1
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Sun T, Korolev N, Minhas V, Mirzoev A, Lyubartsev AP, Nordenskiöld L. Multiscale modeling reveals the ion-mediated phase separation of nucleosome core particles. Biophys J 2024; 123:1414-1434. [PMID: 37915169 PMCID: PMC11163297 DOI: 10.1016/j.bpj.2023.10.030] [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: 07/27/2023] [Revised: 10/05/2023] [Accepted: 10/27/2023] [Indexed: 11/03/2023] Open
Abstract
Due to the vast length scale inside the cell nucleus, multiscale models are required to understand chromatin folding, structure, and dynamics and how they regulate genomic activities such as DNA transcription, replication, and repair. We study the interactions and structure of condensed phases formed by the universal building block of chromatin, the nucleosome core particle (NCP), using bottom-up multiscale coarse-grained (CG) simulations with a model extracted from all-atom MD simulations. In the presence of the multivalent cations Mg(H2O)62+ or CoHex3+, we analyze the internal structures of the NCP aggregates and the contributions of histone tails and ions to the aggregation patterns. We then derive a "super" coarse-grained (SCG) NCP model to study the macroscopic scale phase separation of NCPs. The SCG simulations show the formation of NCP aggregates with Mg(H2O)62+ concentration-dependent densities and sizes. Variation of the CoHex3+ concentrations results in highly ordered lamellocolumnar and hexagonal columnar phases in agreement with experimental data. The results give detailed insights into nucleosome interactions and for understanding chromatin folding in the cell nucleus.
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Affiliation(s)
- Tiedong Sun
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
| | - Nikolay Korolev
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
| | - Vishal Minhas
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
| | - Alexander Mirzoev
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
| | - Alexander P Lyubartsev
- Department of Materials and Environmental Chemistry, Stockholm University, Stockholm, Sweden.
| | - Lars Nordenskiöld
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore.
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2
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Harnett J, Weir S, Michieletto D. Effects of monovalent and divalent cations on the rheology of entangled DNA. SOFT MATTER 2024; 20:3980-3986. [PMID: 38686506 PMCID: PMC11095498 DOI: 10.1039/d3sm00957b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/21/2023] [Accepted: 04/19/2024] [Indexed: 05/02/2024]
Abstract
In this paper we investigate the effects of varying cation valency and concentration on the rheology of entangled λDNA solutions. We show that monovalent cations moderately increase the viscoelasticty of the solutions mainly by stabilising linear concatenation of λDNA "monomers" via hybridisation of their sticky ends. On the contrary, divalent cations have a far more complex and dramatic effect on the rheology of the solution and we observe evidence of inter-molecular DNA-DNA bridging by Mg2+. We argue that these results may be interesting in the context of dense solutions of single and double stranded DNA, e.g. in vivo or in biotechnology applications such as DNA origami and DNA hydrogels.
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Affiliation(s)
- Jennifer Harnett
- School of Physics and Astronomy, University of Edinburgh, Peter Guthrie Tait Road, Edinburgh, EH9 3FD, UK.
| | - Simon Weir
- School of Physics and Astronomy, University of Edinburgh, Peter Guthrie Tait Road, Edinburgh, EH9 3FD, UK.
| | - Davide Michieletto
- School of Physics and Astronomy, University of Edinburgh, Peter Guthrie Tait Road, Edinburgh, EH9 3FD, UK.
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh EH4 2XU, UK
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3
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Chen M, Sahoo B, Mou Z, Song X, Tsai T, Dai X. Genome organization in double-stranded DNA viruses observed by cryoET. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.12.15.571939. [PMID: 38168199 PMCID: PMC10760162 DOI: 10.1101/2023.12.15.571939] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/05/2024]
Abstract
Double-stranded DNA (dsDNA) viruses package their genetic material into protein cages with diameters usually a few hundred times smaller than the length of their genome. Compressing the relatively stiff and highly negatively charged dsDNA into a small volume is energetically costly and mechanistically enigmatic. Multiple models of dsDNA packaging have been proposed based on various experimental evidence and simulation methods, but direct observation of any viral genome organization is lacking. Here, using cryoET and an improved data processing scheme that utilizes information from the encaging protein shell, we present 3D views of dsDNA genome inside individual viral particles at resolution that densities of neighboring DNA duplexes are readily separable. These cryoET observations reveal a "rod-and-coil" fold of the dsDNA that is conserved among herpes simplex virus type 1 (HSV-1) with a spherical capsid, bacteriophage T4 with a prolate capsid, and bacteriophage T7 with a proteinaceous core inside the capsid. Finally, inspired by the genome arrangement in partially packaged T4 particles, we propose a mechanism for the genome packaging process in dsDNA viruses.
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Affiliation(s)
- Muyuan Chen
- Division of CryoEM and Bioimaging, SSRL, SLAC National Accelerator Laboratory, Stanford University, Menlo Park, CA 94025, USA
| | - Bibekananda Sahoo
- Department of Physiology and Biophysics, Case Western Reserve University, Cleveland, OH 44106, USA
| | - Zongjun Mou
- Department of Physiology and Biophysics, Case Western Reserve University, Cleveland, OH 44106, USA
| | - Xiyong Song
- Department of Physiology and Biophysics, Case Western Reserve University, Cleveland, OH 44106, USA
| | - Tiffany Tsai
- Department of Physiology and Biophysics, Case Western Reserve University, Cleveland, OH 44106, USA
| | - Xinghong Dai
- Department of Physiology and Biophysics, Case Western Reserve University, Cleveland, OH 44106, USA
- Lead contact
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4
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Han X, Gao C, Lu W, Yan J, Xu H, Guo Z, Qin W, Lu N, Gao J, Zhu W, Fu Y, Jiao K. Macrophage-Derived Extracellular DNA Initiates Heterotopic Ossification. Inflammation 2023; 46:2225-2240. [PMID: 37458919 DOI: 10.1007/s10753-023-01873-8] [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: 04/24/2023] [Revised: 06/17/2023] [Accepted: 07/04/2023] [Indexed: 11/25/2023]
Abstract
Heterotopic ossification (HO) severely affects people's lives; however, its pathological mechanism remains poorly understood. Although extracellular DNA (ecDNA) has been shown to play important roles in pathological calcification, its effects in HO development and progression remain unknown. The in vivo rat Achilles tendon injury model and in vitro collagen I calcification model were used to evaluate the effects of ecDNA in the ectopic calcifications and the main cell types involved in those pathological process. Histology, immunofluorescent staining, reverse transcriptase-polymerase chain reaction analysis and micro-computed tomography were used to identify the distribution of macrophage-derived ecDNA and elucidate their roles in HO. The results showed that the amount of ecDNA and ectopic calcification increased significantly and exhibited a strong correlation in the injured tendons of HO model compared with those of the controls, which was accompanied by a significantly increased number of M2 macrophages in the injured tendon. During in vitro co-culture experiments, M2 macrophages calcified the reconstituted type I collagen and ectopic bone collected from the injured tendons of HO rats, while those effects were inhibited by deoxyribonuclease. More importantly, deoxyribonuclease reversed the pathological calcification in the injured rat tendon HO model. The present study showed that ecDNA from M2 macrophages initiates pathological calcification in HO, and the elimination of ecDNA might be developed into a clinical strategy to prevent ectopic mineralization diseases. The use of deoxyribonuclease for the targeted degradation of ecDNA at affected tissue sites provides a potential solution to treat diseases associated with ectopic mineralization.
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Affiliation(s)
- Xiaoxiao Han
- Department of Stomatology, Tangdu Hospital, The Fourth Military Medical University, Xi'an, Shaanxi, China
- State Key Laboratory of Oral & Maxillofacial Reconstruction and Regeneration & National Clinical Research Center for Oral Diseases & Shaanxi Key Laboratory of Stomatology, School of Stomatology & Shaanxi Key Laboratory of Stomatology, School of Stomatology, The Fourth Military Medical University, Xi'an, Shaanxi, China
- The College of Life Science, Northwest University, Xi'an, Shaanxi, China
| | - Changhe Gao
- Department of Stomatology, Tangdu Hospital, The Fourth Military Medical University, Xi'an, Shaanxi, China
- State Key Laboratory of Oral & Maxillofacial Reconstruction and Regeneration & National Clinical Research Center for Oral Diseases & Shaanxi Key Laboratory of Stomatology, School of Stomatology & Shaanxi Key Laboratory of Stomatology, School of Stomatology, The Fourth Military Medical University, Xi'an, Shaanxi, China
- The Third Affiliated Hospital of Xinxiang Medical University, Xinxiang, China
| | - Weicheng Lu
- Department of Stomatology, Tangdu Hospital, The Fourth Military Medical University, Xi'an, Shaanxi, China
- State Key Laboratory of Oral & Maxillofacial Reconstruction and Regeneration & National Clinical Research Center for Oral Diseases & Shaanxi Key Laboratory of Stomatology, School of Stomatology & Shaanxi Key Laboratory of Stomatology, School of Stomatology, The Fourth Military Medical University, Xi'an, Shaanxi, China
| | - Jianfei Yan
- Department of Stomatology, Tangdu Hospital, The Fourth Military Medical University, Xi'an, Shaanxi, China
- State Key Laboratory of Oral & Maxillofacial Reconstruction and Regeneration & National Clinical Research Center for Oral Diseases & Shaanxi Key Laboratory of Stomatology, School of Stomatology & Shaanxi Key Laboratory of Stomatology, School of Stomatology, The Fourth Military Medical University, Xi'an, Shaanxi, China
| | - Haoqing Xu
- Department of Stomatology, Tangdu Hospital, The Fourth Military Medical University, Xi'an, Shaanxi, China
- State Key Laboratory of Oral & Maxillofacial Reconstruction and Regeneration & National Clinical Research Center for Oral Diseases & Shaanxi Key Laboratory of Stomatology, School of Stomatology & Shaanxi Key Laboratory of Stomatology, School of Stomatology, The Fourth Military Medical University, Xi'an, Shaanxi, China
- The College of Life Science, Northwest University, Xi'an, Shaanxi, China
| | - Zhenxing Guo
- Department of Stomatology, Tangdu Hospital, The Fourth Military Medical University, Xi'an, Shaanxi, China
- State Key Laboratory of Oral & Maxillofacial Reconstruction and Regeneration & National Clinical Research Center for Oral Diseases & Shaanxi Key Laboratory of Stomatology, School of Stomatology & Shaanxi Key Laboratory of Stomatology, School of Stomatology, The Fourth Military Medical University, Xi'an, Shaanxi, China
| | - Wenpin Qin
- Department of Stomatology, Tangdu Hospital, The Fourth Military Medical University, Xi'an, Shaanxi, China
- State Key Laboratory of Oral & Maxillofacial Reconstruction and Regeneration & National Clinical Research Center for Oral Diseases & Shaanxi Key Laboratory of Stomatology, School of Stomatology & Shaanxi Key Laboratory of Stomatology, School of Stomatology, The Fourth Military Medical University, Xi'an, Shaanxi, China
| | - Naining Lu
- Department of Neurobiology, The Fourth Military Medical University, Xi'an, Shaanxi, China
| | - Jialu Gao
- Department of Stomatology, Tangdu Hospital, The Fourth Military Medical University, Xi'an, Shaanxi, China
- State Key Laboratory of Oral & Maxillofacial Reconstruction and Regeneration & National Clinical Research Center for Oral Diseases & Shaanxi Key Laboratory of Stomatology, School of Stomatology & Shaanxi Key Laboratory of Stomatology, School of Stomatology, The Fourth Military Medical University, Xi'an, Shaanxi, China
| | - Weiwei Zhu
- Department of Stomatology, Tangdu Hospital, The Fourth Military Medical University, Xi'an, Shaanxi, China
- State Key Laboratory of Oral & Maxillofacial Reconstruction and Regeneration & National Clinical Research Center for Oral Diseases & Shaanxi Key Laboratory of Stomatology, School of Stomatology & Shaanxi Key Laboratory of Stomatology, School of Stomatology, The Fourth Military Medical University, Xi'an, Shaanxi, China
- The College of Life Science, Northwest University, Xi'an, Shaanxi, China
| | - Yutong Fu
- State Key Laboratory of Oral & Maxillofacial Reconstruction and Regeneration & National Clinical Research Center for Oral Diseases & Shaanxi Key Laboratory of Stomatology, School of Stomatology & Shaanxi Key Laboratory of Stomatology, School of Stomatology, The Fourth Military Medical University, Xi'an, Shaanxi, China
- The College of Life Science, Northwest University, Xi'an, Shaanxi, China
| | - Kai Jiao
- Department of Stomatology, Tangdu Hospital, The Fourth Military Medical University, Xi'an, Shaanxi, China.
- State Key Laboratory of Oral & Maxillofacial Reconstruction and Regeneration & National Clinical Research Center for Oral Diseases & Shaanxi Key Laboratory of Stomatology, School of Stomatology & Shaanxi Key Laboratory of Stomatology, School of Stomatology, The Fourth Military Medical University, Xi'an, Shaanxi, China.
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5
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Lu W, Onuchic JN, Di Pierro M. An associative memory Hamiltonian model for DNA and nucleosomes. PLoS Comput Biol 2023; 19:e1011013. [PMID: 36972316 PMCID: PMC10079229 DOI: 10.1371/journal.pcbi.1011013] [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: 10/15/2022] [Revised: 04/06/2023] [Accepted: 03/08/2023] [Indexed: 03/29/2023] Open
Abstract
A model for DNA and nucleosomes is introduced with the goal of studying chromosomes from a single base level all the way to higher-order chromatin structures. This model, dubbed the Widely Editable Chromatin Model (WEChroM), reproduces the complex mechanics of the double helix including its bending persistence length and twisting persistence length, and their respective temperature dependence. The WEChroM Hamiltonian is composed of chain connectivity, steric interactions, and associative memory terms representing all remaining interactions leading to the structure, dynamics, and mechanical characteristics of the B-DNA. Several applications of this model are discussed to demonstrate its applicability. WEChroM is used to investigate the behavior of circular DNA in the presence of positive and negative supercoiling. We show that it recapitulates the formation of plectonemes and of structural defects that relax mechanical stress. The model spontaneously manifests an asymmetric behavior with respect to positive or negative supercoiling, similar to what was previously observed in experiments. Additionally, we show that the associative memory Hamiltonian is also capable of reproducing the free energy of partial DNA unwrapping from nucleosomes. WEChroM is designed to emulate the continuously variable mechanical properties of the 10nm fiber and, by virtue of its simplicity, is ready to be scaled up to molecular systems large enough to investigate the structural ensembles of genes. WEChroM is implemented in the OpenMM simulation toolkits and is freely available for public use.
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Affiliation(s)
- Weiqi Lu
- Center for Theoretical Biological Physics, & Department of Physics and Astronomy, Rice University, Houston, Texas, United States of America
| | - José N. Onuchic
- Center for Theoretical Biological Physics, & Department of Physics and Astronomy, Rice University, Houston, Texas, United States of America
- Department of Chemistry, & Department of Biosciences, Rice University, Houston, Texas, United States of America
- * E-mail: (JNO); (MDP)
| | - Michele Di Pierro
- Department of Physics, Northeastern University, Boston, Massachusetts, United States of America
- Center for Theoretical Biological Physics, Northeastern University, Boston, Massachusetts, United States of America
- * E-mail: (JNO); (MDP)
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6
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Unravelling viral dynamics through molecular dynamics simulations - A brief overview. Biophys Chem 2022; 291:106908. [DOI: 10.1016/j.bpc.2022.106908] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2022] [Revised: 09/28/2022] [Accepted: 10/05/2022] [Indexed: 11/24/2022]
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7
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Sun T, Minhas V, Mirzoev A, Korolev N, Lyubartsev AP, Nordenskiöld L. A Bottom-Up Coarse-Grained Model for Nucleosome-Nucleosome Interactions with Explicit Ions. J Chem Theory Comput 2022; 18:3948-3960. [PMID: 35580041 PMCID: PMC9202350 DOI: 10.1021/acs.jctc.2c00083] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The nucleosome core particle (NCP) is a large complex of 145-147 base pairs of DNA and eight histone proteins and is the basic building block of chromatin that forms the chromosomes. Here, we develop a coarse-grained (CG) model of the NCP derived through a systematic bottom-up approach based on underlying all-atom MD simulations to compute the necessary CG interactions. The model produces excellent agreement with known structural features of the NCP and gives a realistic description of the nucleosome-nucleosome attraction in the presence of multivalent cations (Mg(H2O)62+ or Co(NH3)63+) for systems comprising 20 NCPs. The results of the simulations reveal structural details of the NCP-NCP interactions unavailable from experimental approaches, and this model opens the prospect for the rigorous modeling of chromatin fibers.
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Affiliation(s)
- Tiedong Sun
- School of Biological Sciences, Nanyang Technological University, Singapore 639798
| | - Vishal Minhas
- School of Biological Sciences, Nanyang Technological University, Singapore 639798
| | - Alexander Mirzoev
- School of Biological Sciences, Nanyang Technological University, Singapore 639798
| | - Nikolay Korolev
- School of Biological Sciences, Nanyang Technological University, Singapore 639798
| | - Alexander P Lyubartsev
- Department of Materials and Environmental Chemistry, Stockholm University, Stockholm 10691, Sweden
| | - Lars Nordenskiöld
- School of Biological Sciences, Nanyang Technological University, Singapore 639798
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8
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Shen M, Jiao K, Wang C, Ehrlich H, Wan M, Hao D, Li J, Wan Q, Tonggu L, Yan J, Wang K, Ma Y, Chen J, Tay FR, Niu L. Extracellular DNA: A Missing Link in the Pathogenesis of Ectopic Mineralization. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2022; 9:e2103693. [PMID: 34939364 PMCID: PMC8844461 DOI: 10.1002/advs.202103693] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/24/2021] [Revised: 10/10/2021] [Indexed: 05/12/2023]
Abstract
Although deoxyribonucleic acid (DNA) is the genetic coding for the very essence of life, these macromolecules or components thereof are not necessarily lost after a cell dies. There appears to be a link between extracellular DNA and biomineralization. Here the authors demonstrate that extracellular DNA functions as an initiator of collagen intrafibrillar mineralization. This is confirmed with in vitro and in vivo biological mineralization models. Because of their polyanionic property, extracellular DNA molecules are capable of stabilizing supersaturated calcium phosphate solution and mineralizing 2D and 3D collagen matrices completely as early as 24 h. The effectiveness of extracellular DNA in biomineralization of collagen is attributed to the relatively stable formation of amorphous liquid droplets triggered by attraction of DNA to the collagen fibrils via hydrogen bonding. These findings suggest that extracellular DNA is biomimetically significant for fabricating inorganic-organic hybrid materials for tissue engineering. DNA-induced collagen intrafibrillar mineralization provides a clue to the pathogenesis of ectopic mineralization in different body tissues. The use of DNase for targeting extracellular DNA at destined tissue sites provides a potential solution for treatment of diseases associated with ectopic mineralization.
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Affiliation(s)
- Min‐juan Shen
- National Clinical Research Center for Oral Diseases & State Key Laboratory of Military Stomatology & Shaanxi Key Laboratory of Stomatology, School of StomatologyThe Fourth Military Medical UniversityXi'anShaanxi710032P. R. China
| | - Kai Jiao
- National Clinical Research Center for Oral Diseases & State Key Laboratory of Military Stomatology & Shaanxi Key Laboratory of Stomatology, School of StomatologyThe Fourth Military Medical UniversityXi'anShaanxi710032P. R. China
| | - Chen‐yu Wang
- National Clinical Research Center for Oral Diseases & State Key Laboratory of Military Stomatology & Shaanxi Key Laboratory of Stomatology, School of StomatologyThe Fourth Military Medical UniversityXi'anShaanxi710032P. R. China
| | - Hermann Ehrlich
- Institute of Electronic and Sensor MaterialsTU Bergakademie FreibergFreiberg09599Germany
- Center for Advanced TechnologyAdam Mickiewicz UniversityPoznan61‐614Poland
| | - Mei‐chen Wan
- National Clinical Research Center for Oral Diseases & State Key Laboratory of Military Stomatology & Shaanxi Key Laboratory of Stomatology, School of StomatologyThe Fourth Military Medical UniversityXi'anShaanxi710032P. R. China
| | - Dong‐xiao Hao
- National Clinical Research Center for Oral Diseases & State Key Laboratory of Military Stomatology & Shaanxi Key Laboratory of Stomatology, School of StomatologyThe Fourth Military Medical UniversityXi'anShaanxi710032P. R. China
- Department of Applied PhysicsXi'an Jiaotong UniversityXi'anShaanxi710049P. R. China
| | - Jing Li
- National Clinical Research Center for Oral Diseases & State Key Laboratory of Military Stomatology & Shaanxi Key Laboratory of Stomatology, School of StomatologyThe Fourth Military Medical UniversityXi'anShaanxi710032P. R. China
| | - Qian‐qian Wan
- National Clinical Research Center for Oral Diseases & State Key Laboratory of Military Stomatology & Shaanxi Key Laboratory of Stomatology, School of StomatologyThe Fourth Military Medical UniversityXi'anShaanxi710032P. R. China
| | - Lige Tonggu
- School of MedicineUniversity of WashingtonSeattleWA98195USA
| | - Jian‐fei Yan
- National Clinical Research Center for Oral Diseases & State Key Laboratory of Military Stomatology & Shaanxi Key Laboratory of Stomatology, School of StomatologyThe Fourth Military Medical UniversityXi'anShaanxi710032P. R. China
| | - Kai‐yan Wang
- National Clinical Research Center for Oral Diseases & State Key Laboratory of Military Stomatology & Shaanxi Key Laboratory of Stomatology, School of StomatologyThe Fourth Military Medical UniversityXi'anShaanxi710032P. R. China
| | - Yu‐xuan Ma
- National Clinical Research Center for Oral Diseases & State Key Laboratory of Military Stomatology & Shaanxi Key Laboratory of Stomatology, School of StomatologyThe Fourth Military Medical UniversityXi'anShaanxi710032P. R. China
| | - Ji‐hua Chen
- National Clinical Research Center for Oral Diseases & State Key Laboratory of Military Stomatology & Shaanxi Key Laboratory of Stomatology, School of StomatologyThe Fourth Military Medical UniversityXi'anShaanxi710032P. R. China
| | - Franklin R. Tay
- The Dental College of GeorgiaAugusta UniversityAugustaGA30912USA
| | - Li‐na Niu
- National Clinical Research Center for Oral Diseases & State Key Laboratory of Military Stomatology & Shaanxi Key Laboratory of Stomatology, School of StomatologyThe Fourth Military Medical UniversityXi'anShaanxi710032P. R. China
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9
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Li J, Gao J, Wang R. Control of Chromatin Organization and Chromosome Behavior during the Cell Cycle through Phase Separation. Int J Mol Sci 2021; 22:ijms222212271. [PMID: 34830152 PMCID: PMC8621359 DOI: 10.3390/ijms222212271] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2021] [Revised: 10/29/2021] [Accepted: 11/09/2021] [Indexed: 01/02/2023] Open
Abstract
Phase-separated condensates participate in various biological activities. Liquid-liquid phase separation (LLPS) can be driven by collective interactions between multivalent and intrinsically disordered proteins. The manner in which chromatin-with various morphologies and activities-is organized in a complex and small nucleus still remains to be fully determined. Recent findings support the claim that phase separation is involved in the regulation of chromatin organization and chromosome behavior. Moreover, phase separation also influences key events during mitosis and meiosis. This review elaborately dissects how phase separation regulates chromatin and chromosome organization and controls mitotic and meiotic chromosome behavior.
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10
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Vasiliu T, Craciun BF, Neamtu A, Clima L, Isac DL, Maier SS, Pinteala M, Mocci F, Laaksonen A. In silico study of PEI-PEG-squalene-dsDNA polyplex formation: the delicate role of the PEG length in the binding of PEI to DNA. Biomater Sci 2021; 9:6623-6640. [PMID: 34582532 DOI: 10.1039/d1bm00973g] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Biocompatible hydrophilic polyethylene glycol (PEG) is widely used in biomedical applications, such as drug or gene delivery, tissue engineering or as an antifouling component in biomedical devices. Experimental studies have shown that the size of PEG can weaken polycation-polyanion interactions, like those between branched polyethyleneimine (b-PEI) and DNA in gene carriers, but details of its cause and underlying interactions on the atomic scale are still not clear. To better understand the interaction mechanisms in the formation of polyplexes between b-PEI-PEG based carriers and DNA, we have used a combination of in silico tools and experiments on three multicomponent systems differing in PEG MW. Using the PEI-PEG-squalene-dsDNA systems of the same size, both in the all-atom MD simulations and in experimental in-gel electrophoresis measurements, we found that the binding between DNA and the vectors is highly influenced by the size of PEG, with the binding efficiency increasing with a shorter PEG length. The mechanism of how PEG interferes with the binding between PEI and DNA is explained using a two-step MD simulation protocol that showed that the DNA-vector interactions are influenced by the PEG length due to the hydrogen bond formation between PEI and PEG. Although computationally demanding we find it important to study molecular systems of the same size both in silico and in a laboratory and to simulate the behaviour of the carrier prior to the addition of bioactive molecules to understand the molecular mechanisms involved in the formation of the polyplex.
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Affiliation(s)
- Tudor Vasiliu
- Center of Advanced Research in Bionanoconjugates and Biopolymers, "Petru Poni" Institute of Macromolecular Chemistry, Iasi 700487, Romania.
| | - Bogdan Florin Craciun
- Center of Advanced Research in Bionanoconjugates and Biopolymers, "Petru Poni" Institute of Macromolecular Chemistry, Iasi 700487, Romania.
| | - Andrei Neamtu
- Bioinformatics Laboratory, TRANSCEND IRO, Iaşi 700843, Romania
| | - Lilia Clima
- Center of Advanced Research in Bionanoconjugates and Biopolymers, "Petru Poni" Institute of Macromolecular Chemistry, Iasi 700487, Romania.
| | - Dragos Lucian Isac
- Center of Advanced Research in Bionanoconjugates and Biopolymers, "Petru Poni" Institute of Macromolecular Chemistry, Iasi 700487, Romania.
| | - Stelian S Maier
- Center of Advanced Research in Bionanoconjugates and Biopolymers, "Petru Poni" Institute of Macromolecular Chemistry, Iasi 700487, Romania. .,Polymers Research Center, "Gheorghe Asachi" Technical University of Iasi, Iasi, 700487, Romania
| | - Mariana Pinteala
- Center of Advanced Research in Bionanoconjugates and Biopolymers, "Petru Poni" Institute of Macromolecular Chemistry, Iasi 700487, Romania.
| | - Francesca Mocci
- Center of Advanced Research in Bionanoconjugates and Biopolymers, "Petru Poni" Institute of Macromolecular Chemistry, Iasi 700487, Romania. .,Dipartimento di Scienze Chimiche e Geologiche, Università di Cagliari, Monserrato, 09042 Cagliari, Italy
| | - Aatto Laaksonen
- Center of Advanced Research in Bionanoconjugates and Biopolymers, "Petru Poni" Institute of Macromolecular Chemistry, Iasi 700487, Romania. .,Department of Materials and Environmental Chemistry, Division of Physical Chemistry, Arrhenius Laboratory, Stockholm University, 106 91 Stockholm, Sweden.,State Key Laboratory of Materials-Oriented and Chemical Engineering, Nanjing Tech University, 210009 Nanjing, PR China.,Department of Engineering Sciences and Mathematics, Division of Energy Science, Luleå University of Technology, 97187 Luleå, Sweden
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11
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Sun T, Minhas V, Korolev N, Mirzoev A, Lyubartsev AP, Nordenskiöld L. Bottom-Up Coarse-Grained Modeling of DNA. Front Mol Biosci 2021; 8:645527. [PMID: 33816559 PMCID: PMC8010198 DOI: 10.3389/fmolb.2021.645527] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2020] [Accepted: 02/22/2021] [Indexed: 12/22/2022] Open
Abstract
Recent advances in methodology enable effective coarse-grained modeling of deoxyribonucleic acid (DNA) based on underlying atomistic force field simulations. The so-called bottom-up coarse-graining practice separates fast and slow dynamic processes in molecular systems by averaging out fast degrees of freedom represented by the underlying fine-grained model. The resulting effective potential of interaction includes the contribution from fast degrees of freedom effectively in the form of potential of mean force. The pair-wise additive potential is usually adopted to construct the coarse-grained Hamiltonian for its efficiency in a computer simulation. In this review, we present a few well-developed bottom-up coarse-graining methods, discussing their application in modeling DNA properties such as DNA flexibility (persistence length), conformation, "melting," and DNA condensation.
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Affiliation(s)
- Tiedong Sun
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
| | - Vishal Minhas
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
| | - Nikolay Korolev
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
| | - Alexander Mirzoev
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
| | - Alexander P. Lyubartsev
- Department of Materials and Environmental Chemistry, Stockholm University, Stockholm, Sweden
| | - Lars Nordenskiöld
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
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12
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What do we know about DNA mechanics so far? Curr Opin Struct Biol 2020; 64:42-50. [DOI: 10.1016/j.sbi.2020.05.010] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2020] [Accepted: 05/17/2020] [Indexed: 12/14/2022]
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13
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Gallops CE, Ziebarth JD, Wang Y. Coarse‐Grained Simulations of the Impact of Chain Length and Stiffness on the Formation and Aggregation of Polyelectrolyte Complexes. MACROMOL THEOR SIMUL 2020; 29. [DOI: 10.1002/mats.202000015] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Caleb E. Gallops
- Department of ChemistryThe University of Memphis Memphis TN 38152 USA
| | - Jesse D. Ziebarth
- Department of ChemistryThe University of Memphis Memphis TN 38152 USA
| | - Yongmei Wang
- Department of ChemistryThe University of Memphis Memphis TN 38152 USA
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14
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Tanaka H, Shew CY, Yoshikawa Y, Kenmotsu T, Yoshikawa K. Low-efficiency of gene expression with a long diamine is attributable to the effect on DNA zipping. Chem Phys Lett 2020. [DOI: 10.1016/j.cplett.2020.137253] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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15
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Zhai C, Li T, Shi H, Yeo J. Discovery and design of soft polymeric bio-inspired materials with multiscale simulations and artificial intelligence. J Mater Chem B 2020; 8:6562-6587. [DOI: 10.1039/d0tb00896f] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Establishing the “Materials 4.0” paradigm requires intimate knowledge of the virtual space in materials design.
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Affiliation(s)
- Chenxi Zhai
- J2 Lab for Engineering Living Materials
- Sibley School of Mechanical and Aerospace Engineering
- Cornell University
- Ithaca
- USA
| | - Tianjiao Li
- J2 Lab for Engineering Living Materials
- Sibley School of Mechanical and Aerospace Engineering
- Cornell University
- Ithaca
- USA
| | - Haoyuan Shi
- J2 Lab for Engineering Living Materials
- Sibley School of Mechanical and Aerospace Engineering
- Cornell University
- Ithaca
- USA
| | - Jingjie Yeo
- J2 Lab for Engineering Living Materials
- Sibley School of Mechanical and Aerospace Engineering
- Cornell University
- Ithaca
- USA
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16
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Minhas V, Sun T, Mirzoev A, Korolev N, Lyubartsev AP, Nordenskiöld L. Modeling DNA Flexibility: Comparison of Force Fields from Atomistic to Multiscale Levels. J Phys Chem B 2019; 124:38-49. [DOI: 10.1021/acs.jpcb.9b09106] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
- Vishal Minhas
- School of Biological Sciences, Nanyang Technological University, Singapore 637551
| | - Tiedong Sun
- School of Biological Sciences, Nanyang Technological University, Singapore 637551
| | - Alexander Mirzoev
- School of Biological Sciences, Nanyang Technological University, Singapore 637551
| | - Nikolay Korolev
- School of Biological Sciences, Nanyang Technological University, Singapore 637551
| | - Alexander P. Lyubartsev
- Department of Materials and Environmental Chemistry, Stockholm University, 10691 Stockholm, Sweden
| | - Lars Nordenskiöld
- School of Biological Sciences, Nanyang Technological University, Singapore 637551
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17
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Fiorillo L, Bianco S, Esposito A, Conte M, Sciarretta R, Musella F, Chiariello AM. A modern challenge of polymer physics: Novel ways to study, interpret, and reconstruct chromatin structure. WILEY INTERDISCIPLINARY REVIEWS-COMPUTATIONAL MOLECULAR SCIENCE 2019. [DOI: 10.1002/wcms.1454] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- Luca Fiorillo
- Dipartimento di Fisica Università di Napoli Federico II, and INFN Napoli Complesso Universitario di Monte Sant'Angelo Naples Italy
| | - Simona Bianco
- Dipartimento di Fisica Università di Napoli Federico II, and INFN Napoli Complesso Universitario di Monte Sant'Angelo Naples Italy
| | - Andrea Esposito
- Dipartimento di Fisica Università di Napoli Federico II, and INFN Napoli Complesso Universitario di Monte Sant'Angelo Naples Italy
| | - Mattia Conte
- Dipartimento di Fisica Università di Napoli Federico II, and INFN Napoli Complesso Universitario di Monte Sant'Angelo Naples Italy
| | - Renato Sciarretta
- Dipartimento di Fisica Università di Napoli Federico II, and INFN Napoli Complesso Universitario di Monte Sant'Angelo Naples Italy
| | - Francesco Musella
- Dipartimento di Fisica Università di Napoli Federico II, and INFN Napoli Complesso Universitario di Monte Sant'Angelo Naples Italy
| | - Andrea M. Chiariello
- Dipartimento di Fisica Università di Napoli Federico II, and INFN Napoli Complesso Universitario di Monte Sant'Angelo Naples Italy
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