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Zhu Y, Zhao X, Xiang C, Liu X, Li J. Evaluation of Essential Dynamics and Fixed-Length Coarse Graining for Multidomain Proteins. J Phys Chem B 2024; 128:5147-5156. [PMID: 38758598 DOI: 10.1021/acs.jpcb.3c08198] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/19/2024]
Abstract
For multiscale modeling of biomolecules, reliable coarse-grained (CG) models can offer great potential to simulate larger temporal and spatial scales than traditional all-atom (AA) models. In this study, we explore the essential dynamics coarse graining (EDCG) and fixed-length coarse graining (FLCG) approaches for constructing highly coarse-grained models for multidomain proteins (MDPs), with 1 to 10 amino acid residues per CG site. In the studies of 13 MDPs, our data indicate that both EDCG and FLCG can preserve the protein dynamics of MDPs. FLCG, which restricts an equal number of residues in each CG site, represents an excellent approximation to EDCG and a straightforward approach for coarse-graining MDPs. Furthermore, FLCG is tested with a class B G-protein-coupled receptor protein, and the agreement with prior experiments suggests its general application to various MDPs in different environments or conditions. Finally, we demonstrate another application of FLCG through progressive backmapping, showcasing the ability to recover from lower-resolution CG models (6 residues/CG site) to higher-resolution ones (1 residue/CG site). These promising outcomes underscore the broad applicability of FLCG to construct highly or ultra-coarse-grained models of complex biomolecules for multiscale simulations.
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Affiliation(s)
- Yu Zhu
- Borch Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, West Lafayette, Indiana 47907, United States
| | - Xiaochuan Zhao
- Department of Chemistry, University of Vermont, Burlington, Vermont 05405, United States
| | - Chijian Xiang
- Department of Horticulture & Landscape Architecture, Purdue University, West Lafayette, Indiana 47907, United States
| | - Xianshi Liu
- Borch Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, West Lafayette, Indiana 47907, United States
| | - Jianing Li
- Borch Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, West Lafayette, Indiana 47907, United States
- Department of Chemistry, University of Vermont, Burlington, Vermont 05405, United States
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Sharma A, Zhu Y, Spangler EJ, Hoang TB, Laradji M. Highly Ordered Nanoassemblies of Janus Spherocylindrical Nanoparticles Adhering to Lipid Vesicles. ACS NANO 2024; 18:12957-12969. [PMID: 38720633 DOI: 10.1021/acsnano.4c01099] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2024]
Abstract
In recent years, there has been a heightened interest in the self-assembly of nanoparticles (NPs) that is mediated by their adsorption onto lipid membranes. The interplay between the adhesive energy of NPs on a lipid membrane and the membrane's curvature energy causes it to wrap around the NPs. This results in an interesting membrane curvature-mediated interaction, which can lead to the self-assembly of NPs on lipid membranes. Recent studies have demonstrated that Janus spherical NPs, which adhere to lipid vesicles, can self-assemble into well-ordered nanoclusters with various geometries, including a few Platonic solids. The present study explores the additional effect of geometric anisotropy on the self-assembly of Janus NPs on lipid vesicles. Specifically, the current study utilized extensive molecular dynamics simulations to investigate the arrangement of Janus spherocylindrical NPs on lipid vesicles. We found that the additional geometric anisotropy significantly expands the range of NPs' self-assemblies on lipid vesicles. The specific geometries of the resulting nanoclusters depend on several factors, including the number of Janus spherocylindrical NPs adhering to the vesicle and their aspect ratio. The lipid membrane-mediated self-assembly of NPs, demonstrated by this work, provides an alternative cost-effective route for fabricating highly engineered nanoclusters in three dimensions. Such structures, with the current wide range of material choices, have great potential for advanced applications, including biosensing, bioimaging, drug delivery, nanomechanics, and nanophotonics.
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Affiliation(s)
- Abash Sharma
- Department of Physics and Materials Science, The University of Memphis, Memphis, Tennessee 38152, United States
| | - Yu Zhu
- Department of Physics and Materials Science, The University of Memphis, Memphis, Tennessee 38152, United States
- Borch Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, West Lafayette, Indiana 47907, United States
| | - Eric J Spangler
- Department of Physics and Materials Science, The University of Memphis, Memphis, Tennessee 38152, United States
| | - Thang B Hoang
- Department of Physics and Materials Science, The University of Memphis, Memphis, Tennessee 38152, United States
| | - Mohamed Laradji
- Department of Physics and Materials Science, The University of Memphis, Memphis, Tennessee 38152, United States
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Li X, Zou J, He Z, Sun Y, Song X, He W. The interaction between particles and vascular endothelium in blood flow. Adv Drug Deliv Rev 2024; 207:115216. [PMID: 38387770 DOI: 10.1016/j.addr.2024.115216] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2023] [Revised: 01/25/2024] [Accepted: 02/14/2024] [Indexed: 02/24/2024]
Abstract
Particle-based drug delivery systems have shown promising application potential to treat human diseases; however, an incomplete understanding of their interactions with vascular endothelium in blood flow prevents their inclusion into mainstream clinical applications. The flow performance of nano/micro-sized particles in the blood are disturbed by many external/internal factors, including blood constituents, particle properties, and endothelium bioactivities, affecting the fate of particles in vivo and therapeutic effects for diseases. This review highlights how the blood constituents, hemodynamic environment and particle properties influence the interactions and particle activities in vivo. Moreover, we briefly summarized the structure and functions of endothelium and simulated devices for studying particle performance under blood flow conditions. Finally, based on particle-endothelium interactions, we propose future opportunities for novel therapeutic strategies and provide solutions to challenges in particle delivery systems for accelerating their clinical translation. This review helps provoke an increasing in-depth understanding of particle-endothelium interactions and inspires more strategies that may benefit the development of particle medicine.
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Affiliation(s)
- Xiaotong Li
- School of Pharmacy, China Pharmaceutical University, Nanjing 2111198, PR China
| | - Jiahui Zou
- School of Pharmacy, China Pharmaceutical University, Nanjing 2111198, PR China
| | - Zhongshan He
- Department of Critical Care Medicine and Department of Biotherapy, Frontiers Science Center for Disease-related Molecular Network, Cancer Center and State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu 610000, PR China
| | - Yanhua Sun
- Shandong Provincial Key Laboratory of Microparticles Drug Delivery Technology, Qilu Pharmaceutical Co., LtD., Jinan 250000, PR China
| | - Xiangrong Song
- Department of Critical Care Medicine and Department of Biotherapy, Frontiers Science Center for Disease-related Molecular Network, Cancer Center and State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu 610000, PR China.
| | - Wei He
- School of Pharmacy, China Pharmaceutical University, Nanjing 2111198, PR China.
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Zhu Y, Sharma A, Spangler EJ, Laradji M. Non-close-packed hexagonal self-assembly of Janus nanoparticles on planar membranes. SOFT MATTER 2023; 19:7591-7601. [PMID: 37755137 DOI: 10.1039/d3sm00984j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/28/2023]
Abstract
The adhesion modes of an ensemble of spherical Janus nanoparticles on planar membranes are investigated through large-scale molecular dynamics simulations of a coarse-grained implicit-solvent model. We found that the Janus nanoparticles adhering to planar membranes exhibit a rich phase behavior that depends on their adhesion energy density and areal number density. In particular, effective repulsive membrane-curvature-mediated interactions between the Janus nanoparticles lead to their self-assembly into an ordered hexagonal superlattice at intermediate densities and intermediate to high adhesion energy density, with a lattice constant determined by their areal density. The melting behavior of the hexagonal superlattice proceeds through a two-stage melting scenario in agreement with the Kosterlitz-Thouless-Halperin-Nelson-Young classical theory of two-dimensional melting.
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Affiliation(s)
- Yu Zhu
- Department of Physics and Materials Science, The University of Memphis, Memphis, TN 38152, USA.
| | - Abash Sharma
- Department of Physics and Materials Science, The University of Memphis, Memphis, TN 38152, USA.
| | - Eric J Spangler
- Department of Physics and Materials Science, The University of Memphis, Memphis, TN 38152, USA.
| | - Mohamed Laradji
- Department of Physics and Materials Science, The University of Memphis, Memphis, TN 38152, USA.
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Zhu Y, Sharma A, Spangler EJ, Carrillo JMY, Kumar PBS, Laradji M. Lipid vesicles induced ordered nanoassemblies of Janus nanoparticles. SOFT MATTER 2023; 19:2204-2213. [PMID: 36880601 DOI: 10.1039/d2sm01693a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Abstract
Since many advanced applications require specific assemblies of nanoparticles (NPs), considerable efforts have been made to fabricate nanoassemblies with specific geometries. Although nanoassemblies can be fabricated through top-down approaches, recent advances show that intricate nanoassemblies can also be obtained through self-assembly, mediated for example by DNA strands. Here, we show, through extensive molecular dynamics simulations, that highly ordered self-assemblies of NPs can be mediated by their adhesion to lipid vesicles (LVs). Specifically, Janus NPs are considered so that the amount by which they are wrapped by the LV is controlled. The specific geometry of the nanoassembly is the result of effective curvature-mediated repulsion between the NPs and the number of NPs adhering to the LV. The NPs are arranged on the LV into polyhedra which satisfy the upper limit of Euler's polyhedral formula, including several deltahedra and three Platonic solids, corresponding to the tetrahedron, octahedron, and icosahedron.
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Affiliation(s)
- Yu Zhu
- Department of Physics and Materials Science, The University of Memphis, Memphis, TN 38152, USA.
| | - Abash Sharma
- Department of Physics and Materials Science, The University of Memphis, Memphis, TN 38152, USA.
| | - Eric J Spangler
- Department of Physics and Materials Science, The University of Memphis, Memphis, TN 38152, USA.
| | - Jan-Michael Y Carrillo
- Center for Nanophase Materials Sciences, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - P B Sunil Kumar
- Department of Physics, Indian Institute of Technology Madras, Chennai 600036, India
| | - Mohamed Laradji
- Department of Physics and Materials Science, The University of Memphis, Memphis, TN 38152, USA.
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Sharma A, Zhu Y, Spangler EJ, Carrillo JMY, Laradji M. Membrane-mediated dimerization of spherocylindrical nanoparticles. SOFT MATTER 2023; 19:1499-1512. [PMID: 36723357 DOI: 10.1039/d2sm01574a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Abstract
We present a numerical investigation of the modes of adhesion and endocytosis of two spherocylindrical nanoparticles (SCNPs) on planar and tensionless lipid membranes, using systematic molecular dynamics simulations of an implicit-solvent model, with varying values of the SCNPs' adhesion strength and dimensions. We found that at weak values of the adhesion energy per unit of area, ξ, the SCNPs are monomeric and adhere to the membrane in the parallel mode. As ξ is slightly increased, the SCNPs dimerize into wedged dimers, with an obtuse angle between their major axes that decreases with increasing ξ. However, as ξ is further increased, we found that the final adhesion state of the two SCNPs is strongly affected by the initial distance, d0, between their centers of mass, upon their adhesion. Namely, the SCNPs dimerize into wedged dimers, with an acute angle between their major axes, if d0 is relatively small. However, for relatively high d0, they adhere individually to the membrane in the monomeric normal mode. For even higher values of ξ and small values of d0, the SCNPs cluster into tubular dimers. However, they remain monomeric if d0 is high. Finally, the SCNPs endocytose either as a tubular dimer, if d0 is low or as monomers for large d0, with the onset value of ξ of dimeric endocytosis being lower than that of monomeric endocytosis. Dimeric endocytosis requires that the SCNPs adhere simultaneously at nearby locations.
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Affiliation(s)
- Abash Sharma
- Department of Physics and Materials Science, The University of Memphis, Memphis, TN 38152, USA.
| | - Yu Zhu
- Department of Physics and Materials Science, The University of Memphis, Memphis, TN 38152, USA.
| | - Eric J Spangler
- Department of Physics and Materials Science, The University of Memphis, Memphis, TN 38152, USA.
| | - Jan-Michael Y Carrillo
- Center for Nanophase Materials Sciences, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - Mohamed Laradji
- Department of Physics and Materials Science, The University of Memphis, Memphis, TN 38152, USA.
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