modulators of protein conformational states, are key cellular actors to prevent the accumulation of fibrillar aggregates. Here, we integrated kinetic investigations with structural studies to elucidate how the ubiquitous co-chaperonin prefoldin inhibits diabetes associated islet amyloid polypeptide (IAPP) fibril formation. We demonstrated that both human and archaeal prefoldin interfere similarly with the IAPP fibril elongation and secondary nucleation pathways. Using archaeal prefoldin model, we combined nuclear magnetic resonance spectroscopy with electron microscopy to establish that the inhibition of fibril formation is mediated by the binding of prefoldin’s coiled-coil helices to the flexible IAPP N-terminal segment accessible on the fibril surface and fibril ends. Atomic force microscopy demonstrates that binding of prefoldin to IAPP leads to the formation of lower amounts of aggregates, composed of shorter fibrils, clustered together. Linking structural models with observed fibrillation inhibition processes opens perspectives for understanding the interference between natural chaperones and formation of disease-associated amyloids. Integrated kinetic and structural investigations reveal that the ubiquitous co-chaperonin prefoldin interacts with its coiled-coil helices on the islet amyloid polypeptide fibril surface and fibril ends to inhibit fibril elongation and secondary nucleation.
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11
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Atomic-number ( Z)-correlated atomic sizes for deciphering electron microscopic molecular images. Proc Natl Acad Sci U S A 2022; 119:e2114432119. [PMID: 35349339 PMCID: PMC9168473 DOI: 10.1073/pnas.2114432119] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
Abstract
Atomic resolution transmission electron microscopy (TEM) has opened up a new era of molecular science by providing atomic video images of dynamic motions of single organic and inorganic molecules. However, the images often look different from the images of molecular models, because these models are designed to visualize the electronic properties of the molecule instead of nuclear electrostatic potentials that are felt by the e-beam in TEM imaging. Here, we propose a molecular model that reproduces TEM images using atomic radii correlated to atomic number (Z). The model serves to provide a priori a useful idea of how a single molecule, molecular assemblies, and thin crystals of organic or inorganic materials look in TEM. With the advent of atomic resolution transmission electron microscopy (AR-TEM) achieving sub-Ångstrom image resolution and submillisecond time resolution, an era of cinematic molecular science where chemists can visually study the time evolution of molecular motions and reactions at atomistic precision has arrived. However, the appearance of experimental TEM images often differs greatly from that of conventional molecular models, and the images are difficult to decipher unless we know in advance the structure of the specimen molecules. The difference arises from the fundamental design of the molecular models that represent atomic connectivity and/or the electronic properties of molecules rather than the nuclear charge of atoms and electrostatic potentials that are felt by the e-beam in TEM imaging. We found a good correlation between the atomic number (Z) and the atomic size seen in TEM images when we consider shot noise in digital images. We propose Z-correlated (ZC) atomic radii for modeling AR-TEM images of single molecules and ultrathin crystals with which we can develop a good estimate of the molecular structure from the TEM image much more easily than with conventional molecular models. Two parameter sets were developed for TEM images recorded under high-noise (ZCHN) and low-noise (ZCLN) conditions. The molecular models will stimulate the imaginations of chemists planning to use AR-TEM for their research.
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12
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Himes B, Grigorieff N. Cryo-TEM simulations of amorphous radiation-sensitive samples using multislice wave propagation. IUCRJ 2021; 8:943-953. [PMID: 34804546 PMCID: PMC8562658 DOI: 10.1107/s2052252521008538] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/10/2021] [Accepted: 08/16/2021] [Indexed: 06/13/2023]
Abstract
Image simulation plays a central role in the development and practice of high-resolution electron microscopy, including transmission electron microscopy of frozen-hydrated specimens (cryo-EM). Simulating images with contrast that matches the contrast observed in experimental images remains challenging, especially for amorphous samples. Current state-of-the-art simulators apply post hoc scaling to approximate empirical solvent contrast, attenuated image intensity due to specimen thickness and amplitude contrast. This practice fails for images that require spatially variable scaling, e.g. simulations of a crowded or cellular environment. Modeling both the signal and the noise accurately is necessary to simulate images of biological specimens with contrast that is correct on an absolute scale. The 'frozen plasmon' method is introduced to explicitly model spatially variable inelastic scattering processes in cryo-EM specimens. This approach produces amplitude contrast that depends on the atomic composition of the specimen, reproduces the total inelastic mean free path as observed experimentally and allows for the incorporation of radiation damage in the simulation. These improvements are quantified using the matched filter concept to compare simulation and experiment. The frozen plasmon method, in combination with a new mathematical formulation for accurately sampling the tabulated atomic scattering potentials onto a Cartesian grid, is implemented in the open-source software package cisTEM.
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Affiliation(s)
- Benjamin Himes
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, 368 Plantation Street, Worcester, MA 01605, USA
| | - Nikolaus Grigorieff
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, 368 Plantation Street, Worcester, MA 01605, USA
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13
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Narangifard A, Wennberg CL, den Hollander L, Iwai I, Han H, Lundborg M, Masich S, Lindahl E, Daneholt B, Norlén L. Molecular Reorganization during the Formation of the Human Skin Barrier Studied In Situ. J Invest Dermatol 2021; 141:1243-1253.e6. [DOI: 10.1016/j.jid.2020.07.040] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2020] [Revised: 07/01/2020] [Accepted: 07/13/2020] [Indexed: 12/25/2022]
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14
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Reboul CF, Heo J, Machello C, Kiesewetter S, Kim BH, Kim S, Elmlund D, Ercius P, Park J, Elmlund H. SINGLE: Atomic-resolution structure identification of nanocrystals by graphene liquid cell EM. SCIENCE ADVANCES 2021; 7:7/5/eabe6679. [PMID: 33514557 PMCID: PMC7846166 DOI: 10.1126/sciadv.abe6679] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/06/2020] [Accepted: 12/10/2020] [Indexed: 06/12/2023]
Abstract
Analysis of the three-dimensional (3D) structures of nanocrystals with solution-phase transmission electron microscopy is beginning to reveal their unique physiochemical properties. We developed a "one-particle Brownian 3D reconstruction method" based on imaging of ensembles of colloidal nanocrystals using graphene liquid cell electron microscopy. Projection images of differently rotated nanocrystals are acquired using a direct electron detector with high temporal (<2.5 ms) resolution and analyzed to obtain an ensemble of 3D reconstructions. Here, we introduce computational methods required for successful atomic-resolution 3D reconstruction: (i) tracking of the individual particles throughout the time series, (ii) subtraction of the interfering background of the graphene liquid cell, (iii) identification and rejection of low-quality images, and (iv) tailored strategies for 2D/3D alignment and averaging that differ from those used in biological cryo-electron microscopy. Our developments are made available through the open-source software package SINGLE.
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Affiliation(s)
- Cyril F Reboul
- Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Melbourne, Victoria, Australia
- Australian Research Council Centre of Excellence in Advanced Molecular Imaging, Monash University, Melbourne, Victoria, Australia
| | - Junyoung Heo
- Center for Nanoparticle Research, Institute for Basic Science (IBS), Seoul 08826, South Korea
- School of Chemical and Biological Engineering, Institute of Chemical Process, Seoul National University, Seoul 08826, South Korea
| | - Chiara Machello
- Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Melbourne, Victoria, Australia
- Australian Research Council Centre of Excellence in Advanced Molecular Imaging, Monash University, Melbourne, Victoria, Australia
| | - Simon Kiesewetter
- Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Melbourne, Victoria, Australia
- Australian Research Council Centre of Excellence in Advanced Molecular Imaging, Monash University, Melbourne, Victoria, Australia
| | - Byung Hyo Kim
- Center for Nanoparticle Research, Institute for Basic Science (IBS), Seoul 08826, South Korea
- School of Chemical and Biological Engineering, Institute of Chemical Process, Seoul National University, Seoul 08826, South Korea
- Department of Organic Materials and Fiber Engineering, Soongsil University, Seoul 06978, South Korea
| | - Sungin Kim
- Center for Nanoparticle Research, Institute for Basic Science (IBS), Seoul 08826, South Korea
- School of Chemical and Biological Engineering, Institute of Chemical Process, Seoul National University, Seoul 08826, South Korea
| | - Dominika Elmlund
- Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Melbourne, Victoria, Australia
- Australian Research Council Centre of Excellence in Advanced Molecular Imaging, Monash University, Melbourne, Victoria, Australia
| | - Peter Ercius
- National Center for Electron Microscopy, Molecular Foundry, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Jungwon Park
- Center for Nanoparticle Research, Institute for Basic Science (IBS), Seoul 08826, South Korea.
- School of Chemical and Biological Engineering, Institute of Chemical Process, Seoul National University, Seoul 08826, South Korea
| | - Hans Elmlund
- Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Melbourne, Victoria, Australia.
- Australian Research Council Centre of Excellence in Advanced Molecular Imaging, Monash University, Melbourne, Victoria, Australia
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15
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Yao L, Ou Z, Luo B, Xu C, Chen Q. Machine Learning to Reveal Nanoparticle Dynamics from Liquid-Phase TEM Videos. ACS CENTRAL SCIENCE 2020; 6:1421-1430. [PMID: 32875083 PMCID: PMC7453571 DOI: 10.1021/acscentsci.0c00430] [Citation(s) in RCA: 63] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/10/2020] [Indexed: 05/08/2023]
Abstract
Liquid-phase transmission electron microscopy (TEM) has been recently applied to materials chemistry to gain fundamental understanding of various reaction and phase transition dynamics at nanometer resolution. However, quantitative extraction of physical and chemical parameters from the liquid-phase TEM videos remains bottlenecked by the lack of automated analysis methods compatible with the videos' high noisiness and spatial heterogeneity. Here, we integrate, for the first time, liquid-phase TEM imaging with our customized analysis framework based on a machine learning model called U-Net neural network. This combination is made possible by our workflow to generate simulated TEM images as the training data with well-defined ground truth. We apply this framework to three typical systems of colloidal nanoparticles, concerning their diffusion and interaction, reaction kinetics, and assembly dynamics, all resolved in real-time and real-space by liquid-phase TEM. A diversity of properties for differently shaped anisotropic nanoparticles are mapped, including the anisotropic interaction landscape of nanoprisms, curvature-dependent and staged etching profiles of nanorods, and an unexpected kinetic law of first-order chaining assembly of concave nanocubes. These systems representing properties at the nanoscale are otherwise experimentally inaccessible. Compared to the prevalent image segmentation methods, U-Net shows a superior capability to predict the position and shape boundary of nanoparticles from highly noisy and fluctuating background-a challenge common and sometimes inevitable in liquid-phase TEM videos. We expect our framework to push the potency of liquid-phase TEM to its full quantitative level and to shed insights, in high-throughput and statistically significant fashion, on the nanoscale dynamics of synthetic and biological nanomaterials.
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Affiliation(s)
- Lehan Yao
- Department
of Materials Science and Engineering, Materials Research Laboratory, Beckman Institute
for Advanced Science and Technology, and Department of Chemistry, University of Illinois at Urbana−Champaign, Urbana, Illinois 61801, United States
| | - Zihao Ou
- Department
of Materials Science and Engineering, Materials Research Laboratory, Beckman Institute
for Advanced Science and Technology, and Department of Chemistry, University of Illinois at Urbana−Champaign, Urbana, Illinois 61801, United States
| | - Binbin Luo
- Department
of Materials Science and Engineering, Materials Research Laboratory, Beckman Institute
for Advanced Science and Technology, and Department of Chemistry, University of Illinois at Urbana−Champaign, Urbana, Illinois 61801, United States
| | - Cong Xu
- Department
of Materials Science and Engineering, Materials Research Laboratory, Beckman Institute
for Advanced Science and Technology, and Department of Chemistry, University of Illinois at Urbana−Champaign, Urbana, Illinois 61801, United States
| | - Qian Chen
- Department
of Materials Science and Engineering, Materials Research Laboratory, Beckman Institute
for Advanced Science and Technology, and Department of Chemistry, University of Illinois at Urbana−Champaign, Urbana, Illinois 61801, United States
- E-mail:
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16
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Zhang Y, Tammaro R, Peters P, Ravelli R. Could Egg White Lysozyme be Solved by Single Particle Cryo-EM? J Chem Inf Model 2020; 60:2605-2613. [PMID: 32202786 PMCID: PMC7254834 DOI: 10.1021/acs.jcim.9b01176] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2019] [Indexed: 12/29/2022]
Abstract
The combination of high-end cryogenic transmission electron microscopes (cryo-EM), direct electron detectors, and advanced image algorithms allows researchers to obtain the 3D structures of much smaller macromolecules than years ago. However, there are still major challenges for the single-particle cryo-EM method to achieve routine structure determinations for macromolecules much smaller than 100 kDa, which are the majority of all plant and animal proteins. These challenges include sample characteristics such as sample heterogeneity, beam damage, ice layer thickness, stability, and quality, as well as hardware limitations such as detector performance, beam, and phase plate quality. Here, single particle data sets were simulated for samples that were ideal in terms of homogeneity, distribution, and stability, but with realistic parameters for ice layer, dose, detector performance, and beam characteristics. Reference data were calculated for human apo-ferritin using identical parameters reported for an experimental data set downloaded from EMPIAR. Processing of the simulated data set resulted in a value of 1.86 Å from 20 214 particles, similar to a 2 Å density map obtained from 29 224 particles selected from real micrographs. Simulated data sets were then generated for a 14 kDa protein, hen egg white lysozyme (HEWL), with and without an ideal phase plate (PP). Whereas we could not obtain a high-resolution 3D reconstruction of HEWL for the data set without PP, the one with PP resulted in a 2.78 Å resolution density map from 225 751 particles. Our simulator and simulations could help in pushing the size limits of cryo-EM.
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Affiliation(s)
- Y. Zhang
- The Maastricht Multimodal
Molecular Imaging Institute (M4I), Division of Nanoscopy, Maastricht University, 6229ER, Maastricht, The Netherlands
| | - R. Tammaro
- The Maastricht Multimodal
Molecular Imaging Institute (M4I), Division of Nanoscopy, Maastricht University, 6229ER, Maastricht, The Netherlands
| | - P.J. Peters
- The Maastricht Multimodal
Molecular Imaging Institute (M4I), Division of Nanoscopy, Maastricht University, 6229ER, Maastricht, The Netherlands
| | - R.B.G. Ravelli
- The Maastricht Multimodal
Molecular Imaging Institute (M4I), Division of Nanoscopy, Maastricht University, 6229ER, Maastricht, The Netherlands
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17
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Wennberg CL, Narangifard A, Lundborg M, Norlén L, Lindahl E. Structural Transitions in Ceramide Cubic Phases during Formation of the Human Skin Barrier. Biophys J 2019. [PMID: 29539398 DOI: 10.1016/j.bpj.2017.12.039] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022] Open
Abstract
The stratum corneum is the outermost layer of human skin and the primary barrier toward the environment. The barrier function is maintained by stacked layers of saturated long-chain ceramides, free fatty acids, and cholesterol. This structure is formed through a reorganization of glycosylceramide-based bilayers with cubic-like symmetry into ceramide-based bilayers with stacked lamellar symmetry. The process is accompanied by deglycosylation of glycosylceramides and dehydration of the skin barrier lipid structure. Using coarse-grained molecular dynamics simulation, we show the effects of deglycosylation and dehydration on bilayers of human skin glycosylceramides and ceramides, folded in three dimensions with cubic (gyroid) symmetry. Deglycosylation of glycosylceramides destabilizes the cubic lipid bilayer phase and triggers a cubic-to-lamellar phase transition. Furthermore, subsequent dehydration of the deglycosylated lamellar ceramide system closes the remaining pores between adjacent lipid layers and locally induces a ceramide chain transformation from a hairpin-like to a splayed conformation.
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Affiliation(s)
- Christian L Wennberg
- Department of Physics, Swedish e-Science Research Center, KTH Royal Institute of Technology, Stockholm, Sweden; ERCO Pharma AB, Science for Life Laboratory, Stockholm, Sweden
| | - Ali Narangifard
- ERCO Pharma AB, Science for Life Laboratory, Stockholm, Sweden; Department of Cell and Molecular Biology (CMB), Karolinska Institutet, Stockholm, Sweden
| | - Magnus Lundborg
- ERCO Pharma AB, Science for Life Laboratory, Stockholm, Sweden
| | - Lars Norlén
- Department of Cell and Molecular Biology (CMB), Karolinska Institutet, Stockholm, Sweden; Dermatology Clinic, Karolinska University Hospital, Stockholm, Sweden.
| | - Erik Lindahl
- Department of Physics, Swedish e-Science Research Center, KTH Royal Institute of Technology, Stockholm, Sweden; Department of Biophysics and Biochemistry, Science for Life Laboratory, Stockholm University, Solna, Sweden.
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18
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Jiang X, Spencer RK, Sun J, Ophus C, Zuckermann RN, Downing KH, Balsara NP. Resolving the Morphology of Peptoid Vesicles at the 1 nm Length Scale Using Cryogenic Electron Microscopy. J Phys Chem B 2019; 123:1195-1205. [DOI: 10.1021/acs.jpcb.8b11752] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
| | | | - Jing Sun
- Key Laboratory of Biobased Polymer Materials, Shandong Provincial Education Department, School of Polymer Science and Engineering, Qingdao University of Science and Technology, Qingdao 266042, China
| | | | | | | | - Nitash P. Balsara
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, California 94720, United States
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19
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Human skin barrier formation takes place via a cubic to lamellar lipid phase transition as analyzed by cryo-electron microscopy and EM-simulation. Exp Cell Res 2018; 366:139-151. [DOI: 10.1016/j.yexcr.2018.03.010] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2018] [Accepted: 03/06/2018] [Indexed: 01/14/2023]
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20
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Lundborg M, Narangifard A, Wennberg CL, Lindahl E, Daneholt B, Norlén L. Human skin barrier structure and function analyzed by cryo-EM and molecular dynamics simulation. J Struct Biol 2018; 203:149-161. [PMID: 29702212 DOI: 10.1016/j.jsb.2018.04.005] [Citation(s) in RCA: 49] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2018] [Revised: 04/19/2018] [Accepted: 04/22/2018] [Indexed: 11/29/2022]
Abstract
In the present study we have analyzed the molecular structure and function of the human skin's permeability barrier using molecular dynamics simulation validated against cryo-electron microscopy data from near native skin. The skin's barrier capacity is located to an intercellular lipid structure embedding the cells of the superficial most layer of skin - the stratum corneum. According to the splayed bilayer model (Iwai et al., 2012) the lipid structure is organized as stacked bilayers of ceramides in a splayed chain conformation with cholesterol associated with the ceramide sphingoid moiety and free fatty acids associated with the ceramide fatty acid moiety. However, knowledge about the lipid structure's detailed molecular organization, and the roles of its different lipid constituents, remains circumstantial. Starting from a molecular dynamics model based on the splayed bilayer model, we have, by stepwise structural and compositional modifications, arrived at a thermodynamically stable molecular dynamics model expressing simulated electron microscopy patterns matching original cryo-electron microscopy patterns from skin extremely closely. Strikingly, the closer the individual molecular dynamics models' lipid composition was to that reported in human stratum corneum, the better was the match between the models' simulated electron microscopy patterns and the original cryo-electron microscopy patterns. Moreover, the closest-matching model's calculated water permeability and thermotropic behaviour were found compatible with that of human skin. The new model may facilitate more advanced physics-based skin permeability predictions of drugs and toxicants. The proposed procedure for molecular dynamics based analysis of cellular cryo-electron microscopy data might be applied to other biomolecular systems.
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Affiliation(s)
| | - Ali Narangifard
- ERCO Pharma AB, Science for Life Laboratory, Solna, Sweden; Department of Medicine, Solna (MedS), Karolinska Institute, Solna, Sweden
| | - Christian L Wennberg
- ERCO Pharma AB, Science for Life Laboratory, Solna, Sweden; Swedish eScience Research Center, Department of Physics, KTH Royal Institute of Technology, Stockholm, Sweden
| | - Erik Lindahl
- Department of Biochemistry and Biophysics, Science for Life Laboratory, Stockholm University, Stockholm, Sweden; Swedish eScience Research Center, Department of Physics, KTH Royal Institute of Technology, Stockholm, Sweden
| | - Bertil Daneholt
- Department of Cell and Molecular Biology (CMB), Karolinska Institute, Stockholm, Sweden
| | - Lars Norlén
- Department of Cell and Molecular Biology (CMB), Karolinska Institute, Stockholm, Sweden; Dermatology Clinic, Karolinska University Hospital, Stockholm, Sweden.
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21
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Tavabi AH, Beleggia M, Migunov V, Savenko A, Öktem O, Dunin-Borkowski RE, Pozzi G. Tunable Ampere phase plate for low dose imaging of biomolecular complexes. Sci Rep 2018; 8:5592. [PMID: 29618785 PMCID: PMC5884816 DOI: 10.1038/s41598-018-23100-3] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2017] [Accepted: 02/07/2018] [Indexed: 11/09/2022] Open
Abstract
A novel device that can be used as a tunable support-free phase plate for transmission electron microscopy of weakly scattering specimens is described. The device relies on the generation of a controlled phase shift by the magnetic field of a segment of current-carrying wire that is oriented parallel or antiparallel to the electron beam. The validity of the concept is established using both experimental electron holographic measurements and a theoretical model based on Ampere's law. Computer simulations are used to illustrate the resulting contrast enhancement for studies of biological cells and macromolecules.
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Affiliation(s)
- Amir H Tavabi
- Ernst Ruska-Centre for Microscopy and Spectroscopy with Electrons and Peter Grünberg Institute, Forschungszentrum Jülich, 52428, Jülich, Germany.
| | - Marco Beleggia
- Center for Electron Nanoscopy, Technical University of Denmark, 2800, Kgs Lyngby, Denmark
| | - Vadim Migunov
- Ernst Ruska-Centre for Microscopy and Spectroscopy with Electrons and Peter Grünberg Institute, Forschungszentrum Jülich, 52428, Jülich, Germany
| | - Alexey Savenko
- FEI Company, Achtseweg Noord 5, 5600 KA, Eindhoven, The Netherlands
| | - Ozan Öktem
- Centre for Industrial and Applied Mathematics, Department of Mathematics, KTH - Royal Institute of Technology, Stockholm, Sweden
| | - Rafal E Dunin-Borkowski
- Ernst Ruska-Centre for Microscopy and Spectroscopy with Electrons and Peter Grünberg Institute, Forschungszentrum Jülich, 52428, Jülich, Germany
| | - Giulio Pozzi
- Ernst Ruska-Centre for Microscopy and Spectroscopy with Electrons and Peter Grünberg Institute, Forschungszentrum Jülich, 52428, Jülich, Germany.,Department of Physics and Astronomy, University of Bologna, Viale B. Pichat 6/2, 40127, Bologna, Italy
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22
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Haataja JS, Houbenov N, Aseyev V, Fragouli P, Iatrou H, Sougrat R, Hadjichristidis N, Ikkala O. Polymersomes with asymmetric membranes and self-assembled superstructures using pentablock quintopolymers resolved by electron tomography. Chem Commun (Camb) 2018; 54:1085-1088. [DOI: 10.1039/c7cc07306b] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Polystyrene-block-poly(1,4-isoprene)-block-poly(dimethyl siloxane)-block-poly(tert-butyl methacrylate)-block-poly(2-vinyl pyridine), PS-b-PI-b-PDMS-b-PtBMA-b-P2VP, self-assembles in acetone into polymersomes with asymmetric (directional) PI-b-PDMS membranes.
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Affiliation(s)
- J. S. Haataja
- Department of Applied Physics
- Aalto University
- Espoo
- Finland
| | - N. Houbenov
- Department of Applied Physics
- Aalto University
- Espoo
- Finland
| | - V. Aseyev
- Department of Chemistry
- University of Helsinki
- FI-00014 Helsinki
- Finland
| | - P. Fragouli
- Department of Chemistry
- University of Athens
- Panepistimiopolis
- Zografou
- Greece
| | - H. Iatrou
- Department of Chemistry
- University of Athens
- Panepistimiopolis
- Zografou
- Greece
| | - R. Sougrat
- King Abdullah University of Science and Technology (KAUST)
- Thuwal 23955-6900
- Kingdom of Saudi Arabia
| | - N. Hadjichristidis
- King Abdullah University of Science and Technology (KAUST)
- Thuwal 23955-6900
- Kingdom of Saudi Arabia
| | - O. Ikkala
- Department of Applied Physics
- Aalto University
- Espoo
- Finland
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23
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Abstract
Understanding and controlling nucleation is important for many crystallization applications. Calcium carbonate (CaCO3) is often used as a model system to investigate nucleation mechanisms. Despite its great importance in geology, biology, and many industrial applications, CaCO3 nucleation is still a topic of intense discussion, with new pathways for its growth from ions in solution proposed in recent years. These new pathways include the so-called nonclassical nucleation mechanism via the assembly of thermodynamically stable prenucleation clusters, as well as the formation of a dense liquid precursor phase via liquid-liquid phase separation. Here, we present results from a combined experimental and computational investigation on the precipitation of CaCO3 in dilute aqueous solutions. We propose that a dense liquid phase (containing 4-7 H2O per CaCO3 unit) forms in supersaturated solutions through the association of ions and ion pairs without significant participation of larger ion clusters. This liquid acts as the precursor for the formation of solid CaCO3 in the form of vaterite, which grows via a net transfer of ions from solution according to z Ca2+ + z CO32- → z CaCO3 The results show that all steps in this process can be explained according to classical concepts of crystal nucleation and growth, and that long-standing physical concepts of nucleation can describe multistep, multiphase growth mechanisms.
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24
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Rickgauer JP, Grigorieff N, Denk W. Single-protein detection in crowded molecular environments in cryo-EM images. eLife 2017; 6. [PMID: 28467302 PMCID: PMC5453696 DOI: 10.7554/elife.25648] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2017] [Accepted: 05/02/2017] [Indexed: 12/22/2022] Open
Abstract
We present an approach to study macromolecular assemblies by detecting component proteins' characteristic high-resolution projection patterns, calculated from their known 3D structures, in single electron cryo-micrographs. Our method detects single apoferritin molecules in vitreous ice with high specificity and determines their orientation and location precisely. Simulations show that high spatial-frequency information and-in the presence of protein background-a whitening filter are essential for optimal detection, in particular for images taken far from focus. Experimentally, we could detect small viral RNA polymerase molecules, distributed randomly among binding locations, inside rotavirus particles. Based on the currently attainable image quality, we estimate a threshold for detection that is 150 kDa in ice and 300 kDa in 100 nm thick samples of dense biological material.
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Affiliation(s)
| | | | - Winfried Denk
- Howard Hughes Medical Institute, Ashburn, United States.,Department of Electrons - Photons - Neurons, Max Planck Institute of Neurobiology, Martinsried, Germany
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25
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Analytical Review of Direct Stem Imaging Techniques for Thin Samples. ADVANCES IN IMAGING AND ELECTRON PHYSICS 2017. [DOI: 10.1016/bs.aiep.2017.01.006] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
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26
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Kirkland EJ. Computation in electron microscopy. ACTA CRYSTALLOGRAPHICA A-FOUNDATION AND ADVANCES 2016; 72:1-27. [DOI: 10.1107/s205327331501757x] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/09/2015] [Accepted: 09/19/2015] [Indexed: 11/11/2022]
Abstract
Some uses of the computer and computation in high-resolution transmission electron microscopy are reviewed. The theory of image calculation using Bloch wave and multislice methods with and without aberration correction is reviewed and some applications are discussed. The inverse problem of reconstructing the specimen structure from an experimentally measured electron microscope image is discussed. Some future directions of software development are given.
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27
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Lazić I, Bosch EGT, Lazar S. Phase contrast STEM for thin samples: Integrated differential phase contrast. Ultramicroscopy 2015; 160:265-280. [PMID: 26590505 DOI: 10.1016/j.ultramic.2015.10.011] [Citation(s) in RCA: 190] [Impact Index Per Article: 21.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2015] [Revised: 10/08/2015] [Accepted: 10/11/2015] [Indexed: 10/22/2022]
Abstract
It has been known since the 1970s that the movement of the center of mass (COM) of a convergent beam electron diffraction (CBED) pattern is linearly related to the (projected) electrical field in the sample. We re-derive a contrast transfer function (CTF) for a scanning transmission electron microscopy (STEM) imaging technique based on this movement from the point of view of image formation and continue by performing a two-dimensional integration on the two images based on the two components of the COM movement. The resulting integrated COM (iCOM) STEM technique yields a scalar image that is linear in the phase shift caused by the sample and therefore also in the local (projected) electrostatic potential field of a thin sample. We confirm that the differential phase contrast (DPC) STEM technique using a segmented detector with 4 quadrants (4Q) yields a good approximation for the COM movement. Performing a two-dimensional integration, just as for the COM, we obtain an integrated DPC (iDPC) image which is approximately linear in the phase of the sample. Beside deriving the CTFs of iCOM and iDPC, we clearly point out the objects of the two corresponding imaging techniques, and highlight the differences to objects corresponding to COM-, DPC-, and (HA) ADF-STEM. The theory is validated with simulations and we present first experimental results of the iDPC-STEM technique showing its capability for imaging both light and heavy elements with atomic resolution and a good signal to noise ratio (SNR).
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Affiliation(s)
- Ivan Lazić
- FEI Company, Achtseweg Noord 5, PO Box 80066, 5600 KA Eindhoven, The Netherlands.
| | - Eric G T Bosch
- FEI Company, Achtseweg Noord 5, PO Box 80066, 5600 KA Eindhoven, The Netherlands
| | - Sorin Lazar
- FEI Company, Achtseweg Noord 5, PO Box 80066, 5600 KA Eindhoven, The Netherlands
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28
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Bettadapura R, Rasheed M, Vollrath A, Bajaj C. PF2fit: Polar Fast Fourier Matched Alignment of Atomistic Structures with 3D Electron Microscopy Maps. PLoS Comput Biol 2015; 11:e1004289. [PMID: 26469938 PMCID: PMC4607507 DOI: 10.1371/journal.pcbi.1004289] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2014] [Accepted: 04/14/2015] [Indexed: 11/30/2022] Open
Abstract
There continue to be increasing occurrences of both atomistic structure models in the PDB (possibly reconstructed from X-ray diffraction or NMR data), and 3D reconstructed cryo-electron microscopy (3D EM) maps (albeit at coarser resolution) of the same or homologous molecule or molecular assembly, deposited in the EMDB. To obtain the best possible structural model of the molecule at the best achievable resolution, and without any missing gaps, one typically aligns (match and fits) the atomistic structure model with the 3D EM map. We discuss a new algorithm and generalized framework, named PF(2) fit (Polar Fast Fourier Fitting) for the best possible structural alignment of atomistic structures with 3D EM. While PF(2) fit enables only a rigid, six dimensional (6D) alignment method, it augments prior work on 6D X-ray structure and 3D EM alignment in multiple ways: Scoring. PF(2) fit includes a new scoring scheme that, in addition to rewarding overlaps between the volumes occupied by the atomistic structure and 3D EM map, rewards overlaps between the volumes complementary to them. We quantitatively demonstrate how this new complementary scoring scheme improves upon existing approaches. PF(2) fit also includes two scoring functions, the non-uniform exterior penalty and the skeleton-secondary structure score, and implements the scattering potential score as an alternative to traditional Gaussian blurring. Search. PF(2) fit utilizes a fast polar Fourier search scheme, whose main advantage is the ability to search over uniformly and adaptively sampled subsets of the space of rigid-body motions. PF(2) fit also implements a new reranking search and scoring methodology that considerably improves alignment metrics in results obtained from the initial search.
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Affiliation(s)
- Radhakrishna Bettadapura
- Radhakrishna Bettadapura Computational Visualization Center/Department of Mechanical Engineering, University of Texas at Austin, Austin, Texas, United States of America
| | - Muhibur Rasheed
- Muhibur Rasheed Computational Visualization Center/Department of Mechanical Engineering, University of Texas at Austin, Austin, Texas, United States of America
| | - Antje Vollrath
- Antje Vollrath Institut Computational Mathematics, Technische Universität Braunschweig, Braunschweig, Germany
| | - Chandrajit Bajaj
- Chandrajit Bajaj Computational Visualization Center/Institute of Computational Engineering & Sciences/Department of Computer Science, University of Texas at Austin, Austin, Texas, United States of America
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29
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Bosch EG, Lazić I. Analysis of HR-STEM theory for thin specimen. Ultramicroscopy 2015; 156:59-72. [DOI: 10.1016/j.ultramic.2015.02.004] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2014] [Revised: 02/05/2015] [Accepted: 02/12/2015] [Indexed: 11/29/2022]
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30
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KOECK P, KARSHIKOFF A. Limitations of the linear and the projection approximations in three-dimensional transmission electron microscopy of fully hydrated proteins. J Microsc 2015; 259:197-209. [DOI: 10.1111/jmi.12253] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2014] [Accepted: 03/09/2015] [Indexed: 11/29/2022]
Affiliation(s)
- P.J.B. KOECK
- Royal Institute of Technology; School of Technology and Health; Handen Sweden
- Department of Biosciences and Nutrition; Karolinska Institutet; Huddinge Sweden
| | - A. KARSHIKOFF
- Department of Biosciences and Nutrition; Karolinska Institutet; Huddinge Sweden
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31
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When to use the projection assumption and the weak-phase object approximation in phase contrast cryo-EM. Ultramicroscopy 2014; 136:61-6. [DOI: 10.1016/j.ultramic.2013.08.002] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2013] [Revised: 07/31/2013] [Accepted: 08/08/2013] [Indexed: 11/22/2022]
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32
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Vulović M, Ravelli RBG, van Vliet LJ, Koster AJ, Lazić I, Lücken U, Rullgård H, Öktem O, Rieger B. Image formation modeling in cryo-electron microscopy. J Struct Biol 2013; 183:19-32. [PMID: 23711417 DOI: 10.1016/j.jsb.2013.05.008] [Citation(s) in RCA: 59] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2013] [Revised: 05/07/2013] [Accepted: 05/14/2013] [Indexed: 11/16/2022]
Abstract
Accurate modeling of image formation in cryo-electron microscopy is an important requirement for quantitative image interpretation and optimization of the data acquisition strategy. Here we present a forward model that accounts for the specimen's scattering properties, microscope optics, and detector response. The specimen interaction potential is calculated with the isolated atom superposition approximation (IASA) and extended with the influences of solvent's dielectric and ionic properties as well as the molecular electrostatic distribution. We account for an effective charge redistribution via the Poisson-Boltzmann approach and find that the IASA-based potential forms the dominant part of the interaction potential, as the contribution of the redistribution is less than 10%. The electron wave is propagated through the specimen by a multislice approach and the influence of the optics is included via the contrast transfer function. We incorporate the detective quantum efficiency of the camera due to the difference between signal and noise transfer characteristics, instead of using only the modulation transfer function. The full model was validated against experimental images of 20S proteasome, hemoglobin, and GroEL. The simulations adequately predict the effects of phase contrast, changes due to the integrated electron flux, thickness, inelastic scattering, detective quantum efficiency and acceleration voltage. We suggest that beam-induced specimen movements are relevant in the experiments whereas the influence of the solvent amorphousness can be neglected. All simulation parameters are based on physical principles and, when necessary, experimentally determined.
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Affiliation(s)
- Miloš Vulović
- Quantitative Imaging Group, Faculty of Applied Sciences, Delft University of Technology, Lorentzweg 1, 2628 CJ Delft, The Netherlands
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Gopinath A, Xu G, Ress D, Öktem O, Subramaniam S, Bajaj C. Shape-based regularization of electron tomographic reconstruction. IEEE TRANSACTIONS ON MEDICAL IMAGING 2012; 31:2241-52. [PMID: 22922711 PMCID: PMC3513577 DOI: 10.1109/tmi.2012.2214229] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
We introduce a tomographic reconstruction method implemented using a shape-based regularization technique. Spatial models of known features in the structure being reconstructed are integrated into the reconstruction process as regularizers. Our regularization scheme is driven locally through shape information obtained from segmentation and compared with a known spatial model. We demonstrated our method on tomography data from digital phantoms, simulated data, and experimental electron tomography (ET) data of virus complexes. Our reconstruction showed reduced blurring and an improvement in the resolution of the reconstructed volume was also measured. This method also produced improved demarcation of spike boundaries in viral membranes when compared with popular techniques like weighted back projection and the algebraic reconstruction technique. Improved ET reconstructions will provide better structure elucidation and improved feature visualization, which can aid in solving key biological issues. Our method can also be generalized to other tomographic modalities.
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Affiliation(s)
- Ajay Gopinath
- Department of Electrical and Computer Engineering, University of Texas at Austin, Austin, TX 78712 USA.
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Hydration-layer models for cryo-EM image simulation. J Struct Biol 2012; 180:10-6. [PMID: 22609687 DOI: 10.1016/j.jsb.2012.04.021] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2011] [Revised: 04/23/2012] [Accepted: 04/27/2012] [Indexed: 11/21/2022]
Abstract
To compare cryo-EM images and 3D reconstructions with atomic structures in a quantitative way it is essential to model the electron scattering by solvent (water or ice) that surrounds protein assemblies. The most rigorous method for determining the density of solvating water atoms for this purpose has been to perform molecular-dynamics (MD) simulations of the protein-water system. In this paper we adapt the ideas of bulk-water modeling that are used in the refinement of X-ray crystal structures to the cryo-EM solvent-modeling problem. We present a continuum model for solvent density which matches MD-based results to within sampling errors. However, we also find that the simple binary-mask model of Jiang and Brünger (1994) performs nearly as well as the new model. We conclude that several methods are now available for rapid and accurate modeling of cryo-EM images and maps of solvated proteins.
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The human skin barrier is organized as stacked bilayers of fully extended ceramides with cholesterol molecules associated with the ceramide sphingoid moiety. J Invest Dermatol 2012; 132:2215-25. [PMID: 22534876 DOI: 10.1038/jid.2012.43] [Citation(s) in RCA: 157] [Impact Index Per Article: 13.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
The skin barrier is fundamental to terrestrial life and its evolution; it upholds homeostasis and protects against the environment. Skin barrier capacity is controlled by lipids that fill the extracellular space of the skin's surface layer--the stratum corneum. Here we report on the determination of the molecular organization of the skin's lipid matrix in situ, in its near-native state, using a methodological approach combining very high magnification cryo-electron microscopy (EM) of vitreous skin section defocus series, molecular modeling, and EM simulation. The lipids are organized in an arrangement not previously described in a biological system-stacked bilayers of fully extended ceramides (CERs) with cholesterol molecules associated with the CER sphingoid moiety. This arrangement rationalizes the skin's low permeability toward water and toward hydrophilic and lipophilic substances, as well as the skin barrier's robustness toward hydration and dehydration, environmental temperature and pressure changes, stretching, compression, bending, and shearing.
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