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Thekkethil N, Köry J, Guo M, Stewart PS, Hill NA, Luo X. Modelling the rheology of living cell cytoplasm: poroviscoelasticity and fluid-to-solid transition. Biomech Model Mechanobiol 2024:10.1007/s10237-024-01854-2. [PMID: 38976113 DOI: 10.1007/s10237-024-01854-2] [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: 11/30/2023] [Accepted: 04/17/2024] [Indexed: 07/09/2024]
Abstract
Eukaryotic cell rheology has important consequences for vital processes such as adhesion, migration, and differentiation. Experiments indicate that cell cytoplasm can exhibit both elastic and viscous characteristics in different regimes, while the transport of fluid (cytosol) through the cross-linked filamentous scaffold (cytoskeleton) is reminiscent of mass transfer by diffusion through a porous medium. To gain insights into this complex rheological behaviour, we construct a computational model for the cell cytoplasm as a poroviscoelastic material formulated on the principles of nonlinear continuum mechanics, where we model the cytoplasm as a porous viscoelastic scaffold with an embedded viscous fluid flowing between the pores to model the cytosol. Baseline simulations (neglecting the viscosity of the cytosol) indicate that the system exhibits seven different regimes across the parameter space spanned by the viscoelastic relaxation timescale of the cytoskeleton and the poroelastic diffusion timescale; these regimes agree qualitatively with experimental measurements. Furthermore, the theoretical model also allows us to elucidate the additional role of pore fluid viscosity, which enters the system as a distinct viscous timescale. We show that increasing this viscous timescale hinders the passage of the pore fluid (reducing the poroelastic diffusion) and makes the cytoplasm rheology increasingly incompressible, shifting the phase boundaries between the regimes.
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Affiliation(s)
- Namshad Thekkethil
- School of Mathematics and Statistics, University of Glasgow, Glasgow, UK.
| | - Jakub Köry
- School of Mathematics and Statistics, University of Glasgow, Glasgow, UK
| | - Ming Guo
- Department of Mechanical Engineering, Massachusetts Institute of Technology, Cambridge, USA
| | - Peter S Stewart
- School of Mathematics and Statistics, University of Glasgow, Glasgow, UK
| | - Nicholas A Hill
- School of Mathematics and Statistics, University of Glasgow, Glasgow, UK
| | - Xiaoyu Luo
- School of Mathematics and Statistics, University of Glasgow, Glasgow, UK
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2
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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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3
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Pouliquen DL. The biophysics of water in cell biology: perspectives on a keystone for both marine sciences and cancer research. Front Cell Dev Biol 2024; 12:1403037. [PMID: 38803391 PMCID: PMC11128620 DOI: 10.3389/fcell.2024.1403037] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2024] [Accepted: 04/29/2024] [Indexed: 05/29/2024] Open
Abstract
The biophysics of water, has been debated over more than a century. Although its importance is still underestimated, significant breakthroughs occurred in recent years. The influence of protein condensation on water availability control was documented, new findings on water-transport proteins emerged, and the way water molecules rearrange to minimize free energy at interfaces was deciphered, influencing membrane thermodynamics. The state of knowledge continued to progress in the field of deep-sea marine biology, highlighting unknown effects of high hydrostatic pressure and/or temperature on interactions between proteins and ligands in extreme environments, and membrane structure adaptations. The role of osmolytes in protein stability control under stress is also discussed here in relation to fish egg hydration/buoyancy. The complexity of water movements within the cell is updated, all these findings leading to a better view of their impact on many cellular processes. The way water flow and osmotic gradients generated by ion transport work together to produce the driving force behind cell migration is also relevant to both marine biology and cancer research. Additional common points concern water dynamic changes during the neoplastic transformation of cells and tissues, or embryo development. This could improve imaging techniques, early cancer diagnosis, and understanding of the molecular and physiological basis of buoyancy for many marine species.
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Affiliation(s)
- Daniel L. Pouliquen
- Inserm, CNRS, CRCINA, Nantes Université, University of Angers, Angers, France
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4
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Pigozzi F. Pressure-Based Soft Agents. ARTIFICIAL LIFE 2024; 30:240-258. [PMID: 37987673 DOI: 10.1162/artl_a_00415] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2023]
Abstract
Biological agents have bodies that are composed mostly of soft tissue. Researchers have resorted to soft bodies to investigate Artificial Life (ALife)-related questions; similarly, a new era of soft-bodied robots has just begun. Nevertheless, because of their infinite degrees of freedom, soft bodies pose unique challenges in terms of simulation, control, and optimization. Herein I propose a novel soft-bodied agents formalism, namely, pressure-based soft agents (PSAs): spring-mass membranes containing a pressurized medium. Pressure endows the agents with structure, while springs and masses simulate softness and allow the agents to assume a large gamut of shapes. PSAs actuate both locally, by changing the resting lengths of springs, and globally, by modulating global pressure. I optimize the controller of PSAs for a locomotion task on hilly terrain, an escape task from a cage, and an object manipulation task. The results suggest that PSAs are indeed effective at the tasks, especially those requiring a shape change. I envision PSAs as playing a role in modeling soft-bodied agents, such as soft robots and biological cells.
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Affiliation(s)
- Federico Pigozzi
- University of Trieste Department of Engineering and Architecture.
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5
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Khang A, Nguyen Q, Feng X, Howsmon DP, Sacks MS. Three-dimensional analysis of hydrogel-imbedded aortic valve interstitial cell shape and its relation to contractile behavior. Acta Biomater 2023; 163:194-209. [PMID: 35085795 PMCID: PMC9309197 DOI: 10.1016/j.actbio.2022.01.039] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2021] [Revised: 01/11/2022] [Accepted: 01/18/2022] [Indexed: 12/31/2022]
Abstract
Cell-shape is a conglomerate of mechanical, chemical, and biological mechanisms that reflects the cell biophysical state. In a specific application, we consider aortic valve interstitial cells (AVICs), which maintain the structure and function of aortic heart valve leaflets. Actomyosin stress fibers help determine AVIC shape and facilitate processes such as adhesion, contraction, and mechanosensing. However, detailed 3D assessment of stress fiber architecture and function is currently impractical. Herein, we assessed AVIC shape and contractile behaviors using hydrogel-based 3D traction force microscopy to intuit the orientation and behavior of AVIC stress fibers. We utilized spherical harmonics (SPHARM) to quantify AVIC geometries through three days of incubation, which demonstrated a shift from a spherical shape to forming substantial protrusions. Furthermore, we assessed changes in post-three day AVIC shape and contractile function within two testing regimes: (1) normal contractile level to relaxation (cytochalasin D), and (2) normal contractile level to hyper-contraction (endothelin-1). In both scenarios, AVICs underwent isovolumic shape changes and produced complex displacement fields within the hydrogel. AVICs were more elongated when relaxed and more spherical in hyper-contraction. Locally, AVIC protrusions contracted along their long axis and expanded in their circumferential direction, indicating predominately axially aligned stress fibers. Furthermore, the magnitude of protrusion displacements was correlated with protrusion length and approached a consistent displacement plateau at a similar critical length across all AVICs. This implied that stress fiber behavior is conserved, despite great variations in AVIC shapes. We anticipate our findings will bolster future investigations into AVIC stress fiber architecture and function. STATEMENT OF SIGNIFICANCE: Within the aortic valve there exists a population of aortic valve interstitial cells, which orchestrate the turnover, secretion, and remodeling of its extracellular matrix, maintaining tissue integrity and ultimately sustaining the proper mechanical function. Alterations in these processes are thought to underlie diseases of the aortic valve, which affect hundreds of thousands domestically and world-wide. Yet, to date, there are no non-surgical treatments for aortic heart valve disease, in part due to our limited understanding of the underlying disease processes. In the present study, we built upon our previous study to include a full 3D analysis of aortic valve interstitial cell shapes at differing contractile levels. The resulting detailed shape and deformation analysis provided insight into the underlying stress-fiber structures and mechanical behaviors.
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Affiliation(s)
- Alex Khang
- James T. Willerson Center for Cardiovascular Modeling and Simulation, Oden Institute for Computational Engineering and Sciences and the Department of Biomedical Engineering, The University of Texas at Austin, 201 East 24th St, Stop C0200, Austin, TX 78712-1229, USA
| | - Quan Nguyen
- James T. Willerson Center for Cardiovascular Modeling and Simulation, Oden Institute for Computational Engineering and Sciences and the Department of Biomedical Engineering, The University of Texas at Austin, 201 East 24th St, Stop C0200, Austin, TX 78712-1229, USA
| | - Xinzeng Feng
- James T. Willerson Center for Cardiovascular Modeling and Simulation, Oden Institute for Computational Engineering and Sciences and the Department of Biomedical Engineering, The University of Texas at Austin, 201 East 24th St, Stop C0200, Austin, TX 78712-1229, USA
| | - Daniel P Howsmon
- James T. Willerson Center for Cardiovascular Modeling and Simulation, Oden Institute for Computational Engineering and Sciences and the Department of Biomedical Engineering, The University of Texas at Austin, 201 East 24th St, Stop C0200, Austin, TX 78712-1229, USA
| | - Michael S Sacks
- James T. Willerson Center for Cardiovascular Modeling and Simulation, Oden Institute for Computational Engineering and Sciences and the Department of Biomedical Engineering, The University of Texas at Austin, 201 East 24th St, Stop C0200, Austin, TX 78712-1229, USA.
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6
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Shaiken TE, Grimm SL, Siam M, Williams A, Rezaeian AH, Kraushaar D, Ricco E, Robertson MJ, Coarfa C, Jain A, Malovannaya A, Stossi F, Opekun AR, Price AP, Dubrulle J. Transcriptome, proteome, and protein synthesis within the intracellular cytomatrix. iScience 2023; 26:105965. [PMID: 36824274 PMCID: PMC9941065 DOI: 10.1016/j.isci.2023.105965] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2022] [Revised: 11/07/2022] [Accepted: 01/06/2023] [Indexed: 01/15/2023] Open
Abstract
Despite the knowledge that protein translation and various metabolic reactions that create and sustain cellular life occur in the cytoplasm, the structural organization within the cytoplasm remains unclear. Recent models indicate that cytoplasm contains viscous fluid and elastic solid phases. We separated these viscous fluid and solid elastic compartments, which we call the cytosol and cytomatrix, respectively. The distinctive composition of the cytomatrix included structural proteins, ribosomes, and metabolome enzymes. High-throughput analysis revealed unique biosynthetic pathways within the cytomatrix. Enrichment of biosynthetic pathways in the cytomatrix indicated the presence of immobilized biocatalysis. Enzymatic immobilization and segregation can surmount spatial impediments, and the local pathway segregation may form cytoplasmic organelles. Protein translation was reprogrammed within the cytomatrix under the restriction of protein synthesis by drug treatment. The cytosol and cytomatrix are an elaborately interconnected network that promotes operational flexibility in healthy cells and the survival of malignant cells.
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Affiliation(s)
- Tattym E. Shaiken
- Department of Medicine-Gastroenterology and Hepatology Section, Michael E DeBakey Veteran’s Affairs Medical Center, Baylor College of Medicine, Houston, TX 77030, USA
- PeriNuc Labs, University of Houston Technology Bridge, Houston, TX 77023, USA
| | - Sandra L. Grimm
- Advanced Technology Cores, Baylor College of Medicine, Houston, TX 77030, USA
| | - Mohamad Siam
- Department of Medicine-Gastroenterology and Hepatology Section, Michael E DeBakey Veteran’s Affairs Medical Center, Baylor College of Medicine, Houston, TX 77030, USA
- PeriNuc Labs, University of Houston Technology Bridge, Houston, TX 77023, USA
| | - Amanda Williams
- Department of Medicine-Gastroenterology and Hepatology Section, Michael E DeBakey Veteran’s Affairs Medical Center, Baylor College of Medicine, Houston, TX 77030, USA
- PeriNuc Labs, University of Houston Technology Bridge, Houston, TX 77023, USA
| | - Abdol-Hossein Rezaeian
- PeriNuc Labs, University of Houston Technology Bridge, Houston, TX 77023, USA
- Department of Drug Discovery and Biomedical Sciences, University of South Carolina, Columbia, SC 29208, USA
| | - Daniel Kraushaar
- Advanced Technology Cores, Baylor College of Medicine, Houston, TX 77030, USA
| | - Emily Ricco
- Advanced Technology Cores, Baylor College of Medicine, Houston, TX 77030, USA
| | | | - Cristian Coarfa
- Advanced Technology Cores, Baylor College of Medicine, Houston, TX 77030, USA
| | - Antrix Jain
- Advanced Technology Cores, Baylor College of Medicine, Houston, TX 77030, USA
| | - Anna Malovannaya
- Advanced Technology Cores, Baylor College of Medicine, Houston, TX 77030, USA
| | - Fabio Stossi
- Advanced Technology Cores, Baylor College of Medicine, Houston, TX 77030, USA
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Antone R. Opekun
- Department of Medicine-Gastroenterology and Hepatology Section, Michael E DeBakey Veteran’s Affairs Medical Center, Baylor College of Medicine, Houston, TX 77030, USA
- Department of Pediatrics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Alyssa P. Price
- Department of Medicine-Gastroenterology and Hepatology Section, Michael E DeBakey Veteran’s Affairs Medical Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Julien Dubrulle
- Advanced Technology Cores, Baylor College of Medicine, Houston, TX 77030, USA
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7
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Phosphorescent Ir(III) Complexes for Biolabeling and Biosensing. Top Curr Chem (Cham) 2022; 380:35. [PMID: 35948820 DOI: 10.1007/s41061-022-00389-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2021] [Accepted: 05/27/2022] [Indexed: 10/15/2022]
Abstract
Cyclometalated Ir(III) complexes exhibit strong phosphorescence emission with lifetime of submicroseconds to several microseconds at room temperature. Their synthetic versatility enables broad control of physical properties, such as charge and lipophilicity, as well as emission colors. These favorable properties have motivated the use of Ir(III) complexes in luminescent bioimaging applications. This review examines the recent progress in the development of phosphorescent biolabels and sensors based on Ir(III) complexes. It begins with a brief introduction about the basic principles of the syntheses and photophysical processes of cyclometalated Ir(III) complexes. Focus is placed on illustrating the broad imaging utility of Ir(III) complexes. Phosphorescent labels illuminating intracellular organelles, including mitochondria, lysosomes, and cell membranes, are summarized. Ir(III) complexes capable of visualization of tumor spheroids and parasites are also introduced. Facile chemical modification of the cyclometalating ligands endows the Ir(III) complexes with strong sensing ability. Sensors of temperature, pH, CO2, metal ions, anions, biosulfur species, reactive oxygen species, peptides, and viscosity have recently been added to the molecular imaging tools. This diverse utility demonstrates the potential of phosphorescent Ir(III) complexes toward bioimaging applications.
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8
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Pawełkowicz ME, Skarzyńska A, Koter MD, Turek S, Pląder W. miRNA Profiling and Its Role in Multi-Omics Regulatory Networks Connected with Somaclonal Variation in Cucumber ( Cucumis sativus L.). Int J Mol Sci 2022; 23:ijms23084317. [PMID: 35457133 PMCID: PMC9031375 DOI: 10.3390/ijms23084317] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2022] [Revised: 04/10/2022] [Accepted: 04/11/2022] [Indexed: 01/27/2023] Open
Abstract
The role of miRNAs in connection with the phenomenon of somaclonal variation, which occurs during plant in vitro culture, remains uncertain. This study aims to investigate the possible role of miRNAs in multi-omics regulatory pathways in cucumber somaclonal lines. For this purpose, we performed sRNA sequencing (sRNA-seq) from cucumber fruit samples identified 8, 10 and 44 miRNAs that are differentially expressed between somaclones (S1, S2, S3 lines) and the reference B10 line of Cucumis sativus. For miRNA identification, we use ShortStack software designed to filter miRNAs from sRNAs according to specific program criteria. The identification of predicted in-silico targets revealed 2,886 mRNAs encoded by 644 genes. The functional annotation of miRNA's target genes and gene ontology classification revealed their association with metabolic processes, response to stress, multicellular organism development, biosynthetic process and catalytic activity. We checked with bioinformatic analyses for possible interactions at the level of target proteins, differentially expressed genes (DEGs) and genes affected by genomic polymorphisms. We assume that miRNAs can indirectly influence molecular networks and play a role in many different regulatory pathways, leading to somaclonal variation. This regulation is supposed to occur through the process of the target gene cleavage or translation inhibition, which in turn affects the proteome, as we have shown in the example of molecular networks. This is a new approach combining levels from DNA-seq through mRNA-seq, sRNA-seq and in silico PPI in the area of plants' somaclonal variation.
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9
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Psarianos M, Dimopoulos G, Ojha S, Cavini ACM, Bußler S, Taoukis P, Schlüter OK. Effect of pulsed electric fields on cricket (Acheta domesticus) flour: Extraction yield (protein, fat and chitin) and techno-functional properties. INNOV FOOD SCI EMERG 2022. [DOI: 10.1016/j.ifset.2021.102908] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
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10
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Li D, Zhu Z, Sun DW. Visualization of the in situ distribution of contents and hydrogen bonding states of cellular level water in apple tissues by confocal Raman microscopy. Analyst 2020; 145:897-907. [PMID: 31820748 DOI: 10.1039/c9an01743g] [Citation(s) in RCA: 43] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Raman spectroscopy has been employed for studying the hydrogen bonding states of water molecules for decades, however, Raman imaging data contain thousands of spectra, making it challenging to obtain information on water with different hydrogen bonds. In the current study, a novel method combining confocal Raman microscopy (CRM) imaging with the iterative curve fitting algorithms was developed to determine the distribution of water contents at the cellular level and water states with different hydrogen bonds in apple tissues. Raman imaging data ranging from 2700 to 3800 cm-1 were acquired from whole cells in the apple tissue, which were then decomposed into seven sub-peaks using the fixed-position Gaussian iterative curve fitting (FPGICF) algorithm. The content and hydrogen bonding states of cellular water were calculated as the area sum of the OH stretching vibration and the area ratio of DA-OH over DDAA-OH stretching vibration or the number of hydrogen bonds of each water molecule, respectively. Finally, the area of each sub-peak, the area sum of the OH stretching vibration, and the area ratio of DA-OH over DDAA-OH stretching vibration were used to visualize the distribution of each sub-peak, water contents and water states with different hydrogen bonds, respectively. In addition, it was found that the number of hydrogen bonds of each water molecule could also be considered as a criterion to describe the hydrogen bond states of water in apple tissues. The availability of such information should provide new insights for future study of cellular water in other food materials.
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Affiliation(s)
- Dongmei Li
- School of Food Science and Engineering, South China University of Technology, Guangzhou 510641, China.
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11
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Durrani MK, Kang J. Transition-state theory-based analysis of diffusion of water in yeast cells. FEMS Microbiol Lett 2020; 367:5909596. [PMID: 33000144 DOI: 10.1093/femsle/fnaa155] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2020] [Accepted: 09/17/2020] [Indexed: 11/14/2022] Open
Affiliation(s)
- Mehvish K Durrani
- Department of Biology, Valdosta State University, 1500 N. Patterson St., Valdosta, GA 31698, USA
| | - Jonghoon Kang
- Department of Biology, Valdosta State University, 1500 N. Patterson St., Valdosta, GA 31698, USA
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12
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Huang H, Dai C, Shen H, Gu M, Wang Y, Liu J, Chen L, Sun L. Recent Advances on the Model, Measurement Technique, and Application of Single Cell Mechanics. Int J Mol Sci 2020; 21:E6248. [PMID: 32872378 PMCID: PMC7504142 DOI: 10.3390/ijms21176248] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2020] [Revised: 08/19/2020] [Accepted: 08/27/2020] [Indexed: 02/06/2023] Open
Abstract
Since the cell was discovered by humans, it has been an important research subject for researchers. The mechanical response of cells to external stimuli and the biomechanical response inside cells are of great significance for maintaining the life activities of cells. These biomechanical behaviors have wide applications in the fields of disease research and micromanipulation. In order to study the mechanical behavior of single cells, various cell mechanics models have been proposed. In addition, the measurement technologies of single cells have been greatly developed. These models, combined with experimental techniques, can effectively explain the biomechanical behavior and reaction mechanism of cells. In this review, we first introduce the basic concept and biomechanical background of cells, then summarize the research progress of internal force models and experimental techniques in the field of cell mechanics and discuss the latest mechanical models and experimental methods. We summarize the application directions of cell mechanics and put forward the future perspectives of a cell mechanics model.
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Affiliation(s)
| | | | | | | | | | - Jizhu Liu
- School of Mechanical and Electric Engineering, Jiangsu Provincial Key Laboratory of Advanced Robotics, Soochow University, Suzhou 215123, China; (H.H.); (C.D.); (H.S.); (M.G.); (Y.W.); (L.S.)
| | - Liguo Chen
- School of Mechanical and Electric Engineering, Jiangsu Provincial Key Laboratory of Advanced Robotics, Soochow University, Suzhou 215123, China; (H.H.); (C.D.); (H.S.); (M.G.); (Y.W.); (L.S.)
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13
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Shaikh S, Wang Y, ur Rehman F, Jiang H, Wang X. Phosphorescent Ir (III) complexes as cellular staining agents for biomedical molecular imaging. Coord Chem Rev 2020. [DOI: 10.1016/j.ccr.2020.213344] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
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14
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Aboulwafa M, Zhang Z, Saier MH. Protein:Protein interactions in the cytoplasmic membrane apparently influencing sugar transport and phosphorylation activities of the e. coli phosphotransferase system. PLoS One 2019; 14:e0219332. [PMID: 31751341 PMCID: PMC6872149 DOI: 10.1371/journal.pone.0219332] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2019] [Accepted: 10/13/2019] [Indexed: 01/05/2023] Open
Abstract
The multicomponent phosphoenolpyruvate (PEP)-dependent sugar-transporting phosphotransferase system (PTS) in Escherichia coli takes up sugar substrates from the medium and concomitantly phosphorylates them, releasing sugar phosphates into the cytoplasm. We have recently provided evidence that many of the integral membrane PTS permeases interact with the fructose PTS (FruA/FruB) [1]. However, the biochemical and physiological significance of this finding was not known. We have carried out molecular genetic/biochemical/physiological studies that show that interactions of the fructose PTS often enhance, but sometimes inhibit the activities of other PTS transporters many fold, depending on the target PTS system under study. Thus, the glucose (Glc), mannose (Man), mannitol (Mtl) and N-acetylglucosamine (NAG) permeases exhibit enhanced in vivo sugar transport and sometimes in vitro PEP-dependent sugar phosphorylation activities while the galactitol (Gat) and trehalose (Tre) systems show inhibited activities. This is observed when the fructose system is induced to high levels and prevented when the fruA/fruB genes are deleted. Overexpression of the fruA and/or fruB genes in the absence of fructose induction during growth also enhances the rates of uptake of other hexoses. The β-galactosidase activities of man, mtl, and gat-lacZ transcriptional fusions and the sugar-specific transphosphorylation activities of these enzyme transporters were not affected either by frustose induction or by fruAB overexpression, showing that the rates of synthesis of the target PTS permeases were not altered. We thus suggest that specific protein-protein interactions within the cytoplasmic membrane regulate transport in vivo (and sometimes the PEP-dependent phosphorylation activities in vitro) of PTS permeases in a physiologically meaningful way that may help to provide a hierarchy of preferred PTS sugars. These observations appear to be applicable in principle to other types of transport systems as well.
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Affiliation(s)
- Mohammad Aboulwafa
- Department of Molecular Biology, Division of Biological Sciences, University of California at San Diego, La Jolla, CA, United States of America
- Department of Microbiology and Immunology, Faculty of Pharmacy, Ain Shams University, Abbassia, Cairo, Egypt
| | - Zhongge Zhang
- Department of Molecular Biology, Division of Biological Sciences, University of California at San Diego, La Jolla, CA, United States of America
| | - Milton H. Saier
- Department of Molecular Biology, Division of Biological Sciences, University of California at San Diego, La Jolla, CA, United States of America
- * E-mail:
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15
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Foglia F, Hazael R, Meersman F, Wilding MC, Sakai VG, Rogers S, Bove LE, Koza MM, Moulin M, Haertlein M, Forsyth VT, McMillan PF. In Vivo Water Dynamics in Shewanella oneidensis Bacteria at High Pressure. Sci Rep 2019; 9:8716. [PMID: 31213614 PMCID: PMC6581952 DOI: 10.1038/s41598-019-44704-3] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2019] [Accepted: 05/15/2019] [Indexed: 11/10/2022] Open
Abstract
Following observations of survival of microbes and other life forms in deep subsurface environments it is necessary to understand their biological functioning under high pressure conditions. Key aspects of biochemical reactions and transport processes within cells are determined by the intracellular water dynamics. We studied water diffusion and rotational relaxation in live Shewanella oneidensis bacteria at pressures up to 500 MPa using quasi-elastic neutron scattering (QENS). The intracellular diffusion exhibits a significantly greater slowdown (by −10–30%) and an increase in rotational relaxation times (+10–40%) compared with water dynamics in the aqueous solutions used to resuspend the bacterial samples. Those results indicate both a pressure-induced viscosity increase and slowdown in ionic/macromolecular transport properties within the cells affecting the rates of metabolic and other biological processes. Our new data support emerging models for intracellular organisation with nanoscale water channels threading between macromolecular regions within a dynamically organized structure rather than a homogenous gel-like cytoplasm.
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Affiliation(s)
- Fabrizia Foglia
- Chemistry Department, Christopher Ingold Laboratories, University College London, 20 Gordon Street, London, WC1H 0AJ, UK.
| | - Rachael Hazael
- Survivability and Advanced Materials group, Centre for Defence Engineering, Cranfield University at the Defence Academy of the UK, Shrivenham, SN6 8LA, UK
| | - Filip Meersman
- Chemistry Department, Christopher Ingold Laboratories, University College London, 20 Gordon Street, London, WC1H 0AJ, UK.,Biomolecular & Analytical Mass Spectrometry, Department of Chemistry, University of Antwerp, Groenenborgerlaan 171, B-2020, Antwerp, Belgium
| | - Martin C Wilding
- Materials Engineering, Sheffield Hallam University, Howard Street, Sheffield, S1 1WB, UK
| | | | - Sarah Rogers
- ISIS Neutron and Muon Source, Rutherford Appleton Laboratory, Chilton, OX11 0QX, UK
| | - Livia E Bove
- Dipartimento di Fisica, Università di Roma "La Sapienza", 00185, Roma, Italy.,Institut de Minéralogie, de Physique des Matériaux et de Cosmochimie, CNRS UMR 7590, Université Pierre et Marie Curie, F-75252, Paris, France
| | - Michael Marek Koza
- Institut Laue Langevin, 6 Rue Jules Horowitz, BP 156, 38042, Grenoble, Cedex, France
| | - Martine Moulin
- Life Sciences Group, Carl-Ivar Brändén Building, Institut Laue-Langevin, 71 avenue des Martyrs, 38042, Grenoble, cedex 9, France
| | - Michael Haertlein
- Life Sciences Group, Carl-Ivar Brändén Building, Institut Laue-Langevin, 71 avenue des Martyrs, 38042, Grenoble, cedex 9, France
| | - V Trevor Forsyth
- Life Sciences Group, Carl-Ivar Brändén Building, Institut Laue-Langevin, 71 avenue des Martyrs, 38042, Grenoble, cedex 9, France.,Faculty of Natural Sciences/ISTM, Keele University, Staffordshire, ST5 5BG, UK
| | - Paul F McMillan
- Chemistry Department, Christopher Ingold Laboratories, University College London, 20 Gordon Street, London, WC1H 0AJ, UK.
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16
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Toxvaerd S. A Prerequisite for Life. J Theor Biol 2019; 474:48-51. [PMID: 31059714 DOI: 10.1016/j.jtbi.2019.05.001] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2018] [Revised: 03/28/2019] [Accepted: 05/02/2019] [Indexed: 11/28/2022]
Abstract
The complex physicochemical structures and chemical reactions in living organism have some common features: (1) The life processes take place in the cytosol in the cells, which, from a physicochemical point of view is an emulsion of biomolecules in a dilute aqueous suspension. (2) All living systems are homochiral with respect to the units of amino acids and carbohydrates, but (some) proteins are chiral unstable in the cytosol. (3) And living organism are mortal. These three common features together give a prerequisite for the prebiotic self-assembly at the start of the Abiogenesis. Here we argue, that it all together indicates, that the prebiotic self-assembly of structures and reactions took place in a more saline environment, whereby the homochirality of proteins not only could be obtained, but also preserved. A more saline environment for the prebiotic self-assembly of organic molecules and establishment of biochemical reactions could have been the hydrothermal vents.
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Affiliation(s)
- Søren Toxvaerd
- Department of Science and Environment, Roskilde University, Postbox 260, Roskilde DK-4000, Denmark.
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17
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Ruggiero MR, Baroni S, Pezzana S, Ferrante G, Geninatti Crich S, Aime S. Evidence for the Role of Intracellular Water Lifetime as a Tumour Biomarker Obtained by In Vivo Field-Cycling Relaxometry. Angew Chem Int Ed Engl 2018; 57:7468-7472. [PMID: 29575414 PMCID: PMC6175164 DOI: 10.1002/anie.201713318] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2017] [Revised: 02/15/2018] [Indexed: 12/11/2022]
Abstract
It was established through in vivo T1 measurements at low magnetic fields that tumour cells display proton T1 values that are markedly longer than those shown by healthy tissue. Moreover, it has been found that the elongation of T1 parallels the aggressiveness of the investigated tumour. The T1 lengthening is associated with an enhanced water exchange rate across the transcytolemmal membrane through an overexpression/upregulation of GLUT1 and Na+ /K+ ATPase transporters. It follows that the intracellular water lifetime represents a hallmark of tumour cells that can be easily monitored by measuring T1 at different magnetic field strengths ranging from 0.2 to 200 mT.
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Affiliation(s)
- Maria Rosaria Ruggiero
- Department Molecular Biotechnology and Health SciencesUniversity of Torinovia Nizza 52TorinoItaly
| | - Simona Baroni
- Department Molecular Biotechnology and Health SciencesUniversity of Torinovia Nizza 52TorinoItaly
| | - Stefania Pezzana
- Department Molecular Biotechnology and Health SciencesUniversity of Torinovia Nizza 52TorinoItaly
| | | | | | - Silvio Aime
- Department Molecular Biotechnology and Health SciencesUniversity of Torinovia Nizza 52TorinoItaly
- IBB-CNRvia Nizza 52TorinoItaly
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18
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Ruggiero MR, Baroni S, Pezzana S, Ferrante G, Geninatti Crich S, Aime S. Evidence for the Role of Intracellular Water Lifetime as a Tumour Biomarker Obtained by In Vivo Field-Cycling Relaxometry. Angew Chem Int Ed Engl 2018. [DOI: 10.1002/ange.201713318] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Affiliation(s)
- Maria Rosaria Ruggiero
- Department Molecular Biotechnology and Health Sciences; University of Torino; via Nizza 52 Torino Italy
| | - Simona Baroni
- Department Molecular Biotechnology and Health Sciences; University of Torino; via Nizza 52 Torino Italy
| | - Stefania Pezzana
- Department Molecular Biotechnology and Health Sciences; University of Torino; via Nizza 52 Torino Italy
| | | | - Simonetta Geninatti Crich
- Department Molecular Biotechnology and Health Sciences; University of Torino; via Nizza 52 Torino Italy
| | - Silvio Aime
- Department Molecular Biotechnology and Health Sciences; University of Torino; via Nizza 52 Torino Italy
- IBB-CNR; via Nizza 52 Torino Italy
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Abstract
Quantitative magnetic resonance imaging can be combined with advanced biophysical models to measure microstructural features of white matter. Non-invasive microstructural imaging has the potential to revolutionize neuroscience, and acquiring these measures in clinically feasible times would greatly improve patient monitoring and clinical studies of drug efficacy. However, a good understanding of microstructural imaging techniques is essential to set realistic expectations and to prevent over-interpretation of results. This review explains the methodology behind microstructural modeling and imaging, and gives an overview of the breakthroughs and challenges associated with it.
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21
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Higher impact energy in traumatic brain injury interferes with noncovalent and covalent bonds resulting in cytotoxic brain tissue edema as measured with computational simulation. Acta Neurochir (Wien) 2015; 157:639-48; discussion 648. [PMID: 25686919 DOI: 10.1007/s00701-015-2368-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2014] [Accepted: 01/29/2015] [Indexed: 10/24/2022]
Abstract
BACKGROUND Cytotoxic brain tissue edema is a complicated secondary consequence of ischemic injury following cerebral diseases such as traumatic brain injury and stroke. To some extent the pathophysiological mechanisms are known, but far from completely. In this study, a hypothesis is proposed in which protein unfolding and perturbation of nucleotide structures participate in the development of cytotoxic edema following traumatic brain injury (TBI). METHODS An advanced computational simulation model of the human head was used to simulate TBI. The consequences of kinetic energy transfer following an external dynamic impact were analyzed including the intracranial pressure (ICP), strain level, and their potential influences on the noncovalent and covalent bonds in folded protein structures. RESULTS The result shows that although most of the transferred kinetic energy is absorbed in the skin and three bone layers, there is a substantial amount of energy reaching the gray and white matter. The kinetic energy from an external dynamic impact has the theoretical potential to interfere not only with noncovalent but also covalent bonds when high enough. The induced mechanical strain and pressure may further interfere with the proteins, which accumulate water molecules into the interior of the hydrophobic structures of unfolded proteins. Simultaneously, the noncovalent energy-rich bonds in nucleotide adenosine-triphosphates may be perturbed as well. CONCLUSIONS Based on the analysis of the numerical simulation data, the kinetic energy from an external dynamic impact has the theoretical potential to interfere not only with noncovalent, but also with covalent bonds when high enough. The subsequent attraction of increased water molecules into the unfolded protein structures and disruption of adenosine-triphosphate bonds could to some extent explain the etiology to cytotoxic edema.
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22
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Salt and osmosensing: role of cytoplasmic hydrogel. Pflugers Arch 2015; 467:475-87. [DOI: 10.1007/s00424-014-1680-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2014] [Revised: 12/17/2014] [Accepted: 12/18/2014] [Indexed: 12/30/2022]
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23
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Khitrin A, Khitrin K, Model M. A model for membrane potential and intracellular ion distribution. Chem Phys Lipids 2014; 184:76-81. [DOI: 10.1016/j.chemphyslip.2014.10.005] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2014] [Revised: 10/27/2014] [Accepted: 10/31/2014] [Indexed: 10/24/2022]
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24
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Model MA. Possible causes of apoptotic volume decrease: an attempt at quantitative review. Am J Physiol Cell Physiol 2014; 306:C417-24. [DOI: 10.1152/ajpcell.00328.2013] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Cell shrinkage and dehydration are essential characteristics of apoptosis, and loss of as much as half of the initial cell volume is not uncommon. This phenomenon is usually explained by efflux of K+and Cl−. We reexamine this hypothesis on the basis of the available data for ion concentrations and the requirements for osmotic equilibrium and electroneutrality. In addition to ion loss, we discuss the possible impacts of several other processes: efflux of low-molecular-weight osmolytes, acidification of the cytosol, effects of water channels and pumps, heterogeneity of intracellular water, and dissociation of apoptotic bodies. We conclude that most mammalian cells are theoretically capable of reducing their volume by 15–20% through ion loss or a decrease in cytosolic pH, although, in reality, the contribution of these mechanisms to apoptotic shrinkage may be smaller. Transitions between osmotically active and inactive water pools might influence cell volume as well; these mechanisms are poorly understood but are amenable to experimental study. Dissociation of apoptotic bodies is a separate mechanism of volume reduction and should be monitored closely; this can be best achieved by measurement of intracellular water, rather than cell volume.
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Affiliation(s)
- Michael A. Model
- Department of Biological Sciences, Kent State University, Kent, Ohio
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25
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Plankar M, Brežan S, Jerman I. The principle of coherence in multi-level brain information processing. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 2012; 111:8-29. [PMID: 22986048 DOI: 10.1016/j.pbiomolbio.2012.08.006] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/13/2012] [Accepted: 08/02/2012] [Indexed: 02/03/2023]
Abstract
Synchronisation has become one of the major scientific tools to explain biological order at many levels of organisation. In systems neuroscience, synchronised subthreshold and suprathreshold oscillatory neuronal activity within and between distributed neuronal assemblies is acknowledged as a fundamental mode of neuronal information processing. Coherent neuronal oscillations correlate with all basic cognitive functions, mediate local and long-range neuronal communication and affect synaptic plasticity. However, it remains unclear how the very fast and complex changes of functional neuronal connectivity necessary for cognition, as mediated by dynamic patterns of neuronal synchrony, could be explained exclusively based on the well-established synaptic mechanisms. A growing body of research indicates that the intraneuronal matrix, composed of cytoskeletal elements and their binding proteins, structurally and functionally connects the synapses within a neuron, modulates neurotransmission and memory consolidation, and is hypothesised to be involved in signal integration via electric signalling due to its charged surface. Theoretical modelling, as well as emerging experimental evidence indicate that neuronal cytoskeleton supports highly cooperative energy transport and information processing based on molecular coherence. We suggest that long-range coherent dynamics within the intra- and extracellular filamentous matrices could establish dynamic ordered states, capable of rapid modulations of functional neuronal connectivity via their interactions with neuronal membranes and synapses. Coherence may thus represent a common denominator of neurophysiological and biophysical approaches to brain information processing, operating at multiple levels of neuronal organisation, from which cognition may emerge as its cardinal manifestation.
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Affiliation(s)
- Matej Plankar
- BION Institute, Stegne 21, 1000 Ljubljana, Slovenia.
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26
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The molecular stoichiometric hydration model (SHM) as applied to tendon/collagen, globular proteins and cells. Cell Biol Int 2011; 35:1205-15. [DOI: 10.1042/cbi20090226] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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27
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Spitzer J. From water and ions to crowded biomacromolecules: in vivo structuring of a prokaryotic cell. Microbiol Mol Biol Rev 2011; 75:491-506, second page of table of contents. [PMID: 21885682 PMCID: PMC3165543 DOI: 10.1128/mmbr.00010-11] [Citation(s) in RCA: 60] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The interactions and processes which structure prokaryotic cytoplasm (water, ions, metabolites, and biomacromolecules) and ensure the fidelity of the cell cycle are reviewed from a physicochemical perspective. Recent spectroscopic and biological evidence shows that water has no active structuring role in the cytoplasm, an unnecessary notion still entertained in the literature; water acts only as a normal solvent and biochemical reactant. Subcellular structuring arises from localizations and interactions of biomacromolecules and from the growth and modifications of their surfaces by catalytic reactions. Biomacromolecular crowding is a fundamental physicochemical characteristic of cells in vivo. Though some biochemical and physiological effects of crowding (excluded volume effect) have been documented, crowding assays with polyglycols, dextrans, etc., do not properly mimic the compositional variety of biomacromolecules in vivo. In vitro crowding assays are now being designed with proteins, which better reflect biomacromolecular environments in vivo, allowing for hydrophobic bonding and screened electrostatic interactions. I elaborate further the concept of complex vectorial biochemistry, where crowded biomacromolecules structure the cytosol into electrolyte pathways and nanopools that electrochemically "wire" the cell. Noncovalent attractions between biomacromolecules transiently supercrowd biomacromolecules into vectorial, semiconducting multiplexes with a high (35 to 95%)-volume fraction of biomacromolecules; consequently, reservoirs of less crowded cytosol appear in order to maintain the experimental average crowding of ∼25% volume fraction. This nonuniform crowding model allows for fast diffusion of biomacromolecules in the uncrowded cytosolic reservoirs, while the supercrowded vectorial multiplexes conserve the remarkable repeatability of the cell cycle by preventing confusing cross talk of concurrent biochemical reactions.
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Affiliation(s)
- Jan Spitzer
- Mallard Creek Polymers, Inc., 14700 Mallard Creek Road, Charlotte, NC 28262, USA.
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28
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Plankar M, Jerman I, Krašovec R. On the origin of cancer: Can we ignore coherence? PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 2011; 106:380-90. [DOI: 10.1016/j.pbiomolbio.2011.04.001] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/17/2011] [Accepted: 04/09/2011] [Indexed: 01/06/2023]
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29
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Qvist J, Persson E, Mattea C, Halle B. Time scales of water dynamics at biological interfaces: peptides, proteins and cells. Faraday Discuss 2009; 141:131-44; discussion 175-207. [PMID: 19227355 DOI: 10.1039/b806194g] [Citation(s) in RCA: 107] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Water 2H and 17O spin relaxation is used to study water dynamics in the hydration layers of two small peptides, two globular proteins and in living cells of two microorganisms. The dynamical heterogeneity of hydration water is characterized by performing relaxation measurements over a wide temperature range, extending deeply into the supercooled regime, or by covering a wide frequency range. Protein hydration layers can be described by a power-law distribution of rotational correlation times with an exponent close to 2. This distribution comprises a small fraction of protein-specific hydration sites, where water rotation is strongly retarded, and a dominant fraction of generic hydration sites, where water rotation is as fast as in the hydration shells of small peptides. The generic dynamic perturbation factor is less than 2 at room temperature and exhibits a maximum near 260 K. The dynamic perturbation is induced by H-bond constraints that interfere with the cooperative mechanism that facilitates rotation in bulk water. Because these constraints are temperature-independent, hydration water does not follow the super-Arrhenius temperature dependence of bulk water. Water in living cells behaves as expected from studies of simpler model systems, the only difference being a larger fraction of secluded (strongly perturbed) hydration sites associated with the supramolecular organization in the cell. Intracellular water that is not in direct contact with biopolymers has essentially the same dynamics as bulk water. There is no significant difference in cell water dynamics between mesophilic and halophilic organisms, despite the high K+ and Na+ concentrations in the latter.
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Affiliation(s)
- Johan Qvist
- Center for Molecular Protein Science, Department of Biophysical Chemistry, Lund University, SE-22100 Lund, Sweden
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Morán-Zorzano MT, Montero M, Muñoz FJ, Alonso-Casajús N, Viale AM, Eydallin G, Sesma MT, Baroja-Fernández E, Pozueta-Romero J. Cytoplasmic Escherichia coli ADP sugar pyrophosphatase binds to cell membranes in response to extracellular signals as the cell population density increases. FEMS Microbiol Lett 2009; 288:25-32. [PMID: 18778276 DOI: 10.1111/j.1574-6968.2008.01319.x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022] Open
Abstract
ADP sugar pyrophosphatase (AspP) is a member of the 'Nudix' (Nucleoside diphosphate linked to some other moiety X) hydrolase family of enzymes that catalyzes the hydrolytic breakdown of ADP-glucose (ADPG) linked to glycogen biosynthesis. In a previous work, we showed that AspP activity is strongly enhanced by both glucose-1,6-bisphosphate and nucleotide-sugars, and by macromolecular crowding. In this work, we show that AspP binds to cell membranes as the bacterial population density increases, c. 30% of the total enzyme remaining membrane associated as glycogen depletes during the stationary phase. This process is not dependent on the stationary transcription factor RpoS, the producer of the bacterial quorum-sensing autoinducer 2 (LuxS), the presence of glycogen granules or glucose availability, but is stimulated by small soluble heat-labile molecule(s) occurring in cell-free spent supernatants of stationary cultures that are acid stabile and base labile. These data further point to AspP as a highly regulated enzyme, and provide a first set of evidences indicating that glycogen metabolism is subjected to regulation by intercellular communication in Escherichia coli.
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Kurz M. Compatible solute influence on nucleic acids: many questions but few answers. SALINE SYSTEMS 2008; 4:6. [PMID: 18522725 PMCID: PMC2430576 DOI: 10.1186/1746-1448-4-6] [Citation(s) in RCA: 52] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/21/2008] [Accepted: 06/03/2008] [Indexed: 12/21/2022]
Abstract
Compatible solutes are small organic osmolytes including but not limited to sugars, polyols, amino acids, and their derivatives. They are compatible with cell metabolism even at molar concentrations. A variety of organisms synthesize or take up compatible solutes for adaptation to extreme environments. In addition to their protective action on whole cells, compatible solutes display significant effects on biomolecules in vitro. These include stabilization of native protein and nucleic acid structures. They are used as additives in polymerase chain reactions to increase product yield and specificity, but also in other nucleic acid and protein applications. Interactions of compatible solutes with nucleic acids and protein-nucleic acid complexes are much less understood than the corresponding interactions of compatible solutes with proteins. Although we may begin to understand solute/nucleic acid interactions there are only few answers to the many questions we have. I summarize here the current state of knowledge and discuss possible molecular mechanisms and thermodynamics.
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Affiliation(s)
- Matthias Kurz
- Institut für Mikrobiologie & Biotechnologie, Rheinische Friedrich Wilhelms-Universität Bonn, Bonn, Germany.
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33
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Abstract
Water-biomolecule interactions have been extensively studied in dilute solutions, crystals, and rehydrated powders, but none of these model systems may capture the behavior of water in the highly organized intracellular milieu. Because of the experimental difficulty of selectively probing the structure and dynamics of water in intact cells, radically different views about the properties of cell water have proliferated. To resolve this long-standing controversy, we have measured the (2)H spin relaxation rate in living bacteria cultured in D(2)O. The relaxation data, acquired in a wide magnetic field range (0.2 mT-12 T) and analyzed in a model-independent way, reveal water dynamics on a wide range of time scales. Contradicting the view that a substantial fraction of cell water is strongly perturbed, we find that approximately 85% of cell water in Escherichia coli and in the extreme halophile Haloarcula marismortui has bulk-like dynamics. The remaining approximately 15% of cell water interacts directly with biomolecular surfaces and is motionally retarded by a factor 15 +/- 3 on average, corresponding to a rotational correlation time of 27 ps. This dynamic perturbation is three times larger than for small monomeric proteins in solution, a difference we attribute to secluded surface hydration sites in supramolecular assemblies. The relaxation data also show that a small fraction ( approximately 0.1%) of cell water exchanges from buried hydration sites on the microsecond time scale, consistent with the current understanding of protein hydration in solutions and crystals.
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