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Marques MPM, de Carvalho ALMB, Martins CB, Silva JD, Sarter M, García Sakai V, Stewart JR, de Carvalho LAEB. Cellular dynamics as a marker of normal-to-cancer transition in human cells. Sci Rep 2023; 13:21079. [PMID: 38030663 PMCID: PMC10687084 DOI: 10.1038/s41598-023-47649-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2023] [Accepted: 11/16/2023] [Indexed: 12/01/2023] Open
Abstract
Normal-to-cancer (NTC) transition is known to be closely associated to cell´s biomechanical properties which are dependent on the dynamics of the intracellular medium. This study probes different human cancer cells (breast, prostate and lung), concomitantly to their healthy counterparts, aiming at characterising the dynamical profile of water in distinct cellular locations, for each type of cell, and how it changes between normal and cancer states. An increased plasticity of the cytomatrix is observed upon normal-to-malignant transformation, the lung carcinoma cells displaying the highest flexibility followed by prostate and breast cancers. Also, lung cells show a distinct behaviour relative to breast and prostate, with a higher influence from hydration water motions and localised fast rotations upon NTC transformation. Quasielastic neutron scattering techniques allowed to accurately distinguish the different dynamical processes taking place within these highly heterogeneous cellular systems. The results thus obtained suggest that intracellular water dynamics may be regarded as a specific reporter of the cellular conditions-either healthy or malignant.
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Affiliation(s)
- M P M Marques
- Molecular Physical-Chemistry R&D Unit, Department of Chemistry, University of Coimbra, 3004-535, Coimbra, Portugal
- Department of Life Sciences, University of Coimbra, 3000-456, Coimbra, Portugal
| | - A L M Batista de Carvalho
- Molecular Physical-Chemistry R&D Unit, Department of Chemistry, University of Coimbra, 3004-535, Coimbra, Portugal.
| | - C B Martins
- Molecular Physical-Chemistry R&D Unit, Department of Chemistry, University of Coimbra, 3004-535, Coimbra, Portugal
- Department of Life Sciences, University of Coimbra, 3000-456, Coimbra, Portugal
| | - J D Silva
- Molecular Physical-Chemistry R&D Unit, Department of Chemistry, University of Coimbra, 3004-535, Coimbra, Portugal
- Department of Life Sciences, University of Coimbra, 3000-456, Coimbra, Portugal
| | - M Sarter
- STFC Rutherford Appleton Laboratory, ISIS Facility, Chilton, Didcot, OX11 0QX, UK
| | - V García Sakai
- STFC Rutherford Appleton Laboratory, ISIS Facility, Chilton, Didcot, OX11 0QX, UK
| | - J R Stewart
- STFC Rutherford Appleton Laboratory, ISIS Facility, Chilton, Didcot, OX11 0QX, UK
| | - L A E Batista de Carvalho
- Molecular Physical-Chemistry R&D Unit, Department of Chemistry, University of Coimbra, 3004-535, Coimbra, Portugal
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Wilding MC, Sella A, Howard CA, Jorge Sobrido A, Catlow CRA. Exploring the length scales, timescales and chemistry of challenging materials (Part 1). PHILOSOPHICAL TRANSACTIONS. SERIES A, MATHEMATICAL, PHYSICAL, AND ENGINEERING SCIENCES 2023; 381:20220353. [PMID: 37634538 PMCID: PMC10460644 DOI: 10.1098/rsta.2022.0353] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/05/2023] [Accepted: 07/05/2023] [Indexed: 08/29/2023]
Abstract
This themed issue explores the different length scales and timescales that determine the physics and chemistry of a variety of key materials, explored from the perspective of a wide range of disciplines, including physics, chemistry, materials science, Earth science and biochemistry. The topics discussed include catalysis, chemistry under extreme conditions, energy materials, amorphous and liquid structure, hybrid organic materials and biological materials. The issue is in two parts, with the present part exploring glassy and amorphous systems and materials at high pressure. This article is part of the theme issue 'Exploring the length scales, timescales and chemistry of challenging materials (Part 1)'.
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Affiliation(s)
- Martin C. Wilding
- Cardiff Catalysis Institute, School of Chemistry, Cardiff University, Cardiff CF10 3AT, UK
| | - Andrea Sella
- Department of Physics and Astronomy, University College London, London WC1E 6BT, UK
| | - Christopher A. Howard
- School of Engineering and Materials Science, Queen Mary University of London, London E1 4NS, UK
| | - Ana Jorge Sobrido
- Department of Chemistry, University College London, London WC1E 6BT, UK
| | - C. Richard A. Catlow
- Cardiff Catalysis Institute, School of Chemistry, Cardiff University, Cardiff CF10 3AT, UK
- Department of Physics and Astronomy, University College London, London WC1E 6BT, UK
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Belushkin AV. Comparison of the Possibilities of Inelastic Scattering of Synchrotron Radiation and Neutrons for Studying Atomic, Molecular, and Magnetic Dynamics in Condensed Matter. CRYSTALLOGR REP+ 2022. [DOI: 10.1134/s1063774522010035] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Ramos J, Laux V, Haertlein M, Forsyth VT, Mossou E, Larsen S, Langkilde AE. The impact of folding modes and deuteration on the atomic resolution structure of hen egg-white lysozyme. Acta Crystallogr D Struct Biol 2021; 77:1579-1590. [PMID: 34866613 PMCID: PMC8647175 DOI: 10.1107/s2059798321010950] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2021] [Accepted: 10/20/2021] [Indexed: 11/10/2022] Open
Abstract
The biological function of a protein is intimately related to its structure and dynamics, which in turn are determined by the way in which it has been folded. In vitro refolding is commonly used for the recovery of recombinant proteins that are expressed in the form of inclusion bodies and is of central interest in terms of the folding pathways that occur in vivo. Here, biophysical data are reported for in vitro-refolded hydrogenated hen egg-white lysozyme, in combination with atomic resolution X-ray diffraction analyses, which allowed detailed comparisons with native hydrogenated and refolded perdeuterated lysozyme. Distinct folding modes are observed for the hydrogenated and perdeuterated refolded variants, which are determined by conformational changes to the backbone structure of the Lys97-Gly104 flexible loop. Surprisingly, the structure of the refolded perdeuterated protein is closer to that of native lysozyme than that of the refolded hydrogenated protein. These structural differences suggest that the observed decreases in thermal stability and enzymatic activity in the refolded perdeuterated and hydrogenated proteins are consequences of the macromolecular deuteration effect and of distinct folding dynamics, respectively. These results are discussed in the context of both in vitro and in vivo folding, as well as of lysozyme amyloidogenesis.
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Affiliation(s)
- Joao Ramos
- Life Sciences Group, Institute Laue–Langevin, 71 Avenue des Martyrs, 38000 Grenoble, France
- Partnership for Structural Biology (PSB), 71 Avenue des Martyrs, 38000 Grenoble, France
- Department of Drug Design and Pharmacology, University of Copenhagen, Universitetsparken 2, DK-2100 Copenhagen, Denmark
| | - Valerie Laux
- Life Sciences Group, Institute Laue–Langevin, 71 Avenue des Martyrs, 38000 Grenoble, France
- Partnership for Structural Biology (PSB), 71 Avenue des Martyrs, 38000 Grenoble, France
| | - Michael Haertlein
- Life Sciences Group, Institute Laue–Langevin, 71 Avenue des Martyrs, 38000 Grenoble, France
- Partnership for Structural Biology (PSB), 71 Avenue des Martyrs, 38000 Grenoble, France
| | - V. Trevor Forsyth
- Life Sciences Group, Institute Laue–Langevin, 71 Avenue des Martyrs, 38000 Grenoble, France
- Partnership for Structural Biology (PSB), 71 Avenue des Martyrs, 38000 Grenoble, France
- Faculty of Natural Sciences, Keele University, Newcastle ST5 5BG, United Kingdom
- Faculty of Medicine, Lund University, 221 00 Lund, Sweden
- LINXS Institute for Advanced Neutron and X-ray Science, Scheelvagen 19, 223 70 Lund, Sweden
| | - Estelle Mossou
- Partnership for Structural Biology (PSB), 71 Avenue des Martyrs, 38000 Grenoble, France
- European Synchrotron Radiation Facility, 71 Avenue des Martyrs, 38000 Grenoble, France
| | - Sine Larsen
- Department of Chemistry, University of Copenhagen, Universitetsparken 5, DK-2100 Copenhagen, Denmark
| | - Annette E. Langkilde
- Department of Drug Design and Pharmacology, University of Copenhagen, Universitetsparken 2, DK-2100 Copenhagen, Denmark
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Panneels V, Diaz A, Imsand C, Guizar-Sicairos M, Müller E, Bittermann AG, Ishikawa T, Menzel A, Kaech A, Holler M, Grimm C, Schertler G. Imaging of retina cellular and subcellular structures using ptychographic hard X-ray tomography. J Cell Sci 2021; 134:272479. [PMID: 34494099 DOI: 10.1242/jcs.258561] [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: 02/15/2021] [Accepted: 09/01/2021] [Indexed: 11/20/2022] Open
Abstract
Ptychographic hard X-ray computed tomography (PXCT) is a recent method allowing imaging with quantitative electron-density contrast. Here, we imaged, at cryogenic temperature and without sectioning, cellular and subcellular structures of a chemically fixed and stained wild-type mouse retina, including axons and synapses, with complete isotropic 3D information over tens of microns. Comparison with tomograms of degenerative retina from a mouse model of retinitis pigmentosa illustrates the potential of this method for analyzing disease processes like neurodegeneration at sub-200 nm resolution. As a non-destructive imaging method, PXCT is very suitable for correlative imaging. Within the outer plexiform layer containing the photoreceptor synapses, we identified somatic synapses. We used a small region inside the X-ray-imaged sample for further high-resolution focused ion beam/scanning electron microscope tomography. The subcellular structures of synapses obtained with the X-ray technique matched the electron microscopy data, demonstrating that PXCT is a powerful scanning method for tissue volumes of more than 60 cells and sensitive enough for identification of regions as small as 200 nm, which remain available for further structural and biochemical investigations.
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Affiliation(s)
- Valerie Panneels
- Division of Biology and Chemistry, Laboratory for Biomolecular Research, Paul Scherrer Institute, 5232 Villigen, Switzerland
| | - Ana Diaz
- Division of Photon Science, Laboratory for Macromolecules and Bioimaging, Paul Scherrer Institute, 5232 Villigen, Switzerland
| | - Cornelia Imsand
- Laboratory for Retinal Cell Biology, Department of Ophthalmology, University Hospital Zurich, University of Zurich, 8952 Schlieren, Switzerland
| | - Manuel Guizar-Sicairos
- Division of Photon Science, Laboratory for Macromolecules and Bioimaging, Paul Scherrer Institute, 5232 Villigen, Switzerland
| | - Elisabeth Müller
- Division of Biology and Chemistry, Laboratory for Nanoscale Biology, Paul Scherrer Institute, 5232 Villigen, Switzerland
| | - Anne Greet Bittermann
- ScopeM, Scientific Center for Optical and Electron Microscopy, ETH Zurich, 8093 Zurich, Switzerland
| | - Takashi Ishikawa
- Division of Biology and Chemistry, Laboratory for Biomolecular Research, Paul Scherrer Institute, 5232 Villigen, Switzerland.,Department of Biology, ETH Zurich, 8093 Zurich, Switzerland
| | - Andreas Menzel
- Division of Photon Science, Laboratory for Macromolecules and Bioimaging, Paul Scherrer Institute, 5232 Villigen, Switzerland
| | - Andres Kaech
- Center for Microscopy and Image Analysis, University of Zurich, 8006 Zurich, Switzerland
| | - Mirko Holler
- Division of Photon Science, Laboratory for Macromolecules and Bioimaging, Paul Scherrer Institute, 5232 Villigen, Switzerland
| | - Christian Grimm
- Laboratory for Retinal Cell Biology, Department of Ophthalmology, University Hospital Zurich, University of Zurich, 8952 Schlieren, Switzerland
| | - Gebhard Schertler
- Division of Biology and Chemistry, Laboratory for Biomolecular Research, Paul Scherrer Institute, 5232 Villigen, Switzerland.,Department of Biology, ETH Zurich, 8093 Zurich, Switzerland
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Eves BJ, Doutch JJ, Terry AE, Yin H, Moulin M, Haertlein M, Forsyth VT, Flagmeier P, Knowles TPJ, Dias DM, Lotze G, Seddon AM, Squires AM. Elongation rate and average length of amyloid fibrils in solution using isotope-labelled small-angle neutron scattering. RSC Chem Biol 2021; 2:1232-1238. [PMID: 34458836 PMCID: PMC8341957 DOI: 10.1039/d1cb00001b] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2021] [Accepted: 04/06/2021] [Indexed: 12/22/2022] Open
Abstract
We demonstrate a solution method that allows both elongation rate and average fibril length of assembling amyloid fibrils to be estimated. The approach involves acquisition of real-time neutron scattering data during the initial stages of seeded growth, using contrast matched buffer to make the seeds effectively invisible to neutrons. As deuterated monomers add on to the seeds, the labelled growing ends give rise to scattering patterns that we model as cylinders whose increase in length with time gives an elongation rate. In addition, the absolute intensity of the signal can be used to determine the number of growing ends per unit volume, which in turn provides an estimate of seed length. The number of ends did not change significantly during elongation, demonstrating that any spontaneous or secondary nucleation was not significant compared with growth on the ends of pre-existing fibrils, and in addition providing a method of internal validation for the technique. Our experiments on initial growth of alpha synuclein fibrils using 1.2 mg ml-1 seeds in 2.5 mg ml-1 deuterated monomer at room temperature gave an elongation rate of 6.3 ± 0.5 Å min-1, and an average seed length estimate of 4.2 ± 1.3 μm.
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Affiliation(s)
- Ben J Eves
- Department of Chemistry, University of Bath Bath UK
| | - James J Doutch
- ISIS Facility, Rutherford Appleton Laboratory, STFC, Chilton Didcot OX11 0QX UK
| | - Ann E Terry
- MAX IV Laboratory, Lund University P.O. Box 118 Lund 221 00 Sweden
| | - Han Yin
- Department of Chemistry, University of Bath Bath UK
| | - Martine Moulin
- Life Sciences Group, Institut Laue Langevin 38042 Grenoble Cedex 9 France
| | - Michael Haertlein
- Life Sciences Group, Institut Laue Langevin 38042 Grenoble Cedex 9 France
| | - V Trevor Forsyth
- Life Sciences Group, Institut Laue Langevin 38042 Grenoble Cedex 9 France
- School of Chemistry & Physics Keele University Staffordshire ST5 5BG UK
| | - Patrick Flagmeier
- Department of Chemistry, University of Cambridge Cambridge CB2 1EW UK
- Centre for Misfolding Diseases, University of Cambridge Cambridge CB2 1EW UK
| | - Tuomas P J Knowles
- Department of Chemistry, University of Cambridge Cambridge CB2 1EW UK
- Centre for Misfolding Diseases, University of Cambridge Cambridge CB2 1EW UK
| | - David M Dias
- Department of Chemistry, Physical and Theoretical Chemistry Laboratory, University of Oxford South Parks Road Oxford OX1 3QZ UK
| | - Gudrun Lotze
- MAX IV Laboratory, Lund University P.O. Box 118 Lund 221 00 Sweden
| | - Annela M Seddon
- School of Physics, HH Wills Physics Laboratory, Tyndall Avenue, University of Bristol Bristol BS8 1TL UK
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Ando N, Barquera B, Bartlett DH, Boyd E, Burnim AA, Byer AS, Colman D, Gillilan RE, Gruebele M, Makhatadze G, Royer CA, Shock E, Wand AJ, Watkins MB. The Molecular Basis for Life in Extreme Environments. Annu Rev Biophys 2021; 50:343-372. [PMID: 33637008 DOI: 10.1146/annurev-biophys-100120-072804] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Sampling and genomic efforts over the past decade have revealed an enormous quantity and diversity of life in Earth's extreme environments. This new knowledge of life on Earth poses the challenge of understandingits molecular basis in such inhospitable conditions, given that such conditions lead to loss of structure and of function in biomolecules from mesophiles. In this review, we discuss the physicochemical properties of extreme environments. We present the state of recent progress in extreme environmental genomics. We then present an overview of our current understanding of the biomolecular adaptation to extreme conditions. As our current and future understanding of biomolecular structure-function relationships in extremophiles requires methodologies adapted to extremes of pressure, temperature, and chemical composition, advances in instrumentation for probing biophysical properties under extreme conditions are presented. Finally, we briefly discuss possible future directions in extreme biophysics.
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Affiliation(s)
- Nozomi Ando
- Department of Chemistry & Chemical Biology, Cornell University, Ithaca, New York 14853, USA.,Department of Chemistry, Princeton University, Princeton, New Jersey 08544, USA
| | - Blanca Barquera
- Department of Biological Sciences, Rensselaer Polytechnic Institute, Troy, New York 12180, USA;
| | - Douglas H Bartlett
- Marine Biology Research Division, Scripps Institution of Oceanography, University of California, San Diego, La Jolla, California 92093-0202, USA
| | - Eric Boyd
- Department of Microbiology and Immunology, Montana State University, Bozeman, Montana 59717, USA
| | - Audrey A Burnim
- Department of Chemistry & Chemical Biology, Cornell University, Ithaca, New York 14853, USA
| | - Amanda S Byer
- Department of Chemistry & Chemical Biology, Cornell University, Ithaca, New York 14853, USA
| | - Daniel Colman
- Department of Microbiology and Immunology, Montana State University, Bozeman, Montana 59717, USA
| | - Richard E Gillilan
- Center for High Energy X-ray Sciences (CHEXS), Ithaca, New York 14853, USA
| | - Martin Gruebele
- Department of Chemistry, University of Illinois, Urbana-Champaign, Illinois 61801, USA.,Department of Physics, University of Illinois, Urbana-Champaign, Illinois 61801, USA.,Center for Biophysics and Quantitative Biology, University of Illinois, Urbana-Champaign, Illinois 61801, USA
| | - George Makhatadze
- Department of Biological Sciences, Rensselaer Polytechnic Institute, Troy, New York 12180, USA;
| | - Catherine A Royer
- Department of Biological Sciences, Rensselaer Polytechnic Institute, Troy, New York 12180, USA;
| | - Everett Shock
- GEOPIG, School of Earth & Space Exploration, School of Molecular Sciences, Center for Fundamental and Applied Microbiomics, Arizona State University, Tempe, Arizona 85287, USA
| | - A Joshua Wand
- Department of Biochemistry & Biophysics, Texas A&M University, College Station, Texas 77845, USA.,Department of Chemistry, Texas A&M University, College Station, Texas 77845, USA.,Department of Molecular & Cellular Medicine, Texas A&M University, College Station, Texas 77845, USA
| | - Maxwell B Watkins
- Department of Chemistry & Chemical Biology, Cornell University, Ithaca, New York 14853, USA.,Department of Chemistry, Princeton University, Princeton, New Jersey 08544, USA
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