Chemically specific coarse-grained models to investigate the structure of biomimetic membranes

Kowalik, Małgorzata; Schantz, Allen B.; Naqi, Abdullah; Shen, Yuexiao; Sines, Ian; Maranas, Janna K.; Kumar, Manish

doi:10.1039/C7RA10573H

Title: Chemically specific coarse-grained models to investigate the structure of biomimetic membranes

Journal Article · 01 January 2017 · RSC Advances

DOI: https://doi.org/10.1039/C7RA10573H · OSTI ID:1410586

Kowalik, Małgorzata ^[1]; Schantz, Allen B. ^[1]; Naqi, Abdullah ^[1]; Shen, Yuexiao ^[2]; Sines, Ian ^[3]; Maranas, Janna K. ^[1];

^[4]

Department of Chemical Engineering, The Pennsylvania State University, University Park, USA
Department of Chemical Engineering, The Pennsylvania State University, University Park, USA, Department of Chemistry
Department of Chemical Engineering, The Pennsylvania State University, University Park, USA, Surface Conditioning Business Unit
Department of Chemical Engineering, The Pennsylvania State University, University Park, USA, Department of Civil and Environmental Engineering

Biomimetic polymer/protein membranes are promising materials for DNA sequencing, sensors, drug delivery and water purification.

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Research Organization:: Pennsylvania State Univ., University Park, PA (United States)

Sponsoring Organization:: USDOE Office of Science (SC), Advanced Scientific Computing Research (ASCR) (SC-21); USDOE Office of Science (SC), Basic Energy Sciences (BES)

Grant/Contract Number:: FG02-02ER25535

OSTI ID:: 1410586

Journal Information:: RSC Advances, Journal Name: RSC Advances Journal Issue: 86 Vol. 7; ISSN 2046-2069; ISSN RSCACL

Publisher:: Royal Society of Chemistry (RSC)Copyright Statement

Country of Publication:: United Kingdom

Language:: English

References (59)

Coarse-Graining in Polymer Simulation: From the Atomistic to the Mesoscopic Scale and Back Müller-Plathe, Florian ChemPhysChem, Vol. 3, Issue 9 https://doi.org/10.1002/1439-7641(20020916)3:9<754::AID-CPHC754>3.0.CO;2-U	journal	September 2002
Deriving effective mesoscale potentials from atomistic simulations: Mesoscale Potentials from Atomistic Simulations Reith, Dirk; Pütz, Mathias; Müller-Plathe, Florian Journal of Computational Chemistry, Vol. 24, Issue 13 https://doi.org/10.1002/jcc.10307	journal	August 2003
New combining rules for rare gas van der waals parameters Waldman, Marvin; Hagler, A. T. Journal of Computational Chemistry, Vol. 14, Issue 9 https://doi.org/10.1002/jcc.540140909	journal	September 1993
A method for estimating both the solubility parameters and molar volumes of liquids Fedors, Robert F. Polymer Engineering and Science, Vol. 14, Issue 2 https://doi.org/10.1002/pen.760140211	journal	February 1974
Fast Parallel Algorithms for Short-Range Molecular Dynamics Plimpton, Steve Journal of Computational Physics, Vol. 117, Issue 1 https://doi.org/10.1006/jcph.1995.1039	journal	March 1995
Chain Dimensions and Entanglement Spacings Fetters, L. J.; Lohse, D. J.; Colby, R. H. Physical Properties of Polymers Handbook https://doi.org/10.1007/978-0-387-69002-5_25	book	January 2007
Boltzmann's principle, knowledge-based mean fields and protein folding. An approach to the computational determination of protein structures Sippl, Manfred J. Journal of Computer-Aided Molecular Design, Vol. 7, Issue 4 https://doi.org/10.1007/BF02337562	journal	August 1993
Chemical stability of liposomes: implications for their physical stability Grit, Mustafa; Crommelin, Daan J. A. Chemistry and Physics of Lipids, Vol. 64, Issue 1-3 https://doi.org/10.1016/0009-3084(93)90053-6	journal	September 1993
The Effect of Chain Length on Protein Solubilization in Polymer-Based Vesicles (Polymersomes) Pata, Veena; Dan, Nily Biophysical Journal, Vol. 85, Issue 4 https://doi.org/10.1016/S0006-3495(03)74639-6	journal	October 2003
Molecular dynamics simulation of cis-1,4-polybutadiene. 1. Comparison with experimental data for static and dynamic properties Okada, O. Polymer, Vol. 43, Issue 3 https://doi.org/10.1016/S0032-3861(01)00628-0	journal	February 2002
Desalination by biomimetic aquaporin membranes: Review of status and prospects Tang, C. Y.; Zhao, Y.; Wang, R. Desalination, Vol. 308 https://doi.org/10.1016/j.desal.2012.07.007	journal	January 2013
Phase behavior of carbon dioxide mixtures with n-alkanes and n-perfluoroalkanes Colina, C. M.; Galindo, A.; Blas, F. J. Fluid Phase Equilibria, Vol. 222-223 https://doi.org/10.1016/j.fluid.2004.06.021	journal	August 2004
Aquaporin-embedded biomimetic membranes for nanofiltration Zhong, Pei Shan; Chung, Tai-Shung; Jeyaseelan, Kandiah Journal of Membrane Science, Vol. 407-408 https://doi.org/10.1016/j.memsci.2012.03.033	journal	July 2012
Biomimetic membranes: A review Shen, Yue-xiao; Saboe, Patrick O.; Sines, Ian T. Journal of Membrane Science, Vol. 454 https://doi.org/10.1016/j.memsci.2013.12.019	journal	March 2014
Influence of the solvent and the end groups on the morphology of cross-linked amphiphilic poly(1,2-butadiene)-b-poly(ethylene oxide) nanoparticles Maskos, Michael Polymer, Vol. 47, Issue 4 https://doi.org/10.1016/j.polymer.2005.12.045	journal	February 2006
Emerging applications of polymersomes in delivery: From molecular dynamics to shrinkage of tumors Discher, Dennis E.; Ortiz, Vanessa; Srinivas, Goundla Progress in Polymer Science, Vol. 32, Issue 8-9 https://doi.org/10.1016/j.progpolymsci.2007.05.011	journal	August 2007
Free Energy-Based Coarse-Grained Force Field for Binary Mixtures of Hydrocarbons, Nitrogen, Oxygen, and Carbon Dioxide Cao, Fenglei; Deetz, Joshua D.; Sun, Huai Journal of Chemical Information and Modeling, Vol. 57, Issue 1 https://doi.org/10.1021/acs.jcim.6b00685	journal	December 2016
Polymeric Vesicles: From Drug Carriers to Nanoreactors and Artificial Organelles Tanner, Pascal; Baumann, Patric; Enea, Ramona Accounts of Chemical Research, Vol. 44, Issue 10 https://doi.org/10.1021/ar200036k	journal	October 2011
Micellization Studied by GPU-Accelerated Coarse-Grained Molecular Dynamics Levine, Benjamin G.; LeBard, David N.; DeVane, Russell Journal of Chemical Theory and Computation, Vol. 7, Issue 12 https://doi.org/10.1021/ct2005193	journal	October 2011
The OPLS [optimized potentials for liquid simulations] potential functions for proteins, energy minimizations for crystals of cyclic peptides and crambin Jorgensen, William L.; Tirado-Rives, Julian Journal of the American Chemical Society, Vol. 110, Issue 6 https://doi.org/10.1021/ja00214a001	journal	March 1988
Biocompatible Functionalization of Polymersome Surfaces: A New Approach to Surface Immobilization and Cell Targeting Using Polymersomes Egli, Stefan; Nussbaumer, Martin G.; Balasubramanian, Vimalkumar Journal of the American Chemical Society, Vol. 133, Issue 12 https://doi.org/10.1021/ja110275f	journal	March 2011
High-Density Reconstitution of Functional Water Channels into Vesicular and Planar Block Copolymer Membranes Kumar, Manish; Habel, Joachim E. O.; Shen, Yue-xiao Journal of the American Chemical Society, Vol. 134, Issue 45 https://doi.org/10.1021/ja304721r	journal	November 2012
Development and Testing of the OPLS All-Atom Force Field on Conformational Energetics and Properties of Organic Liquids Jorgensen, William L.; Maxwell, David S.; Tirado-Rives, Julian Journal of the American Chemical Society, Vol. 118, Issue 45 https://doi.org/10.1021/ja9621760	journal	January 1996
Segment Distribution of the Micellar Brushes of Poly(ethylene oxide) via Small-Angle Neutron Scattering Won, You-Yeon; Davis, H. Ted; Bates, Frank S. The Journal of Physical Chemistry B, Vol. 104, Issue 30 https://doi.org/10.1021/jp000457v	journal	August 2000
Cryogenic Transmission Electron Microscopy (Cryo-TEM) of Micelles and Vesicles Formed in Water by Poly(ethylene oxide)-Based Block Copolymers Won, You-Yeon; Brannan, Aaron K.; Davis, H. Ted The Journal of Physical Chemistry B, Vol. 106, Issue 13 https://doi.org/10.1021/jp013639d	journal	April 2002
Simulation of Diblock Copolymer Self-Assembly, Using a Coarse-Grain Model Srinivas, Goundla; Shelley, John C.; Nielsen, Steve O. The Journal of Physical Chemistry B, Vol. 108, Issue 24 https://doi.org/10.1021/jp037842f	journal	June 2004
Mapping Atomistic Simulations to Mesoscopic Models: A Systematic Coarse-Graining Procedure for Vinyl Polymer Chains Milano, Giuseppe; Müller-Plathe, Florian The Journal of Physical Chemistry B, Vol. 109, Issue 39 https://doi.org/10.1021/jp0523571	journal	October 2005
A Quantitative Coarse-Grain Model for Lipid Bilayers Orsi, Mario; Haubertin, David Y.; Sanderson, Wendy E. The Journal of Physical Chemistry B, Vol. 112, Issue 3 https://doi.org/10.1021/jp076139e	journal	January 2008
Coarse-Graining Poly(ethylene oxide)–Poly(propylene oxide)–Poly(ethylene oxide) (PEO–PPO–PEO) Block Copolymers Using the MARTINI Force Field Nawaz, Selina; Carbone, Paola The Journal of Physical Chemistry B, Vol. 118, Issue 6 https://doi.org/10.1021/jp4092249	journal	January 2014
Theory of the grafted polymer brush Milner, S. T.; Witten, T. A.; Cates, M. E. Macromolecules, Vol. 21, Issue 8 https://doi.org/10.1021/ma00186a051	journal	August 1988
Molecular Weight Dependence of Polymersome Membrane Structure, Elasticity, and Stability Bermudez, Harry; Brannan, Aaron K.; Hammer, Daniel A. Macromolecules, Vol. 35, Issue 21 https://doi.org/10.1021/ma020669l	journal	October 2002
Hierarchical Modeling of Polystyrene: From Atomistic to Coarse-Grained Simulations Harmandaris, V. A.; Adhikari, N. P.; van der Vegt, N. F. A. Macromolecules, Vol. 39, Issue 19 https://doi.org/10.1021/ma0606399	journal	September 2006
Conformations of Polymers Attached to an Interface de Gennes, P. G. Macromolecules, Vol. 13, Issue 5 https://doi.org/10.1021/ma60077a009	journal	September 1980
Coarse-Grained Polymer Melts Based on Isolated Atomistic Chains: Simulation of Polystyrene of Different Tacticities Fritz, Dominik; Harmandaris, Vagelis A.; Kremer, Kurt Macromolecules, Vol. 42, Issue 19 https://doi.org/10.1021/ma901242h	journal	October 2009
Synthesis and Characterization of Model Polyalkane−Poly(ethylene oxide) Block Copolymers Hillmyer, Marc A.; Bates, Frank S. Macromolecules, Vol. 29, Issue 22 https://doi.org/10.1021/ma960774t	journal	January 1996
Self-assembly and properties of diblock copolymers by coarse-grain molecular dynamics Srinivas, Goundla; Discher, Dennis E.; Klein, Michael L. Nature Materials, Vol. 3, Issue 9 https://doi.org/10.1038/nmat1185	journal	August 2004
Stimuli-responsive nanocarriers for drug delivery Mura, Simona; Nicolas, Julien; Couvreur, Patrick Nature Materials, Vol. 12, Issue 11 https://doi.org/10.1038/nmat3776	journal	October 2013
Continuous base identification for single-molecule nanopore DNA sequencing Clarke, James; Wu, Hai-Chen; Jayasinghe, Lakmal Nature Nanotechnology, Vol. 4, Issue 4, p. 265-270 https://doi.org/10.1038/nnano.2009.12	journal	February 2009
Systematic coarse-graining methods for soft matter simulations – a review Brini, Emiliano; Algaer, Elena A.; Ganguly, Pritam Soft Matter, Vol. 9, Issue 7 https://doi.org/10.1039/C2SM27201F	journal	January 2013
A transferable coarse-grained model for hydrogen-bonding liquids Golubkov, Pavel A.; Wu, Johnny C.; Ren, Pengyu Physical Chemistry Chemical Physics, Vol. 10, Issue 15 https://doi.org/10.1039/b715841f	journal	January 2008
Coarse-grained molecular modeling of non-ionic surfactant self-assembly Shinoda, Wataru; DeVane, Russell; Klein, Michael L. Soft Matter, Vol. 4, Issue 12 https://doi.org/10.1039/b808701f	journal	January 2008
Polymersomes hydrophilic brush scaling relations Smart, Thomas P.; Mykhaylyk, Oleksandr O.; Ryan, Anthony J. Soft Matter, Vol. 5, Issue 19 https://doi.org/10.1039/b908731a	journal	January 2009
Adsorption of chain molecules with a polar head a scaling description Alexander, S. Journal de Physique, Vol. 38, Issue 8 https://doi.org/10.1051/jphys:01977003808098300	journal	January 1977
Phase behavior of n -alkanes in supercritical solution: A Monte Carlo study Virnau, Peter; Müller, Marcus; MacDowell, L. G. The Journal of Chemical Physics, Vol. 121, Issue 5 https://doi.org/10.1063/1.1765103	journal	August 2004
Computer simulations of bilayer membranes: Self-assembly and interfacial tension Goetz, Rüdiger; Lipowsky, Reinhard The Journal of Chemical Physics, Vol. 108, Issue 17 https://doi.org/10.1063/1.476160	journal	May 1998
Perspective: Coarse-grained models for biomolecular systems Noid, W. G. The Journal of Chemical Physics, Vol. 139, Issue 9 https://doi.org/10.1063/1.4818908	journal	September 2013
Flory-Huggins parameter χ, from binary mixtures of Lennard-Jones particles to block copolymer melts Chremos, Alexandros; Nikoubashman, Arash; Panagiotopoulos, Athanassios Z. The Journal of Chemical Physics, Vol. 140, Issue 5 https://doi.org/10.1063/1.4863331	journal	February 2014
Highly permeable polymeric membranes based on the incorporation of the functional water channel protein Aquaporin Z Kumar, M.; Grzelakowski, M.; Zilles, J. Proceedings of the National Academy of Sciences, Vol. 104, Issue 52 https://doi.org/10.1073/pnas.0708762104	journal	December 2007
Exploring the utility of coarse-grained water models for computational studies of interfacial systems He, Xibing; Shinoda, Wataru; DeVane, Russell Molecular Physics, Vol. 108, Issue 15 https://doi.org/10.1080/00268976.2010.503197	journal	August 2010
Thermodynamic analysis of micellization in PEO–PPO–PEO block copolymer solutions from the hydrogen bonding point of view Chen, S.; Guo, C.; Liu, H. -Z. Molecular Simulation, Vol. 32, Issue 5 https://doi.org/10.1080/08927020600717103	journal	April 2006
Multi-property fitting and parameterization of a coarse grained model for aqueous surfactants Shinoda, W.; DeVane, R.; Klein, M. L. Molecular Simulation, Vol. 33, Issue 1-2 https://doi.org/10.1080/08927020601054050	journal	January 2007
Phase separation kinetics in compressible polymer solutions: computer simulation of the early stages Virnau, Peter; Müller, Marcus; MacDowell, Luis González New Journal of Physics, Vol. 6 https://doi.org/10.1088/1367-2630/6/1/007	journal	January 2004
Canonical dynamics: Equilibrium phase-space distributions Hoover, William G. Physical Review A, Vol. 31, Issue 3 https://doi.org/10.1103/PhysRevA.31.1695	journal	March 1985
Polymer Vesicles Discher, D. E. Science, Vol. 297, Issue 5583 https://doi.org/10.1126/science.1074972	journal	August 2002
Polymer Brushes Milner, S. T. Science, Vol. 251, Issue 4996 https://doi.org/10.1126/science.251.4996.905	journal	February 1991
Polymersomes: Tough Vesicles Made from Diblock Copolymers Discher, B. M. Science, Vol. 284, Issue 5417 https://doi.org/10.1126/science.284.5417.1143	journal	May 1999
De Novo Assembly of Human Herpes Virus Type 1 (HHV-1) Genome, Mining of Non-Canonical Structures and Detection of Novel Drug-Resistance Mutations Using Short- and Long-Read Next Generation Sequencing Technologies Karamitros, Timokratis; Harrison, Ian; Piorkowska, Renata PLOS ONE, Vol. 11, Issue 6 https://doi.org/10.1371/journal.pone.0157600	journal	June 2016
A Molecular View of Melting in Anhydrous Phospholipidic Membranes Doxastakis, M.; Sakai, V. García; Ohtake, S. Biophysical Journal, Vol. 92, Issue 1 https://doi.org/10.1529/biophysj.106.089631	journal	January 2007
Lipid Bilayer Structure Determined by the Simultaneous Analysis of Neutron and X-Ray Scattering Data Kučerka, Norbert; Nagle, John F.; Sachs, Jonathan N. Biophysical Journal, Vol. 95, Issue 5 https://doi.org/10.1529/biophysj.108.132662	journal	September 2008

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