1
|
Abramova A, Glagolev M, Vasilevskaya V. Structured globules with twisted arrangement of helical blocks: Computer simulation. POLYMER 2022. [DOI: 10.1016/j.polymer.2022.124974] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
|
2
|
Lee JY, Song Y, Wessels MG, Jayaraman A, Wooley KL, Pochan DJ. Hierarchical Self-Assembly of Poly(d-glucose carbonate) Amphiphilic Block Copolymers in Mixed Solvents. Macromolecules 2020. [DOI: 10.1021/acs.macromol.0c01575] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Affiliation(s)
- Jee Young Lee
- Department of Materials Science and Engineering, University of Delaware, Newark, Delaware 19716, United States
| | - Yue Song
- Departments of Chemistry, Chemical Engineering, and Materials Science & Engineering, Texas A&M University, College Station, Texas 77842, United States
| | - Michiel G. Wessels
- Department of Chemical and Biomolecular Engineering, University of Delaware, Newark, Delaware 19716, United States
| | - Arthi Jayaraman
- Department of Materials Science and Engineering, University of Delaware, Newark, Delaware 19716, United States
- Department of Chemical and Biomolecular Engineering, University of Delaware, Newark, Delaware 19716, United States
| | - Karen L. Wooley
- Departments of Chemistry, Chemical Engineering, and Materials Science & Engineering, Texas A&M University, College Station, Texas 77842, United States
| | - Darrin J. Pochan
- Department of Materials Science and Engineering, University of Delaware, Newark, Delaware 19716, United States
| |
Collapse
|
3
|
Diagrams of States of Single Flexible-Semiflexible Multi-Block Copolymer Chains: A Flat-Histogram Monte Carlo Study. Polymers (Basel) 2019; 11:polym11050757. [PMID: 31052227 PMCID: PMC6571722 DOI: 10.3390/polym11050757] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2019] [Revised: 04/24/2019] [Accepted: 04/26/2019] [Indexed: 01/16/2023] Open
Abstract
The combination of flexibility and semiflexibility in a single molecule is a powerful design principle both in nature and in materials science. We present results on the conformational behavior of a single multiblock-copolymer chain, consisting of equal amounts of Flexible (F) and Semiflexible (S) blocks with different affinity to an implicit solvent. We consider a manifold of macrostates defined by two terms in the total energy: intermonomer interaction energy and stiffness energy. To obtain diagrams of states (pseudo-phase diagrams), we performed flat-histogram Monte Carlo simulations using the Stochastic Approximation Monte Carlo algorithm (SAMC). We have accumulated two-Dimensional Density of States (2D DoS) functions (defined on the 2D manifold of macrostates) for a SF-multiblock-copolymer chain of length N=64 with block lengths b = 4, 8, 16, and 32 in two different selective solvents. In an analysis of the canonical ensemble, we calculated the heat capacity and determined its maxima and the most probable morphologies in different regions of the state diagrams. These are rich in various, non-trivial morphologies, which are formed without any specific interactions, and depend on the block length and the type of solvent selectivity (preferring S or F blocks, respectively). We compared the diagrams with those for the non-selective solvent and reveal essential changes in some cases. Additionally, we implemented microcanonical analysis in the “conformational” microcanonical (NVU, where U is the potential energy) and the true microcanonical (NVE, where E is the total energy) ensembles with the aim to reveal and classify pseudo-phase transitions, occurring under the change of temperature.
Collapse
|
4
|
Zablotskiy SV, Martemyanova JA, Ivanov VA, Paul W. Diagram of states and morphologies of flexible-semiflexible copolymer chains: A Monte Carlo simulation. J Chem Phys 2016; 144:244903. [PMID: 27369540 DOI: 10.1063/1.4946035] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
A single copolymer chain consisting of multiple flexible (F) and semiflexible (S) blocks has been studied using a continuum bead-spring model by Stochastic Approximation Monte Carlo simulations, which determine the density of states of the model. The only difference between F and S blocks is the intramolecular bending potential, all non-bonded interactions are equal. The state diagrams for this class of models display multiple nematic phases in the collapsed state, characterized through a demixing of the blocks of different stiffness and orientational ordering of the stiff blocks. We observe dumbbell-like morphologies, lamellar phases, and for the larger block lengths also Saturn-like structures with a core of flexible segments and the stiff segments forming a ring around the core.
Collapse
Affiliation(s)
| | | | - Viktor A Ivanov
- Faculty of Physics, Moscow State University, Moscow 119991, Russia
| | - Wolfgang Paul
- Institut für Physik, Martin-Luther-Universität Halle-Wittenberg, Halle (Saale) 06099, Germany
| |
Collapse
|
5
|
Ivanov VA, Martemyanova JA, Rodionova AS, Stukan MR. Computer simulation of stiff-chain polymers. POLYMER SCIENCE SERIES C 2013. [DOI: 10.1134/s1811238213060039] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
|
6
|
Structure of metaphase chromosomes: a role for effects of macromolecular crowding. PLoS One 2012; 7:e36045. [PMID: 22540018 PMCID: PMC3335069 DOI: 10.1371/journal.pone.0036045] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2012] [Accepted: 03/29/2012] [Indexed: 12/12/2022] Open
Abstract
In metaphase chromosomes, chromatin is compacted to a concentration of several hundred mg/ml by mechanisms which remain elusive. Effects mediated by the ionic environment are considered most frequently because mono- and di-valent cations cause polynucleosome chains to form compact ~30-nm diameter fibres in vitro, but this conformation is not detected in chromosomes in situ. A further unconsidered factor is predicted to influence the compaction of chromosomes, namely the forces which arise from crowding by macromolecules in the surrounding cytoplasm whose measured concentration is 100-200 mg/ml. To mimic these conditions, chromosomes were released from mitotic CHO cells in solutions containing an inert volume-occupying macromolecule (8 kDa polyethylene glycol, 10.5 kDa dextran, or 70 kDa Ficoll) in 100 µM K-Hepes buffer, with contaminating cations at only low micromolar concentrations. Optical and electron microscopy showed that these chromosomes conserved their characteristic structure and compaction, and their volume varied inversely with the concentration of a crowding macromolecule. They showed a canonical nucleosomal structure and contained the characteristic proteins topoisomerase IIα and the condensin subunit SMC2. These observations, together with evidence that the cytoplasm is crowded in vivo, suggest that macromolecular crowding effects should be considered a significant and perhaps major factor in compacting chromosomes. This model may explain why ~30-nm fibres characteristic of cation-mediated compaction are not seen in chromosomes in situ. Considering that crowding by cytoplasmic macromolecules maintains the compaction of bacterial chromosomes and has been proposed to form the liquid crystalline chromosomes of dinoflagellates, a crowded environment may be an essential characteristic of all genomes.
Collapse
|
7
|
Neratova IV, Komarov PV, Pavlov AS, Ivanov VA. Collapse of an AB copolymer single chain with alternating blocks of different stiffness. Russ Chem Bull 2011. [DOI: 10.1007/s11172-011-0038-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
|
8
|
Das S, Chakraborty S. Probing solvation decay length in order to characterize hydrophobicity-induced bead-bead attractive interactions in polymer chains. J Mol Model 2010; 17:1911-8. [PMID: 21110052 DOI: 10.1007/s00894-010-0899-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2010] [Accepted: 11/09/2010] [Indexed: 11/24/2022]
Abstract
In this paper, we quantitatively demonstrate that exponentially decaying attractive potentials can effectively mimic strong hydrophobic interactions between monomer units of a polymer chain dissolved in aqueous solvent. Classical approaches to modeling hydrophobic solvation interactions are based on invariant attractive length scales. However, we demonstrate here that the solvation interaction decay length may need to be posed as a function of the relative separation distances and the sizes of the interacting species (or beads or monomers) to replicate the necessary physical interactions. As an illustrative example, we derive a universal scaling relationship for a given solute-solvent combination between the solvation decay length, the bead radius, and the distance between the interacting beads. With our formalism, the hydrophobic component of the net attractive interaction between monomer units can be synergistically accounted for within the unified framework of a simple exponentially decaying potential law, where the characteristic decay length incorporates the distinctive and critical physical features of the underlying interaction. The present formalism, even in a mesoscopic computational framework, is capable of incorporating the essential physics of the appropriate solute-size dependence and solvent-interaction dependence in the hydrophobic force estimation, without explicitly resolving the underlying molecular level details.
Collapse
Affiliation(s)
- Siddhartha Das
- Department of Mechanical Engineering, Indian Institute of Technology, Kharagpur 721302, India
| | | |
Collapse
|
9
|
Self-association of polynucleosome chains by macromolecular crowding. EUROPEAN BIOPHYSICS JOURNAL: EBJ 2008; 37:1059-64. [PMID: 18259740 DOI: 10.1007/s00249-008-0276-1] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/23/2007] [Revised: 01/18/2008] [Accepted: 01/22/2008] [Indexed: 10/22/2022]
Abstract
The crowding of macromolecules in the cell nucleus, where their concentration is in the range of 100 mg/ml, is predicted to result in strong entropic forces between them. Here the effects of crowding on polynucleosome chains in vitro were studied to evaluate if these forces could contribute to the packing of chromatin in the nucleus in vivo. Soluble polynucleosomes approximately 20 nucleosomes in length formed fast-sedimenting complexes in the presence of inert, volume-occupying agents poly(ethylene glycol) (PEG) or dextran. This self-association was reversible and consistent with the effect of macromolecular crowding. In the presence of these crowding agents, polynucleosomes formed large assemblies as seen by fluorescence microscopy after labelling DNA with the fluorescent stain DAPI, and formed rods and sheets at a higher concentration of crowding agent. Self-association caused by crowding does not require exogenous cations. Single, approximately 800 nucleosome-long chains prepared in 100 microM Hepes buffer with no added cations, labelled with the fluorescent DNA stain YOYO-1, and spread on a polylysine-coated surface formed compact 3-D clusters in the presence of PEG or dextran. This reversible packing of polynucleosome chains by crowding may help to understand their compact conformations in the nucleus. These results, together with the known collapse of linear polymers in crowded milieux, suggest that entropic forces due to crowding, which have not been considered previously, may be an important factor in the packing of nucleosome chains in the nucleus.
Collapse
|
10
|
Hancock R. Packing of the polynucleosome chain in interphase chromosomes: evidence for a contribution of crowding and entropic forces. Semin Cell Dev Biol 2007; 18:668-75. [PMID: 17904880 DOI: 10.1016/j.semcdb.2007.08.006] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2007] [Accepted: 08/22/2007] [Indexed: 11/23/2022]
Abstract
In the crowded intranuclear environment, entropic depletion forces between macromolecules are expected to be strong. A review of simulations of linear polymers leads to several predictions about probable conformations of a polynucleosome chain in these conditions. These include a globular conformation, variable compaction due to different local rigidity or curvature of the mosaic of isochores, satellite sequences, and nucleosomes containing different histone variants, and the possibility that chromosomes represent separate phases like those seen in heterogeneous particle mixtures by experiment and simulation. Experimental results which show that macromolecular crowding alone, in the absence of exogenous cations, can stabilise interphase chromosomes and cause self-association of polynucleosome chains are presented. Together, these considerations suggest that macromolecular crowding and entropic forces are major factors in packing polynucleosome chains in vivo.
Collapse
Affiliation(s)
- Ronald Hancock
- Laval University Cancer Research Centre, Hôtel-Dieu Hospital, 9 rue MacMahon, Québec, QC, Canada G1R 2J6.
| |
Collapse
|
11
|
Yoshinaga N, Yoshikawa K. Core-shell structures in single flexible-semiflexible block copolymers: Finding the free energy minimum for the folding transition. J Chem Phys 2007; 127:044902. [PMID: 17672720 DOI: 10.1063/1.2753838] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
We investigate the folding transition of a single diblock copolymer consisting of a semiflexible and a flexible block. We obtain a Saturn-shaped core-shell conformation in the folded state, in which the flexible block forms a core and the semiflexible block wraps around it. We demonstrate two distinctive features of the core-shell structures: (i) The kinetics of the folding transition in the copolymer are significantly more efficient than those of a semiflexible homopolymer. (ii) The core-shell structure does not depend on the transition pathway.
Collapse
Affiliation(s)
- Natsuhiko Yoshinaga
- Department of Physics, Graduate School of Sciences, The University of Tokyo, Tokyo 113-0033, Japan
| | | |
Collapse
|