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Lang X, Shi L, Zhao Z, Min W. Probing the structure of water in individual living cells. Nat Commun 2024; 15:5271. [PMID: 38902250 PMCID: PMC11190263 DOI: 10.1038/s41467-024-49404-9] [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: 10/16/2023] [Accepted: 06/04/2024] [Indexed: 06/22/2024] Open
Abstract
Water regulates or even governs a wide range of biological processes. Despite its fundamental importance, surprisingly little is known about the structure of intracellular water. Herein we employ a Raman micro-spectroscopy technique to uncover the composition, abundance and vibrational spectra of intracellular water in individual living cells. In three different cell types, we show a small but consistent population (~3%) of non-bulk-like water. It exhibits a weakened hydrogen-bonded network and a more disordered tetrahedral structure. We attribute this population to biointerfacial water located in the vicinity of biomolecules. Moreover, our whole-cell modeling suggests that all soluble (globular) proteins inside cells are surrounded by, on average, one full molecular layer (about 2.6 Angstrom) of biointerfacial water. Furthermore, relative invariance of biointerfacial water is observed among different single cells. Overall, our study not only opens up experimental possibilities of interrogating water structure in vivo but also provides insights into water in life.
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Affiliation(s)
- Xiaoqi Lang
- Department of Chemistry, Columbia University, New York, NY, 10027, USA
| | - Lixue Shi
- Shanghai Xuhui Central Hospital, Zhongshan-Xuhui Hospital, and Shanghai Key Laboratory of Medical Epigenetics, International Co-laboratory of Medical Epigenetics and Metabolism, Institutes of Biomedical Sciences, Shanghai Medical College, Fudan University, Shanghai, 200032, China
| | - Zhilun Zhao
- Department of Chemistry, Columbia University, New York, NY, 10027, USA
| | - Wei Min
- Department of Chemistry, Columbia University, New York, NY, 10027, USA.
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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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Theillet FX, Luchinat E. In-cell NMR: Why and how? PROGRESS IN NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY 2022; 132-133:1-112. [PMID: 36496255 DOI: 10.1016/j.pnmrs.2022.04.002] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/15/2021] [Revised: 04/19/2022] [Accepted: 04/27/2022] [Indexed: 06/17/2023]
Abstract
NMR spectroscopy has been applied to cells and tissues analysis since its beginnings, as early as 1950. We have attempted to gather here in a didactic fashion the broad diversity of data and ideas that emerged from NMR investigations on living cells. Covering a large proportion of the periodic table, NMR spectroscopy permits scrutiny of a great variety of atomic nuclei in all living organisms non-invasively. It has thus provided quantitative information on cellular atoms and their chemical environment, dynamics, or interactions. We will show that NMR studies have generated valuable knowledge on a vast array of cellular molecules and events, from water, salts, metabolites, cell walls, proteins, nucleic acids, drugs and drug targets, to pH, redox equilibria and chemical reactions. The characterization of such a multitude of objects at the atomic scale has thus shaped our mental representation of cellular life at multiple levels, together with major techniques like mass-spectrometry or microscopies. NMR studies on cells has accompanied the developments of MRI and metabolomics, and various subfields have flourished, coined with appealing names: fluxomics, foodomics, MRI and MRS (i.e. imaging and localized spectroscopy of living tissues, respectively), whole-cell NMR, on-cell ligand-based NMR, systems NMR, cellular structural biology, in-cell NMR… All these have not grown separately, but rather by reinforcing each other like a braided trunk. Hence, we try here to provide an analytical account of a large ensemble of intricately linked approaches, whose integration has been and will be key to their success. We present extensive overviews, firstly on the various types of information provided by NMR in a cellular environment (the "why", oriented towards a broad readership), and secondly on the employed NMR techniques and setups (the "how", where we discuss the past, current and future methods). Each subsection is constructed as a historical anthology, showing how the intrinsic properties of NMR spectroscopy and its developments structured the accessible knowledge on cellular phenomena. Using this systematic approach, we sought i) to make this review accessible to the broadest audience and ii) to highlight some early techniques that may find renewed interest. Finally, we present a brief discussion on what may be potential and desirable developments in the context of integrative studies in biology.
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Affiliation(s)
- Francois-Xavier Theillet
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198 Gif-sur-Yvette, France.
| | - Enrico Luchinat
- Dipartimento di Scienze e Tecnologie Agro-Alimentari, Alma Mater Studiorum - Università di Bologna, Piazza Goidanich 60, 47521 Cesena, Italy; CERM - Magnetic Resonance Center, and Neurofarba Department, Università degli Studi di Firenze, 50019 Sesto Fiorentino, Italy
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Li Y, Han Z, Ma C, Hong L, Ding Y, Chen Y, Zhao J, Liu D, Sun G, Zuo T, Cheng H, Han CC. Structure and dynamics of supercooled water in the hydration layer of poly(ethylene glycol). STRUCTURAL DYNAMICS (MELVILLE, N.Y.) 2022; 9:054901. [PMID: 36090796 PMCID: PMC9462885 DOI: 10.1063/4.0000158] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/08/2022] [Accepted: 08/11/2022] [Indexed: 06/15/2023]
Abstract
The statics and dynamics of supercooled water in the hydration layer of poly(ethylene glycol) (PEG) were studied by a combination of quasi-elastic neutron scattering (QENS) and molecular dynamics (MD) simulations. Two samples, that is, hydrogenated PEG/deuterated water (h-PEG/D2O) and fully deuterated PEG/hydrogenated water (d-PEG/H2O) with the same molar ratio of ethylene glycol (EG) monomer to water, 1:1, are compared. The QENS data of h-PEG/D2O show the dynamics of PEG, and that of d-PEG/H2O reveals the motion of water. The temperature-dependent elastic scattering intensity of both samples has shown transitions at supercooled temperature, and these transition temperatures depend on the energy resolution of the instruments. Therefore, neither one is a phase transition, but undergoes dynamic process. The dynamic of water can be described as an Arrhenius to super-Arrhenius transition, and it reveals the hydrogen bonding network relaxation of hydration water around PEG at supercooled temperature. Since the PEG-water hydrogen bond structural relaxation time from MD is in good agreement with the average relaxation time from QENS (d-PEG/H2O), MD may further reveal the atomic pictures of the supercooled hydration water. It shows that hydration water molecules form a series of pools around the hydrophilic oxygen atom of PEG. At supercooled temperature, they have a more bond ordered structure than bulk water, proceed a trapping sites diffusion on the PEG surface, and facilitate the structural relaxation of PEG backbone.
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Affiliation(s)
| | | | | | - Liang Hong
- School of Physics and Astronomy, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Yanwei Ding
- Department of Chemical Physics, University of Science and Technology of China, Hefei 230026, China
| | - Ye Chen
- Faculty of Materials Science and Engineering, South China University of Technology, Guangzhou 510640, China
| | - Junpeng Zhao
- Faculty of Materials Science and Engineering, South China University of Technology, Guangzhou 510640, China
| | - Dong Liu
- Key Laboratory of Neutron Physics, Institute of Nuclear Physics and Chemistry, China Academy of Engineering Physics, Mianyang 621999, China
| | - Guangai Sun
- Key Laboratory of Neutron Physics, Institute of Nuclear Physics and Chemistry, China Academy of Engineering Physics, Mianyang 621999, China
| | | | - He Cheng
- Author to whom correspondence should be addressed: . Tel.: +86-769-8915-6445. Fax: +86-769-8915-6441
| | - Charles C. Han
- Institute for Advanced Study, Shenzhen University, Shenzhen 508060, China
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Marques MPM, Santos IP, Batista de Carvalho ALM, Mamede AP, Martins CB, Figueiredo P, Sarter M, Sakai VG, Batista de Carvalho LAE. Water dynamics in human cancer and non-cancer tissues. Phys Chem Chem Phys 2022; 24:15406-15415. [PMID: 35704895 DOI: 10.1039/d2cp00621a] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Normal-to-malignant transformation is a poorly understood process associated with cellular biomechanical properties. These are strongly dependent on the dynamical behaviour of water, known to play a fundamental role in normal cellular activity and in the maintenance of the three-dimensional architecture of the tissue and the functional state of biopolymers. In this study, quasi-elastic neutron scattering was used to probe the dynamical behaviour of water in human cancer specimens and their respective surrounding normal tissue from breast and tongue, as an innovative approach for identifying particular features of malignancy. This methodology has been successfully used by the authors in human cells and was the first study of human tissues by neutron scattering techniques. A larger flexibility was observed for breast versus tongue tissues. Additionally, different dynamics were found for malignant and non-malignant specimens, depending on the tissue: higher plasticity for breast invasive cancer versus the normal, and an opposite effect for tongue. The data were interpreted in the light of two different water populations within the samples: one displaying bulk-like dynamics (extracellular and intracellular/cytoplasmic) and another with constrained flexibility (extracellular/interstitial and intracellular/hydration layers).
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Affiliation(s)
- M P M Marques
- University of Coimbra, Molecular Physical-Chemistry R&D Unit, Department of Chemistry, 3004-535 Coimbra, Portugal. .,University of Coimbra, Department of Life Sciences, 3000-456 Coimbra, Portugal
| | - I P Santos
- University of Coimbra, Molecular Physical-Chemistry R&D Unit, Department of Chemistry, 3004-535 Coimbra, Portugal.
| | - A L M Batista de Carvalho
- University of Coimbra, Molecular Physical-Chemistry R&D Unit, Department of Chemistry, 3004-535 Coimbra, Portugal.
| | - A P Mamede
- University of Coimbra, Molecular Physical-Chemistry R&D Unit, Department of Chemistry, 3004-535 Coimbra, Portugal.
| | - C B Martins
- University of Coimbra, Molecular Physical-Chemistry R&D Unit, Department of Chemistry, 3004-535 Coimbra, Portugal.
| | - P Figueiredo
- Oncology Institute of Coimbra Francisco Gentil, 3000-075 Coimbra, Portugal
| | - M Sarter
- ISIS Neutron and Muon Facility, STFC Rutherford Appleton Laboratory, Chilton, Didcot, OX11 0QX, UK
| | - V García Sakai
- ISIS Neutron and Muon Facility, STFC Rutherford Appleton Laboratory, Chilton, Didcot, OX11 0QX, UK
| | - L A E Batista de Carvalho
- University of Coimbra, Molecular Physical-Chemistry R&D Unit, Department of Chemistry, 3004-535 Coimbra, Portugal.
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Campo MG, Corral GM. Structural, dynamic, and hydration properties of quercetin and its aggregates in solution. JOURNAL OF PHYSICS. CONDENSED MATTER : AN INSTITUTE OF PHYSICS JOURNAL 2022; 34:294001. [PMID: 35472688 DOI: 10.1088/1361-648x/ac6a99] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/05/2022] [Accepted: 04/26/2022] [Indexed: 06/14/2023]
Abstract
Quercetin is a flavonoid present in the human diet with multiple health benefits. Quercetin solutions are inhomogeneous even at very low concentrations due to quercetin's tendency to aggregate. We simulate, using molecular dynamics, three systems of quercetin solutions: infinite dilution, 0.22 M, and 0.46 M. The systems at the two highest concentrations represent regions of the quercetin aggregates, in which the concentration of this molecule is unusually high. We study the behavior of this molecule, its aggregates, and the modifications in the surrounding water. In the first three successive layers of quercetin hydration, the density of water and the hydrogen bonds formations between water molecules are smaller than that of bulk. Quercetin has a hydrophilic surface region that preferentially establishes donor hydrogen bonds with water molecules with relative frequencies from 0.12 to 0.46 at infinite dilution. Also, it has two hydrophobic regions above and below the planes of its rings, whose first hydration layers are further out from quercetin (≈0.3 Å) and their water molecules do not establish hydrogen bonds with it. Water density around the hydrophobic regions is smaller than that of the hydrophilic. Quercetin molecules aggregate inπ-stacking configurations, with a distance of ≈0.37 nm between the planes of their rings, and form bonds between their hydroxyl groups. The formation of quercetin aggregates decreases the hydrogen bonds between quercetin and the surrounding water and produces a subdiffusive behavior in water molecules. Quercetin has a subdiffusive behavior even at infinite dilution, which increases with the number of molecules within the aggregates and the time they remain within them.
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Affiliation(s)
- M G Campo
- Facultad de Ciencias Exactas y Naturales, Universidad Nacional de La Pampa, Uruguay 151, (6300) Santa Rosa, Argentina
| | - G M Corral
- Facultad de Ciencias Exactas y Naturales, Universidad Nacional de La Pampa, Uruguay 151, (6300) Santa Rosa, Argentina
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Atamas N, Gavryushenko D, Yablochkova K, Lazarenko M, Taranyik G. Temperature and temporal heterogeneities of water dynamics in the physiological temperature range. J Mol Liq 2021. [DOI: 10.1016/j.molliq.2021.117201] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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