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Dorenbos G. How fork-length asymmetry affects solvent connectivity and diffusion in grafted polymeric model membranes. J Chem Phys 2024; 160:064901. [PMID: 38341779 DOI: 10.1063/5.0193120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2023] [Accepted: 01/15/2024] [Indexed: 02/13/2024] Open
Abstract
The hydrophilic pore morphology and solvent diffusion within model (amphiphilic) polymer membranes are simulated by dissipative particle dynamics (DPD). The polymers are composed of a backbone of 18 covalently bonded A beads to which at regular intervals side chains are attached. The side chains are composed of linear Ap chains (i.e., -A1-A2…Ap) from which two branches, [AsC] and [ArC], split off (s ≤ r). C beads serve as functionalized hydrophilic pendent sites. The branch lengths (s + 1 and r + 1) are varied. Five repeat unit designs (with general formula A3[Ap[AsC][ArC]]) are considered: A2[A3C][A3C] (symmetric branching), A2[A2C][A4C], A2[AC][A5C], A2[C][A6C] (highly asymmetric branching), and A4[AC][A3C]. The distribution of water (W) and W diffusion through nanophase segregated hydrophilic pores is studied. For similar primary length p, an increase in side chain symmetry favors hydrophilic pore connectivity and long-range water transport. C beads located on the longer [ArC] branches reveal the highest C bead mobility and are more strongly associated with water than the C beads on the shorter [AsC] branches. The connectivity of hydrophilic (W and W + C) phases through mapped replica of selected snapshots obtained from Monte Carlo tracer diffusion simulations is in line with trends found from the W bead diffusivities during DPD simulations. The diffusive pathways for protons (H+) in proton exchange membranes and for hydronium (OH-) in anion exchange membranes are the same as for solvents. Therefore, control of the side chain architecture is an interesting design parameter for optimizing membrane conductivities.
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Affiliation(s)
- G Dorenbos
- Private research, Sano 1107-2, Belle Crea 502, 410-1118 Susono, Japan
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2
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Gilbert BR, Luthey-Schulten Z. Replicating Chromosomes in Whole-Cell Models of Bacteria. Methods Mol Biol 2024; 2819:625-653. [PMID: 39028527 DOI: 10.1007/978-1-0716-3930-6_29] [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] [Indexed: 07/20/2024]
Abstract
Computational models of cells cannot be considered complete unless they include the most fundamental process of life, the replication of genetic material. In a recent study, we presented a computational framework to model systems of replicating bacterial chromosomes as polymers at 10 bp resolution with Brownian dynamics. This approach was used to investigate changes in chromosome organization during replication and extend the applicability of an existing whole-cell model (WCM) for a genetically minimal bacterium, JCVI-syn3A, to the entire cell cycle. To achieve cell-scale chromosome structures that are realistic, we modeled the chromosome as a self-avoiding homopolymer with bending and torsional stiffnesses that capture the essential mechanical properties of dsDNA in Syn3A. Additionally, the polymer interacts with ribosomes distributed according to cryo-electron tomograms of Syn3A. The polymer model was further augmented by computational models of loop extrusion by structural maintenance of chromosomes (SMC) protein complexes and topoisomerase action, and the modeling and analysis of multi-fork replication states.
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Affiliation(s)
- Benjamin R Gilbert
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Zaida Luthey-Schulten
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL, USA.
- Department of Physics, University of Illinois at Urbana-Champaign, Urbana, IL, USA.
- NIH Center for Macromolecular Modeling and Bioinformatics, Beckman Institute, University of Illinois at Urbana-Champaign, Urbana, IL, USA.
- NSF Science and Technology Center for Quantitative Cell Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA.
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龚 海, 麻 付, 张 晓. [Advances in methods and applications of single-cell Hi-C data analysis]. SHENG WU YI XUE GONG CHENG XUE ZA ZHI = JOURNAL OF BIOMEDICAL ENGINEERING = SHENGWU YIXUE GONGCHENGXUE ZAZHI 2023; 40:1033-1039. [PMID: 37879935 PMCID: PMC10600426 DOI: 10.7507/1001-5515.202303046] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Received: 03/20/2023] [Revised: 08/29/2023] [Indexed: 10/27/2023]
Abstract
Chromatin three-dimensional genome structure plays a key role in cell function and gene regulation. Single-cell Hi-C techniques can capture genomic structure information at the cellular level, which provides an opportunity to study changes in genomic structure between different cell types. Recently, some excellent computational methods have been developed for single-cell Hi-C data analysis. In this paper, the available methods for single-cell Hi-C data analysis were first reviewed, including preprocessing of single-cell Hi-C data, multi-scale structure recognition based on single-cell Hi-C data, bulk-like Hi-C contact matrix generation based on single-cell Hi-C data sets, pseudo-time series analysis, and cell classification. Then the application of single-cell Hi-C data in cell differentiation and structural variation was described. Finally, the future development direction of single-cell Hi-C data analysis was also prospected.
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Affiliation(s)
- 海燕 龚
- 北京科技大学 新材料技术研究院 (北京 100083)Institute for Advanced Materials and Technology, University of Science and Technology Beijing, Beijing 100083, P. R. China
- 北京科技大学 计算机与通信工程学院(北京 100083)School of Computer and Communication Engineering, University of Science and Technology Beijing, Beijing 100083, P. R. China
| | - 付强 麻
- 北京科技大学 新材料技术研究院 (北京 100083)Institute for Advanced Materials and Technology, University of Science and Technology Beijing, Beijing 100083, P. R. China
| | - 晓彤 张
- 北京科技大学 新材料技术研究院 (北京 100083)Institute for Advanced Materials and Technology, University of Science and Technology Beijing, Beijing 100083, P. R. China
- 北京科技大学 计算机与通信工程学院(北京 100083)School of Computer and Communication Engineering, University of Science and Technology Beijing, Beijing 100083, P. R. China
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Gilbert BR, Thornburg ZR, Brier TA, Stevens JA, Grünewald F, Stone JE, Marrink SJ, Luthey-Schulten Z. Dynamics of chromosome organization in a minimal bacterial cell. Front Cell Dev Biol 2023; 11:1214962. [PMID: 37621774 PMCID: PMC10445541 DOI: 10.3389/fcell.2023.1214962] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2023] [Accepted: 07/10/2023] [Indexed: 08/26/2023] Open
Abstract
Computational models of cells cannot be considered complete unless they include the most fundamental process of life, the replication and inheritance of genetic material. By creating a computational framework to model systems of replicating bacterial chromosomes as polymers at 10 bp resolution with Brownian dynamics, we investigate changes in chromosome organization during replication and extend the applicability of an existing whole-cell model (WCM) for a genetically minimal bacterium, JCVI-syn3A, to the entire cell-cycle. To achieve cell-scale chromosome structures that are realistic, we model the chromosome as a self-avoiding homopolymer with bending and torsional stiffnesses that capture the essential mechanical properties of dsDNA in Syn3A. In addition, the conformations of the circular DNA must avoid overlapping with ribosomes identitied in cryo-electron tomograms. While Syn3A lacks the complex regulatory systems known to orchestrate chromosome segregation in other bacteria, its minimized genome retains essential loop-extruding structural maintenance of chromosomes (SMC) protein complexes (SMC-scpAB) and topoisomerases. Through implementing the effects of these proteins in our simulations of replicating chromosomes, we find that they alone are sufficient for simultaneous chromosome segregation across all generations within nested theta structures. This supports previous studies suggesting loop-extrusion serves as a near-universal mechanism for chromosome organization within bacterial and eukaryotic cells. Furthermore, we analyze ribosome diffusion under the influence of the chromosome and calculate in silico chromosome contact maps that capture inter-daughter interactions. Finally, we present a methodology to map the polymer model of the chromosome to a Martini coarse-grained representation to prepare molecular dynamics models of entire Syn3A cells, which serves as an ultimate means of validation for cell states predicted by the WCM.
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Affiliation(s)
- Benjamin R. Gilbert
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL, United States
| | - Zane R. Thornburg
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL, United States
| | - Troy A. Brier
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL, United States
| | - Jan A. Stevens
- Molecular Dynamics Group, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, Netherlands
| | - Fabian Grünewald
- Molecular Dynamics Group, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, Netherlands
| | - John E. Stone
- NVIDIA Corporation, Santa Clara, CA, United States
- NIH Center for Macromolecular Modeling and Bioinformatics, Beckman Institute, University of Illinois at Urbana-Champaign, Urbana, IL, United States
| | - Siewert J. Marrink
- Molecular Dynamics Group, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, Netherlands
| | - Zaida Luthey-Schulten
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL, United States
- NIH Center for Macromolecular Modeling and Bioinformatics, Beckman Institute, University of Illinois at Urbana-Champaign, Urbana, IL, United States
- NSF Center for the Physics of Living Cells, Department of Physics, University of Illinois at Urbana-Champaign, Urbana, IL, United States
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Madsen-Østerbye J, Bellanger A, Galigniana NM, Collas P. Biology and Model Predictions of the Dynamics and Heterogeneity of Chromatin-Nuclear Lamina Interactions. Front Cell Dev Biol 2022; 10:913458. [PMID: 35693945 PMCID: PMC9178083 DOI: 10.3389/fcell.2022.913458] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2022] [Accepted: 05/12/2022] [Indexed: 11/13/2022] Open
Abstract
Associations of chromatin with the nuclear lamina, at the nuclear periphery, help shape the genome in 3 dimensions. The genomic landscape of lamina-associated domains (LADs) is well characterized, but much remains unknown on the physical and mechanistic properties of chromatin conformation at the nuclear lamina. Computational models of chromatin folding at, and interactions with, a surface representing the nuclear lamina are emerging in attempts to characterize these properties and predict chromatin behavior at the lamina in health and disease. Here, we highlight the heterogeneous nature of the nuclear lamina and LADs, outline the main 3-dimensional chromatin structural modeling methods, review applications of modeling chromatin-lamina interactions and discuss biological insights inferred from these models in normal and disease states. Lastly, we address perspectives on future developments in modeling chromatin interactions with the nuclear lamina.
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Affiliation(s)
- Julia Madsen-Østerbye
- Department of Molecular Medicine, Institute of Basic Medical Sciences, Faculty of Medicine, University of Oslo, Oslo, Norway
| | - Aurélie Bellanger
- Department of Molecular Medicine, Institute of Basic Medical Sciences, Faculty of Medicine, University of Oslo, Oslo, Norway
| | - Natalia M. Galigniana
- Department of Molecular Medicine, Institute of Basic Medical Sciences, Faculty of Medicine, University of Oslo, Oslo, Norway
- Department of Immunology and Transfusion Medicine, Oslo University Hospital, Oslo, Norway
| | - Philippe Collas
- Department of Molecular Medicine, Institute of Basic Medical Sciences, Faculty of Medicine, University of Oslo, Oslo, Norway
- Department of Immunology and Transfusion Medicine, Oslo University Hospital, Oslo, Norway
- *Correspondence: Philippe Collas,
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Super-resolution visualization of chromatin loop folding in human lymphoblastoid cells using interferometric photoactivated localization microscopy. Sci Rep 2022; 12:8582. [PMID: 35595799 PMCID: PMC9122977 DOI: 10.1038/s41598-022-12568-9] [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] [Received: 01/25/2022] [Accepted: 05/10/2022] [Indexed: 11/18/2022] Open
Abstract
The three-dimensional (3D) genome structure plays a fundamental role in gene regulation and cellular functions. Recent studies in 3D genomics inferred the very basic functional chromatin folding structures known as chromatin loops, the long-range chromatin interactions that are mediated by protein factors and dynamically extruded by cohesin. We combined the use of FISH staining of a very short (33 kb) chromatin fragment, interferometric photoactivated localization microscopy (iPALM), and traveling salesman problem-based heuristic loop reconstruction algorithm from an image of the one of the strongest CTCF-mediated chromatin loops in human lymphoblastoid cells. In total, we have generated thirteen good quality images of the target chromatin region with 2–22 nm oligo probe localization precision. We visualized the shape of the single chromatin loops with unprecedented genomic resolution which allowed us to study the structural heterogeneity of chromatin looping. We were able to compare the physical distance maps from all reconstructed image-driven computational models with contact frequencies observed by ChIA-PET and Hi-C genomic-driven methods to examine the concordance between single cell imaging and population based genomic data.
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Gong W, Wee J, Wu MC, Sun X, Li C, Xia K. Persistent spectral simplicial complex-based machine learning for chromosomal structural analysis in cellular differentiation. Brief Bioinform 2022; 23:6583209. [PMID: 35536545 DOI: 10.1093/bib/bbac168] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2022] [Revised: 04/12/2022] [Accepted: 03/13/2022] [Indexed: 11/13/2022] Open
Abstract
The three-dimensional (3D) chromosomal structure plays an essential role in all DNA-templated processes, including gene transcription, DNA replication and other cellular processes. Although developing chromosome conformation capture (3C) methods, such as Hi-C, which can generate chromosomal contact data characterized genome-wide chromosomal structural properties, understanding 3D genomic nature-based on Hi-C data remains lacking. Here, we propose a persistent spectral simplicial complex (PerSpectSC) model to describe Hi-C data for the first time. Specifically, a filtration process is introduced to generate a series of nested simplicial complexes at different scales. For each of these simplicial complexes, its spectral information can be calculated from the corresponding Hodge Laplacian matrix. PerSpectSC model describes the persistence and variation of the spectral information of the nested simplicial complexes during the filtration process. Different from all previous models, our PerSpectSC-based features provide a quantitative global-scale characterization of chromosome structures and topology. Our descriptors can successfully classify cell types and also cellular differentiation stages for all the 24 types of chromosomes simultaneously. In particular, persistent minimum best characterizes cell types and Dim (1) persistent multiplicity best characterizes cellular differentiation. These results demonstrate the great potential of our PerSpectSC-based models in polymeric data analysis.
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Affiliation(s)
- Weikang Gong
- Faculty of Environmental and Life Sciences, Beijing University of Technology, Beijing, China 100124.,Division of Mathematical Sciences, School of Physical and Mathematical Sciences, Nanyang Technological University, Singapore 637371
| | - JunJie Wee
- Division of Mathematical Sciences, School of Physical and Mathematical Sciences, Nanyang Technological University, Singapore 637371
| | - Min-Chun Wu
- Division of Mathematical Sciences, School of Physical and Mathematical Sciences, Nanyang Technological University, Singapore 637371
| | - Xiaohan Sun
- Faculty of Environmental and Life Sciences, Beijing University of Technology, Beijing, China 100124
| | - Chunhua Li
- Faculty of Environmental and Life Sciences, Beijing University of Technology, Beijing, China 100124
| | - Kelin Xia
- Division of Mathematical Sciences, School of Physical and Mathematical Sciences, Nanyang Technological University, Singapore 637371
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