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Vögele M, Köfinger J, Hummer G. Nanoporous Membranes of Densely Packed Carbon Nanotubes Formed by Lipid-Mediated Self-Assembly. ACS Appl Bio Mater 2024; 7:528-534. [PMID: 36070609 PMCID: PMC10880049 DOI: 10.1021/acsabm.2c00585] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2022] [Accepted: 08/29/2022] [Indexed: 11/29/2022]
Abstract
Nanofiltration technology faces the competing challenges of achieving high fluid flux through uniformly narrow pores of a mechanically and chemically stable filter. Supported dense-packed 2D-crystals of single-walled carbon nanotube (CNT) porins with ∼1 nm wide pores could, in principle, meet these challenges. However, such CNT membranes cannot currently be synthesized at high pore density. Here, we use computer simulations to explore lipid-mediated self-assembly as a route toward densely packed CNT membranes, motivated by the analogy to membrane-protein 2D crystallization. In large-scale coarse-grained molecular dynamics (MD) simulations, we find that CNTs in lipid membranes readily self-assemble into large clusters. Lipids trapped between the CNTs lubricate CNT repacking upon collisions of diffusing clusters, thereby facilitating the formation of large ordered structures. Cluster diffusion follows the Saffman-Delbrück law and its generalization by Hughes, Pailthorpe, and White. On longer time scales, we expect the formation of close-packed CNT structures by depletion of the intervening shared annular lipid shell, depending on the relative strength of CNT-CNT and CNT-lipid interactions. Our simulations identify CNT length, diameter, and end functionalization as major factors for the self-assembly of CNT membranes.
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Affiliation(s)
- Martin Vögele
- Department
of Theoretical Biophysics, Max Planck Institute
of Biophysics, Max-von-Laue-Str. 3, 60438 Frankfurt am Main, Germany
| | - Jürgen Köfinger
- Department
of Theoretical Biophysics, Max Planck Institute
of Biophysics, Max-von-Laue-Str. 3, 60438 Frankfurt am Main, Germany
| | - Gerhard Hummer
- Department
of Theoretical Biophysics, Max Planck Institute
of Biophysics, Max-von-Laue-Str. 3, 60438 Frankfurt am Main, Germany
- Institute
for Biophysics, Goethe University Frankfurt, Max-von-Laue-Str. 1, 60438 Frankfurt am Main, Germany
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2
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Vögele M, Zhang BW, Kaindl J, Wang L. Is the Functional Response of a Receptor Determined by the Thermodynamics of Ligand Binding? J Chem Theory Comput 2023; 19:8414-8422. [PMID: 37943175 DOI: 10.1021/acs.jctc.3c00899] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2023]
Abstract
For an effective drug, strong binding to the target protein is a prerequisite, but it is not enough. To produce a particular functional response, drugs need to either block the proteins' functions or modulate their activities by changing their conformational equilibrium. The binding free energy of a compound to its target is routinely calculated, but the timescales for the protein conformational changes are prohibitively long to be efficiently modeled via physics-based simulations. Thermodynamic principles suggest that the binding free energies of the ligands with different receptor conformations may infer their efficacy. However, this hypothesis has not been thoroughly validated. We present an actionable protocol and a comprehensive study to show that binding thermodynamics provides a strong predictor of the efficacy of a ligand. We apply the absolute binding free energy perturbation method to ligands bound to active and inactive states of eight G protein-coupled receptors and a nuclear receptor and then compare the resulting binding free energies. We find that carefully designed restraints are often necessary to efficiently model the corresponding conformational ensembles for each state. Our method achieves unprecedented performance in classifying ligands as agonists or antagonists across the various investigated receptors, all of which are important drug targets.
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Affiliation(s)
- Martin Vögele
- Schrödinger, Inc., 1540 Broadway 24th Floor, New York, New York 10036, United States
| | - Bin W Zhang
- Schrödinger, Inc., 1540 Broadway 24th Floor, New York, New York 10036, United States
| | - Jonas Kaindl
- Schrödinger GmbH, Glücksteinallee 25, Mannheim 68163, Germany
| | - Lingle Wang
- Schrödinger, Inc., 1540 Broadway 24th Floor, New York, New York 10036, United States
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3
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Tsutsumi N, Maeda S, Qu Q, Vögele M, Jude KM, Suomivuori CM, Panova O, Waghray D, Kato HE, Velasco A, Dror RO, Skiniotis G, Kobilka BK, Garcia KC. Atypical structural snapshots of human cytomegalovirus GPCR interactions with host G proteins. Sci Adv 2022; 8:eabl5442. [PMID: 35061538 PMCID: PMC8782444 DOI: 10.1126/sciadv.abl5442] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/20/2021] [Accepted: 11/29/2021] [Indexed: 05/12/2023]
Abstract
Human cytomegalovirus (HCMV) encodes G protein-coupled receptors (GPCRs) US28 and US27, which facilitate viral pathogenesis through engagement of host G proteins. Here we report cryo-electron microscopy structures of US28 and US27 forming nonproductive and productive complexes with Gi and Gq, respectively, exhibiting unusual features with functional implications. The "orphan" GPCR US27 lacks a ligand-binding pocket and has captured a guanosine diphosphate-bound inactive Gi through a tenuous interaction. The docking modes of CX3CL1-US28 and US27 to Gi favor localization to endosome-like curved membranes, where US28 and US27 can function as nonproductive Gi sinks to attenuate host chemokine-dependent Gi signaling. The CX3CL1-US28-Gq/11 complex likely represents a trapped intermediate during productive signaling, providing a view of a transition state in GPCR-G protein coupling for signaling. Our collective results shed new insight into unique G protein-mediated HCMV GPCR structural mechanisms, compared to mammalian GPCR counterparts, for subversion of host immunity.
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Affiliation(s)
- Naotaka Tsutsumi
- Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA, USA
- Department of Structural Biology, Stanford University School of Medicine, Stanford, CA, USA
- Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, CA, USA
| | - Shoji Maeda
- Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA, USA
| | - Qianhui Qu
- Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA, USA
- Department of Structural Biology, Stanford University School of Medicine, Stanford, CA, USA
| | - Martin Vögele
- Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA, USA
- Department of Structural Biology, Stanford University School of Medicine, Stanford, CA, USA
- Department of Computer Science, Stanford University, Stanford, CA, USA
- Institute for Computational and Mathematical Engineering, Stanford University, Stanford, CA, USA
| | - Kevin M. Jude
- Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA, USA
- Department of Structural Biology, Stanford University School of Medicine, Stanford, CA, USA
- Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, CA, USA
| | - Carl-Mikael Suomivuori
- Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA, USA
- Department of Structural Biology, Stanford University School of Medicine, Stanford, CA, USA
- Department of Computer Science, Stanford University, Stanford, CA, USA
- Institute for Computational and Mathematical Engineering, Stanford University, Stanford, CA, USA
| | - Ouliana Panova
- Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA, USA
- Department of Structural Biology, Stanford University School of Medicine, Stanford, CA, USA
| | - Deepa Waghray
- Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA, USA
| | - Hideaki E. Kato
- Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA, USA
| | - Andrew Velasco
- Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA, USA
| | - Ron O. Dror
- Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA, USA
- Department of Structural Biology, Stanford University School of Medicine, Stanford, CA, USA
- Department of Computer Science, Stanford University, Stanford, CA, USA
- Institute for Computational and Mathematical Engineering, Stanford University, Stanford, CA, USA
| | - Georgios Skiniotis
- Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA, USA
- Department of Structural Biology, Stanford University School of Medicine, Stanford, CA, USA
| | - Brian K. Kobilka
- Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA, USA
| | - K. Christopher Garcia
- Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA, USA
- Department of Structural Biology, Stanford University School of Medicine, Stanford, CA, USA
- Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, CA, USA
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Vögele M, Bhaskara RM, Mulvihill E, van Pee K, Yildiz Ö, Kühlbrandt W, Müller DJ, Hummer G. Membrane Perforation by the Pore-Forming Toxin Pneumolysin. Biophys J 2020. [DOI: 10.1016/j.bpj.2019.11.1397] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022] Open
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5
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Sánchez PA, Vögele M, Smiatek J, Qiao B, Sega M, Holm C. Atomistic simulation of PDADMAC/PSS oligoelectrolyte multilayers: overall comparison of tri- and tetra-layer systems. Soft Matter 2019; 15:9437-9451. [PMID: 31720676 DOI: 10.1039/c9sm02010a] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
By employing large-scale molecular dynamics simulations of atomistically resolved oligoelectrolytes in aqueous solutions, we study in detail the first four layer-by-layer deposition cycles of an oligoelectrolyte multilayer made of poly(diallyl dimethyl ammonium chloride)/poly(styrene sulfonate sodium salt) (PDADMAC/PSS). The multilayers are grown on a silica substrate in 0.1 M NaCl electrolyte solutions and the swollen structures are then subsequently exposed to varying added salt concentration. We investigated the microscopic properties of the films, analyzing in detail the differences between three- and four-layer systems. Our simulations provide insights into the early stages of growth of a multilayer, which are particularly challenging for experimental observations. We found rather strong complexation of the oligoelectrolytes, with fuzzy layering of the film structure. The main charge compensation mechanism is for all cases intrinsic, whereas extrinsic compensation is relatively enhanced for the layer of the last deposition cycle. In addition, we quantified other fundamental observables of these systems, such as the film thickness, water uptake, and overcharge fractions for each deposition layer.
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Affiliation(s)
- Pedro A Sánchez
- Ural Federal University, 51 Lenin av., Ekaterinburg, 620000, Russian Federation. and Institute of Ion Beam Physics and Materials Research, Helmholtz-Zentrum Dresden-Rossendorf e.V., Dresden, Germany
| | - Martin Vögele
- Department of Computer Science, Stanford University, Stanford, California, USA
| | - Jens Smiatek
- Institut für Computerphysik, Universität Stuttgart, 70569 Stuttgart, Germany
| | - Baofu Qiao
- Chemical Sciences and Engineering Division, Argonne National Laboratory, Argonne, Illinois, USA
| | - Marcello Sega
- Forschungszentrum Jülich, Helmholtz Institute Erlangen-Nuremberg, Nuremberg, Germany
| | - Christian Holm
- Institut für Computerphysik, Universität Stuttgart, 70569 Stuttgart, Germany
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6
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Wu CM, Regler B, Bäuerle FK, Vögele M, Einhorn L, Elizarova S, Förste S, Shenolikar J, Lasser J. Perceptions of publication pressure in the Max Planck Society. Nat Hum Behav 2019; 3:1029-1030. [PMID: 31602033 DOI: 10.1038/s41562-019-0728-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
| | - Charley M Wu
- Max Planck Institute for Human Development, Berlin, Germany.
| | - Benjamin Regler
- Fritz Haber Institute of the Max Planck Society, Berlin, Germany
| | - Felix K Bäuerle
- Max Planck Institute for Dynamics and Self-Organization, Göttingen, Germany
| | | | - Laura Einhorn
- Max Planck Institute for the Study of Societies, Köln, Germany
| | - Sofia Elizarova
- Max Planck Institute of Experimental Medicine, Göttingen, Germany
| | - Stefanie Förste
- Max Planck Institute of Colloids and Interfaces, Potsdam, Germany
| | | | - Jana Lasser
- Max Planck Institute for Dynamics and Self-Organization, Göttingen, Germany
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7
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Vögele M, Köfinger J, Hummer G. Finite-Size-Corrected Rotational Diffusion Coefficients of Membrane Proteins and Carbon Nanotubes from Molecular Dynamics Simulations. J Phys Chem B 2019; 123:5099-5106. [PMID: 31132280 PMCID: PMC6750896 DOI: 10.1021/acs.jpcb.9b01656] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
![]()
We investigate
system-size effects on the rotational diffusion of membrane proteins
and other membrane-embedded molecules in molecular dynamics simulations. We find that
the rotational diffusion coefficient slows down relative to the infinite-system
value by a factor of one minus the ratio of protein and box areas.
This correction factor follows from the hydrodynamics of rotational
flows under periodic boundary conditions and is rationalized in terms
of Taylor–Couette flow. For membrane proteins like transporters,
channels, or receptors in typical simulation setups, the protein-covered
area tends to be relatively large, requiring a significant finite-size
correction. Molecular dynamics simulations of the protein adenine
nucleotide translocase (ANT1) and of a carbon nanotube porin in lipid
membranes show that the hydrodynamic finite-size correction for rotational
diffusion is accurate in standard-use cases. The dependence of the
rotational diffusion on box size can be used to determine the membrane
viscosity.
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Affiliation(s)
- Martin Vögele
- Department of Theoretical Biophysics , Max Planck Institute of Biophysics , Max-von-Laue Str. 3 , 60438 Frankfurt am Main , Germany
| | - Jürgen Köfinger
- Department of Theoretical Biophysics , Max Planck Institute of Biophysics , Max-von-Laue Str. 3 , 60438 Frankfurt am Main , Germany
| | - Gerhard Hummer
- Department of Theoretical Biophysics , Max Planck Institute of Biophysics , Max-von-Laue Str. 3 , 60438 Frankfurt am Main , Germany.,Institute for Biophysics , Goethe University Frankfurt , 60438 Frankfurt am Main , Germany
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8
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Abstract
By performing molecular dynamics simulations with up to 132 million coarse-grained particles in half-micron sized boxes, we show that hydrodynamics quantitatively explains the finite-size effects on diffusion of lipids, proteins, and carbon nanotubes in membranes. The resulting Oseen correction allows us to extract infinite-system diffusion coefficients and membrane surface viscosities from membrane simulations despite the logarithmic divergence of apparent diffusivities with increasing box width. The hydrodynamic theory of diffusion applies also to membranes with asymmetric leaflets and embedded proteins, and to a complex plasma-membrane mimetic.
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Affiliation(s)
- Martin Vögele
- Department of Theoretical Biophysics, Max Planck Institute of Biophysics, Max-von-Laue Straße 3, 60438 Frankfurt am Main, Germany
| | - Jürgen Köfinger
- Department of Theoretical Biophysics, Max Planck Institute of Biophysics, Max-von-Laue Straße 3, 60438 Frankfurt am Main, Germany
| | - Gerhard Hummer
- Department of Theoretical Biophysics, Max Planck Institute of Biophysics, Max-von-Laue Straße 3, 60438 Frankfurt am Main, Germany
- Institute for Biophysics, Goethe University, 60438 Frankfurt am Main, Germany
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9
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Baaden M, Barboiu M, Bill RM, Chen CL, Davis J, Di Vincenzo M, Freger V, Fröba M, Gale PA, Gong B, Hélix-Nielsen C, Hickey R, Hinds B, Hou JL, Hummer G, Kumar M, Legrand YM, Lokesh M, Mi B, Murail S, Pohl P, Sansom M, Song Q, Song W, Törnroth-Horsefield S, Vashisth H, Vögele M. Biomimetic water channels: general discussion. Faraday Discuss 2018; 209:205-229. [DOI: 10.1039/c8fd90020e] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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10
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Abstract
Carbon nanotube porins embedded in lipid membranes are studied by molecular dynamics simulations.
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Affiliation(s)
- Martin Vögele
- Department of Theoretical Biophysics
- Max Planck Institute of Biophysics
- 60438 Frankfurt am Main
- Germany
| | - Jürgen Köfinger
- Department of Theoretical Biophysics
- Max Planck Institute of Biophysics
- 60438 Frankfurt am Main
- Germany
| | - Gerhard Hummer
- Department of Theoretical Biophysics
- Max Planck Institute of Biophysics
- 60438 Frankfurt am Main
- Germany
- Institute for Biophysics
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11
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Baaden M, Borthakur MP, Casanova S, Coalson R, Freger V, Gonzalez M, Góra A, Hinds B, Hirunpinyopas W, Hummer G, Kumar M, Lynch C, Murail S, Noy A, Sansom M, Song Q, Vashisth H, Vögele M. The modelling and enhancement of water hydrodynamics: general discussion. Faraday Discuss 2018; 209:273-285. [DOI: 10.1039/c8fd90021c] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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12
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Abstract
The fusion of lipid membranes is opposed by high energetic barriers. In living organisms, complex protein machineries carry out this biologically essential process. Here we show that membrane-spanning carbon nanotubes (CNTs) can trigger spontaneous fusion of small lipid vesicles. In coarse-grained molecular dynamics simulations, we find that a CNT bridging between two vesicles locally perturbs their lipid structure. Their outer leaflets merge as the CNT pulls lipids out of the membranes, creating an hourglass-shaped fusion intermediate with still intact inner leaflets. As the CNT moves away from the symmetry axis connecting the vesicle centers, the inner leaflets merge, forming a pore that completes fusion. The distinct mechanism of CNT-mediated membrane fusion may be transferable, providing guidance in the development of fusion agents, e.g., for the targeted delivery of drugs or nucleic acids.
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Affiliation(s)
- Ramachandra M Bhaskara
- Department of Theoretical Biophysics, Max Planck Institute of Biophysics , Max-von-Laue Straße 3, 60438 Frankfurt am Main, Germany
| | - Stephanie M Linker
- Department of Theoretical Biophysics, Max Planck Institute of Biophysics , Max-von-Laue Straße 3, 60438 Frankfurt am Main, Germany
| | - Martin Vögele
- Department of Theoretical Biophysics, Max Planck Institute of Biophysics , Max-von-Laue Straße 3, 60438 Frankfurt am Main, Germany
| | - Jürgen Köfinger
- Department of Theoretical Biophysics, Max Planck Institute of Biophysics , Max-von-Laue Straße 3, 60438 Frankfurt am Main, Germany
| | - Gerhard Hummer
- Department of Theoretical Biophysics, Max Planck Institute of Biophysics , Max-von-Laue Straße 3, 60438 Frankfurt am Main, Germany
- Institute for Biophysics, Goethe University Frankfurt , 60438 Frankfurt am Main, Germany
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Vögele M, Holm C, Smiatek J. Coarse-grained simulations of polyelectrolyte complexes: MARTINI models for poly(styrene sulfonate) and poly(diallyldimethylammonium). J Chem Phys 2016; 143:243151. [PMID: 26723636 DOI: 10.1063/1.4937805] [Citation(s) in RCA: 58] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
We present simulations of aqueous polyelectrolyte complexes with new MARTINI models for the charged polymers poly(styrene sulfonate) and poly(diallyldimethylammonium). Our coarse-grained polyelectrolyte models allow us to study large length and long time scales with regard to chemical details and thermodynamic properties. The results are compared to the outcomes of previous atomistic molecular dynamics simulations and verify that electrostatic properties are reproduced by our MARTINI coarse-grained approach with reasonable accuracy. Structural similarity between the atomistic and the coarse-grained results is indicated by a comparison between the pair radial distribution functions and the cumulative number of surrounding particles. Our coarse-grained models are able to quantitatively reproduce previous findings like the correct charge compensation mechanism and a reduced dielectric constant of water. These results can be interpreted as the underlying reason for the stability of polyelectrolyte multilayers and complexes and validate the robustness of the proposed models.
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Affiliation(s)
- Martin Vögele
- Institute for Computational Physics, University of Stuttgart, Stuttgart, Germany
| | - Christian Holm
- Institute for Computational Physics, University of Stuttgart, Stuttgart, Germany
| | - Jens Smiatek
- Institute for Computational Physics, University of Stuttgart, Stuttgart, Germany
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