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Collette D, Dunlap D, Finzi L. Macromolecular Crowding and DNA: Bridging the Gap between In Vitro and In Vivo. Int J Mol Sci 2023; 24:17502. [PMID: 38139331 PMCID: PMC10744201 DOI: 10.3390/ijms242417502] [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: 09/13/2023] [Revised: 11/29/2023] [Accepted: 12/05/2023] [Indexed: 12/24/2023] Open
Abstract
The cellular environment is highly crowded, with up to 40% of the volume fraction of the cell occupied by various macromolecules. Most laboratory experiments take place in dilute buffer solutions; by adding various synthetic or organic macromolecules, researchers have begun to bridge the gap between in vitro and in vivo measurements. This is a review of the reported effects of macromolecular crowding on the compaction and extension of DNA, the effect of macromolecular crowding on DNA kinetics, and protein-DNA interactions. Theoretical models related to macromolecular crowding and DNA are briefly reviewed. Gaps in the literature, including the use of biologically relevant crowders, simultaneous use of multi-sized crowders, empirical connections between macromolecular crowding and liquid-liquid phase separation of nucleic materials are discussed.
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Affiliation(s)
| | | | - Laura Finzi
- Department of Physics, College of Arts & Sciences, Emory University, Atlanta, GA 30322, USA; (D.C.); (D.D.)
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2
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Zhang B, Tan F, Zhao N. Polymer looping kinetics in active heterogeneous environments. SOFT MATTER 2021; 17:10334-10349. [PMID: 34734953 DOI: 10.1039/d1sm01259b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
A typical biological environment is usually featured by crowding and heterogeneity, leading to complex reaction kinetics of the immersed macromolecules. In the present work, we adopt Langevin dynamics simulations to systematically investigate polymer looping kinetics in active heterogeneous media crowded with a mixture of mobile active particles and immobile obstacles. For comparison, a parallel study is also performed in the passive heterogeneous media. We explicitly analyze the change of looping time and looping probability with the variation of obstacle ratio, volume fraction and crowder size. We reveal the novel phenomena of inhibition-facilitation transition of the looping rate induced by heterogeneity, crowdedness and activity. In addition, our results demonstrate a very non-trivial crowder size effect on the looping kinetics. The underlying mechanism is rationalized by the interplay of polymer diffusion, conformational change and looping free-energy barrier. The competing effect arising from active particles and obstacles on structural and dynamical properties of the polymer yields a consistent scenario for our observations. Lastly, the non-exponential kinetics of the looping process is also analyzed. We find that both activity and crowding can strengthen the heterogeneity degree of the looping kinetics.
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Affiliation(s)
- Bingjie Zhang
- College of Chemistry, Sichuan University, Chengdu 610064, China.
| | - Fei Tan
- College of Chemistry, Sichuan University, Chengdu 610064, China.
| | - Nanrong Zhao
- College of Chemistry, Sichuan University, Chengdu 610064, China.
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3
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Zhang B, Lei T, Zhao N. Comparative study of polymer looping kinetics in passive and active environments. Phys Chem Chem Phys 2021; 23:12171-12190. [PMID: 34008649 DOI: 10.1039/d1cp00591j] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Intra-chain looping in complex environments is significant in advancing our understanding of biological processes in life. We adopt Langevin dynamics simulations to perform a comparative study of polymer looping kinetics in passive and active environments. From the analysis of looping quantities, including looping-unlooping times and looping probabilities, we unraveled the intriguing effects of active crowder size, activity and crowding. Firstly, we figured out the phase diagram involving a novel facilitation-inhibition transition in the parameter space of active crowder size and active force, and the two-fold roles of activity are clarified. In particular, we find that active particles of a size comparable to the polymer monomer are most favorable for facilitated looping, while those with a similar size to the polymer gyration radius impede the looping most seriously. Secondly, the underlying looping mechanisms in different active crowder size regimes are rationalized by the interplay among diffusion, polymer conformational change and the free-energy barrier. For small active crowders, activity significantly promotes end-to-end distance diffusion, which dominantly facilitates both looping and unlooping processes. In the case of moderate active crowders, the polymer chain suffers from prominent swelling, and thus inevitable inhibited looping will occur. For large active crowders, activity induces a counterintuitive non-cage effect on the looping kinetics, through yielding a higher effective temperature and larger unlooping free-energy barrier. This is in sharp contrast to the caging phenomena observed in passive media. Lastly, the volume-fraction dependence of the looping quantities in an active bath demonstrates dramatic discrepancies from that in a passive bath, which highlights the contrasting effects of activity and crowding.
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Affiliation(s)
- Bingjie Zhang
- College of Chemistry, Sichuan University, Chengdu 610064, China.
| | - Ting Lei
- College of Chemistry, Sichuan University, Chengdu 610064, China.
| | - Nanrong Zhao
- College of Chemistry, Sichuan University, Chengdu 610064, China.
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4
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Tan F, Chen Y, Zhao N. Effects of active crowder size and activity-crowding coupling on polymer translocation. SOFT MATTER 2021; 17:1940-1954. [PMID: 33427276 DOI: 10.1039/d0sm01906b] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Polymer translocation in complex environments is crucially important to many biological processes in life. In the present work, we adopted two-dimensional Langevin dynamics simulations to study the forced and unbiased polymer translocation dynamics in active and crowded media. The translocation time and probability are analyzed in terms of active force Fa, volume fraction φ and also the crowder size. The non-trivial active crowder size effect and activity-crowding coupling effect as well as the novel mechanism of unbiased translocation between two active environments with different active particle sizes are clarified. Firstly, for forced translocation, we reveal an intriguing non-monotonic dependence of the translocation time on the crowder size in the case of large activity. In particular, crowders of intermediate size similar to the polymer segment are proven to be the most favorable for translocation. Moreover, a facilitation-inhibition crossover of the translocation time with increasing volume fraction is observed, indicating a crucial activity-crowding coupling effect. Secondly, for unbiased translocation driven by different active crowder sizes, the translocation probability demonstrates a novel turnover phenomenon, implying the appearance of an opposite directional preference as the active force exceeds a critical value. The translocation time in both directions decreases monotonically with the active force. The asymmetric activity effect together with the entropic driving scenario provides a reasonable picture for the peculiar behavior observed in unbiased translocation.
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Affiliation(s)
- Fei Tan
- College of Chemistry, Sichuan University, Chengdu 610064, China.
| | - Ying Chen
- College of Chemistry, Sichuan University, Chengdu 610064, China.
| | - Nanrong Zhao
- College of Chemistry, Sichuan University, Chengdu 610064, China.
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5
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Abstract
Chromatin ‘blobs’ were recently identified by live super-resolution imaging of labeled nucleosomes as pervasive but fleeting structural entities. However, the mechanisms leading to the formation of these blobs and their functional implications are unknown. We explore here whether causal relationships exist between parameters that characterize the chromatin blob dynamics and structure, by adapting a framework for spatio-temporal Granger-causality inference. Our analysis reveals that chromatin dynamics is a key determinant for both blob area and local density. Such causality, however, could be demonstrated only in 10–20% of the nucleus, suggesting that chromatin dynamics and structure at the nanometer scale are dominated by stochasticity. We show that the theory of active semiflexible polymers can be invoked to provide potential mechanisms leading to the organization of chromatin into blobs. Our results represent a first step toward elucidating the mechanisms that govern the dynamic and stochastic organization of chromatin in the cell nucleus.
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Affiliation(s)
- Roman Barth
- Department of Bionanoscience, Delft University of Technology , Delft, The Netherlands
| | - Genevieve Fourel
- Laboratory of Biology and Modelling of the Cell, University of Lyon, ENS de Lyon, University of Claude Bernard, CNRS UMR 5239, Inserm U1210 , Lyon, France.,Centre Blaise Pascal, ENS de Lyon , Lyon, France
| | - Haitham A Shaban
- Spectroscopy Department, Physics Division, National Research Centre , Cairo, Egypt.,Center for Advanced Imaging, Faculty of Arts and Sciences, Harvard University , Cambridge, MA, USA
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Joo S, Durang X, Lee OC, Jeon JH. Anomalous diffusion of active Brownian particles cross-linked to a networked polymer: Langevin dynamics simulation and theory. SOFT MATTER 2020; 16:9188-9201. [PMID: 32840541 DOI: 10.1039/d0sm01200a] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Quantitatively understanding the dynamics of an active Brownian particle (ABP) interacting with a viscoelastic polymer environment is a scientific challenge. It is intimately related to several interdisciplinary topics such as the microrheology of active colloids in a polymer matrix and the athermal dynamics of the in vivo chromosomes or cytoskeletal networks. Based on Langevin dynamics simulation and analytic theory, here we explore such a viscoelastic active system in depth using a star polymer of functionality f with the center cross-linker particle being ABP. We observe that the ABP cross-linker, despite its self-propelled movement, attains an active subdiffusion with the scaling ΔR2(t) ∼ tα with α ≤ 1/2, through the viscoelastic feedback from the polymer. Counter-intuitively, the apparent anomaly exponent α becomes smaller as the ABP is driven by a larger propulsion velocity, but is independent of functionality f or the boundary conditions of the polymer. We set forth an exact theory and show that the motion of the active cross-linker is a Gaussian non-Markovian process characterized by two distinct power-law displacement correlations. At a moderate Péclet number, it seemingly behaves as fractional Brownian motion with a Hurst exponent H = α/2, whereas, at a high Péclet number, the self-propelled noise in the polymer environment leads to a logarithmic growth of the mean squared displacement (∼ln t) and a velocity autocorrelation decaying as -t-2. We demonstrate that the anomalous diffusion of the active cross-linker is precisely described by a fractional Langevin equation with two distinct random noises.
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Affiliation(s)
- Sungmin Joo
- Department of Physics, POSTECH, Pohang, Republic of Korea.
| | - Xavier Durang
- Department of Physics, POSTECH, Pohang, Republic of Korea.
| | - O-Chul Lee
- Department of Physics, POSTECH, Pohang, Republic of Korea.
| | - Jae-Hyung Jeon
- Department of Physics, POSTECH, Pohang, Republic of Korea.
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Wang H, Gu L, Tan R, Ma X, Zhou X, Liu Y. Macromolecule crowding effects on the phase separation of semi-flexible polymer in spherical confined space. J Biol Phys 2020; 46:223-231. [PMID: 32613446 DOI: 10.1007/s10867-020-09550-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2020] [Accepted: 05/13/2020] [Indexed: 11/27/2022] Open
Abstract
Current works focus on detecting macromolecule crowding effects on the phase separation of the mixture between semi-flexible polymer and crowders (hydrophilic polymers) in confined space by Monte Carlo simulations. With the increasing addition of crowders into the spherical confined space, the semi-flexible polymer was first compressed into a condensed state from the initial coil state, and then the condensed conformation expanded and deposited on the inner surface of the spherical confined space with an extended state. The phase diagram in the phase space of the volume fraction of crowders and the scaled radius of spherical confined space by crowder diameter, and the direct conformation transition of semi-flexible polymer have validated the phase transition process successfully. In addition, the deposition of extended conformation on the inner surface of the spherical confined space was qualified by the vertex density, its curve shifted along the radial direction with the increasing volume fraction of crowder. During the phase separation process, the critical volume fraction φ∗ relates to the crowder diameter approximately linearly and the relation between the critical volume fraction and the crowder diameter strongly depends on the size of the spherical confined space.
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Affiliation(s)
- Hongchang Wang
- School of Physics and Electronic Science, Guizhou Normal University, Guiyang, 550025, China
| | - Lingyun Gu
- School of Physics and Astronomy, Sun Yat-Sen University, Zhuhai, 519082, China
| | - Rongri Tan
- College of Communication and Electronics, Jiangxi Science and Technology Normal University, Nanchang, 330013, China
| | - Xiaotian Ma
- School of Physics and Electronic Science, Guizhou Normal University, Guiyang, 550025, China
| | - Xun Zhou
- School of Physics and Electronic Science, Guizhou Normal University, Guiyang, 550025, China.
| | - Yanhui Liu
- College of Physics, Guizhou University, Guiyang, 550025, China.
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Chen A, Zhang B, Zhao N. A comparative study of semi-flexible linear and ring polymer conformational change in an anisotropic environment. Phys Chem Chem Phys 2020; 22:9137-9147. [PMID: 32301953 DOI: 10.1039/c9cp07018d] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
We adopt a Langevin-dynamics based simulation to systematically study the conformational change of a semi-flexible probed polymer in a rod crowding environment. Two topologically different probed polymer types, linear and ring polymers, are specifically considered. Our results unravel the significance of the interplay of probed polymer's semi-flexibility and crowding anisotropy. Firstly, both ring and linear polymers show a non-trivial dimensional change including nonmonotonicity and collapse-swelling crossover as their stiffness increases. Secondly, we modulate rod crowder length to investigate the anisotropic effect. We reveal that the formation of an ordered parallel arrangement of the environment can effectively lead to a remarkable stretching effect on the probed polymer. The coupling between the crowding anisotropy-induced stretching and the polymer stiffness can account for the unusual swelling behavior. Lastly, nonmonotonic swelling and shape change of the ring polymer are analyzed. We find out that the ring polymer is subject to most pronounced swelling at robust stiffness. Moreover, the maximum prolate shape is also observed at the same robust location.
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Affiliation(s)
- Anpu Chen
- College of Chemistry, Sichuan University, Chengdu 610064, China.
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9
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Cao X, Zhang B, Zhao N. Effective temperature scaled dynamics of a flexible polymer in an active bath. Mol Phys 2020. [DOI: 10.1080/00268976.2020.1730992] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Affiliation(s)
- Xiuli Cao
- College of Chemistry, Sichuan University, Chengdu, China
| | - Bingjie Zhang
- College of Chemistry, Sichuan University, Chengdu, China
| | - Nanrong Zhao
- College of Chemistry, Sichuan University, Chengdu, China
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