1
|
Neusch A, Wiedwald U, Novoselova IP, Kuckla DA, Tetos N, Sadik S, Hagemann P, Farle M, Monzel C. Semisynthetic ferritin-based nanoparticles with high magnetic anisotropy for spatial magnetic manipulation and inductive heating. NANOSCALE 2024; 16:15113-15127. [PMID: 39054876 DOI: 10.1039/d4nr01652a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/27/2024]
Abstract
The human iron storage protein ferritin represents an appealing template to obtain a semisynthetic magnetic nanoparticle (MNP) for spatial manipulation or inductive heating applications on a nanoscale. Ferritin consists of a protein cage of well-defined size (12 nm), which is genetically modifiable and biocompatible, and into which a magnetic core is synthesised. Here, we probed the magnetic response and hence the MNP's suitability for (bio-)nanotechnological or nanomedical applications when the core is doped with 7% cobalt or 7% zinc in comparison with the undoped iron oxide MNP. The samples exhibit almost identical core and hydrodynamic sizes, along with their tunable magnetic core characteristics as verified by structural and magnetic characterisation. Cobalt doping significantly increased the MNP's anisotropy and hence the heating power in comparison with other magnetic cores with potential application as a mild heat mediator. Spatial magnetic manipulation was performed with MNPs inside droplets, the cell cytoplasm, or the cell nucleus, where the MNP surface conjugation with mEGFP and poly(ethylene glycol) gave rise to excellent intracellular stability and traceability within the complex biological environment. A magnetic stimulus (smaller than fN forces) results in the quick and reversible redistribution of the MNPs. The obtained data suggest that semisynthetic ferritin MNPs are highly versatile nanoagents and promising candidates for theranostic or (bio-)nanotechnological applications.
Collapse
Affiliation(s)
- Andreas Neusch
- Experimental Medical Physics, Heinrich-Heine University Düsseldorf, 40225 Düsseldorf, Germany.
| | - Ulf Wiedwald
- Faculty of Physics and Center for Nanointegration (CENIDE), University of Duisburg-Essen, 47057 Duisburg, Germany
| | - Iuliia P Novoselova
- Experimental Medical Physics, Heinrich-Heine University Düsseldorf, 40225 Düsseldorf, Germany.
| | - Daniel A Kuckla
- Experimental Medical Physics, Heinrich-Heine University Düsseldorf, 40225 Düsseldorf, Germany.
| | - Nikolaos Tetos
- Faculty of Physics and Center for Nanointegration (CENIDE), University of Duisburg-Essen, 47057 Duisburg, Germany
| | - Sarah Sadik
- Experimental Medical Physics, Heinrich-Heine University Düsseldorf, 40225 Düsseldorf, Germany.
| | - Philipp Hagemann
- Experimental Medical Physics, Heinrich-Heine University Düsseldorf, 40225 Düsseldorf, Germany.
| | - Michael Farle
- Faculty of Physics and Center for Nanointegration (CENIDE), University of Duisburg-Essen, 47057 Duisburg, Germany
| | - Cornelia Monzel
- Experimental Medical Physics, Heinrich-Heine University Düsseldorf, 40225 Düsseldorf, Germany.
| |
Collapse
|
2
|
Speckner K, Rehfeldt F, Weiss M. Intermittent subdiffusion of short nuclear actin rods due to interactions with chromatin. Phys Rev E 2024; 110:014406. [PMID: 39160992 DOI: 10.1103/physreve.110.014406] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2023] [Accepted: 06/25/2024] [Indexed: 08/21/2024]
Abstract
The interior of cellular nuclei, the nucleoplasm, is a crowded fluid that is pervaded by protein-decorated DNA polymers, the chromatin. Due to the complex architecture of chromatin and a multitude of associated nonequilibrium processes, e.g., DNA repair, the nucleoplasm can be expected to feature nontrivial material properties and hence anomalous transport phenomena. Here, we have used single-particle tracking on nuclear actin rods to probe such transport phenomena. Our analysis reveals that short actin rods in the nucleus show an intermittent, antipersistent subdiffusion with clear signatures of fractional Brownian motion. Moreover, the diffusive motion is heterogeneous with clear signatures of an intermittent switching of trajectories between at least two different mobilities, most likely due to transient associations with chromatin. In line with this interpretation, hyperosmotic stress is seen to stall the motion of nuclear actin rods, whereas hypo-osmotic conditions yield a reptationlike motion. Our data highlights the heterogeneity of transport in the nucleoplasm that needs to be taken into account for an understanding of nucleoplasmic organization and the mechanobiology of nuclei.
Collapse
|
3
|
Sakai K, Kondo Y, Goto Y, Aoki K. Cytoplasmic fluidization contributes to breaking spore dormancy in fission yeast. Proc Natl Acad Sci U S A 2024; 121:e2405553121. [PMID: 38889144 PMCID: PMC11214080 DOI: 10.1073/pnas.2405553121] [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: 04/02/2024] [Accepted: 05/09/2024] [Indexed: 06/20/2024] Open
Abstract
The cytoplasm is a complex, crowded environment that influences myriad cellular processes including protein folding and metabolic reactions. Recent studies have suggested that changes in the biophysical properties of the cytoplasm play a key role in cellular homeostasis and adaptation. However, it still remains unclear how cells control their cytoplasmic properties in response to environmental cues. Here, we used fission yeast spores as a model system of dormant cells to elucidate the mechanisms underlying regulation of the cytoplasmic properties. By tracking fluorescent tracer particles, we found that particle mobility decreased in spores compared to vegetative cells and rapidly increased at the onset of dormancy breaking upon glucose addition. This cytoplasmic fluidization depended on glucose-sensing via the cyclic adenosine monophosphate-protein kinase A pathway. PKA activation led to trehalose degradation through trehalase Ntp1, thereby increasing particle mobility as the amount of trehalose decreased. In contrast, the rapid cytoplasmic fluidization did not require de novo protein synthesis, cytoskeletal dynamics, or cell volume increase. Furthermore, the measurement of diffusion coefficients with tracer particles of different sizes suggests that the spore cytoplasm impedes the movement of larger protein complexes (40 to 150 nm) such as ribosomes, while allowing free diffusion of smaller molecules (~3 nm) such as second messengers and signaling proteins. Our experiments have thus uncovered a series of signaling events that enable cells to quickly fluidize the cytoplasm at the onset of dormancy breaking.
Collapse
Affiliation(s)
- Keiichiro Sakai
- Quantitative Biology Research Group, Exploratory Research Center on Life and Living Systems, National Institutes of Natural Sciences, Myodaiji-cho, Okazaki, Aichi444-8787, Japan
- Division of Quantitative Biology, National Institute for Basic Biology, National Institutes of Natural Sciences, Myodaiji-cho, Okazaki, Aichi444-8787, Japan
| | - Yohei Kondo
- Quantitative Biology Research Group, Exploratory Research Center on Life and Living Systems, National Institutes of Natural Sciences, Myodaiji-cho, Okazaki, Aichi444-8787, Japan
- Division of Quantitative Biology, National Institute for Basic Biology, National Institutes of Natural Sciences, Myodaiji-cho, Okazaki, Aichi444-8787, Japan
- Department of Basic Biology, School of Life Science, SOKENDAI (The Graduate University for Advanced Studies), Myodaiji-cho, Okazaki, Aichi444-8787, Japan
- Division of Integrated Life Science, Department of Gene Mechanisms, Laboratory of Cell Cycle Regulation, Graduate School of Biostudies, Kyoto University, Kyoto606-8315, Japan
- Center for Living Systems Information Science, Graduate School of Biostudies, Kyoto University, Kyoto606-8315, Japan
| | - Yuhei Goto
- Quantitative Biology Research Group, Exploratory Research Center on Life and Living Systems, National Institutes of Natural Sciences, Myodaiji-cho, Okazaki, Aichi444-8787, Japan
- Division of Quantitative Biology, National Institute for Basic Biology, National Institutes of Natural Sciences, Myodaiji-cho, Okazaki, Aichi444-8787, Japan
- Department of Basic Biology, School of Life Science, SOKENDAI (The Graduate University for Advanced Studies), Myodaiji-cho, Okazaki, Aichi444-8787, Japan
- Division of Integrated Life Science, Department of Gene Mechanisms, Laboratory of Cell Cycle Regulation, Graduate School of Biostudies, Kyoto University, Kyoto606-8315, Japan
- Center for Living Systems Information Science, Graduate School of Biostudies, Kyoto University, Kyoto606-8315, Japan
| | - Kazuhiro Aoki
- Quantitative Biology Research Group, Exploratory Research Center on Life and Living Systems, National Institutes of Natural Sciences, Myodaiji-cho, Okazaki, Aichi444-8787, Japan
- Division of Quantitative Biology, National Institute for Basic Biology, National Institutes of Natural Sciences, Myodaiji-cho, Okazaki, Aichi444-8787, Japan
- Department of Basic Biology, School of Life Science, SOKENDAI (The Graduate University for Advanced Studies), Myodaiji-cho, Okazaki, Aichi444-8787, Japan
- Division of Integrated Life Science, Department of Gene Mechanisms, Laboratory of Cell Cycle Regulation, Graduate School of Biostudies, Kyoto University, Kyoto606-8315, Japan
- Center for Living Systems Information Science, Graduate School of Biostudies, Kyoto University, Kyoto606-8315, Japan
| |
Collapse
|
4
|
Simon AA, Haye L, Alhalabi A, Gresil Q, Muñoz BM, Mornet S, Reisch A, Le Guével X, Cognet L. Expanding the Palette of SWIR Emitting Nanoparticles Based on Au Nanoclusters for Single-Particle Tracking Microscopy. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024; 11:e2309267. [PMID: 38639398 PMCID: PMC11199965 DOI: 10.1002/advs.202309267] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/05/2023] [Revised: 03/28/2024] [Indexed: 04/20/2024]
Abstract
Single-molecule localization microscopy has proved promising to unravel the dynamics and molecular architecture of thin biological samples down to nanoscales. For applications in complex, thick biological tissues shifting single-particle emission wavelengths to the shortwave infrared (SWIR also called NIR II) region between 900 to 2100 nm, where biological tissues are more transparent is key. To date, mainly single-walled carbon nanotubes (SWCNTs) enable such applications, but they are inherently 1D objects. Here, 0D ultra-small luminescent gold nanoclusters (AuNCs, <3 nm) and ≈25 nm AuNC-loaded-polymeric particles that can be detected at the single-particle level in the SWIR are presented. Thanks to high brightness and excellent photostability, it is shown that the dynamics of the spherical polymeric particles can be followed at the single-particle level in solution at video rates for minutes. We compared single particle tracking of AuNC-loaded-polymeric particles with that of SWCNT diffusing in agarose gels demonstrating the specificity and complementarity of diffusion properties of these SWIR-emitting nano-objects when exploring a complex environment. This extends the library of photostable SWIR emitting nanomaterials to 0D nano-objects of variable size for single-molecule localization microscopy in the second biological window, opening unprecedented possibilities for mapping the structure and dynamics of complex biological systems.
Collapse
Affiliation(s)
- Apolline A. Simon
- Univ. BordeauxLaboratoire Photonique Numérique et Nanosciences (LP2N)UMR 5298TalenceF‐33400France
- Institut d'Optique Graduate School & CNRSLP2N UMR 5298TalenceF‐33400France
- Univ. BordeauxCNRSBordeaux INPICMCBUMR 5026Pessac33600France
| | - Lucie Haye
- Université de StrasbourgCNRSLaboratoire de Bioimagerie et Pathologies UMR 7021StrasbourgF‐67000France
| | - Abdallah Alhalabi
- University of Grenoble AlpesInstitute for Advanced BiosciencesINSERM1209/CNRS‐UMR5309GrenobleF‐38700France
| | - Quentin Gresil
- Univ. BordeauxLaboratoire Photonique Numérique et Nanosciences (LP2N)UMR 5298TalenceF‐33400France
- Institut d'Optique Graduate School & CNRSLP2N UMR 5298TalenceF‐33400France
| | - Blanca Martín Muñoz
- Univ. BordeauxLaboratoire Photonique Numérique et Nanosciences (LP2N)UMR 5298TalenceF‐33400France
- Institut d'Optique Graduate School & CNRSLP2N UMR 5298TalenceF‐33400France
| | - Stéphane Mornet
- Univ. BordeauxCNRSBordeaux INPICMCBUMR 5026Pessac33600France
| | - Andreas Reisch
- Université de StrasbourgCNRSLaboratoire de Bioimagerie et Pathologies UMR 7021StrasbourgF‐67000France
- Inserm UMR_S 1121CNRS EMR 7003Université de StrasbourgBiomaterials and BioengineeringCentre de Recherche en Biomédecine de Strasbourg1 rue Eugène BoeckelStrasbourgF‐67000France
| | - Xavier Le Guével
- University of Grenoble AlpesInstitute for Advanced BiosciencesINSERM1209/CNRS‐UMR5309GrenobleF‐38700France
| | - Laurent Cognet
- Univ. BordeauxLaboratoire Photonique Numérique et Nanosciences (LP2N)UMR 5298TalenceF‐33400France
- Institut d'Optique Graduate School & CNRSLP2N UMR 5298TalenceF‐33400France
| |
Collapse
|
5
|
Liang Y, Wang W, Metzler R. Aging and confinement in subordinated fractional Brownian motion. Phys Rev E 2024; 109:064144. [PMID: 39020934 DOI: 10.1103/physreve.109.064144] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2024] [Accepted: 05/29/2024] [Indexed: 07/20/2024]
Abstract
We study the effects of aging properties of subordinated fractional Brownian motion (FBM) with drift and in harmonic confinement, when the measurement of the stochastic process starts a time t_{a}>0 after its original initiation at t=0. Specifically, we consider the aged versions of the ensemble mean-squared displacement (MSD) and the time-averaged MSD (TAMSD), along with the aging factor. Our results are favorably compared with simulations results. The aging subordinated FBM exhibits a disparity between MSD and TAMSD and is thus weakly nonergodic, while strong aging is shown to effect a convergence of the MSD and TAMSD. The information on the aging factor with respect to the lag time exhibits an identical form to the aging behavior of subdiffusive continuous-time random walks (CTRW). The statistical properties of the MSD and TAMSD for the confined subordinated FBM are also derived. At long times, the MSD in the harmonic potential has a stationary value, that depends on the Hurst index of the parental (nonequilibrium) FBM. The TAMSD of confined subordinated FBM does not relax to a stationary value but increases sublinearly with lag time, analogously to confined CTRW. Specifically, short aging times t_{a} in confined subordinated FBM do not affect the aged MSD, while for long aging times the aged MSD has a power-law increase and is identical to the aged TAMSD.
Collapse
|
6
|
Rajyaguru A, Metzler R, Dror I, Grolimund D, Berkowitz B. Diffusion in Porous Rock Is Anomalous. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2024; 58:8946-8954. [PMID: 38736287 PMCID: PMC11112742 DOI: 10.1021/acs.est.4c01386] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/06/2024] [Revised: 04/30/2024] [Accepted: 05/01/2024] [Indexed: 05/14/2024]
Abstract
Molecular diffusion of chemical species in subsurface environments─rock formations, soil sediments, marine, river, and lake sediments─plays a critical role in a variety of dynamic processes, many of which affect water chemistry. We investigate and demonstrate the occurrence of anomalous (non-Fickian) diffusion behavior, distinct from classically assumed Fickian diffusion. We measured molecular diffusion through a series of five chalk and dolomite rock samples over a period of about two months. We demonstrate that in all cases, diffusion behavior is significantly different than Fickian. We then analyze the results using a continuous time random walk framework that can describe anomalous diffusion in heterogeneous porous materials such as rock. This methodology shows extreme long-time tailing of tracer advance as compared to conventional Fickian diffusion processes. The finding that distinct anomalous diffusion occurs ubiquitously implies that diffusion-driven processes in subsurface zones should be analyzed using tools that account for non-Fickian diffusion.
Collapse
Affiliation(s)
- Ashish Rajyaguru
- Department
of Earth and Planetary Sciences, Weizmann
Institute of Science, Rehovot 7610001, Israel
| | - Ralf Metzler
- Institute
for Physics and Astronomy, University of
Potsdam, 14476 Potsdam, Germany
- Asia
Pacific Centre for Theoretical Physics, Pohang 37673, Republic of Korea
| | - Ishai Dror
- Department
of Earth and Planetary Sciences, Weizmann
Institute of Science, Rehovot 7610001, Israel
| | | | - Brian Berkowitz
- Department
of Earth and Planetary Sciences, Weizmann
Institute of Science, Rehovot 7610001, Israel
| |
Collapse
|
7
|
Voce N, Stevenson P. Experimentally Probing the Effect of Confinement Geometry on Lipid Diffusion. J Phys Chem B 2024; 128:4404-4413. [PMID: 38574293 PMCID: PMC11089508 DOI: 10.1021/acs.jpcb.3c07388] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2023] [Revised: 03/18/2024] [Accepted: 03/19/2024] [Indexed: 04/06/2024]
Abstract
The lateral mobility of molecules within the cell membrane is ultimately governed by the local environment of the membrane. Confined regions induced by membrane structures, such as protein aggregates or the actin meshwork, occur over a wide range of length scales and can impede or steer the diffusion of membrane components. However, a detailed picture of the origins and nature of these confinement effects remains elusive. Here, we prepare model lipid systems on substrates patterned with confined domains of varying geometries constructed with different materials to explore the influences of physical boundary conditions and specific molecular interactions on diffusion. We demonstrate a platform that is capable of significantly altering and steering the long-range diffusion of lipids by using simple oxide deposition approaches, enabling us to systematically explore how confinement size and shape impact diffusion over multiple length scales. While we find that a "boundary condition" description of the system captures underlying trends in some cases, we are also able to directly compare our systems to analytical models, revealing the unexpected breakdown of several approximate solutions. Our results highlight the importance of considering the length scale dependence when discussing properties such as diffusion.
Collapse
Affiliation(s)
- Nicole Voce
- Department of Physics, Northeastern University, Boston, Massachusetts 02115, United States
| | - Paul Stevenson
- Department of Physics, Northeastern University, Boston, Massachusetts 02115, United States
| |
Collapse
|
8
|
Raczyłło E, Gołowicz D, Skóra T, Kazimierczuk K, Kondrat S. Size Sensitivity of Metabolite Diffusion in Macromolecular Crowds. NANO LETTERS 2024; 24. [PMID: 38607288 PMCID: PMC11057039 DOI: 10.1021/acs.nanolett.3c05100] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/25/2023] [Revised: 04/02/2024] [Accepted: 04/03/2024] [Indexed: 04/13/2024]
Abstract
Metabolites play crucial roles in cellular processes, yet their diffusion in the densely packed interiors of cells remains poorly understood, compounded by conflicting reports in existing studies. Here, we employ pulsed-gradient stimulated-echo NMR and Brownian/Stokesian dynamics simulations to elucidate the behavior of nano- and subnanometer-sized tracers in crowded environments. Using Ficoll as a crowder, we observe a linear decrease in tracer diffusivity with increasing occupied volume fraction, persisting─somewhat surprisingly─up to volume fractions of 30-40%. While simulations suggest a linear correlation between diffusivity slowdown and particle size, experimental findings hint at a more intricate relationship, possibly influenced by Ficoll's porosity. Simulations and numerical calculations of tracer diffusivity in the E. coli cytoplasm show a nonlinear yet monotonic diffusion slowdown with particle size. We discuss our results in the context of nanoviscosity and discrepancies with existing studies.
Collapse
Affiliation(s)
- Edyta Raczyłło
- Institute
of Physical Chemistry, Polish Academy of Sciences, 01-224 Warsaw, Poland
- Department
of Theoretical Chemistry, Institute of Chemical Sciences, Faculty
of Chemistry, Maria Curie-Skłodowska
University in Lublin, 20-031 Lublin, Poland
| | - Dariusz Gołowicz
- Institute
of Physical Chemistry, Polish Academy of Sciences, 01-224 Warsaw, Poland
| | - Tomasz Skóra
- Institute
of Physical Chemistry, Polish Academy of Sciences, 01-224 Warsaw, Poland
- Scientific
Computing and Imaging Institute, University
of Utah, Salt Lake City, Utah 84112, United States
| | | | - Svyatoslav Kondrat
- Institute
of Physical Chemistry, Polish Academy of Sciences, 01-224 Warsaw, Poland
- Institute
for Computational Physics, University of
Stuttgart 70569, Stuttgart, Germany
| |
Collapse
|
9
|
Yanagawa M, Shimobayashi SF. Multi-dimensional condensation of intracellular biomolecules. J Biochem 2024; 175:179-186. [PMID: 37993409 DOI: 10.1093/jb/mvad095] [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: 09/12/2023] [Accepted: 11/09/2023] [Indexed: 11/24/2023] Open
Abstract
Liquid-liquid phase separation has been recognized as universal mechanisms in living cells for the formation of RNA-protein condensates and ordered lipid domains. These biomolecular condensates or domains nucleate, diffuse and interact with each other across physical dimensions to perform their biological functions. Here we summarize key features of biophysical principles underlying the multi-dimensional condensation of RNA-protein condensates and ordered lipid domains, which are related to nuclear transcription, and signaling on cell membranes. Uncovering physicochemical factors that govern the spatiotemporal coupling of those condensates presents a new avenue in their functions and associated human diseases.
Collapse
Affiliation(s)
- Masataka Yanagawa
- Molecular and Cellular Biochemistry, Graduate School of Pharmaceutical Sciences, Tohoku University, 6-3, Aoba, Aramaki, Aoba-ku, Sendai, Miyagi 980-8578, Japan
- Cellular Informatics Laboratory, RIKEN Cluster for Pioneering Research, Wako, Saitama 351-0198, Japan
| | - Shunsuke F Shimobayashi
- Department of Life Science Frontiers, Center for iPS Cell Research and Application, Kyoto University, 53 Kawahara-cho, Shogoin, Sakyo-ku, Kyoto 606-8507, Japan
| |
Collapse
|
10
|
Kompella VPS, Romano MC, Stansfield I, Mancera RL. What determines sub-diffusive behavior in crowded protein solutions? Biophys J 2024; 123:134-146. [PMID: 38073154 PMCID: PMC10808025 DOI: 10.1016/j.bpj.2023.12.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2023] [Revised: 10/07/2023] [Accepted: 12/04/2023] [Indexed: 12/22/2023] Open
Abstract
The aqueous environment inside cells is densely packed. A typical cell has a macromolecular concentration in the range 90-450 g/L, with 5%-40% of its volume being occupied by macromolecules, resulting in what is known as macromolecular crowding. The space available for the free diffusion of metabolites and other macromolecules is thus greatly reduced, leading to so-called excluded volume effects. The slow diffusion of macromolecules under crowded conditions has been explained using transient complex formation. However, sub-diffusion noted in earlier works is not well characterized, particularly the role played by transient complex formation and excluded volume effects. We have used Brownian dynamics simulations to characterize the diffusion of chymotrypsin inhibitor 2 in protein solutions of bovine serum albumin and lysozyme at concentrations ranging from 50 to 300 g/L. The predicted changes in diffusion coefficient as a function of crowder concentration are consistent with NMR experiments. The sub-diffusive behavior observed in the sub-microsecond timescale can be explained in terms of a so-called cage effect, arising from rattling motion in a local molecular cage as a consequence of excluded volume effects. By selectively manipulating the nature of interactions between protein molecules, we determined that excluded volume effects induce sub-diffusive dynamics at sub-microsecond timescales. These findings may help to explain the diffusion-mediated effects of protein crowding on cellular processes.
Collapse
Affiliation(s)
- Vijay Phanindra Srikanth Kompella
- Curtin Medical School, Curtin Health Innovation Research Institute, Curtin Institute for Data Science, Curtin University, Perth, Western Australia, Australia; Department of Physics, Institute for Complex Systems and Mathematical Biology, University of Aberdeen, Aberdeen, United Kingdom
| | - Maria Carmen Romano
- Department of Physics, Institute for Complex Systems and Mathematical Biology, University of Aberdeen, Aberdeen, United Kingdom; Institute of Medical Sciences, University of Aberdeen, Aberdeen, United Kingdom
| | - Ian Stansfield
- Institute of Medical Sciences, University of Aberdeen, Aberdeen, United Kingdom
| | - Ricardo L Mancera
- Curtin Medical School, Curtin Health Innovation Research Institute, Curtin Institute for Data Science, Curtin University, Perth, Western Australia, Australia.
| |
Collapse
|
11
|
Li Y, Suleiman K, Xu Y. Anomalous diffusion, non-Gaussianity, nonergodicity, and confinement in stochastic-scaled Brownian motion with diffusing diffusivity dynamics. Phys Rev E 2024; 109:014139. [PMID: 38366530 DOI: 10.1103/physreve.109.014139] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2023] [Accepted: 12/07/2023] [Indexed: 02/18/2024]
Abstract
Scaled Brownian motions (SBMs) with power-law time-dependent diffusivity have been used to describe various types of anomalous diffusion yet Gaussian observed in granular gases kinetics, turbulent diffusion, and molecules mobility in cells, to name a few. However, some of these systems may exhibit non-Gaussian behavior which can be described by SBM with diffusing diffusivity (DD-SBM). Here, we numerically investigate both free and confined DD-SBM models characterized by fixed or stochastic scaling exponent of time-dependent diffusivity. The effects of distributed scaling exponent, random diffusivity, and confinement are considered. Different regimes of ultraslow diffusion, subdiffusion, normal diffusion, and superdiffusion are observed. In addition, weak ergodic and non-Gaussian behaviors are also detected. These results provide insights into diffusion in time-fluctuating diffusivity landscapes with potential applications to time-dependent temperature systems spreading in heterogeneous environments.
Collapse
Affiliation(s)
- Yongge Li
- School of Mathematics and Statistics, Northwestern Polytechnical University, Xi'an 710072, China
| | - Kheder Suleiman
- School of Mathematics and Statistics, Northwestern Polytechnical University, Xi'an 710072, China
| | - Yong Xu
- School of Mathematics and Statistics, Northwestern Polytechnical University, Xi'an 710072, China
- MOE Key Laboratory for Complexity Science in Aerospace, Northwestern Polytechnical University, Xi'an 710072, China
| |
Collapse
|
12
|
Arjona MI, Najafi J, Minc N. Cytoplasm mechanics and cellular organization. Curr Opin Cell Biol 2023; 85:102278. [PMID: 37979412 DOI: 10.1016/j.ceb.2023.102278] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2023] [Revised: 10/17/2023] [Accepted: 10/18/2023] [Indexed: 11/20/2023]
Abstract
As cells organize spatially or divide, they translocate many micron-scale organelles in their cytoplasm. These include endomembrane vesicles, nuclei, microtubule asters, mitotic spindles, or chromosomes. Organelle motion is powered by cytoskeleton forces but is opposed by viscoelastic forces imparted by the surrounding crowded cytoplasm medium. These resistive forces associated to cytoplasm physcial properties remain generally underappreciated, yet reach significant values to slow down organelle motion or even limit their displacement by springing them back towards their original position. The cytoplasm may also be itself organized in time and space, being for example stiffer or more fluid at certain locations or during particular cell cycle phases. Thus, cytoplasm mechanics may be viewed as a labile module that contributes to organize cells. We here review emerging methods, mechanisms, and concepts to study cytoplasm mechanical properties and their function in organelle positioning, cellular organization and division.
Collapse
Affiliation(s)
- María Isabel Arjona
- Université de Paris, CNRS, Institut Jacques Monod, F-75006 Paris, France; Equipe Labellisée LIGUE Contre le Cancer, France
| | - Javad Najafi
- Université de Paris, CNRS, Institut Jacques Monod, F-75006 Paris, France; Equipe Labellisée LIGUE Contre le Cancer, France
| | - Nicolas Minc
- Université de Paris, CNRS, Institut Jacques Monod, F-75006 Paris, France; Equipe Labellisée LIGUE Contre le Cancer, France.
| |
Collapse
|
13
|
Waigh TA, Korabel N. Heterogeneous anomalous transport in cellular and molecular biology. REPORTS ON PROGRESS IN PHYSICS. PHYSICAL SOCIETY (GREAT BRITAIN) 2023; 86:126601. [PMID: 37863075 DOI: 10.1088/1361-6633/ad058f] [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: 12/21/2022] [Accepted: 10/20/2023] [Indexed: 10/22/2023]
Abstract
It is well established that a wide variety of phenomena in cellular and molecular biology involve anomalous transport e.g. the statistics for the motility of cells and molecules are fractional and do not conform to the archetypes of simple diffusion or ballistic transport. Recent research demonstrates that anomalous transport is in many cases heterogeneous in both time and space. Thus single anomalous exponents and single generalised diffusion coefficients are unable to satisfactorily describe many crucial phenomena in cellular and molecular biology. We consider advances in the field ofheterogeneous anomalous transport(HAT) highlighting: experimental techniques (single molecule methods, microscopy, image analysis, fluorescence correlation spectroscopy, inelastic neutron scattering, and nuclear magnetic resonance), theoretical tools for data analysis (robust statistical methods such as first passage probabilities, survival analysis, different varieties of mean square displacements, etc), analytic theory and generative theoretical models based on simulations. Special emphasis is made on high throughput analysis techniques based on machine learning and neural networks. Furthermore, we consider anomalous transport in the context of microrheology and the heterogeneous viscoelasticity of complex fluids. HAT in the wavefronts of reaction-diffusion systems is also considered since it plays an important role in morphogenesis and signalling. In addition, we present specific examples from cellular biology including embryonic cells, leucocytes, cancer cells, bacterial cells, bacterial biofilms, and eukaryotic microorganisms. Case studies from molecular biology include DNA, membranes, endosomal transport, endoplasmic reticula, mucins, globular proteins, and amyloids.
Collapse
Affiliation(s)
- Thomas Andrew Waigh
- Biological Physics, School of Physics and Astronomy, University of Manchester, Manchester M13 9PL, United Kingdom
| | - Nickolay Korabel
- Department of Mathematics, The University of Manchester, Manchester M13 9PL, United Kingdom
| |
Collapse
|
14
|
Bonucci M, Shu T, Holt LJ. How it feels in a cell. Trends Cell Biol 2023; 33:924-938. [PMID: 37286396 PMCID: PMC10592589 DOI: 10.1016/j.tcb.2023.05.002] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2023] [Revised: 05/01/2023] [Accepted: 05/02/2023] [Indexed: 06/09/2023]
Abstract
Life emerges from thousands of biochemical processes occurring within a shared intracellular environment. We have gained deep insights from in vitro reconstitution of isolated biochemical reactions. However, the reaction medium in test tubes is typically simple and diluted. The cell interior is far more complex: macromolecules occupy more than a third of the space, and energy-consuming processes agitate the cell interior. Here, we review how this crowded, active environment impacts the motion and assembly of macromolecules, with an emphasis on mesoscale particles (10-1000 nm diameter). We describe methods to probe and analyze the biophysical properties of cells and highlight how changes in these properties can impact physiology and signaling, and potentially contribute to aging, and diseases, including cancer and neurodegeneration.
Collapse
Affiliation(s)
- Martina Bonucci
- Institute for Systems Genetics, New York University Langone Medical Center, 435 E 30th Street, New York, NY 10016, USA
| | - Tong Shu
- Institute for Systems Genetics, New York University Langone Medical Center, 435 E 30th Street, New York, NY 10016, USA
| | - Liam J Holt
- Institute for Systems Genetics, New York University Langone Medical Center, 435 E 30th Street, New York, NY 10016, USA.
| |
Collapse
|
15
|
Saxton MN, Morisaki T, Krapf D, Kimura H, Stasevich TJ. Live-cell imaging uncovers the relationship between histone acetylation, transcription initiation, and nucleosome mobility. SCIENCE ADVANCES 2023; 9:eadh4819. [PMID: 37792937 PMCID: PMC10550241 DOI: 10.1126/sciadv.adh4819] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/08/2023] [Accepted: 09/01/2023] [Indexed: 10/06/2023]
Abstract
Histone acetylation and RNA polymerase II phosphorylation are associated with transcriptionally active chromatin, but their spatiotemporal relationship in live cells remains poorly understood. To address this problem, we combine Fab-based labeling of endogenous protein modifications with single-molecule tracking to quantify the dynamics of chromatin enriched with histone H3 lysine-27 acetylation (H3K27ac) and RNA polymerase II serine-5 phosphorylation (RNAP2-Ser5ph). Our analysis reveals that chromatin enriched with these two modifications is generally separate. In these separated sites, we show that the two modifications are inversely correlated with one another on the minutes time scale and that single nucleosomes within each region display distinct and opposing dynamics on the subsecond time scale. While nucleosomes diffuse ~15% faster in chromatin enriched with H3K27ac, they diffuse ~15% slower in chromatin enriched with RNAP2-Ser5ph. These results argue that high levels of H3K27ac and RNAP2-Ser5ph are not often present together at the same place and time, but rather each marks distinct transcriptionally poised or active sites, respectively.
Collapse
Affiliation(s)
- Matthew N. Saxton
- Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, CO, USA
| | - Tatsuya Morisaki
- Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, CO, USA
| | - Diego Krapf
- Department of Electrical and Computer Engineering, and School of Biomedical Engineering, Colorado State University, Fort Collins, CO, USA
| | - Hiroshi Kimura
- Cell Biology Center and World Research Hub Initiative, Tokyo Institute of Technology, Yokohama, Japan
- School of Life Science and Technology, Tokyo Institute of Technology, Yokohama, Japan
| | - Timothy J. Stasevich
- Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, CO, USA
- Cell Biology Center and World Research Hub Initiative, Tokyo Institute of Technology, Yokohama, Japan
| |
Collapse
|
16
|
Luo MB, Hua DY. Simulation Study on the Mechanism of Intermediate Subdiffusion of Diffusive Particles in Crowded Systems. ACS OMEGA 2023; 8:34188-34195. [PMID: 37744832 PMCID: PMC10515404 DOI: 10.1021/acsomega.3c05945] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/12/2023] [Accepted: 08/29/2023] [Indexed: 09/26/2023]
Abstract
The intermediate subdiffusion of diffusive particles in crowded systems is studied for two model systems: the continuous time random walk (CTRW) model and the obstruction-binding model. For the CTRW model with an arbitrarily given longest waiting time τmax, we find that the diffusive particle exhibits subdiffusion below τmax and recovers normal diffusion above τmax. For the obstruction-binding model with randomly distributed attractive obstacles, the diffusion of the diffusive particle is dependent on the binding energy and the density of obstacles. Interestingly, diffusion curves for different binding strengths can be overlapped by rescaling the simulation time, indicating that the diffusive particle in the obstruction-binding model can change from the intermediate subdiffusion to the normal diffusion at a long-term simulation scale. The results of the two model systems show that the diffusive particles only exhibit intermediate subdiffusion below the longest waiting time. Therefore, long timescale subdiffusion would only be observed in the CTRW model with an infinitely long waiting time and in the obstruction-binding model with an infinitely large binding strength.
Collapse
Affiliation(s)
- Meng-Bo Luo
- School of Physics, Zhejiang University, Hangzhou 310027, China
| | - Dao-Yang Hua
- School of Physics, Zhejiang University, Hangzhou 310027, China
| |
Collapse
|
17
|
Fournier M, Leclerc P, Leray A, Champelovier D, Agbazahou F, Dahmani F, Bidaux G, Furlan A, Héliot L. Combined SPT and FCS methods reveal a mechanism of RNAP II oversampling in cell nuclei. Sci Rep 2023; 13:14633. [PMID: 37669988 PMCID: PMC10480184 DOI: 10.1038/s41598-023-38668-8] [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: 01/05/2023] [Accepted: 07/12/2023] [Indexed: 09/07/2023] Open
Abstract
Gene expression orchestration is a key question in fundamental and applied research. Different models for transcription regulation were proposed, yet the dynamic regulation of RNA polymerase II (RNAP II) activity remains a matter of debate. To improve our knowledge of this topic, we investigated RNAP II motility in eukaryotic cells by combining single particle tracking (SPT) and fluorescence correlation spectroscopy (FCS) techniques, to take advantage of their different sensitivities in order to analyze together slow and fast molecular movements. Thanks to calibrated samples, we developed a benchmark for quantitative analysis of molecular dynamics, to eliminate the main potential instrumental biases. We applied this workflow to study the diffusion of RPB1, the catalytic subunit of RNAP II. By a cross-analysis of FCS and SPT, we could highlight different RPB1 motility states and identifyed a stationary state, a slow diffusion state, and two different modes of subdiffusion. Interestingly, our analysis also unveiled the oversampling by RPB1 of nuclear subdomains. Based on these data, we propose a novel model of spatio-temporal transcription regulation. Altogether, our results highlight the importance of combining microscopy approaches at different time scales to get a full insight into the real complexity of molecular kinetics in cells.
Collapse
Affiliation(s)
- Marie Fournier
- Univ. Lille, CNRS, UMR 8523, PhLAM Laboratoire de Physique des Lasers, Atomes et Molécules, Lille, France
- CNRS, Groupement de Recherche ImaBio, 59655, Villeneuve d'Ascq, France
| | - Pierre Leclerc
- Univ. Lille, CNRS, UMR 8523, PhLAM Laboratoire de Physique des Lasers, Atomes et Molécules, Lille, France
- CNRS, Groupement de Recherche ImaBio, 59655, Villeneuve d'Ascq, France
| | - Aymeric Leray
- Laboratoire Interdisciplinaire Carnot de Bourgogne, UMR 6303 CNRS, Université de Bourgogne Franche Comte, Dijon, France
- CNRS, Groupement de Recherche ImaBio, 59655, Villeneuve d'Ascq, France
| | - Dorian Champelovier
- Univ. Lille, CNRS, UMR 8523, PhLAM Laboratoire de Physique des Lasers, Atomes et Molécules, Lille, France
- CNRS, Groupement de Recherche ImaBio, 59655, Villeneuve d'Ascq, France
| | - Florence Agbazahou
- Univ. Lille, CNRS, UMR 8523, PhLAM Laboratoire de Physique des Lasers, Atomes et Molécules, Lille, France
- CNRS, Groupement de Recherche ImaBio, 59655, Villeneuve d'Ascq, France
| | - Fatima Dahmani
- Univ. Lille, CNRS, UMR 8523, PhLAM Laboratoire de Physique des Lasers, Atomes et Molécules, Lille, France
- CNRS, Groupement de Recherche ImaBio, 59655, Villeneuve d'Ascq, France
| | - Gabriel Bidaux
- INSERM UMR 1060, CarMeN Laboratory, IHU OPERA, Hôpital Louis Pradel, Hospices Civils de Lyon, Univ Lyon1, Lyon, France
- CNRS, Groupement de Recherche ImaBio, 59655, Villeneuve d'Ascq, France
| | - Alessandro Furlan
- Univ. Lille, CNRS, UMR 8523, PhLAM Laboratoire de Physique des Lasers, Atomes et Molécules, Lille, France.
- Univ. Lille, CNRS, Inserm, CHU Lille, UMR9020-U1277 -CANTHER -Cancer Heterogeneity Plasticity and Resistance to Therapies, Lille, 59000, France.
- Unité Tumorigenèse et Résistance aux Traitements, Centre Oscar Lambret, 59000, Lille, France.
- CNRS, Groupement de Recherche ImaBio, 59655, Villeneuve d'Ascq, France.
| | - Laurent Héliot
- Univ. Lille, CNRS, UMR 8523, PhLAM Laboratoire de Physique des Lasers, Atomes et Molécules, Lille, France.
- CNRS, Groupement de Recherche ImaBio, 59655, Villeneuve d'Ascq, France.
| |
Collapse
|
18
|
Liang Y, Wang W, Metzler R, Cherstvy AG. Anomalous diffusion, nonergodicity, non-Gaussianity, and aging of fractional Brownian motion with nonlinear clocks. Phys Rev E 2023; 108:034113. [PMID: 37849140 DOI: 10.1103/physreve.108.034113] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2023] [Accepted: 08/07/2023] [Indexed: 10/19/2023]
Abstract
How do nonlinear clocks in time and/or space affect the fundamental properties of a stochastic process? Specifically, how precisely may ergodic processes such as fractional Brownian motion (FBM) acquire predictable nonergodic and aging features being subjected to such conditions? We address these questions in the current study. To describe different types of non-Brownian motion of particles-including power-law anomalous, ultraslow or logarithmic, as well as superfast or exponential diffusion-we here develop and analyze a generalized stochastic process of scaled-fractional Brownian motion (SFBM). The time- and space-SFBM processes are, respectively, constructed based on FBM running with nonlinear time and space clocks. The fundamental statistical characteristics such as non-Gaussianity of particle displacements, nonergodicity, as well as aging are quantified for time- and space-SFBM by selecting different clocks. The latter parametrize power-law anomalous, ultraslow, and superfast diffusion. The results of our computer simulations are fully consistent with the analytical predictions for several functional forms of clocks. We thoroughly examine the behaviors of the probability-density function, the mean-squared displacement, the time-averaged mean-squared displacement, as well as the aging factor. Our results are applicable for rationalizing the impact of nonlinear time and space properties superimposed onto the FBM-type dynamics. SFBM offers a general framework for a universal and more precise model-based description of anomalous, nonergodic, non-Gaussian, and aging diffusion in single-molecule-tracking observations.
Collapse
Affiliation(s)
- Yingjie Liang
- College of Mechanics and Materials, Hohai University, 211100 Nanjing, China
- Institute of Physics and Astronomy, University of Potsdam, 14476 Potsdam, Germany
| | - Wei Wang
- Institute of Physics and Astronomy, University of Potsdam, 14476 Potsdam, Germany
| | - Ralf Metzler
- Institute of Physics and Astronomy, University of Potsdam, 14476 Potsdam, Germany
- Asia Pacific Center for Theoretical Physics, Pohang 37673, Republic of Korea
| | - Andrey G Cherstvy
- Institute of Physics and Astronomy, University of Potsdam, 14476 Potsdam, Germany
| |
Collapse
|
19
|
Jiang C, Luo HY, Xu X, Dou SX, Li W, Guan D, Ye F, Chen X, Guo M, Wang PY, Li H. Switch of cell migration modes orchestrated by changes of three-dimensional lamellipodium structure and intracellular diffusion. Nat Commun 2023; 14:5166. [PMID: 37620390 PMCID: PMC10449835 DOI: 10.1038/s41467-023-40858-x] [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: 11/28/2022] [Accepted: 08/14/2023] [Indexed: 08/26/2023] Open
Abstract
Cell migration plays important roles in many biological processes, but how migrating cells orchestrate intracellular molecules and subcellular structures to regulate their speed and direction is still not clear. Here, by characterizing the intracellular diffusion and the three-dimensional lamellipodium structures of fish keratocyte cells, we observe a strong positive correlation between the intracellular diffusion and cell migration speed and, more importantly, discover a switching of cell migration modes with reversible intracellular diffusion variation and lamellipodium structure deformation. Distinct from the normal fast mode, cells migrating in the newly-found slow mode have a deformed lamellipodium with swollen-up front and thinned-down rear, reduced intracellular diffusion and compartmentalized macromolecule distribution in the lamellipodium. Furthermore, in turning cells, both lamellipodium structure and intracellular diffusion dynamics are also changed, with left-right symmetry breaking. We propose a mechanism involving the front-localized actin polymerization and increased molecular crowding in the lamellipodium to explain how cells spatiotemporally coordinate the intracellular diffusion dynamics and the lamellipodium structure in regulating their migrations.
Collapse
Affiliation(s)
- Chao Jiang
- Beijing National Laboratory for Condensed Matter Physics and Laboratory of Soft Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing, 100190, China
- School of Systems Science and Institute of Nonequilibrium Systems, Beijing Normal University, Beijing, 100875, China
- School of Physical Sciences and School of Engineering Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Hong-Yu Luo
- Beijing National Laboratory for Condensed Matter Physics and Laboratory of Soft Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing, 100190, China
- School of Physical Sciences and School of Engineering Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Xinpeng Xu
- Physics Program, Guangdong Technion-Israel Institute of Technology, 241 Daxue Road, Shantou, Guangdong, 515063, China
- Technion-Israel Institute of Technology, Haifa, 32000, Israel
| | - Shuo-Xing Dou
- Beijing National Laboratory for Condensed Matter Physics and Laboratory of Soft Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing, 100190, China
- School of Physical Sciences and School of Engineering Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Wei Li
- Beijing National Laboratory for Condensed Matter Physics and Laboratory of Soft Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing, 100190, China
- Songshan Lake Materials Laboratory, Dongguan, Guangdong, 523808, China
| | - Dongshi Guan
- School of Physical Sciences and School of Engineering Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
- State Key Laboratory of Nonlinear Mechanics, Institute of Mechanics, Chinese Academy of Sciences, Beijing, 100190, China
| | - Fangfu Ye
- Beijing National Laboratory for Condensed Matter Physics and Laboratory of Soft Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing, 100190, China
- School of Physical Sciences and School of Engineering Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
- Songshan Lake Materials Laboratory, Dongguan, Guangdong, 523808, China
- Wenzhou Institute, University of Chinese Academy of Sciences, Wenzhou, Zhejiang, 325001, China
| | - Xiaosong Chen
- School of Systems Science and Institute of Nonequilibrium Systems, Beijing Normal University, Beijing, 100875, China
| | - Ming Guo
- Department of Mechanical Engineering, MIT, 77 Massachusetts Ave, Cambridge, MA, 02139, USA
| | - Peng-Ye Wang
- Beijing National Laboratory for Condensed Matter Physics and Laboratory of Soft Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing, 100190, China.
- School of Physical Sciences and School of Engineering Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China.
- Songshan Lake Materials Laboratory, Dongguan, Guangdong, 523808, China.
| | - Hui Li
- School of Systems Science and Institute of Nonequilibrium Systems, Beijing Normal University, Beijing, 100875, China.
| |
Collapse
|
20
|
Liang Y, Wang W, Metzler R. Anomalous diffusion, non-Gaussianity, and nonergodicity for subordinated fractional Brownian motion with a drift. Phys Rev E 2023; 108:024143. [PMID: 37723819 DOI: 10.1103/physreve.108.024143] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2023] [Accepted: 08/11/2023] [Indexed: 09/20/2023]
Abstract
The stochastic motion of a particle with long-range correlated increments (the moving phase) which is intermittently interrupted by immobilizations (the trapping phase) in a disordered medium is considered in the presence of an external drift. In particular, we consider trapping events whose times follow a scale-free distribution with diverging mean trapping time. We construct this process in terms of fractional Brownian motion with constant forcing in which the trapping effect is introduced by the subordination technique, connecting "operational time" with observable "real time." We derive the statistical properties of this process such as non-Gaussianity and nonergodicity, for both ensemble and single-trajectory (time) averages. We demonstrate nice agreement with extensive simulations for the probability density function, skewness, kurtosis, as well as ensemble and time-averaged mean-squared displacements. We place a specific emphasis on the comparisons between the cases with and without drift.
Collapse
Affiliation(s)
- Yingjie Liang
- College of Mechanics and Materials, Hohai University, 211100 Nanjing, China
- University of Potsdam, Institute of Physics and Astronomy, 14476 Potsdam-Golm, Germany
| | - Wei Wang
- University of Potsdam, Institute of Physics and Astronomy, 14476 Potsdam-Golm, Germany
| | - Ralf Metzler
- University of Potsdam, Institute of Physics and Astronomy, 14476 Potsdam-Golm, Germany
- Asia Pacific Centre for Theoretical Physics, Pohang 37673, Republic of Korea
| |
Collapse
|
21
|
Delille F, Balloul E, Hajj B, Hanafi M, Morand C, Xu XZ, Dumas S, Coulon A, Lequeux N, Pons T. Sulfobetaine-Phosphonate Block Copolymer Coated Iron Oxide Nanoparticles for Genomic Locus Targeting and Magnetic Micromanipulation in the Nucleus of Living Cells. NANO LETTERS 2023. [PMID: 37390368 DOI: 10.1021/acs.nanolett.3c00688] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/02/2023]
Abstract
Exerting forces on biomolecules inside living cells would allow us to probe their dynamic interactions in their native environment. Magnetic iron oxide nanoparticles represent a unique tool capable of pulling on biomolecules with the application of an external magnetic field gradient; however, their use has been restricted to biomolecules accessible from the extracellular medium. Targeting intracellular biomolecules represents an additional challenge due to potential nonspecific interactions with cytoplasmic or nuclear components. We present the synthesis of sulfobetaine-phosphonate block copolymer ligands, which provide magnetic nanoparticles that are stealthy and targetable in living cells. We demonstrate, for the first time, their efficient targeting in the nucleus and their use for magnetic micromanipulation of a specific genomic locus in living cells. We believe that these stable and sensitive magnetic nanoprobes represent a promising tool to manipulate specific biomolecules in living cells and probe the mechanical properties of living matter at the molecular scale.
Collapse
Affiliation(s)
- Fanny Delille
- Laboratoire Physique et Etude des Matériaux, ESPCI-Paris, PSL Research University, CNRS, Sorbonne Université, UMR 8213, 10, rue Vauquelin, 75005 Paris, France
| | - Elie Balloul
- Laboratoire Physico Chimie Curie, Institut Curie, PSL Research University, Sorbonne Université, CNRS UMR168, 75005 Paris, France
| | - Bassam Hajj
- Laboratoire Physico Chimie Curie, Institut Curie, PSL Research University, Sorbonne Université, CNRS UMR168, 75005 Paris, France
| | - Mohamed Hanafi
- Sciences et Ingénierie de la Matière Molle, UMR 7615, ESPCI Paris PSL-CNRS-Sorbonne Université, 10 Rue Vauquelin, 75005 Paris, France
| | - Colin Morand
- Laboratoire Physico Chimie Curie, Institut Curie, PSL Research University, Sorbonne Université, CNRS UMR168, 75005 Paris, France
- Laboratoire Dynamique du Noyau, Institut Curie, PSL Research University, Sorbonne Université, CNRS UMR3664, 75005 Paris, France
| | - Xiang Zhen Xu
- Laboratoire Physique et Etude des Matériaux, ESPCI-Paris, PSL Research University, CNRS, Sorbonne Université, UMR 8213, 10, rue Vauquelin, 75005 Paris, France
| | - Simon Dumas
- Institut Pierre-Gilles de Gennes, Institut Curie, Sorbonne Université, PSL Research University, 6 rue Jean Calvin, 75005 Paris, France
| | - Antoine Coulon
- Laboratoire Physico Chimie Curie, Institut Curie, PSL Research University, Sorbonne Université, CNRS UMR168, 75005 Paris, France
- Laboratoire Dynamique du Noyau, Institut Curie, PSL Research University, Sorbonne Université, CNRS UMR3664, 75005 Paris, France
| | - Nicolas Lequeux
- Laboratoire Physique et Etude des Matériaux, ESPCI-Paris, PSL Research University, CNRS, Sorbonne Université, UMR 8213, 10, rue Vauquelin, 75005 Paris, France
| | - Thomas Pons
- Laboratoire Physique et Etude des Matériaux, ESPCI-Paris, PSL Research University, CNRS, Sorbonne Université, UMR 8213, 10, rue Vauquelin, 75005 Paris, France
| |
Collapse
|
22
|
Korabel N, Taloni A, Pagnini G, Allan V, Fedotov S, Waigh TA. Ensemble heterogeneity mimics ageing for endosomal dynamics within eukaryotic cells. Sci Rep 2023; 13:8789. [PMID: 37258614 DOI: 10.1038/s41598-023-35903-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2023] [Accepted: 05/25/2023] [Indexed: 06/02/2023] Open
Abstract
Transport processes of many structures inside living cells display anomalous diffusion, such as endosomes in eukaryotic cells. They are also heterogeneous in space and time. Large ensembles of single particle trajectories allow the heterogeneities to be quantified in detail and provide insights for mathematical modelling. The development of accurate mathematical models for heterogeneous dynamics has the potential to enable the design and optimization of various technological applications, for example, the design of effective drug delivery systems. Central questions in the analysis of anomalous dynamics are ergodicity and statistical ageing which allow for selecting the proper model for the description. It is believed that non-ergodicity and ageing occur concurrently. However, we found that the anomalous dynamics of endosomes is paradoxical since it is ergodic but shows ageing. We show that this behaviour is caused by ensemble heterogeneity that, in addition to space-time heterogeneity within a single trajectory, is an inherent property of endosomal motion. Our work introduces novel approaches for the analysis and modelling of heterogeneous dynamics.
Collapse
Affiliation(s)
- Nickolay Korabel
- Department of Mathematics, The University of Manchester, Manchester, M13 9PL, UK.
| | - Alessandro Taloni
- CNR-Consiglio Nazionale delle Ricerche, Istituto dei Sistemi Complessi, via dei Taurini 19, 00185, Rome, Italy
| | - Gianni Pagnini
- BCAM-Basque Center for Applied Mathematics, Mazarredo 14, 48009, Bilbao, Basque Country, Spain
- Ikerbasque-Basque Foundation for Science, Plaza Euskadi 5, 48009, Bilbao, Basque Country, Spain
| | - Viki Allan
- School of Biological Sciences, The University of Manchester, Manchester, M13 9PT, UK
| | - Sergei Fedotov
- Department of Mathematics, The University of Manchester, Manchester, M13 9PL, UK
| | - Thomas Andrew Waigh
- Biological Physics, Department of Physics and Astronomy, The University of Manchester, Manchester, M13 9PL, UK.
| |
Collapse
|
23
|
Arbel-Goren R, McKeithen-Mead SA, Voglmaier D, Afremov I, Teza G, Grossman A, Stavans J. Target search by an imported conjugative DNA element for a unique integration site along a bacterial chromosome during horizontal gene transfer. Nucleic Acids Res 2023; 51:3116-3129. [PMID: 36762480 PMCID: PMC10123120 DOI: 10.1093/nar/gkad068] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2022] [Revised: 01/18/2023] [Accepted: 01/25/2023] [Indexed: 02/11/2023] Open
Abstract
Integrative and conjugative elements (ICEs) are mobile genetic elements that can transfer by conjugation to recipient cells. Some ICEs integrate into a unique site in the genome of their hosts. We studied quantitatively the process by which an ICE searches for its unique integration site in the Bacillus subtilis chromosome. We followed the motion of both ICEBs1 and the chromosomal integration site in real time within individual cells. ICEBs1 exhibited a wide spectrum of dynamical behaviors, ranging from rapid sub-diffusive displacements crisscrossing the cell, to kinetically trapped states. The chromosomal integration site moved sub-diffusively and exhibited pronounced dynamical asymmetry between longitudinal and transversal motions, highlighting the role of chromosomal structure and the heterogeneity of the bacterial interior in the search. The successful search for and subsequent recombination into the integration site is a key step in the acquisition of integrating mobile genetic elements. Our findings provide new insights into intracellular transport processes involving large DNA molecules.
Collapse
Affiliation(s)
- Rinat Arbel-Goren
- Department of Physics of Complex Systems, Weizmann Institute of Science, Rehovot 76100, Israel
| | | | - Dominik Voglmaier
- Department of Physics of Complex Systems, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Idana Afremov
- Department of Physics of Complex Systems, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Gianluca Teza
- Department of Physics of Complex Systems, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Alan D Grossman
- Department of Biology Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Joel Stavans
- Department of Physics of Complex Systems, Weizmann Institute of Science, Rehovot 76100, Israel
| |
Collapse
|
24
|
Itto Y. Conditional Entropic Approach to Nonequilibrium Complex Systems with Weak Fluctuation Correlation. ENTROPY (BASEL, SWITZERLAND) 2023; 25:e25040556. [PMID: 37190346 PMCID: PMC10137531 DOI: 10.3390/e25040556] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/22/2023] [Revised: 03/21/2023] [Accepted: 03/21/2023] [Indexed: 05/17/2023]
Abstract
A conditional entropic approach is discussed for nonequilibrium complex systems with a weak correlation between spatiotemporally fluctuating quantities on a large time scale. The weak correlation is found to constitute the fluctuation distribution that maximizes the entropy associated with the conditional fluctuations. The approach is illustrated in diffusion phenomenon of proteins inside bacteria. A further possible illustration is also presented for membraneless organelles in embryos and beads in cell extracts, which share common natures of fluctuations in their diffusion.
Collapse
Affiliation(s)
- Yuichi Itto
- Science Division, Center for General Education, Aichi Institute of Technology, Toyota 470-0392, Aichi, Japan
- Institut für Computerphysik, Universität Stuttgart, 70569 Stuttgart, Germany
| |
Collapse
|
25
|
Xie Y, Gresham D, Holt L. Increased mesoscale diffusivity in response to acute glucose starvation. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.01.10.523352. [PMID: 36711511 PMCID: PMC9882054 DOI: 10.1101/2023.01.10.523352] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
Macromolecular crowding is an important parameter that impacts multiple biological processes. Passive microrheology using single particle tracking is a powerful means of studying macromolecular crowding. Here we monitored the diffusivity of self-assembling fluorescent nanoparticles (μNS) in response to acute glucose starvation. mRNP diffusivity was reduced upon glucose starvation as previously reported. In contrast, we observed increased diffusivity of μNS particles. Our results suggest that, upon glucose starvation, mRNP granule diffusivity may be reduced due to changes in physical interactions, while global crowding in the cytoplasm may be reduced.
Collapse
Affiliation(s)
- Ying Xie
- New York University, School of Medicine, Institute for Systems Genetics, New York, USA
- New York University, Center for Genomics and Systems Biology, Department of Biology, New York, USA
| | - David Gresham
- New York University, Center for Genomics and Systems Biology, Department of Biology, New York, USA
| | - Liam Holt
- New York University, School of Medicine, Institute for Systems Genetics, New York, USA
| |
Collapse
|
26
|
Xie Y, Gresham D, Holt LJ. Increased mesoscale diffusivity in response to acute glucose starvation. MICROPUBLICATION BIOLOGY 2023; 2023:10.17912/micropub.biology.000729. [PMID: 36908311 PMCID: PMC9996311 DOI: 10.17912/micropub.biology.000729] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Figures] [Subscribe] [Scholar Register] [Received: 12/21/2022] [Revised: 02/16/2023] [Accepted: 02/20/2023] [Indexed: 03/14/2023]
Abstract
Macromolecular crowding is an important property of cells that impacts multiple biological processes. Passive microrheology using single particle tracking is a powerful means of studying macromolecular crowding. Here we monitored the diffusivity of self-assembling fluorescent nanoparticles (μNS) and mRNPs ( GFA1 -PP7) in response to acute glucose starvation. mRNP diffusivity was reduced upon glucose starvation as previously reported. By contrast, we observed increased diffusivity of μNS particles. Our results suggest that, upon glucose starvation, mRNP granule diffusivity may be reduced due to increased physical interactions, whereas macromolecular crowding in the cytoplasm may be globally reduced.
Collapse
Affiliation(s)
- Ying Xie
- Institute for Systems Genetics, New York University Langone Medical Center, New York, New York, United States
- Department of Biology, New York University, New York, New York, United States
| | - David Gresham
- Department of Biology, New York University, New York, New York, United States
- Correspondence to: David Gresham (
)
| | - Liam J Holt
- Institute for Systems Genetics, New York University Langone Medical Center, New York, New York, United States
- Correspondence to: Liam J Holt (
)
| |
Collapse
|
27
|
Liu J, Jin Y, Bao JD, Chen X. Coexistence of ergodicity and nonergodicity in the aging two-state random walks. SOFT MATTER 2022; 18:8687-8699. [PMID: 36349834 DOI: 10.1039/d2sm01093c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
The two-state stochastic phenomenon is observed in various systems and is attracting more interest, and it can be described by the two-state random walk (TSRW) model. The TSRW model is a typical two-state renewal process alternating between the continuous-time random walk state and the Lévy walk state, in both of which the sojourn time distributions follow a power law. In this paper, by discussing the statistical properties and calculating the ensemble averaged and time averaged mean squared displacement, the ergodic property and the ultimate diffusive behavior of the aging TSRW is studied. Results reveal that because of the two-state intermittent feature, ergodicity and nonergodicity can coexist in the aging TSRW, which behave as the time scalings of the time averages and ensemble averages not being identically equal. In addition, we find that the unique state occupation mechanism caused by the diverging mean of the sojourn times of one state, determines the aging TSRW's ultimate diffusive behavior at extremely large timescales, i.e., instead of the term with the larger diffusion exponent, the diffusion is surprisingly characterized by the term with the smaller one, which is distinctly different from previous conclusions and known results. At last, we note that the Lévy walk with rests model which also displays aging and ergodicity breaking, can be generalized by the TSRW model.
Collapse
Affiliation(s)
- Jian Liu
- Department of Physics, Beijing Technology and Business University, Beijing, 100048, China.
- Institute of Systems Science, Beijing Technology and Business University, Beijing, 100048, China
- Institute of Theoretical Physics, Chinese Academy of Sciences, Beijing 100190, China
| | - Yuliang Jin
- Institute of Theoretical Physics, Chinese Academy of Sciences, Beijing 100190, China
- School of Physical Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
- Wenzhou Institute, University of Chinese Academy of Sciences, Wenzhou, Zhejiang 325000, China
| | - Jing-Dong Bao
- Department of Physics, Beijing Normal University, Beijing, 100875, China
| | - Xiaosong Chen
- School of Systems Science, Beijing Normal University, Beijing, 100875, China
| |
Collapse
|
28
|
Xue J, Fu Y, Fan S, Cao X, Huang W, Zhang J, Zhao Y, Chen F. Branched immunochip-integrated pairwise barcoding amplification exploring the spatial proximity of two post-translational modifications in distinct cell subpopulations. Chem Commun (Camb) 2022; 58:10020-10023. [PMID: 35983894 DOI: 10.1039/d2cc03833a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Investigating the spatial information of post-translational modifications (PTMs) in distinct cell subpopulations represents a new direction toward single-cell analysis. The specific capture of cell populations combined with PTM spatial proximity visualization making it practically challenging. Here, we develop branched immunochip-integrated pairwise barcoding amplification, termed biChip-PBA, which can perform the respective capture of cell subpopulations expressing different membrane proteins and successive PBA-based fluorescence imaging of PTM proximities. Our work may provide multilevel information for new insights into epigenetic regulation and cell function.
Collapse
Affiliation(s)
- Jing Xue
- Institute of Analytical Chemistry and Instrument for Life Science, The Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, Shaanxi 710049, China.
| | - Youlan Fu
- Institute of Analytical Chemistry and Instrument for Life Science, The Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, Shaanxi 710049, China.
| | - Siyue Fan
- Institute of Analytical Chemistry and Instrument for Life Science, The Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, Shaanxi 710049, China.
| | - Xiaowen Cao
- Institute of Analytical Chemistry and Instrument for Life Science, The Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, Shaanxi 710049, China.
| | - Wei Huang
- Institute of Analytical Chemistry and Instrument for Life Science, The Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, Shaanxi 710049, China.
| | - Jin Zhang
- Institute of Analytical Chemistry and Instrument for Life Science, The Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, Shaanxi 710049, China.
| | - Yongxi Zhao
- Institute of Analytical Chemistry and Instrument for Life Science, The Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, Shaanxi 710049, China.
| | - Feng Chen
- Institute of Analytical Chemistry and Instrument for Life Science, The Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, Shaanxi 710049, China.
| |
Collapse
|
29
|
Kim Y, Joo S, Kim WK, Jeon JH. Active Diffusion of Self-Propelled Particles in Flexible Polymer Networks. Macromolecules 2022. [DOI: 10.1021/acs.macromol.2c00610] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Affiliation(s)
- Yeongjin Kim
- Department of Physics, Pohang University of Science and Technology (POSTECH), Pohang37673, Republic of Korea
| | - Sungmin Joo
- Department of Physics, Pohang University of Science and Technology (POSTECH), Pohang37673, Republic of Korea
| | - Won Kyu Kim
- School of Computational Sciences, Korea Institute for Advanced Study (KIAS), Seoul02455, Republic of Korea
| | - Jae-Hyung Jeon
- Department of Physics, Pohang University of Science and Technology (POSTECH), Pohang37673, Republic of Korea
- Asia Pacific Center for Theoretical Physics (APCTP), Pohang37673, Republic of Korea
| |
Collapse
|
30
|
Szarek D, Jabłoński I, Krapf D, Wyłomańska A. Multifractional Brownian motion characterization based on Hurst exponent estimation and statistical learning. CHAOS (WOODBURY, N.Y.) 2022; 32:083148. [PMID: 36049911 DOI: 10.1063/5.0093836] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/30/2022] [Accepted: 08/02/2022] [Indexed: 06/15/2023]
Abstract
This paper proposes an approach for the estimation of a time-varying Hurst exponent to allow accurate identification of multifractional Brownian motion (MFBM). The contribution provides a prescription for how to deal with the MFBM measurement data to solve regression and classification problems. Theoretical studies are supplemented with computer simulations and real-world examples. Those prove that the procedure proposed in this paper outperforms the best-in-class algorithm.
Collapse
Affiliation(s)
- Dawid Szarek
- Chair of Applied Mathematics, Faculty of Pure and Applied Mathematics, Hugo Steinhaus Center, Wroclaw University of Science and Technology, Wyspianskiego 27, 50-370 Wroclaw, Poland
| | - Ireneusz Jabłoński
- Chair of Electronic and Photonic Metrology, Faculty of Electronics, Photonics and Microsystems, Wroclaw University of Science and Technology, B. Prusa 53/55, 50-317 Wroclaw, Poland
| | - Diego Krapf
- Department of Electrical and Computer Engineering, Colorado State University, Fort Collins, Colorado 80523, USA
| | - Agnieszka Wyłomańska
- Chair of Applied Mathematics, Faculty of Pure and Applied Mathematics, Hugo Steinhaus Center, Wroclaw University of Science and Technology, Wyspianskiego 27, 50-370 Wroclaw, Poland
| |
Collapse
|
31
|
Ferdinandus, Suzuki M, Vu CQ, Harada Y, Sarker SR, Ishiwata S, Kitaguchi T, Arai S. Modulation of Local Cellular Activities using a Photothermal Dye-Based Subcellular-Sized Heat Spot. ACS NANO 2022; 16:9004-9018. [PMID: 35675905 PMCID: PMC9245347 DOI: 10.1021/acsnano.2c00285] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/10/2022] [Accepted: 05/19/2022] [Indexed: 08/25/2023]
Abstract
Thermal engineering at the microscale, such as the regulation and precise evaluation of the temperature within cellular environments, is a major challenge for basic biological research and biomaterials development. We engineered a polymeric nanoparticle having a fluorescent temperature sensory dye and a photothermal dye embedded in the polymer matrix, named nanoheater-thermometer (nanoHT). When nanoHT is illuminated with a near-infrared laser at 808 nm, a subcellular-sized heat spot is generated in a live cell. Fluorescence thermometry allows the temperature increment to be read out concurrently at individual heat spots. Within a few seconds of an increase in temperature by approximately 11.4 °C from the base temperature (37 °C), we observed the death of HeLa cells. The cell death was observed to be triggered from the exact local heat spot at the subcellular level under the fluorescence microscope. Furthermore, we demonstrate the application of nanoHT for the induction of muscle contraction in C2C12 myotubes by heat release. We successfully showed heat-induced contraction to occur in a limited area of a single myotube based on the alteration of protein-protein interactions related to the contraction event. These results demonstrate that even a single heat spot provided by a photothermal material can be extremely effective in altering cellular functions.
Collapse
Affiliation(s)
- Ferdinandus
- Waseda
Bioscience Research Institute in Singapore (WABIOS), Singapore 138667, Singapore
| | - Madoka Suzuki
- Institute
for Protein Research, Osaka University, 3-2 Yamadaoka,
Suita, Osaka 565-0871, Japan
| | - Cong Quang Vu
- Nano
Life Science Institute (WPI-NanoLSI), Kanazawa
University, Kakuma-machi, Kanazawa, 920-1192, Japan
| | - Yoshie Harada
- Institute
for Protein Research, Osaka University, 3-2 Yamadaoka,
Suita, Osaka 565-0871, Japan
- Center
for Quantum Information and Quantum Biology, Osaka University, Osaka 565-0871, Japan
| | - Satya Ranjan Sarker
- Nano
Life Science Institute (WPI-NanoLSI), Kanazawa
University, Kakuma-machi, Kanazawa, 920-1192, Japan
| | - Shin’ichi Ishiwata
- Department
of Physics, Faculty of Science and Engineering, Waseda University, 3-4-1 Okubo, Shinjuku-ku, Tokyo 169-8555, Japan
| | - Tetsuya Kitaguchi
- Laboratory
for Chemistry and Life Science, Institute of Innovative Research, Tokyo Institute of Technology, Kanagawa 226-8503, Japan
| | - Satoshi Arai
- Nano
Life Science Institute (WPI-NanoLSI), Kanazawa
University, Kakuma-machi, Kanazawa, 920-1192, Japan
| |
Collapse
|
32
|
Tang B, Liu BH, Liu ZY, Luo MY, Shi XH, Pang DW. Quantum Dots with a Compact Amphiphilic Zwitterionic Coating. ACS APPLIED MATERIALS & INTERFACES 2022; 14:28097-28104. [PMID: 35686447 DOI: 10.1021/acsami.2c04438] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Generally speaking, it is difficult to keep nanomaterials encapsulated in amphiphilic polymers like octylamine-grafted poly(acrylic acid) (OPA) compact in coating-layer, with a small hydrodynamic size. Here, we prepared stable hydrophilic quantum dots (QDs) via encapsulation in ∼3 nm-long amphiphilic and zwitterionic (AZ) molecules. After encapsulation with AZ molecules, the coated QDs are only 2.1 nm thicker in coating, instead of 5.4 nm with OPA. Meanwhile, the hydrodynamic sizes of CdSe/CdS, ZnCdSeS, ZnCdSe/ZnS, and CdSe/ZnS QDs encapsulated in AZ molecules (AZ-QDs) are less than 15 nm, and 6-7 nm smaller than those of QDs in OPA (OPA-QDs). Notably, both extracellular and intracellular nonspecific binding of AZ-QDs is approximately 100-folds lower than that of OPA-QDs.
Collapse
Affiliation(s)
- Bo Tang
- College of Chemistry and Molecular Sciences, Wuhan University, Wuhan 430072, PR China
| | - Bing-Hua Liu
- College of Chemistry and Molecular Sciences, Wuhan University, Wuhan 430072, PR China
| | - Zhen-Ya Liu
- College of Chemistry and Molecular Sciences, Wuhan University, Wuhan 430072, PR China
| | - Meng-Yao Luo
- College of Chemistry and Molecular Sciences, Wuhan University, Wuhan 430072, PR China
| | - Xue-Hui Shi
- State Key Laboratory of Medicinal Chemical Biology, Tianjin Key Laboratory of Biosensing and Molecular Recognition, Frontiers Science Center for New Organic Matter, Research Center for Analytical Sciences, College of Chemistry, Frontiers Science Center for Cell Responses, Nankai University, Haihe Laboratory of Sustainable Chemical Transformations, Tianjin 300071, P. R. China
| | - Dai-Wen Pang
- College of Chemistry and Molecular Sciences, Wuhan University, Wuhan 430072, PR China
- State Key Laboratory of Medicinal Chemical Biology, Tianjin Key Laboratory of Biosensing and Molecular Recognition, Frontiers Science Center for New Organic Matter, Research Center for Analytical Sciences, College of Chemistry, Frontiers Science Center for Cell Responses, Nankai University, Haihe Laboratory of Sustainable Chemical Transformations, Tianjin 300071, P. R. China
| |
Collapse
|
33
|
Han Z, Vaidya RM, Arogundade OH, Ma L, Zahid MU, Sarkar S, Kuo CW, Selvin PR, Smith AM. Structural Design of Multidentate Copolymers as Compact Quantum Dot Coatings for Live-Cell Single-Particle Imaging. CHEMISTRY OF MATERIALS : A PUBLICATION OF THE AMERICAN CHEMICAL SOCIETY 2022; 34:4621-4632. [PMID: 36968145 PMCID: PMC10038122 DOI: 10.1021/acs.chemmater.2c00498] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
Quantum dots (QDs) are a class of semiconductor nanocrystal used broadly as fluorescent emitters for analytical studies in the life sciences. These nanomaterials are particularly valuable for single-particle imaging and tracking applications in cells and tissues. An ongoing technological goal is to reduce the hydrodynamic size of QDs to enhance access to sterically hindered biological targets. Multidentate polymer coatings are a focus of these efforts and have resulted in compact and stable QDs with hydrodynamic diameters near 10 nm. New developments are needed to reach smaller sizes to further enhance transport through pores in cells and tissues. Here, we describe how structural characteristics of linear multidentate copolymers determine hydrodynamic size, colloidal stability, and biomolecular interactions of coated QDs. We tune copolymer composition, degree of polymerization, and hydrophilic group length, and coat polymers on CdSe and (core)shell (HgCdSe)CdZnS QDs. We find that a broad range of polymer structures and compositions yield stable colloidal dispersions; however, hydrodynamic size minimization and nonspecific binding resistance can only be simultaneously achieved within a narrow range of properties, requiring short polymers, balanced compositions, and small nanocrystals. In quantitative single-molecule imaging assays in synapses of live neurons, size reduction progressively increases labeling specificity of neurotransmitter receptors. Our findings provide a design roadmap to next-generation QDs with sizes approaching fluorescent protein labels that are the standard of many live-cell biomolecular studies.
Collapse
Affiliation(s)
- Zhiyuan Han
- Department of Materials Science and Engineering and Holonyak Micro and Nanotechnology Laboratory, University of Illinois Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Rohit M Vaidya
- Center for Biophysics and Quantitative Biology, University of Illinois Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Opeyemi H Arogundade
- Holonyak Micro and Nanotechnology Laboratory and Department of Bioengineering, University of Illinois Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Liang Ma
- Department of Materials Science and Engineering and Holonyak Micro and Nanotechnology Laboratory, University of Illinois Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Mohammad U Zahid
- Holonyak Micro and Nanotechnology Laboratory and Department of Bioengineering, University of Illinois Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Suresh Sarkar
- Holonyak Micro and Nanotechnology Laboratory and Department of Bioengineering, University of Illinois Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Chia-Wei Kuo
- Department of Bioengineering, University of Illinois Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Paul R Selvin
- Center for Biophysics and Quantitative Biology, Center for the Physics of Living Cells, and Department of Physics, University of Illinois Urbana-Champaign, Urbana, Illinois 61801, United States-8163
| | - Andrew M Smith
- Department of Materials Science and Engineering, Holonyak Micro and Nanotechnology Laboratory, Department of Bioengineering, Cancer Center at Illinois, and Carl R. Woese Institute for Genomic Biology, University of Illinois Urbana-Champaign, Urbana, Illinois 61801, United States
- Carle Illinois College of Medicine, Urbana, Illinois 61801, United States
| |
Collapse
|
34
|
Wang YF, Zhang Q, Tian F, Wang H, Wang Y, Ma X, Huang Q, Cai M, Ji Y, Wu X, Gan Y, Yan Y, Dawson KA, Guo S, Zhang J, Shi X, Shan Y, Liang XJ. Spatiotemporal Tracing of the Cellular Internalization Process of Rod-Shaped Nanostructures. ACS NANO 2022; 16:4059-4071. [PMID: 35191668 DOI: 10.1021/acsnano.1c09684] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Endocytosis, as one of the main ways for nanostructures enter cells, is affected by several aspects, and shape is an especially critical aspect during the endocytosis of nanostructures. However, it has remained challenging to capture the dynamic internalization behaviors of rod-shaped nanostructures while also probing the mechanical aspects of the internalization. Here, using the atomic force microscopy-based force tracing technique, transmission electron microscopy, and molecular dynamic simulation, we mapped the detailed internalization behaviors of rod-shaped nanostructures with different aspect ratios at the single-particle level. We found that the gold nanorod is endocytosed in a noncontinuous and force-rebound rotation manner, herein named "intermittent rotation". The force tracing test indicated that the internalization force (∼81 pN, ∼108 pN, and ∼157 pN) and time (∼0.56 s, ∼0.66 s, and ∼1.14 s for a 12.10 nm × 11.96 nm gold nanosphere and 26.15 nm × 13.05 nm and 48.71 nm × 12.45 nm gold nanorods, respectively) are positively correlated with the aspect ratios. However, internalization speed is negatively correlated with internalization time, irrespective of the aspect ratio. Further, the energy analysis suggested that intermittent rotation from the horizontal to vertical direction can reduce energy dissipation during the internalization process. Thus, to overcome the energy barrier of internalization, the number and angle of rotation increases with aspect ratios. Our findings provide critical missing evidence of rod-shaped nanostructure's internalization, which is essential for fundamentally understanding the internalization mechanism in living cells.
Collapse
Affiliation(s)
- Yi-Feng Wang
- Laboratory of Controllable Nanopharmaceuticals, CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety, CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology, Beijing 100190, P.R. China
- University of Chinese Academy of Sciences, Beijing 100049, P.R. China
| | - Qingrong Zhang
- School of Chemistry and Life Science, Advanced Institute of Materials Science, Changchun University of Technology, Changchun 130012, P.R. China
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun 130022, P.R. China
| | - Falin Tian
- Laboratory of Theoretical and Computational Nanoscience, CAS Key Laboratory for Nanosystem and Hierarchy Fabrication, CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology, Beijing 100190, P.R. China
| | - Hongda Wang
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun 130022, P.R. China
| | - Yufei Wang
- Laboratory of Controllable Nanopharmaceuticals, CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety, CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology, Beijing 100190, P.R. China
- University of Chinese Academy of Sciences, Beijing 100049, P.R. China
| | - Xiaowei Ma
- Laboratory of Controllable Nanopharmaceuticals, CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety, CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology, Beijing 100190, P.R. China
| | - Qianqian Huang
- Laboratory of Controllable Nanopharmaceuticals, CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety, CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology, Beijing 100190, P.R. China
- University of Chinese Academy of Sciences, Beijing 100049, P.R. China
| | - Mingjun Cai
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun 130022, P.R. China
| | - Yinglu Ji
- CAS Key Laboratory of Standardization and Measurement for Nanotechnology, CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology, Beijing 100190, P.R. China
| | - Xiaochun Wu
- CAS Key Laboratory of Standardization and Measurement for Nanotechnology, CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology, Beijing 100190, P.R. China
| | - Yaling Gan
- Laboratory of Controllable Nanopharmaceuticals, CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety, CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology, Beijing 100190, P.R. China
| | - Yan Yan
- Centre for BioNano Interactions, School of Chemistry, School of Biomolecular and Biomedical Science, University College Dublin, Dublin D04 V1W8, Ireland
| | - Kenneth A Dawson
- Centre for BioNano Interactions, School of Chemistry, School of Biomolecular and Biomedical Science, University College Dublin, Dublin D04 V1W8, Ireland
- Guangdong Provincial Education Department Key Laboratory of Nano-Immunoregulation Tumor Microenvironment, The Second Affiliated Hospital, Guangzhou Medical University, Guangzhou 510260, P.R. China
| | - Shutao Guo
- Key Laboratory of Functional Polymer Materials of Ministry of Education, State Key Laboratory of Medicinal Chemical Biology and Institute of Polymer Chemistry, College of Chemistry, Nankai University, Tianjin 300071, P.R. China
| | - Jinchao Zhang
- Key Laboratory of Medicinal Chemistry and Molecular Diagnosis of the Ministry of Education, Key Laboratory of Chemical Biology of Hebei Province, College of Chemistry and Environmental Science, Hebei University, Baoding 071002, P.R China
| | - Xinghua Shi
- University of Chinese Academy of Sciences, Beijing 100049, P.R. China
- Laboratory of Theoretical and Computational Nanoscience, CAS Key Laboratory for Nanosystem and Hierarchy Fabrication, CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology, Beijing 100190, P.R. China
| | - Yuping Shan
- School of Chemistry and Life Science, Advanced Institute of Materials Science, Changchun University of Technology, Changchun 130012, P.R. China
| | - Xing-Jie Liang
- Laboratory of Controllable Nanopharmaceuticals, CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety, CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology, Beijing 100190, P.R. China
- University of Chinese Academy of Sciences, Beijing 100049, P.R. China
| |
Collapse
|
35
|
Khatri D, Brugière T, Athale CA, Delattre M. Evolutionary divergence of anaphase spindle mechanics in nematode embryos constrained by antagonistic pulling and viscous forces. Mol Biol Cell 2022; 33:ar61. [PMID: 35235368 PMCID: PMC9265157 DOI: 10.1091/mbc.e21-10-0532] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
Abstract
Cellular functions like cell division are remarkably conserved across phyla. However the evolutionary principles of cellular organization that drive it are less well explored. Thus, an essential question remains: to what extent cellular parameters evolve without altering the basic function they sustain? Here we have observed 6 different nematode species for which the mitotic spindle is positioned asymmetrically during the first embryonic division. Whereas the C. elegans spindle undergoes oscillations during its displacement, the spindle elongates without oscillations in other species. We asked which evolutionary changes in biophysical parameters could explain differences in spindle motion while maintaining a constant output. Using laser microsurgery of the spindle we revealed that all species are subjected to cortical pulling forces, of varying magnitudes. Using a viscoelastic model to fit the recoil trajectories and with an independent measurement of cytoplasmic viscosity, we extracted the values of cytoplasmic drag, cortical pulling forces and spindle elasticity for all species. We found large variations in cytoplasmic viscosity whereas cortical pulling forces and elasticity were often more constrained. In agreement with previous simulations, we found that increased viscosity correlates with decreased oscillation speeds across species. However, the absence of oscillations despite low viscosity in some species, can only be explained by smaller pulling forces. Consequently, we find that spindle mobility across the species analyzed here is characterized by a tradeoff between cytoplasmic viscosity and pulling forces normalized by the size of the embryo. Our work provides a framework for understanding mechanical constraints on evolutionary diversification of spindle mobility.
Collapse
Affiliation(s)
- Dhruv Khatri
- Div. of Biology, IISER Pune, Dr. Homi Bhabha Road, Pashan, Pune 411008, India
| | - Thibault Brugière
- Laboratory of Biology and Modeling of the Cell, Ecole Normale Supérieure de Lyon, CNRS, Inserm, UCBL, 69007 Lyon, France
| | - Chaitanya A Athale
- Div. of Biology, IISER Pune, Dr. Homi Bhabha Road, Pashan, Pune 411008, India
| | - Marie Delattre
- Laboratory of Biology and Modeling of the Cell, Ecole Normale Supérieure de Lyon, CNRS, Inserm, UCBL, 69007 Lyon, France
| |
Collapse
|
36
|
Lu RX, Huang JH, Luo MB. A simulation study on the subdiffusion of polymer chains in crowded environments containing nanoparticles. Phys Chem Chem Phys 2022; 24:3078-3085. [PMID: 35040462 DOI: 10.1039/d1cp03926a] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Polymer chains in crowded environments often show subdiffusive behavior. We adopt molecular dynamics simulations to study the conditions for the subdiffusion of polymer chains in crowded environments containing randomly distributed, immobile, attractive nanoparticles (NPs). The attraction is strong enough to adsorb polymer chains on NPs. The results show that subdiffusion occurs at a low concentration of polymer chains (cp). A transition from subdiffusion to normal diffusion is observed when cp exceeds the transition concentration , which increases with increasing concentration of NPs while decreases with increasing size of NPs. The high concentration and small size of NPs exert a big effect on the subdiffusion of polymer chains. The subdiffusive behavior of polymer chains can be attributed to the strong adsorption of polymer chains on the attractive NPs. For the subdiffusion case, polymer chains are adsorbed strongly on multiple NPs, and they diffuse via the NP-exchange diffusion mechanism. However for the normal diffusion case, polymer chains are either free or weakly adsorbed on one or a few NPs, and they diffuse mainly via the adsorption-and-desorption diffusion mechanism.
Collapse
Affiliation(s)
- Rong-Xing Lu
- Department of Chemistry, Key Laboratory of Surface & Interface Science of Polymer Materials of Zhejiang Province, Zhejiang Sci-Tech University, Hangzhou 310018, China.
| | - Jian-Hua Huang
- Department of Chemistry, Key Laboratory of Surface & Interface Science of Polymer Materials of Zhejiang Province, Zhejiang Sci-Tech University, Hangzhou 310018, China.
| | - Meng-Bo Luo
- Department of Physics, Zhejiang University, Hangzhou 310027, China
| |
Collapse
|
37
|
Wang W, Metzler R, Cherstvy AG. Anomalous diffusion, aging, and nonergodicity of scaled Brownian motion with fractional Gaussian noise: overview of related experimental observations and models. Phys Chem Chem Phys 2022; 24:18482-18504. [DOI: 10.1039/d2cp01741e] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
How does a systematic time-dependence of the diffusion coefficient $D (t)$ affect the ergodic and statistical characteristics of fractional Brownian motion (FBM)? Here, we examine how the behavior of the...
Collapse
|
38
|
Liu J, Zhu P, Bao JD, Chen X. Strong anomalous diffusive behaviors of the two-state random walk process. Phys Rev E 2022; 105:014122. [PMID: 35193269 DOI: 10.1103/physreve.105.014122] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2021] [Accepted: 01/06/2022] [Indexed: 06/14/2023]
Abstract
The phenomenon of the two-state process is observed in various systems and is increasingly attracting attention, such that there is a need for a theoretical model of the process. In this paper, we present a prototypal two-state random walk (TSRW) model of a renewal process alternating between the continuous-time random walk (CTRW) state and Lévy walk (LW) state. The jump length distribution of the CTRW state is assumed to be Gaussian whereas the time distributions of the two states are both considered to follow a power law. The diffusive behavior is analyzed and discussed by calculating the mean squared displacement (MSD) analytically and numerically. The results reveal that it displays strong anomalous diffusive behaviors caused by random motions of both states, i.e., two anomalous diffusion terms coexist in the expression of the MSD, and the time distribution which has the heavier tail determines their forms. Moreover, because the two diffusion terms originate from different mechanisms, we find that the diffusion can be characterized by either the term with the largest diffusion exponent or the term with the largest diffusion coefficient at long timescales, which shows very different properties from the single-state process. In addition, the two-state nature of the process of the particle moving in a velocity field makes the TSRW model applicable to describe it. Results obtained from the two-state model reveal that the diffusion can even exhibit subdiffusive behavior, which is significantly different from known results obtained using the single-state model.
Collapse
Affiliation(s)
- Jian Liu
- Department of Physics, Institute of Systems Science, Beijing Technology and Business University, Beijing 100048, China
| | - Ping Zhu
- Department of Physics, Institute of Systems Science, Beijing Technology and Business University, Beijing 100048, China
| | - Jing-Dong Bao
- Department of Physics, Beijing Normal University, Beijing 100875, China
| | - Xiaosong Chen
- School of Systems Science, Beijing Normal University, Beijing 100875, China
| |
Collapse
|
39
|
Bellotto N, Agudo-Canalejo J, Colin R, Golestanian R, Malengo G, Sourjik V. Dependence of diffusion in Escherichia coli cytoplasm on protein size, environmental conditions, and cell growth. eLife 2022; 11:82654. [PMID: 36468683 PMCID: PMC9810338 DOI: 10.7554/elife.82654] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2022] [Accepted: 12/02/2022] [Indexed: 12/12/2022] Open
Abstract
Inside prokaryotic cells, passive translational diffusion typically limits the rates with which cytoplasmic proteins can reach their locations. Diffusion is thus fundamental to most cellular processes, but the understanding of protein mobility in the highly crowded and non-homogeneous environment of a bacterial cell is still limited. Here, we investigated the mobility of a large set of proteins in the cytoplasm of Escherichia coli, by employing fluorescence correlation spectroscopy (FCS) combined with simulations and theoretical modeling. We conclude that cytoplasmic protein mobility could be well described by Brownian diffusion in the confined geometry of the bacterial cell and at the high viscosity imposed by macromolecular crowding. We observed similar size dependence of protein diffusion for the majority of tested proteins, whether native or foreign to E. coli. For the faster-diffusing proteins, this size dependence is well consistent with the Stokes-Einstein relation once taking into account the specific dumbbell shape of protein fusions. Pronounced subdiffusion and hindered mobility are only observed for proteins with extensive interactions within the cytoplasm. Finally, while protein diffusion becomes markedly faster in actively growing cells, at high temperature, or upon treatment with rifampicin, and slower at high osmolarity, all of these perturbations affect proteins of different sizes in the same proportions, which could thus be described as changes of a well-defined cytoplasmic viscosity.
Collapse
Affiliation(s)
- Nicola Bellotto
- Max Planck Institute for Terrestrial Microbiology and Center for Synthetic Microbiology (SYNMIKRO)MarburgGermany
| | | | - Remy Colin
- Max Planck Institute for Terrestrial Microbiology and Center for Synthetic Microbiology (SYNMIKRO)MarburgGermany
| | - Ramin Golestanian
- Max Planck Institute for Dynamics and Self-OrganizationGöttingenGermany,Rudolf Peierls Centre for Theoretical Physics, University of OxfordOxfordUnited Kingdom
| | - Gabriele Malengo
- Max Planck Institute for Terrestrial Microbiology and Center for Synthetic Microbiology (SYNMIKRO)MarburgGermany
| | - Victor Sourjik
- Max Planck Institute for Terrestrial Microbiology and Center for Synthetic Microbiology (SYNMIKRO)MarburgGermany
| |
Collapse
|
40
|
Liu J, Zhang C, Bao JD, Chen X. Correlated continuous-time random walk in the velocity field: the role of velocity and weak asymptotics. SOFT MATTER 2021; 17:9786-9798. [PMID: 34657952 DOI: 10.1039/d1sm00995h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Within the framework of a space-time correlated continuous-time random walk model, anomalous diffusion of particles moving in the velocity field is studied in this paper. The weak asymptotic form ω(t) ∼ t-(1+α), 1 < α < 2 for large t, is considered to be the waiting time distribution. The analytical results reveal that the diffusion in the velocity field, i.e., the mean squared displacement, can display a multi-fractional form caused by dispersive bias and space-time correlation. The numerical results indicate that the multi-fractional diffusion leads to a crossover phenomenon in-between the process at an intermediate timescale, followed by a steady state which is always determined by the largest diffusion exponent term. In addition, the role of velocity and weak asymptotics is discussed. The extremely small fluid velocity can characterize the diffusion by a diffusion coefficient instead of diffusion exponent, which is distinctly different from the former definition. In particular, for the waiting time displaying a weak asymptotic property, if the anomalous part is suppressed by the normal part, a second crossover phenomenon appears at an intermediate timescale, followed by a steady normal diffusion, which implies that the anomalies underlying the process are smoothed out at large timescales. Moreover, we discuss that the consideration of bias and correlation could help to avoid a possible not readily noticeable mistake in studying the topic concerned in this paper, which may be helpful in the relevant experimental research.
Collapse
Affiliation(s)
- Jian Liu
- Department of Physics, Beijing Technology and Business University, Beijing, 100048, China.
- Institute of Systems Science, Beijing Technology and Business University, Beijing, 100048, China
| | - Caiyun Zhang
- Department of Physics, Beijing Technology and Business University, Beijing, 100048, China.
- Institute of Systems Science, Beijing Technology and Business University, Beijing, 100048, China
| | - Jing-Dong Bao
- Department of Physics, Beijing Normal University, Beijing, 100875, China
| | - Xiaosong Chen
- School of Systems Science, Beijing Normal University, Beijing, 100875, China
| |
Collapse
|
41
|
Fox ZR, Barkai E, Krapf D. Aging power spectrum of membrane protein transport and other subordinated random walks. Nat Commun 2021; 12:6162. [PMID: 34697310 PMCID: PMC8546023 DOI: 10.1038/s41467-021-26465-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2021] [Accepted: 10/04/2021] [Indexed: 11/09/2022] Open
Abstract
Single-particle tracking offers detailed information about the motion of molecules in complex environments such as those encountered in live cells, but the interpretation of experimental data is challenging. One of the most powerful tools in the characterization of random processes is the power spectral density. However, because anomalous diffusion processes in complex systems are usually not stationary, the traditional Wiener-Khinchin theorem for the analysis of power spectral densities is invalid. Here, we employ a recently developed tool named aging Wiener-Khinchin theorem to derive the power spectral density of fractional Brownian motion coexisting with a scale-free continuous time random walk, the two most typical anomalous diffusion processes. Using this analysis, we characterize the motion of voltage-gated sodium channels on the surface of hippocampal neurons. Our results show aging where the power spectral density can either increase or decrease with observation time depending on the specific parameters of both underlying processes.
Collapse
Affiliation(s)
- Zachary R Fox
- School of Biomedical Engineering, Colorado State University, Fort Collins, CO, USA
- The Center for Nonlinear Studies and Computational and Statistical Sciences Division, Los Alamos National Laboratory, Los Alamos, NM, USA
| | - Eli Barkai
- Department of Physics, Institute of Nanotechnology and Advanced Materials, Bar-Ilan University, Ramat-Gan, Israel
| | - Diego Krapf
- School of Biomedical Engineering, Colorado State University, Fort Collins, CO, USA.
- Electrical and Computer Engineering, Colorado State University, Fort Collins, CO, USA.
| |
Collapse
|
42
|
Zhao Y, Lu Y, Wang D. Tracking of Nanoparticle Diffusion at a Liquid-Liquid Interface Adsorbed by Nonionic Surfactants. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2021; 37:12118-12127. [PMID: 34610245 DOI: 10.1021/acs.langmuir.1c01978] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Emulsions stabilized by both nanoparticles and surfactants often display longer shelf life than those stabilized by nanoparticles or surfactants alone. Although numerous works have been conducted to understand the effect of nanoparticles and surfactants on the variation of interfacial tension, little is known about interfacial diffusion when both nanoparticles and surfactants are present at interfaces. In this work, we used single-particle fluorescence tracking to study the lateral diffusion of individual hydrophobic nanoparticles at hexane-glycerol interfaces adsorbed by different amounts of nonionic surfactants. When the surfactant concentration is over a threshold, we found that the nanoparticle diffusion exhibits a two-regime behavior involving short-time Brownian and the emergence of subdiffusive, non-Gaussian, and dynamically anticorrelated diffusion in the long lag time regime. A stepwise analysis rationalized diffusion in different lag time regimes, leading to a mechanistic interpretation regarding the two-regime behavior. These results could provide insight into the understanding of the synergistic effect for the surfactant-assistant Pickering emulsion.
Collapse
Affiliation(s)
- Yuehua Zhao
- State Key Laboratory of Polymer Physics and Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun 130022, P. R. China
- University of Science and Technology of China, Hefei 230026, P. R. China
| | - Yuyuan Lu
- State Key Laboratory of Polymer Physics and Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun 130022, P. R. China
| | - Dapeng Wang
- State Key Laboratory of Polymer Physics and Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun 130022, P. R. China
- University of Science and Technology of China, Hefei 230026, P. R. China
| |
Collapse
|
43
|
Briane V, Vimond M, Kervrann C. An overview of diffusion models for intracellular dynamics analysis. Brief Bioinform 2021; 21:1136-1150. [PMID: 31204428 DOI: 10.1093/bib/bbz052] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2019] [Revised: 03/15/2019] [Accepted: 04/09/2019] [Indexed: 11/13/2022] Open
Abstract
We present an overview of diffusion models commonly used for quantifying the dynamics of intracellular particles (e.g. biomolecules) inside eukaryotic living cells. It is established that inference on the modes of mobility of molecules is central in cell biology since it reflects interactions between structures and determines functions of biomolecules in the cell. In that context, Brownian motion is a key component in short distance transportation (e.g. connectivity for signal transduction). Another dynamical process that has been heavily studied in the past decade is the motor-mediated transport (e.g. dynein, kinesin and myosin) of molecules. Primarily supported by actin filament and microtubule network, it ensures spatial organization and temporal synchronization in the intracellular mechanisms and structures. Nevertheless, the complexity of internal structures and molecular processes in the living cell influence the molecular dynamics and prevent the systematic application of pure Brownian or directed motion modeling. On the one hand, cytoskeleton density will hinder the free displacement of the particle, a phenomenon called subdiffusion. On the other hand, the cytoskeleton elasticity combined with thermal bending can contribute a phenomenon called superdiffusion. This paper discusses the basics of diffusion modes observed in eukariotic cells, by introducing the essential properties of these processes. Applications of diffusion models include protein trafficking and transport and membrane diffusion.
Collapse
Affiliation(s)
- Vincent Briane
- Inria, Centre Rennes-Bretagne Atlantique, SERPICO Project Team, Rennes, France.,CREST (Ensai, Université Bretagne Loire), Bruz, France
| | - Myriam Vimond
- CREST (Ensai, Université Bretagne Loire), Bruz, France
| | - Charles Kervrann
- Inria, Centre Rennes-Bretagne Atlantique, SERPICO Project Team, Rennes, France
| |
Collapse
|
44
|
Zhang P, Wang S. Real-Time analysis of exosome secretion of single cells with single molecule imaging. ACTA ACUST UNITED AC 2021; 45:1449-1451. [PMID: 34539042 PMCID: PMC8445240 DOI: 10.32604/biocell.2021.017607] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
The exosome-mediated response can promote or restrain the diseases by regulating the intracellular pathways, making the exosome become an effective marker for diagnosis and therapeutic control at the single-cell level. However, real-time analysis is hard to be achieved with traditional approaches because the exosomes usually need to be enriched by ultracentrifugation for a measurable signal-to-noise ratio. Recently developed label-free single-molecule imaging approaches may become an real-time quantitative tool for the analysis of single exosomes and related secretion behaviors of single living cells owing to their extreme sensitivity.
Collapse
Affiliation(s)
- Pengfei Zhang
- Biodesign Center for Bioelectronics and Biosensors, Arizona State University, Tempe, 85287, USA
| | - Shaopeng Wang
- Biodesign Center for Bioelectronics and Biosensors, Arizona State University, Tempe, 85287, USA.,School of Biological and Health Systems Engineering, Arizona State University, Tempe, 85287, USA
| |
Collapse
|
45
|
Magnetic Nanoprobes for Spatio-Mechanical Manipulation in Single Cells. NANOMATERIALS 2021; 11:nano11092267. [PMID: 34578584 PMCID: PMC8471295 DOI: 10.3390/nano11092267] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/30/2021] [Revised: 08/25/2021] [Accepted: 08/27/2021] [Indexed: 02/08/2023]
Abstract
Magnetic nanoparticles (MNPs) are widely known as valuable agents for biomedical applications. Recently, MNPs were further suggested to be used for a remote and non-invasive manipulation, where their spatial redistribution or force response in a magnetic field provides a fine-tunable stimulus to a cell. Here, we investigated the properties of two different MNPs and assessed their suitability for spatio-mechanical manipulations: semisynthetic magnetoferritin nanoparticles and fully synthetic 'nanoflower'-shaped iron oxide nanoparticles. As well as confirming their monodispersity in terms of structure, surface potential, and magnetic response, we monitored the MNP performance in a living cell environment using fluorescence microscopy and asserted their biocompatibility. We then demonstrated facilitated spatial redistribution of magnetoferritin compared to 'nanoflower'-NPs after microinjection, and a higher magnetic force response of these NPs compared to magnetoferritin inside a cell. Our remote manipulation assays present these tailored magnetic materials as suitable agents for applications in magnetogenetics, biomedicine, or nanomaterial research.
Collapse
|
46
|
Korabel N, Han D, Taloni A, Pagnini G, Fedotov S, Allan V, Waigh TA. Local Analysis of Heterogeneous Intracellular Transport: Slow and Fast Moving Endosomes. ENTROPY (BASEL, SWITZERLAND) 2021; 23:958. [PMID: 34441098 PMCID: PMC8394768 DOI: 10.3390/e23080958] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/14/2021] [Revised: 07/19/2021] [Accepted: 07/23/2021] [Indexed: 01/14/2023]
Abstract
Trajectories of endosomes inside living eukaryotic cells are highly heterogeneous in space and time and diffuse anomalously due to a combination of viscoelasticity, caging, aggregation and active transport. Some of the trajectories display switching between persistent and anti-persistent motion, while others jiggle around in one position for the whole measurement time. By splitting the ensemble of endosome trajectories into slow moving subdiffusive and fast moving superdiffusive endosomes, we analyzed them separately. The mean squared displacements and velocity auto-correlation functions confirm the effectiveness of the splitting methods. Applying the local analysis, we show that both ensembles are characterized by a spectrum of local anomalous exponents and local generalized diffusion coefficients. Slow and fast endosomes have exponential distributions of local anomalous exponents and power law distributions of generalized diffusion coefficients. This suggests that heterogeneous fractional Brownian motion is an appropriate model for both fast and slow moving endosomes. This article is part of a Special Issue entitled: "Recent Advances In Single-Particle Tracking: Experiment and Analysis" edited by Janusz Szwabiński and Aleksander Weron.
Collapse
Affiliation(s)
- Nickolay Korabel
- Department of Mathematics, The University of Manchester, Manchester M13 9PL, UK; (D.H.); (S.F.)
| | - Daniel Han
- Department of Mathematics, The University of Manchester, Manchester M13 9PL, UK; (D.H.); (S.F.)
- School of Biological Sciences, The University of Manchester, Manchester M13 9PT, UK;
- Biological Physics, Department of Physics and Astronomy, The University of Manchester, Manchester M13 9PL, UK
| | - Alessandro Taloni
- CNR—Consiglio Nazionale delle Ricerche, Istituto dei Sistemi Complessi, Via dei Taurini 19, 00185 Roma, Italy;
| | - Gianni Pagnini
- BCAM—Basque Center for Applied Mathematics, Mazarredo 14, 48009 Bilbao, Spain;
- Ikerbasque—Basque Foundation for Science, Plaza Euskadi 5, 48009 Bilbao, Spain
| | - Sergei Fedotov
- Department of Mathematics, The University of Manchester, Manchester M13 9PL, UK; (D.H.); (S.F.)
| | - Viki Allan
- School of Biological Sciences, The University of Manchester, Manchester M13 9PT, UK;
| | - Thomas Andrew Waigh
- Biological Physics, Department of Physics and Astronomy, The University of Manchester, Manchester M13 9PL, UK
| |
Collapse
|
47
|
Speckner K, Weiss M. Single-Particle Tracking Reveals Anti-Persistent Subdiffusion in Cell Extracts. ENTROPY (BASEL, SWITZERLAND) 2021; 23:892. [PMID: 34356433 PMCID: PMC8303845 DOI: 10.3390/e23070892] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/15/2021] [Revised: 07/06/2021] [Accepted: 07/09/2021] [Indexed: 01/08/2023]
Abstract
Single-particle tracking (SPT) has become a powerful tool to quantify transport phenomena in complex media with unprecedented detail. Based on the reconstruction of individual trajectories, a wealth of informative measures become available for each particle, allowing for a detailed comparison with theoretical predictions. While SPT has been used frequently to explore diffusive transport in artificial fluids and inside living cells, intermediate systems, i.e., biochemically active cell extracts, have been studied only sparsely. Extracts derived from the eggs of the clawfrog Xenopus laevis, for example, are known for their ability to support and mimic vital processes of cells, emphasizing the need to explore also the transport phenomena of nano-sized particles in such extracts. Here, we have performed extensive SPT on beads with 20 nm radius in native and chemically treated Xenopus extracts. By analyzing a variety of distinct measures, we show that these beads feature an anti-persistent subdiffusion that is consistent with fractional Brownian motion. Chemical treatments did not grossly alter this finding, suggesting that the high degree of macromolecular crowding in Xenopus extracts equips the fluid with a viscoelastic modulus, hence enforcing particles to perform random walks with a significant anti-persistent memory kernel.
Collapse
Affiliation(s)
| | - Matthias Weiss
- Experimental Physics I, University of Bayreuth, Universitätsstr. 30, D-95447 Bayreuth, Germany;
| |
Collapse
|
48
|
Definition of the immune evasion-replication interface of rabies virus P protein. PLoS Pathog 2021; 17:e1009729. [PMID: 34237115 PMCID: PMC8291714 DOI: 10.1371/journal.ppat.1009729] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2021] [Revised: 07/20/2021] [Accepted: 06/18/2021] [Indexed: 12/24/2022] Open
Abstract
Rabies virus phosphoprotein (P protein) is a multifunctional protein that plays key roles in replication as the polymerase cofactor that binds to the complex of viral genomic RNA and the nucleoprotein (N protein), and in evading the innate immune response by binding to STAT transcription factors. These interactions are mediated by the C-terminal domain of P (PCTD). The colocation of these binding sites in the small globular PCTD raises the question of how these interactions underlying replication and immune evasion, central to viral infection, are coordinated and, potentially, coregulated. While direct data on the binding interface of the PCTD for STAT1 is available, the lack of direct structural data on the sites that bind N protein limits our understanding of this interaction hub. The PCTD was proposed to bind via two sites to a flexible loop of N protein (Npep) that is not visible in crystal structures, but no direct analysis of this interaction has been reported. Here we use Nuclear Magnetic Resonance, and molecular modelling to show N protein residues, Leu381, Asp383, Asp384 and phosphor-Ser389, are likely to bind to a ‘positive patch’ of the PCTD formed by Lys211, Lys214 and Arg260. Furthermore, in contrast to previous predictions we identify a single site of interaction on the PCTD by this Npep. Intriguingly, this site is proximal to the defined STAT1 binding site that includes Ile201 to Phe209. However, cell-based assays indicate that STAT1 and N protein do not compete for P protein. Thus, it appears that interactions critical to replication and immune evasion can occur simultaneously with the same molecules of P protein so that the binding of P protein to activated STAT1 can potentially occur without interrupting interactions involved in replication. These data suggest that replication complexes might be directly involved in STAT1 antagonism. For viruses to infect cells and generate progeny, they must be able to mediate replication, while simultaneously evading the innate immune system. Viruses with small genomes often achieve this through multifunctional proteins that have roles in both replication and immune evasion, such as the phosphoprotein (P protein) of rabies virus. P protein is an essential cofactor in genome replication and transcription, dependent on the well-folded C-terminal domain (PCTD), which binds to the nucleoprotein (N protein) when complexed with RNA. The PCTD can also bind and antagonize signal transducers and activators of transcription (STAT) proteins, that are essential for activating antiviral mechanisms. Here we show using Nuclear Magnetic Resonance spectroscopy and cell-based assays, that the STAT1-binding and N-binding interfaces are proximal but, nevertheless, it appears that the same molecule of PCTD can simultaneously bind STAT1 and N protein. These data suggest that P-protein-STAT1 interaction, critical to immune evasion, can occur without interrupting interactions underlying replication, and so replication complexes might be directly involved in STAT1 antagonism.
Collapse
|
49
|
Miangolarra AM, Duperray-Susini A, Coppey M, Castellana M. Two timescales control the creation of large protein aggregates in cells. Biophys J 2021; 120:2394-2399. [PMID: 33961867 DOI: 10.1016/j.bpj.2021.04.032] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2020] [Revised: 03/30/2021] [Accepted: 04/29/2021] [Indexed: 11/27/2022] Open
Abstract
Protein aggregation is of particular interest because of its connection with many diseases and disorders. Many factors can alter the dynamics and result of this process, one of them being the diffusivity of the monomers and aggregates in the system. Here, we study experimentally and theoretically an aggregation process in cells, and we identify two distinct physical timescales that set the number and size of aggregates. The first timescale involves fast aggregation of small clusters freely diffusing in the cytoplasm, whereas in the second one, the aggregates are larger than the pore size of the cytoplasm and thus barely diffuse, and the aggregation process is slowed down. However, the process is not entirely halted, potentially reflecting a myriad of active but random forces that stir the aggregates. Such a slow timescale is essential to account for the experimental results of the aggregation process. These results could also have implications in other processes of spatial organization in cell biology, such as phase-separated droplets.
Collapse
Affiliation(s)
- Ander Movilla Miangolarra
- Laboratoire Physico Chimie Curie, Institut Curie, PSL Research University, CNRS UMR 168, Paris, France; Sorbonne Universités, UPMC University Paris 06, Paris, France
| | - Aléria Duperray-Susini
- Laboratoire Physico Chimie Curie, Institut Curie, PSL Research University, CNRS UMR 168, Paris, France; Sorbonne Universités, UPMC University Paris 06, Paris, France
| | - Mathieu Coppey
- Laboratoire Physico Chimie Curie, Institut Curie, PSL Research University, CNRS UMR 168, Paris, France; Sorbonne Universités, UPMC University Paris 06, Paris, France
| | - Michele Castellana
- Laboratoire Physico Chimie Curie, Institut Curie, PSL Research University, CNRS UMR 168, Paris, France; Sorbonne Universités, UPMC University Paris 06, Paris, France.
| |
Collapse
|
50
|
Zhang P, Ma G, Wan Z, Wang S. Quantification of Single-Molecule Protein Binding Kinetics in Complex Media with Prism-Coupled Plasmonic Scattering Imaging. ACS Sens 2021; 6:1357-1366. [PMID: 33720692 DOI: 10.1021/acssensors.0c02729] [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: 12/18/2022]
Abstract
Measuring molecular binding is critical for understanding molecular-scale biological processes and screening drugs. Label-free detection technologies, such as surface plasmon resonance (SPR), have been developed for analyzing analytes in their natural forms. However, the specificity of these methods is solely relying on surface chemistry and has often nonspecific binding issues when working with samples in complex media. Herein, we show that single-molecule-based measurement can distinct specific and nonspecific binding processes by quantifying the mass and binding dynamics of individual-bound analyte molecules, thus allowing the binding kinetic analysis in complex media such as serum. In addition, this single-molecule imaging is realized in a commonly used Kretschmann prism-coupled SPR system, thus providing a convenient solution to realize high-resolution imaging on widely used prism-coupled SPR systems.
Collapse
Affiliation(s)
- Pengfei Zhang
- Biodesign Center for Bioelectronics and Biosensors, Arizona State University, Tempe, Arizona 85287 United States
| | - Guangzhong Ma
- Biodesign Center for Bioelectronics and Biosensors, Arizona State University, Tempe, Arizona 85287 United States
| | - Zijian Wan
- Biodesign Center for Bioelectronics and Biosensors, Arizona State University, Tempe, Arizona 85287 United States
- School of Electrical, Energy and Computer Engineering, Arizona State University, Tempe, Arizona 85287, United States
| | - Shaopeng Wang
- Biodesign Center for Bioelectronics and Biosensors, Arizona State University, Tempe, Arizona 85287 United States
| |
Collapse
|