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Huguet C, Fietz S, Rosell-Melé A, Daura X, Costenaro L. Molecular dynamics simulation study of the effect of glycerol dialkyl glycerol tetraether hydroxylation on membrane thermostability. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2017; 1859:966-974. [DOI: 10.1016/j.bbamem.2017.02.009] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/30/2016] [Revised: 02/12/2017] [Accepted: 02/14/2017] [Indexed: 01/21/2023]
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2
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Mustafa G, Nandekar PP, Yu X, Wade RC. On the application of the MARTINI coarse-grained model to immersion of a protein in a phospholipid bilayer. J Chem Phys 2015; 143:243139. [DOI: 10.1063/1.4936909] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
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3
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Koprowski P, Grajkowski W, Balcerzak M, Filipiuk I, Fabczak H, Kubalski A. Cytoplasmic Domain of MscS Interacts with Cell Division Protein FtsZ: A Possible Non-Channel Function of the Mechanosensitive Channel in Escherichia Coli. PLoS One 2015; 10:e0127029. [PMID: 25996836 PMCID: PMC4440785 DOI: 10.1371/journal.pone.0127029] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2014] [Accepted: 04/10/2015] [Indexed: 01/03/2023] Open
Abstract
Bacterial mechano-sensitive (MS) channels reside in the inner membrane and are considered to act as emergency valves whose role is to lower cell turgor when bacteria enter hypo-osmotic environments. However, there is emerging evidence that members of the Mechano-sensitive channel Small (MscS) family play additional roles in bacterial and plant cell physiology. MscS has a large cytoplasmic C-terminal region that changes its shape upon activation and inactivation of the channel. Our pull-down and co-sedimentation assays show that this domain interacts with FtsZ, a bacterial tubulin-like protein. We identify point mutations in the MscS C-terminal domain that reduce binding to FtsZ and show that bacteria expressing these mutants are compromised in growth on sublethal concentrations of β-lactam antibiotics. Our results suggest that interaction between MscS and FtsZ could occur upon inactivation and/or opening of the channel and could be important for the bacterial cell response against sustained stress upon stationary phase and in the presence of β-lactam antibiotics.
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Affiliation(s)
- Piotr Koprowski
- Department of Cell Biology, Nencki Institute of Experimental Biology, Polish Academy of Sciences, Pasteur 3, Warsaw, Poland
- * E-mail:
| | - Wojciech Grajkowski
- Department of Cell Biology, Nencki Institute of Experimental Biology, Polish Academy of Sciences, Pasteur 3, Warsaw, Poland
| | - Marcin Balcerzak
- Department of Cell Biology, Nencki Institute of Experimental Biology, Polish Academy of Sciences, Pasteur 3, Warsaw, Poland
| | - Iwona Filipiuk
- Department of Cell Biology, Nencki Institute of Experimental Biology, Polish Academy of Sciences, Pasteur 3, Warsaw, Poland
| | - Hanna Fabczak
- Department of Cell Biology, Nencki Institute of Experimental Biology, Polish Academy of Sciences, Pasteur 3, Warsaw, Poland
| | - Andrzej Kubalski
- Department of Cell Biology, Nencki Institute of Experimental Biology, Polish Academy of Sciences, Pasteur 3, Warsaw, Poland
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Li Y, Zhang X, Cao D. Nanoparticle hardness controls the internalization pathway for drug delivery. NANOSCALE 2015; 7:2758-2769. [PMID: 25585060 DOI: 10.1039/c4nr05575f] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Nanoparticle (NP)-based drug delivery systems offer fundamental advantages over current therapeutic agents that commonly display a longer circulation time, lower toxicity, specific targeted release, and greater bioavailability. For successful NP-based drug delivery it is essential that the drug-carrying nanocarriers can be internalized by the target cells and transported to specific sites, and the inefficient internalization of nanocarriers is often one of the major sources for drug resistance. In this work, we use the dissipative particle dynamics simulation to investigate the effect of NP hardness on their internalization efficiency. Three simplified models of NP platforms for drug delivery, including polymeric NP, liposome and solid NP, are designed here to represent increasing nanocarrier hardness. Simulation results indicate that NP hardness controls the internalization pathway for drug delivery. Rigid NPs can enter the cell by a pathway of endocytosis, whereas for soft NPs the endocytosis process can be inhibited or frustrated due to wrapping-induced shape deformation and non-uniform ligand distribution. Instead, soft NPs tend to find one of three penetration pathways to enter the cell membrane via rearranging their hydrophobic and hydrophilic segments. Finally, we show that the interaction between nanocarriers and drug molecules is also essential for effective drug delivery.
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Affiliation(s)
- Ye Li
- State Key Laboratory of Organic-Inorganic Composites, Beijing University of Chemical Technology, Beijing 100029, China.
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5
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Tian F, Yue T, Li Y, Zhang X. Computer simulation studies on the interactions between nanoparticles and cell membrane. Sci China Chem 2014. [DOI: 10.1007/s11426-014-5231-7] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
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6
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Tian F, Zhang X, Dong W. How hydrophobic nanoparticles aggregate in the interior of membranes: A computer simulation. PHYSICAL REVIEW. E, STATISTICAL, NONLINEAR, AND SOFT MATTER PHYSICS 2014; 90:052701. [PMID: 25493810 DOI: 10.1103/physreve.90.052701] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/02/2014] [Indexed: 05/21/2023]
Abstract
Lipid-based dispersion of hydrophobic nanoparticles (NPs) not only gives fundamental insight into how nanomaterials distribute in live cells and organisms, but also provides a quite general route to designing nanocarrier agents in triggered drug delivery and medical imaging. It is not clearly understood how hydrophobic NPs arrange in the interior of a membrane. In this paper, with computer simulation techniques, we demonstrate that hydrophobic NPs having a diameter compared to the hydrophobic thickness of the membrane are capable of clustering in the hydrophobic interior of a cell membrane. Except from the isotropic aggregation, an unexpected linear arrangement of spherical NPs, which is still not found from experiments, is identified here. The free-energy costs associated with linear and isotropic aggregations are computed explicitly to interpret aggregation behavior and the obtained phase diagrams give us a comprehensive understanding of where linear aggregation is expected. In this work we also shows that NP size and membrane tension play key roles in determining the NP aggregate, while the effects of NP concentration and membrane curvature seem to be relatively weak.
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Affiliation(s)
- Falin Tian
- State Key Laboratory of Organic-Inorganic Composites, Beijing University of Chemical Technology, Beijing 100029, China and Laboratoire de Chimie, Ecole Normale Superieure de Lyon, 46 Allee d'Italie, 69364 Lyon Cedex 07, France
| | - Xianren Zhang
- State Key Laboratory of Organic-Inorganic Composites, Beijing University of Chemical Technology, Beijing 100029, China
| | - Wei Dong
- Laboratoire de Chimie, Ecole Normale Superieure de Lyon, 46 Allee d'Italie, 69364 Lyon Cedex 07, France
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Li Y, Zhang X, Cao D. A spontaneous penetration mechanism of patterned nanoparticles across a biomembrane. SOFT MATTER 2014; 10:6844-6856. [PMID: 25082334 DOI: 10.1039/c4sm00236a] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
Recent experimental studies have shown the ability of tailoring the nanoparticle (NP)-cell interaction via the engineering of NP surfaces. Although the considerable progress has been made in design of patterned NPs for drug delivery, the effect of surface pattern on the NP-cell interaction is not fully understood yet. In this work, we used a dissipative particle dynamics method to systematically investigate the effects of NP surface pattern on its penetration across a membrane. For stripy NPs or patchy NPs having a large stripe width or patch size, an "insertion-rotation" penetration mechanism is found. Results indicate that stripy NPs and patchy NPs coated with narrow stripes or small patches can directly penetrate the cell membrane with a less constrained rotation. By considering the spontaneous penetration of many NPs into a vesicle, we found that NP aggregation would lead to the shape change of the vesicle, and therefore cause the leakage of encapsulated solvent or membrane rupture, implying the possible cytotoxicity. In short, this work gives a fundamental understanding for the penetration mechanism of the ligand patterned NPs, which provides useful reference for the design of NPs for controllable cell penetrability and targeted delivery of drugs.
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Affiliation(s)
- Ye Li
- Division of Molecular and Materials Simulation, State Key Laboratory of Organic-Inorganic Composites, Beijing University of Chemical Technology, Beijing 100029, China.
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8
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Gao X, Dong J, Zhang X. The effect of nanoparticle size on endocytosis dynamics depends on membrane–nanoparticle interaction. MOLECULAR SIMULATION 2014. [DOI: 10.1080/08927022.2014.896995] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
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9
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Li Y, Zhang X, Cao D. The role of shape complementarity in the protein-protein interactions. Sci Rep 2013; 3:3271. [PMID: 24253561 PMCID: PMC3834541 DOI: 10.1038/srep03271] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2013] [Accepted: 10/31/2013] [Indexed: 11/23/2022] Open
Abstract
We use a dissipative particle dynamic simulation to investigate the effects of shape complementarity on the protein-protein interactions. By monitoring different kinds of protein shape-complementarity modes, we gave a clear mechanism to reveal the role of the shape complementarity in the protein-protein interactions, i.e., when the two proteins with shape complementarity approach each other, the conformation of lipid chains between two proteins would be restricted significantly. The lipid molecules tend to leave the gap formed by two proteins to maximize the configuration entropy, and therefore yield an effective entropy-induced protein-protein attraction, which enhances the protein aggregation. In short, this work provides an insight into understanding the importance of the shape complementarity in the protein-protein interactions especially for protein aggregation and antibody-antigen complexes. Definitely, the shape complementarity is the third key factor affecting protein aggregation and complex, besides the electrostatic-complementarity and hydrophobic complementarity.
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Affiliation(s)
- Ye Li
- Division of Molecular and Materials Simulation, State Key Laboratory of Organic-Inorganic Composites, Beijing University of Chemical Technology, Beijing 100029, People's Republic of China
| | - Xianren Zhang
- Division of Molecular and Materials Simulation, State Key Laboratory of Organic-Inorganic Composites, Beijing University of Chemical Technology, Beijing 100029, People's Republic of China
| | - Dapeng Cao
- Division of Molecular and Materials Simulation, State Key Laboratory of Organic-Inorganic Composites, Beijing University of Chemical Technology, Beijing 100029, People's Republic of China
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Li Y, Zhang X, Cao D. Self-Assembly of Patterned Nanoparticles on Cellular Membranes: Effect of Charge Distribution. J Phys Chem B 2013; 117:6733-40. [DOI: 10.1021/jp312124x] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
- Ye Li
- Division of Molecular and
Materials Simulation, State
Key Laboratory of Organic−Inorganic Composites, Beijing University of Chemical Technology, Beijing
100029, People’s Republic of China
| | - Xianren Zhang
- Division of Molecular and
Materials Simulation, State
Key Laboratory of Organic−Inorganic Composites, Beijing University of Chemical Technology, Beijing
100029, People’s Republic of China
| | - Dapeng Cao
- Division of Molecular and
Materials Simulation, State
Key Laboratory of Organic−Inorganic Composites, Beijing University of Chemical Technology, Beijing
100029, People’s Republic of China
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Maffeo C, Bhattacharya S, Yoo J, Wells D, Aksimentiev A. Modeling and simulation of ion channels. Chem Rev 2012; 112:6250-84. [PMID: 23035940 PMCID: PMC3633640 DOI: 10.1021/cr3002609] [Citation(s) in RCA: 148] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Christopher Maffeo
- Department of Physics, University of Illinois, 1110 W. Green St., Urbana, IL
| | - Swati Bhattacharya
- Department of Physics, University of Illinois, 1110 W. Green St., Urbana, IL
| | - Jejoong Yoo
- Department of Physics, University of Illinois, 1110 W. Green St., Urbana, IL
| | - David Wells
- Department of Physics, University of Illinois, 1110 W. Green St., Urbana, IL
| | - Aleksei Aksimentiev
- Department of Physics, University of Illinois, 1110 W. Green St., Urbana, IL
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12
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Molecular modeling of the relationship between nanoparticle shape anisotropy and endocytosis kinetics. Biomaterials 2012; 33:4965-73. [DOI: 10.1016/j.biomaterials.2012.03.044] [Citation(s) in RCA: 128] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2012] [Accepted: 03/13/2012] [Indexed: 01/19/2023]
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13
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Chen X, Dong W, Zhang X. Self-assembly of amphiphilic molecules: A review on the recent computer simulation results. Sci China Chem 2010. [DOI: 10.1007/s11426-010-4064-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Li S, Zhang X, Wang W. Cluster formation of anchored proteins induced by membrane-mediated interaction. Biophys J 2010; 98:2554-63. [PMID: 20513399 PMCID: PMC2877327 DOI: 10.1016/j.bpj.2010.02.032] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2009] [Revised: 01/16/2010] [Accepted: 02/17/2010] [Indexed: 11/16/2022] Open
Abstract
Computer simulations were used to study the cluster formation of anchored proteins in a membrane. The rate and extent of clustering was found to be dependent upon the hydrophobic length of the anchored proteins embedded in the membrane. The cluster formation mechanism of anchored proteins in our work was ascribed to the different local perturbations on the upper and lower monolayers of the membrane and the intermonolayer coupling. Simulation results demonstrated that only when the penetration depth of anchored proteins was larger than half the membrane thickness, could the structure of the lower monolayer be significantly deformed. Additionally, studies on the local structures of membranes indicated weak perturbation of bilayer thickness for a shallowly inserted protein, while there was significant perturbation for a more deeply inserted protein. The origin of membrane-mediated protein-protein interaction is therefore due to the local perturbation of the membrane thickness, and the entropy loss-both of which are caused by the conformation restriction on the lipid chains and the enhanced intermonolayer coupling for a deeply inserted protein. Finally, in this study we addressed the difference of cluster formation mechanisms between anchored proteins and transmembrane proteins.
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Affiliation(s)
| | - Xianren Zhang
- Division of Molecular and Materials Simulation, Key Laboratory for Nanomaterials, Ministry of Education, Beijing University of Chemical Technology, Beijing, China
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15
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Bringing ion channel crystal structures into sharper focus with computer modeling: examples from mechanosensitive channels. Future Med Chem 2010; 2:909-13. [DOI: 10.4155/fmc.10.28] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
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16
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Gao J, Li S, Zhang X, Wang W. Computer simulations of micelle fission. Phys Chem Chem Phys 2010; 12:3219-28. [DOI: 10.1039/b918449j] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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