1
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Singh A, Thutupalli S, Kumar M, Ameta S. Constrained dynamics of DNA oligonucleotides in phase-separated droplets. Biophys J 2024; 123:1458-1466. [PMID: 38169216 PMCID: PMC11163293 DOI: 10.1016/j.bpj.2023.12.025] [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: 10/13/2023] [Revised: 12/20/2023] [Accepted: 12/28/2023] [Indexed: 01/05/2024] Open
Abstract
Understanding the dynamics of biomolecules in complex environments is crucial for elucidating the effect of condensed and heterogeneous environments on their functional properties. A relevant environment-and one that can also be mimicked easily in vitro-is that of phase-separated droplets. While phase-separated droplet systems have been shown to compartmentalize a wide range of functional biomolecules, the effects of internal structuration of droplets on the dynamics and mobility of internalized molecules remain poorly understood. Here, we use fluorescence correlation spectroscopy to measure the dynamics of short oligonucleotides encapsulated within two representative kinds of uncharged and charged phase-separated droplets. We find that the internal structuration controls the oligonucleotide dynamics in these droplets, revealed by measuring physical parameters at high spatiotemporal resolution. By varying oligonucleotide length and salt concentrations (and thereby charge screening), we found that the dynamics are significantly affected in the noncharged droplets compared to the charged system. Our work lays the foundation for unraveling and quantifying the physical parameters governing biomolecular transport in the condensed environment.
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Affiliation(s)
- Anupam Singh
- Simons Centre for the Study of Living Machines, National Centre for Biological Sciences, Tata Institute of Fundamental Research, Bengaluru, India
| | - Shashi Thutupalli
- Simons Centre for the Study of Living Machines, National Centre for Biological Sciences, Tata Institute of Fundamental Research, Bengaluru, India; International Centre for Theoretical Sciences, Tata Institute of Fundamental Research, Bengaluru, India
| | - Manoj Kumar
- Simons Centre for the Study of Living Machines, National Centre for Biological Sciences, Tata Institute of Fundamental Research, Bengaluru, India.
| | - Sandeep Ameta
- Simons Centre for the Study of Living Machines, National Centre for Biological Sciences, Tata Institute of Fundamental Research, Bengaluru, India; Trivedi School of Biosciences, Ashoka University, Sonepat, India.
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2
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Shi H, Du L, Huang F, Guo W. Weak ergodicity breaking and anomalous diffusion in collective motion of active particles under spatiotemporal disorder. Phys Rev E 2023; 107:024114. [PMID: 36932613 DOI: 10.1103/physreve.107.024114] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2021] [Accepted: 01/12/2023] [Indexed: 06/18/2023]
Abstract
The effects of spatiotemporal disorder, i.e., both the noise and quenched disorder, on the dynamics of active particles in two dimensions are investigated. We demonstrate that within the tailored parameter regime, nonergodic superdiffusion and nonergodic subdiffusion occur in the system, identified by the observable quantities (the mean squared displacement and ergodicity-breaking parameter) averaged over both the noise and realizations of quenched disorder. Their origins are attributed to the competition effects between the neighbor alignment and spatiotemporal disorder on the collective motion of active particles. These results may be helpful for further understanding the nonequilibrium transport process of active particles, as well as for detection of the transport of self-propelled particles in complex and crowded environments.
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Affiliation(s)
- Hongda Shi
- Key Laboratory of Artificial Microstructures in Yunnan Higher Education Institutions, School of Physical Science and Technology, Kunming University, Kunming 650214, China
| | - Luchun Du
- Department of Physics, Yunnan University, Kunming 650091, China
| | - Feijie Huang
- Key Laboratory of Artificial Microstructures in Yunnan Higher Education Institutions, School of Physical Science and Technology, Kunming University, Kunming 650214, China
| | - Wei Guo
- Key Laboratory of Artificial Microstructures in Yunnan Higher Education Institutions, School of Physical Science and Technology, Kunming University, Kunming 650214, China
- Yunnan Key Laboratory of Metal-Organic Molecular Materials and Devices, Kunming University, Kunming 650214, China
- National Laboratory of Solid State Microstructures, Department of Physics, Nanjing University, Nanjing 210093, China
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3
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Moud AA. Fluorescence Recovery after Photobleaching in Colloidal Science: Introduction and Application. ACS Biomater Sci Eng 2022; 8:1028-1048. [PMID: 35201752 DOI: 10.1021/acsbiomaterials.1c01422] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
FRAP (fluorescence recovery after photo bleaching) is a method for determining diffusion in material science. In industrial applications such as medications, foods, Medtech, hygiene, and textiles, the diffusion process has a substantial influence on the overall qualities of goods. All these complex and heterogeneous systems have diffusion-based processes at the local level. FRAP is a fluorescence-based approach for detecting diffusion; in this method, a high-intensity laser is made for a brief period and then applied to the samples, bleaching the fluorescent chemical inside the region, which is subsequently filled up by natural diffusion. This brief Review will focus on the existing research on employing FRAP to measure colloidal system heterogeneity and explore diffusion into complicated structures. This description of FRAP will be followed by a discussion of how FRAP is intended to be used in colloidal science. When constructing the current Review, the most recent publications were reviewed for this assessment. Because of the large number of FRAP articles in colloidal research, there is currently a dearth of knowledge regarding the growth of FRAP's significance to colloidal science. Colloids make up only 2% of FRAP papers, according to ISI Web of Knowledge.
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Affiliation(s)
- Aref Abbasi Moud
- Department of Chemical and Biological Engineering, The University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada
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4
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Pastore R, Ciarlo A, Pesce G, Greco F, Sasso A. Rapid Fickian Yet Non-Gaussian Diffusion after Subdiffusion. PHYSICAL REVIEW LETTERS 2021; 126:158003. [PMID: 33929249 DOI: 10.1103/physrevlett.126.158003] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/02/2021] [Accepted: 03/11/2021] [Indexed: 05/23/2023]
Abstract
The recently discovered Fickian yet non-Gaussian diffusion (FnGD) is here finely tuned and investigated over a wide range of probabilities and timescales using a quasi-2D suspension of colloidal beads under the action of a static and spatially random optical force field. This experimental model allows one to demonstrate that a "rapid" FnGD regime with a diffusivity close to that of free suspension can originate from earlier subdiffusion. We show that these two regimes are strictly tangled: as subdiffusion deepens upon increasing the optical force, deviations from Gaussianity in the FnGD regime become larger and more persistent in time. In addition, the distinctive exponential tails of FnGD are quickly built up in the subdiffusive regime. Our results shed new light on previous experimental observations and suggest that FnGD may generally be a memory effect of earlier subdiffusive processes.
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Affiliation(s)
- Raffaele Pastore
- Department of Chemical, Materials and Production Engineering, University of Naples Federico II, P.le Tecchio 80, Napoli 80125, Italy
| | - Antonio Ciarlo
- Department of Physics E. Pancini, University of Naples Federico II, Complesso Universitario Monte S. Angelo, Via Cintia, I-80126 Naples, Italy
| | - Giuseppe Pesce
- Department of Physics E. Pancini, University of Naples Federico II, Complesso Universitario Monte S. Angelo, Via Cintia, I-80126 Naples, Italy
| | - Francesco Greco
- Department of Chemical, Materials and Production Engineering, University of Naples Federico II, P.le Tecchio 80, Napoli 80125, Italy
| | - Antonio Sasso
- Department of Physics E. Pancini, University of Naples Federico II, Complesso Universitario Monte S. Angelo, Via Cintia, I-80126 Naples, Italy
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5
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Cho HW, Kim H, Sung BJ, Kim JS. Tracer Diffusion in Tightly-Meshed Homogeneous Polymer Networks: A Brownian Dynamics Simulation Study. Polymers (Basel) 2020; 12:E2067. [PMID: 32932910 PMCID: PMC7569880 DOI: 10.3390/polym12092067] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2020] [Revised: 09/07/2020] [Accepted: 09/09/2020] [Indexed: 12/02/2022] Open
Abstract
We report Brownian dynamics simulations of tracer diffusion in regularly crosslinked polymer networks in order to elucidate the transport of a tracer particle in polymer networks. The average mesh size of homogeneous polymer networks is varied by assuming different degrees of crosslinking or swelling, and the size of a tracer particle is comparable to the average mesh size. Simulation results show subdiffusion of a tracer particle at intermediate time scales and normal diffusion at long times. In particular, the duration of subdiffusion is significantly prolonged as the average mesh size decreases with increasing degree of crosslinking, for which long-time diffusion occurs via the hopping processes of a tracer particle after undergoing rattling motions within a cage of the network mesh for an extended period of time. On the other hand, the cage dynamics and hopping process are less pronounced as the mesh size decreases with increasing polymer volume fractions. The interpretation is provided in terms of fluctuations in network mesh size: at higher polymer volume fractions, the network fluctuations are large enough to allow for collective, structural changes of network meshes, so that a tracer particle can escape from the cage, whereas, at lower volume fractions, the fluctuations are so small that a tracer particle remains trapped within the cage for a significant period of time before making infrequent jumps out of the cage. This work suggests that fluctuation in mesh size, as well as average mesh size itself, plays an important role in determining the dynamics of molecules and nanoparticles that are embedded in tightly meshed polymer networks.
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Affiliation(s)
- Hyun Woo Cho
- Department of Chemistry, Sogang University, Seoul 04107, Korea;
| | - Haein Kim
- Department of Chemistry and Nanoscience, Ewha Womans University, Seoul 03760, Korea;
| | - Bong June Sung
- Department of Chemistry, Sogang University, Seoul 04107, Korea;
| | - Jun Soo Kim
- Department of Chemistry and Nanoscience, Ewha Womans University, Seoul 03760, Korea;
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6
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Kumar P, Theeyancheri L, Chaki S, Chakrabarti R. Transport of probe particles in a polymer network: effects of probe size, network rigidity and probe-polymer interaction. SOFT MATTER 2019; 15:8992-9002. [PMID: 31681926 DOI: 10.1039/c9sm01822k] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Fundamental understanding of the effect of microscopic parameters on the dynamics of probe particles in different complex environments has wide implications. Examples include diffusion of proteins in biological hydrogels, porous media, polymer matrix, etc. Here, we use extensive molecular dynamics simulations to investigate the dynamics of the probe particle in a polymer network on a diamond lattice, which provides substantial crowding to mimic the cellular environment. Our simulations show that the dynamics of the probe increasingly becomes restricted, non-Gaussian and subdiffusive on increasing the network rigidity, binding affinity and probe size. In addition, the velocity autocorrelation functions show negative dips owing to the viscoelasticity and caging due to the surrounding network. These observations go with the general experimental findings. Importantly, for a probe particle of size comparable to the mesh size, unrestricted motion engulfing large length scales has been observed. This happens with a more flexible polymer network, which is easily pushed by the bigger probe. On increasing the rigidity of the network, the bigger probe can not efficiently push the network and as a result the long tail disappears. Our study gives a general qualitative picture of the transport of probes in a gel-like medium, as encountered in different contexts.
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Affiliation(s)
- Praveen Kumar
- Department of Chemistry, Indian Institute of Technology Bombay, Powai, Mumbai, 400076, India.
| | - Ligesh Theeyancheri
- Department of Chemistry, Indian Institute of Technology Bombay, Powai, Mumbai, 400076, India.
| | - Subhasish Chaki
- Department of Chemistry, Indian Institute of Technology Bombay, Powai, Mumbai, 400076, India.
| | - Rajarshi Chakrabarti
- Department of Chemistry, Indian Institute of Technology Bombay, Powai, Mumbai, 400076, India.
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7
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Senanayake KK, Mukhopadhyay A. Nanoparticle Diffusion within Dilute and Semidilute Xanthan Solutions. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2019; 35:7978-7984. [PMID: 31117734 DOI: 10.1021/acs.langmuir.9b01029] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
We measured the translation diffusion coefficient ( D) of nanoparticles within dilute and semidilute solutions of a semiflexible polymer, xanthan. Our results showed that for particle diameters ( d) of 5 and 10 nm, the obstruction theory can explain the concentration ( c) dependence of D in the dilute regime. Diffusion in semidilute solutions is better explained by additionally considering the modified Darcy flow with the hydrodynamic screening length varying according to κ ≈ c-0.76. The depletion effect is operative for larger particles ( d = 30 nm) within semidilute solutions. We used a scaling relation for the depletion layer thickness δ ≈ ξν, where ξ is the static correlation length and the exponent ν ≈ 0.42 that can explain our data. This is in contrast with a flat surface, where the exponent is expected to be 1. Our results showed that in the situation, when the polymer network relaxation is much slower compared to the diffusive time-scale of particles, no single theory is capable to describe the concentration and size dependence of particle mobility.
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Affiliation(s)
- Kavindya K Senanayake
- Department of Physics , Wayne State University , Detroit , Michigan 48201 , United States
| | - Ashis Mukhopadhyay
- Department of Physics , Wayne State University , Detroit , Michigan 48201 , United States
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8
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Clarkson CG, Johnson A, Leggett GJ, Geoghegan M. Slow polymer diffusion on brush-patterned surfaces in aqueous solution. NANOSCALE 2019; 11:6052-6061. [PMID: 30869707 DOI: 10.1039/c9nr00341j] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
A model system for the investigation of diffusional transport in compartmentalized nanosystems is described. Arrays of "corrals" enclosed within poly[oligo(ethylene glycol)methyl ether methacrylate] (POEGMA) "walls" were fabricated using double-exposure interferometric lithography to deprotect aminosilane films protected by a nitrophenyl group. In exposed regions, removal of the nitrophenyl group enabled attachment of an initiator for the atom-transfer radical polymerization of end-grafted POEGMA (brushes). Diffusion coefficients for poly(ethylene glycol) in these corrals were obtained by fluorescence correlation spectroscopy. Two modes of surface diffusion were observed: one which is similar to diffusion on the unpatterned surface and a very slow mode of surface diffusion that becomes increasingly important as confinement increases. Diffusion within the POEGMA brushes does not significantly contribute to the results.
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9
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Barabás K, Godó S, Lengyel F, Ernszt D, Pál J, Ábrahám IM. Rapid non-classical effects of steroids on the membrane receptor dynamics and downstream signaling in neurons. Horm Behav 2018; 104:183-191. [PMID: 29775570 DOI: 10.1016/j.yhbeh.2018.05.008] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/28/2018] [Revised: 05/08/2018] [Accepted: 05/09/2018] [Indexed: 12/26/2022]
Abstract
Contribution to Special Issue on Fast effects of steroids. Although rapid effects of steroid hormones on membrane receptors and intracellular signaling molecules have been extensively studied in neurons, we are only beginning to understand the molecular mechanisms behind these non-classical steroid actions. Single molecule tracking (SMT) studies on live cells demonstrated that surface trafficking of membrane receptors determines their ligand binding properties and downstream signaling events. Recent findings suggest that one of the underlying mechanisms of non-classical steroid actions is the alteration of receptor movements on the membrane surface. In order to highlight this novel aspect of steroid effects, we first address the types of receptor movements in the plasma membrane and the role of cortical actin dynamics in receptor movement. We then discuss how single molecules and the surface movements of receptors can be detected in live cells. Next, we review the fundamental processes, which determine the effect of steroids on the plasma membrane: steroid movement through the lipid bilayer and the role of steroid membrane receptors. Using glutamate and neurotrophin receptors (NTRs) as examples, we demonstrate the features of receptor dynamics in the membrane. In addition, we survey the available data of rapid steroid actions on membrane receptor trafficking: we discuss how glucocorticoids act on the surface diffusion of glutamate receptor molecules and how estradiol acts on NTRs and gamma-aminobutyric acid type A receptors (GABAARs) and their related signaling events as well as on cortical actin. Finally, we address the physiological relevance of rapid steroid action on membrane receptors dynamics.
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Affiliation(s)
- Klaudia Barabás
- MTA NAP-B Molecular Neuroendocrinology Research Group, Institute of Physiology, Medical School, Centre for Neuroscience, Szentágothai Research Institute, University of Pécs, Pécs, Hungary
| | - Soma Godó
- MTA NAP-B Molecular Neuroendocrinology Research Group, Institute of Physiology, Medical School, Centre for Neuroscience, Szentágothai Research Institute, University of Pécs, Pécs, Hungary
| | - Ferenc Lengyel
- MTA NAP-B Molecular Neuroendocrinology Research Group, Institute of Physiology, Medical School, Centre for Neuroscience, Szentágothai Research Institute, University of Pécs, Pécs, Hungary
| | - Dávid Ernszt
- MTA NAP-B Molecular Neuroendocrinology Research Group, Institute of Physiology, Medical School, Centre for Neuroscience, Szentágothai Research Institute, University of Pécs, Pécs, Hungary
| | - József Pál
- MTA NAP-B Molecular Neuroendocrinology Research Group, Institute of Physiology, Medical School, Centre for Neuroscience, Szentágothai Research Institute, University of Pécs, Pécs, Hungary
| | - István M Ábrahám
- MTA NAP-B Molecular Neuroendocrinology Research Group, Institute of Physiology, Medical School, Centre for Neuroscience, Szentágothai Research Institute, University of Pécs, Pécs, Hungary.
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10
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Ren KX, Jia XM, Jiao GS, Chen T, Qian HJ, Lu ZY. Interfacial Properties and Hopping Diffusion of Small Nanoparticle in Polymer/Nanoparticle Composite with Attractive Interaction on Side Group. Polymers (Basel) 2018; 10:E598. [PMID: 30966632 PMCID: PMC6403981 DOI: 10.3390/polym10060598] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2018] [Revised: 05/21/2018] [Accepted: 05/25/2018] [Indexed: 12/03/2022] Open
Abstract
The diffusion dynamics of fullerene (C 60 ) in unentangled linear atactic polystyrene (PS) and polypropylene (PP) melts and the structure and dynamic properties of polymers in interface area are investigated by performing all-atom molecular dynamics simulations. The comparison of the results in two systems emphasises the influence of local interactions exerted by polymer side group on the diffusion dynamics of the nanoparticle. In the normal diffusive regime at long time scales, the displacement distribution function (DDF) follows a Gaussian distribution in PP system, indicating a normal diffusion of C 60 . However, we observe multiple peaks in the DDF curve for C 60 diffusing in PS melt, which indicates a diffusion mechanism of hopping of C 60 . The attractive interaction between C 60 and phenyl ring side groups are found to be responsible for the observed hopping diffusion. In addition, we find that the C 60 is dynamically coupled with a subsection of a tetramer on PS chain, which has a similar size with C 60 . The phenyl ring on PS chain backbone tends to have a parallel configuration in the vicinity of C 60 surface, therefore neighbouring phenyl rings can form chelation effect on the C 60 surface. Consequently, the rotational dynamics of phenyl ring and the translational diffusion of styrene monomers are found to be slowed down in this interface area. We hope our results can be helpful for understanding of the influence of the local interactions on the nanoparticle diffusion dynamics and interfacial properties in polymer/nanoparticle composites.
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Affiliation(s)
- Kai-Xin Ren
- State Key Laboratory of Supramolecular Structure and Materials, and Laboratory of Theoretical and Computational Chemistry, Institute of Theoretical Chemistry, Jilin University, Changchun 130023, China.
| | - Xiang-Meng Jia
- State Key Laboratory of Supramolecular Structure and Materials, and Laboratory of Theoretical and Computational Chemistry, Institute of Theoretical Chemistry, Jilin University, Changchun 130023, China.
| | - Gui-Sheng Jiao
- State Key Laboratory of Supramolecular Structure and Materials, and Laboratory of Theoretical and Computational Chemistry, Institute of Theoretical Chemistry, Jilin University, Changchun 130023, China.
| | - Tao Chen
- State Key Laboratory of Supramolecular Structure and Materials, and Laboratory of Theoretical and Computational Chemistry, Institute of Theoretical Chemistry, Jilin University, Changchun 130023, China.
| | - Hu-Jun Qian
- State Key Laboratory of Supramolecular Structure and Materials, and Laboratory of Theoretical and Computational Chemistry, Institute of Theoretical Chemistry, Jilin University, Changchun 130023, China.
| | - Zhong-Yuan Lu
- State Key Laboratory of Supramolecular Structure and Materials, and Laboratory of Theoretical and Computational Chemistry, Institute of Theoretical Chemistry, Jilin University, Changchun 130023, China.
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11
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Watanabe C, Yanagisawa M. Cell-size confinement effect on protein diffusion in crowded poly(ethylene)glycol solution. Phys Chem Chem Phys 2018. [PMID: 29542748 DOI: 10.1039/c7cp08199e] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Micrometric membrane confinements and macromolecular crowding of cytoplasm are key factors that regulate molecular diffusion in live cells. Previous studies have shown that macromolecular crowding delays molecular diffusion. However, the effect of cell-size confinement on diffusion in the crowding environment is yet to be elucidated. Using fluorescence correlation spectroscopy (FCS), we analyzed protein diffusion in microdroplets containing polymer solution covered with lipid membranes that mimic cells. As a result, we found that a synergistic condition of crowding and micrometric confinement results in accelerated protein diffusion on a sub-millisecond time scale. This acceleration rate strongly depended on the size of the confined space and the degree of crowding. These findings indicate that cell-size confinement supports protein diffusion in highly crowded cytoplasm.
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Affiliation(s)
- Chiho Watanabe
- Department of Applied Physics, Faculty of Engineering, Tokyo University of Agriculture and Technology, Koganei, Tokyo 184-8588, Japan.
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12
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Bag N, Ng XW, Sankaran J, Wohland T. Spatiotemporal mapping of diffusion dynamics and organization in plasma membranes. Methods Appl Fluoresc 2016; 4:034003. [PMID: 28355150 DOI: 10.1088/2050-6120/4/3/034003] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Imaging fluorescence correlation spectroscopy (FCS) and the related FCS diffusion law have been applied in recent years to investigate the diffusion modes of lipids and proteins in membranes. These efforts have provided new insights into the membrane structure below the optical diffraction limit, new information on the existence of lipid domains, and on the influence of the cytoskeleton on membrane dynamics. However, there has been no systematic study to evaluate how domain size, domain density, and the probe partition coefficient affect the resulting imaging FCS diffusion law parameters. Here, we characterize the effects of these factors on the FCS diffusion law through simulations and experiments on lipid bilayers and live cells. By segmenting images into smaller 7 × 7 pixel areas, we can evaluate the FCS diffusion law on areas smaller than 2 µm and thus provide detailed maps of information on the membrane structure and heterogeneity at this length scale. We support and extend this analysis by deriving a mathematical expression to calculate the mean squared displacement (MSDACF) from the autocorrelation function of imaging FCS, and demonstrate that the MSDACF plots depend on the existence of nanoscopic domains. Based on the results, we derive limits for the detection of domains depending on their size, density, and relative viscosity in comparison to the surroundings. Finally, we apply these measurements to bilayers and live cells using imaging total internal reflection FCS and single plane illumination microscopy FCS.
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Affiliation(s)
- Nirmalya Bag
- Department of Biological Sciences, National University of Singapore, 14 Science Drive 4, Singapore 117543, Singapore. NUS Centre for Bio-Imaging Sciences, National University of Singapore, 14 Science Drive 4, Singapore 117557, Singapore
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13
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Kubečka J, Uhlík F, Košovan P. Mean squared displacement from fluorescence correlation spectroscopy. SOFT MATTER 2016; 12:3760-3769. [PMID: 26996953 DOI: 10.1039/c6sm00296j] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
Under certain conditions, the mean squared displacement (MSD) can be retrieved from fluorescence correlation spectroscopy (FCS) measurements. However, in the general case this procedure is not valid, and the apparent MSD obtained from FCS data may substantially differ from the true one. In this work we discuss under which conditions this procedure can be applied. Furthermore, we use computer simulations to obtain the MSD and the apparent MSD for the diffusion of a single polymer chain under various approximations. Based on the simulation results we discuss the reliability of the apparent MSD obtained from FCS, showing that it systematically deviates from the true MSD. We also propose a general procedure to verify the reliability of the apparent MSD by measurements at various focal spot sizes.
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Affiliation(s)
- Jakub Kubečka
- Department of Physical and Macromolecular Chemistry, Faculty of Science, Charles University in Prague, Hlavova 8, 128 00 Praha 2, Czech Republic.
| | - Filip Uhlík
- Department of Physical and Macromolecular Chemistry, Faculty of Science, Charles University in Prague, Hlavova 8, 128 00 Praha 2, Czech Republic.
| | - Peter Košovan
- Department of Physical and Macromolecular Chemistry, Faculty of Science, Charles University in Prague, Hlavova 8, 128 00 Praha 2, Czech Republic.
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14
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Xue C, Zheng X, Chen K, Tian Y, Hu G. Probing Non-Gaussianity in Confined Diffusion of Nanoparticles. J Phys Chem Lett 2016; 7:514-9. [PMID: 26784864 DOI: 10.1021/acs.jpclett.5b02624] [Citation(s) in RCA: 62] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/14/2023]
Abstract
Confined diffusion is ubiquitous in nature. Ever since the "anomalous yet Brownian" motion was observed, the non-Gaussianity in confined diffusion has been unveiled as an important issue. In this Letter, we experimentally investigate the characteristics and source of non-Gaussian behavior in confined diffusion of nanoparticles suspended in polymer solutions. A time-varied and size-dependent non-Gaussianity is reported based on the non-Gaussian parameter and displacement probability distribution, especially when the nanoparticle's size is smaller than the typical polymer mesh size. This non-Gaussianity does not vanish even at the long-time Brownian stage. By inspecting the displacement autocorrelation, we observe that the nanoparticle-structure interaction, indicated by the anticorrelation, is limited in the short-time stage and makes little contribution to the non-Gaussianity in the long-time stage. The main source of the non-Gaussianity can therefore be attributed to hopping diffusion that results in an exponential probability distribution with the large displacements, which may also explain certain processes dominated by rare events in the biological environment.
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Affiliation(s)
- Chundong Xue
- State Key Laboratory of Nonlinear Mechanics, Beijing Key Laboratory of Engineered Construction and Mechanobiology, Institute of Mechanics, Chinese Academy of Sciences , Beijing 100190, China
| | - Xu Zheng
- State Key Laboratory of Nonlinear Mechanics, Beijing Key Laboratory of Engineered Construction and Mechanobiology, Institute of Mechanics, Chinese Academy of Sciences , Beijing 100190, China
| | - Kaikai Chen
- State Key Laboratory of Tribology, Tsinghua University , Beijing 100084, China
| | - Yu Tian
- State Key Laboratory of Tribology, Tsinghua University , Beijing 100084, China
| | - Guoqing Hu
- State Key Laboratory of Nonlinear Mechanics, Beijing Key Laboratory of Engineered Construction and Mechanobiology, Institute of Mechanics, Chinese Academy of Sciences , Beijing 100190, China
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15
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Affiliation(s)
- Lydia Kisley
- Department of Chemistry and Department of Electrical and Computer
Engineering,
Rice Quantum Institute, Rice University, 6100 Main Street, MS-60, Houston, Texas 77005, United States
| | - Christy F. Landes
- Department of Chemistry and Department of Electrical and Computer
Engineering,
Rice Quantum Institute, Rice University, 6100 Main Street, MS-60, Houston, Texas 77005, United States
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16
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Ghosh SK, Cherstvy AG, Metzler R. Non-universal tracer diffusion in crowded media of non-inert obstacles. Phys Chem Chem Phys 2015; 17:1847-58. [DOI: 10.1039/c4cp03599b] [Citation(s) in RCA: 98] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
For tracer motion in an array of attractive obstacles we observe transient, non-ergodic anomalous diffusion depending on the obstacle density.
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Affiliation(s)
- Surya K. Ghosh
- Institute for Physics & Astronomy
- University of Potsdam
- 14476 Potsdam-Golm
- Germany
| | - Andrey G. Cherstvy
- Institute for Physics & Astronomy
- University of Potsdam
- 14476 Potsdam-Golm
- Germany
| | - Ralf Metzler
- Institute for Physics & Astronomy
- University of Potsdam
- 14476 Potsdam-Golm
- Germany
- Department of Physics
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