Using extensive molecular dynamics simulations, we obtain the conformational phase diagram of a charged polymer in the presence of oppositely charged counterions and neutral attractive crowders for monovalent, divalent, and trivalent counterion valencies. We demonstrate that the charged polymer can exist in three phases: (1) an extended phase for low charge densities and weak polymer-crowder attractive interactions [Charged Extended (CE)]; (2) a collapsed phase for high charge densities and weak polymer-crowder attractive interactions, primarily driven by counterion condensation [Charged Collapsed due to Intra-polymer interactions [(CCI)]; and (3) a collapsed phase for strong polymer-crowder attractive interactions, irrespective of the charge density, driven by crowders acting as bridges or cross-links [Charged Collapsed due to Bridging interactions [(CCB)]. Importantly, simulations reveal that the interaction with crowders can induce collapse, despite the presence of strong repulsive electrostatic interactions, and can replace condensed counterions to facilitate a direct transition from the CCI and CE phases to the CCB phase.
Download full-text PDF |
Source |
|---|---|
| http://dx.doi.org/10.1063/5.0172696 | DOI Listing |
Publication Analysis
Top Keywords
Similar Publications
Attractive crowding effect on passive and active polymer looping kinetics.
J Chem Phys
April 2024
College of Chemistry, Sichuan University, Chengdu 610064, China.
Loop formation in complex environments is crucially important to many biological processes in life. In the present work, we adopt three-dimensional Langevin dynamics simulations to investigate passive and active polymer looping kinetics in crowded media featuring polymer-crowder attraction. We find polymers undergo a remarkable coil-globule-coil transition, highlighted by a marked change in the Flory scaling exponent of the gyration radius.
View Article and Find Full Text PDFThe conformational phase diagram of charged polymers in the presence of attractive bridging crowders.
J Chem Phys
November 2023
The Institute of Mathematical Sciences, C.I.T. Campus, Taramani, Chennai 600113, India.
Using extensive molecular dynamics simulations, we obtain the conformational phase diagram of a charged polymer in the presence of oppositely charged counterions and neutral attractive crowders for monovalent, divalent, and trivalent counterion valencies. We demonstrate that the charged polymer can exist in three phases: (1) an extended phase for low charge densities and weak polymer-crowder attractive interactions [Charged Extended (CE)]; (2) a collapsed phase for high charge densities and weak polymer-crowder attractive interactions, primarily driven by counterion condensation [Charged Collapsed due to Intra-polymer interactions [(CCI)]; and (3) a collapsed phase for strong polymer-crowder attractive interactions, irrespective of the charge density, driven by crowders acting as bridges or cross-links [Charged Collapsed due to Bridging interactions [(CCB)]. Importantly, simulations reveal that the interaction with crowders can induce collapse, despite the presence of strong repulsive electrostatic interactions, and can replace condensed counterions to facilitate a direct transition from the CCI and CE phases to the CCB phase.
View Article and Find Full Text PDFMolecular Crowders Can Induce Collapse in Hydrophilic Polymers via Soft Attractive Interactions.
J Phys Chem B
July 2023
Department of Materials Science and Engineering, Indian Institute of Technology Delhi, New Delhi 110016, India.
A comprehensive understanding of protein folding and biomolecular self-assembly in the intracellular environment requires obtaining a microscopic view of the crowding effects. The classical view of crowding explains biomolecular collapse in such an environment in terms of the entropic solvent excluded volume effects subjected to hard-core repulsions exerted by the inert crowders, neglecting their soft chemical interactions. In this study, the effects of nonspecific, soft interactions of molecular crowders in regulating the conformational equilibrium of hydrophilic (charged) polymers are examined.
View Article and Find Full Text PDFThe conformational phase diagram of neutral polymers in the presence of attractive crowders.
J Chem Phys
March 2023
The Institute of Mathematical Sciences, C.I.T. Campus, Taramani, Chennai 600113, India.
Extensive coarse-grained molecular dynamics simulations are performed to investigate the conformational phase diagram of a neutral polymer in the presence of attractive crowders. We show that, for low crowder densities, the polymer predominantly shows three phases as a function of both intra-polymer and polymer-crowder interactions: (1) weak intra-polymer and weak polymer-crowder attractive interactions induce extended or coil polymer conformations (phase E), (2) strong intra-polymer and relatively weak polymer-crowder attractive interactions induce collapsed or globular conformations (phase CI), and (3) strong polymer-crowder attractive interactions, regardless of intra-polymer interactions, induce a second collapsed or globular conformation that encloses bridging crowders (phase CB). The detailed phase diagram is obtained by determining the phase boundaries delineating the different phases based on an analysis of the radius of gyration as well as bridging crowders.
View Article and Find Full Text PDFSmall crowder interactions can drive hydrophobic polymer collapse as well as unfolding.
Phys Chem Chem Phys
August 2020
Centre for Computational and Data Sciences, Indian Institute of Technology Kharagpur, West Bengal 721302, India.
Biomolecules evolve and function in the intracellular crowded environment that is densely packed with macromolecules. Yet, a microscopic understanding of the effects of such an environment on the conformational preferences of biomolecules remains elusive. While prior investigations have attributed crowding effects mainly to the excluded volume (size) effects of the crowders, very little is known about the effects exerted due to their chemical interactions.
View Article and Find Full Text PDFWant AI Summaries of new PubMed Abstracts delivered to your In-box?
Enter search terms and have AI summaries delivered each week - change queries or unsubscribe any time!