1
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Conde-Torres D, Calvelo M, Rovira C, Piñeiro Á, Garcia-Fandino R. Unlocking the specificity of antimicrobial peptide interactions for membrane-targeted therapies. Comput Struct Biotechnol J 2024; 25:61-74. [PMID: 38695015 PMCID: PMC11061258 DOI: 10.1016/j.csbj.2024.04.022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2023] [Revised: 04/06/2024] [Accepted: 04/07/2024] [Indexed: 05/04/2024] Open
Abstract
Antimicrobial peptides (AMPs) are increasingly recognized as potent therapeutic agents, with their selective affinity for pathological membranes, low toxicity profile, and minimal resistance development making them particularly attractive in the pharmaceutical landscape. This study offers a comprehensive analysis of the interaction between specific AMPs, including magainin-2, pleurocidin, CM15, LL37, and clavanin, with lipid bilayer models of very different compositions that have been ordinarily used as biological membrane models of healthy mammal, cancerous, and bacterial cells. Employing unbiased molecular dynamics simulations and metadynamics techniques, we have deciphered the intricate mechanisms by which these peptides recognize pathogenic and pathologic lipid patterns and integrate into lipid assemblies. Our findings reveal that the transverse component of the peptide's hydrophobic dipole moment is critical for membrane interaction, decisively influencing the molecule's orientation and expected therapeutic efficacy. Our approach also provides insight on the kinetic and dynamic dependence on the peptide orientation in the axial and azimuthal angles when coming close to the membrane. The aim is to establish a robust framework for the rational design of peptide-based, membrane-targeted therapies, as well as effective quantitative descriptors that can facilitate the automated design of novel AMPs for these therapies using machine learning methods.
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Affiliation(s)
- Daniel Conde-Torres
- Center for Research in Biological Chemistry and Molecular Materials, Departamento de Química Orgánica, Universidade de Santiago de Compostela, Campus Vida s/n, 15782 Santiago de Compostela, Spain
- Departamento de Física Aplicada, Facultade de Física, Universidade de Santiago de Compostela, 15782 Santiago de Compostela, Spain
| | - Martín Calvelo
- Departament de Química Orgànica and Institut de Química Teòrica i Computacional (IQTCUB), Universitat de Barcelona, Barcelona, Spain
| | - Carme Rovira
- Departament de Química Orgànica and Institut de Química Teòrica i Computacional (IQTCUB), Universitat de Barcelona, Barcelona, Spain
- Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain
| | - Ángel Piñeiro
- Departamento de Física Aplicada, Facultade de Física, Universidade de Santiago de Compostela, 15782 Santiago de Compostela, Spain
| | - Rebeca Garcia-Fandino
- Center for Research in Biological Chemistry and Molecular Materials, Departamento de Química Orgánica, Universidade de Santiago de Compostela, Campus Vida s/n, 15782 Santiago de Compostela, Spain
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2
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Blanco-González A, Wurl A, Mendes Ferreira T, Piñeiro Á, Garcia-Fandino R. Simulating Bacterial Membrane Models at the Atomistic Level: A Force Field Comparison. J Chem Theory Comput 2024. [PMID: 39226695 DOI: 10.1021/acs.jctc.4c00204] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/05/2024]
Abstract
Molecular dynamics (MD) simulations are currently an indispensable tool to understand both the dynamic and nanoscale organization of cell membrane models. A large number of quantitative parameters can be extracted from these simulations, but their reliability is determined by the quality of the employed force field and the simulation parameters. Much of the work on parametrizing and optimizing force fields for biomembrane modeling has been focused on homogeneous bilayers with a single phospholipid type. However, these may not perform effectively or could even be unsuitable for lipid mixtures commonly employed in membrane models. This work aims to fill this gap by comparing MD simulation results of several bacterial membrane models using different force fields and simulation parameters, namely, CHARMM36, Slipids, and GROMOS-CKP. Furthermore, the hydrogen isotope exchange (HIE) method, combined with GROMOS-CKP (GROMOS-H2Q), was also tested to check for the impact of this acceleration strategy on the performance of the force field. A common set of simulation parameters was employed for all of the force fields in addition to those corresponding to the original parametrization of each of them. Furthermore, new experimental order parameter values determined from NMR of several lipid mixtures are also reported to compare them with those determined from MD simulations. Our results reveal that most of the calculated physical properties of bacterial membrane models from MD simulations are substantially force field and lipid composition dependent. Some lipid mixtures exhibit nearly ideal behaviors, while the interaction of different lipid types in other mixtures is highly synergistic. None of the employed force fields seem to be clearly superior to the other three, each having its own strengths and weaknesses. Slipids are notably effective at replicating the order parameters for all acyl chains, including those in lipid mixtures, but they offer the least accurate results for headgroup parameters. Conversely, CHARMM provides almost perfect estimates for the order parameters of the headgroups but tends to overestimate those of the lipid tails. The GROMOS parametrizations deliver reasonable order parameters for entire lipid molecules, including multicomponent bilayers, although they do not reach the accuracy of Slipids for tails or CHARMM for headgroups. Importantly, GROMOS-H2Q stands out for its computational efficiency, being at least 3 times faster than GROMOS, which is already faster than both CHARMM and Slipids. In turn, GROMOS-H2Q yields much higher compressibilities compared to all other parametrizations.
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Affiliation(s)
- Alexandre Blanco-González
- Facultad de Física, University of Santiago de Compostela (USC), 15782 Santiago de Compostela, Spain
- Singular Research Centre in Chemical Biology and Molecular Materials, (CIQUS), Organic Chemistry Department, University of Santiago de Compostela (USC), 15782 Santiago de Compostela, Spain
- MD.USE Innovations S.L, Edificio Emprendia, 15782 Santiago de Compostela, Spain
| | - Anika Wurl
- Institute of Physics, Faculty of Natural Sciences II, Betty-Heimann-Str. 7, 06120 Halle/Saale, Germany
| | - Tiago Mendes Ferreira
- Institute of Physics, Faculty of Natural Sciences II, Betty-Heimann-Str. 7, 06120 Halle/Saale, Germany
| | - Ángel Piñeiro
- Facultad de Física, University of Santiago de Compostela (USC), 15782 Santiago de Compostela, Spain
| | - Rebeca Garcia-Fandino
- Singular Research Centre in Chemical Biology and Molecular Materials, (CIQUS), Organic Chemistry Department, University of Santiago de Compostela (USC), 15782 Santiago de Compostela, Spain
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3
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Ju H, Cheng L, Li M, Mei K, He S, Jia C, Guo X. Single-Molecule Electrical Profiling of Peptides and Proteins. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024; 11:e2401877. [PMID: 38639403 PMCID: PMC11267281 DOI: 10.1002/advs.202401877] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/22/2024] [Revised: 04/03/2024] [Indexed: 04/20/2024]
Abstract
In recent decades, there has been a significant increase in the application of single-molecule electrical analysis platforms in studying proteins and peptides. These advanced analysis methods have the potential for deep investigation of enzymatic working mechanisms and accurate monitoring of dynamic changes in protein configurations, which are often challenging to achieve in ensemble measurements. In this work, the prominent research progress in peptide and protein-related studies are surveyed using electronic devices with single-molecule/single-event sensitivity, including single-molecule junctions, single-molecule field-effect transistors, and nanopores. In particular, the successful commercial application of nanopores in DNA sequencing has made it one of the most promising techniques in protein sequencing at the single-molecule level. From single peptides to protein complexes, the correlation between their electrical characteristics, structures, and biological functions is gradually being established. This enables to distinguish different molecular configurations of these biomacromolecules through real-time electrical monitoring of their life activities, significantly improving the understanding of the mechanisms underlying various life processes.
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Affiliation(s)
- Hongyu Ju
- School of Pharmaceutical Science and TechnologyTianjin UniversityTianjin300072P. R. China
- Center of Single‐Molecule SciencesInstitute of Modern OpticsFrontiers Science Center for New Organic MatterTianjin Key Laboratory of Microscale Optical Information Science and TechnologyCollege of Electronic Information and Optical EngineeringNankai UniversityTianjin300350P. R. China
| | - Li Cheng
- Center of Single‐Molecule SciencesInstitute of Modern OpticsFrontiers Science Center for New Organic MatterTianjin Key Laboratory of Microscale Optical Information Science and TechnologyCollege of Electronic Information and Optical EngineeringNankai UniversityTianjin300350P. R. China
| | - Mengmeng Li
- Center of Single‐Molecule SciencesInstitute of Modern OpticsFrontiers Science Center for New Organic MatterTianjin Key Laboratory of Microscale Optical Information Science and TechnologyCollege of Electronic Information and Optical EngineeringNankai UniversityTianjin300350P. R. China
| | - Kunrong Mei
- School of Pharmaceutical Science and TechnologyTianjin UniversityTianjin300072P. R. China
| | - Suhang He
- Center of Single‐Molecule SciencesInstitute of Modern OpticsFrontiers Science Center for New Organic MatterTianjin Key Laboratory of Microscale Optical Information Science and TechnologyCollege of Electronic Information and Optical EngineeringNankai UniversityTianjin300350P. R. China
| | - Chuancheng Jia
- Center of Single‐Molecule SciencesInstitute of Modern OpticsFrontiers Science Center for New Organic MatterTianjin Key Laboratory of Microscale Optical Information Science and TechnologyCollege of Electronic Information and Optical EngineeringNankai UniversityTianjin300350P. R. China
| | - Xuefeng Guo
- Center of Single‐Molecule SciencesInstitute of Modern OpticsFrontiers Science Center for New Organic MatterTianjin Key Laboratory of Microscale Optical Information Science and TechnologyCollege of Electronic Information and Optical EngineeringNankai UniversityTianjin300350P. R. China
- Beijing National Laboratory for Molecular SciencesNational Biomedical Imaging CenterCollege of Chemistry and Molecular EngineeringPeking UniversityBeijing100871P. R. China
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4
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Voce N, Stevenson P. Experimentally Probing the Effect of Confinement Geometry on Lipid Diffusion. J Phys Chem B 2024; 128:4404-4413. [PMID: 38574293 PMCID: PMC11089508 DOI: 10.1021/acs.jpcb.3c07388] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2023] [Revised: 03/18/2024] [Accepted: 03/19/2024] [Indexed: 04/06/2024]
Abstract
The lateral mobility of molecules within the cell membrane is ultimately governed by the local environment of the membrane. Confined regions induced by membrane structures, such as protein aggregates or the actin meshwork, occur over a wide range of length scales and can impede or steer the diffusion of membrane components. However, a detailed picture of the origins and nature of these confinement effects remains elusive. Here, we prepare model lipid systems on substrates patterned with confined domains of varying geometries constructed with different materials to explore the influences of physical boundary conditions and specific molecular interactions on diffusion. We demonstrate a platform that is capable of significantly altering and steering the long-range diffusion of lipids by using simple oxide deposition approaches, enabling us to systematically explore how confinement size and shape impact diffusion over multiple length scales. While we find that a "boundary condition" description of the system captures underlying trends in some cases, we are also able to directly compare our systems to analytical models, revealing the unexpected breakdown of several approximate solutions. Our results highlight the importance of considering the length scale dependence when discussing properties such as diffusion.
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Affiliation(s)
- Nicole Voce
- Department of Physics, Northeastern University, Boston, Massachusetts 02115, United States
| | - Paul Stevenson
- Department of Physics, Northeastern University, Boston, Massachusetts 02115, United States
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5
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Vögele M, Köfinger J, Hummer G. Nanoporous Membranes of Densely Packed Carbon Nanotubes Formed by Lipid-Mediated Self-Assembly. ACS APPLIED BIO MATERIALS 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] [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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6
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Cabezón A, Calvelo M, Granja JR, Piñeiro Á, Garcia-Fandino R. Uncovering the mechanisms of cyclic peptide self-assembly in membranes with the chirality-aware MA(R/S)TINI forcefield. J Colloid Interface Sci 2023; 642:84-99. [PMID: 37001460 DOI: 10.1016/j.jcis.2023.03.101] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2023] [Revised: 02/19/2023] [Accepted: 03/16/2023] [Indexed: 03/31/2023]
Abstract
Cyclic peptides (CPs) formed by alternation of D- and L-amino acids (D,L-CPs) can self-assemble into nanotubes (SCPNs) by parallel or/and antiparallel stacking. Different applications have been attributed to these nanotubes, including the disruption of lipid bilayers of specific compositions and the selective transport of ions throughout membranes. Molecular dynamics (MD) simulations have significantly contributed to understand the interaction between CPs, including the structural, dynamic and transport properties of their supramolecular aggregates. The high computational cost of atomic resolution forcefields makes them impractical for simulating the self-assembly of macromolecules, so coarse-grained (CG) models might represent a more feasible solution for this purpose. However, general CG models used for the simulation of biomolecules such as the MARTINI forcefield do not explicitly consider the non-covalent interactions leading to the formation of secondary structure patterns in proteins. This becomes particularly important in the case of CPs due to the D- and L-chirality alternation in their sequence, leading to opposite orientations of the backbone polar groups on both sides of the cyclic ring plane. In order to overcome this limitation, we have extended the MARTINI forcefield to introduce chirality in each residue of the CPs. The new parametrization, which we have called MA(R/S)TINI, reproduces the expected self-assembly patterns for several CP sequences in the presence of different membrane models, explicitly considering the chirality of the CPs and with no significant extra computational cost. Our simulations provide new mechanistic information of how these systems self-assemble in presence of different lipid scenarios, showing that the CP-CP and CP-membrane interactions are sensitive to the peptide sequence chirality. This opens the door to design new bioactive CPs based on CG-MD simulations. A web-based tool for the automatic parameterization of new CP sequences using MA(R/S)TINI, among other functionalities, is under construction (see http://cyclopep.com).
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7
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Suárez-Lestón F, Garrido PF, Piñeiro Á, Garcia-Fandino R. Not so rigid capsids based on cyclodextrin complexes: Keys to design. J Colloid Interface Sci 2022; 623:938-946. [DOI: 10.1016/j.jcis.2022.05.098] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2022] [Revised: 05/14/2022] [Accepted: 05/16/2022] [Indexed: 11/26/2022]
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8
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Chan SY, Lee D, Meivita MP, Li L, Tan YS, Bajalovic N, Loke DK. Ultrasensitive Detection of MCF-7 Cells with a Carbon Nanotube-Based Optoelectronic-Pulse Sensor Framework. ACS OMEGA 2022; 7:18459-18470. [PMID: 35694527 PMCID: PMC9178712 DOI: 10.1021/acsomega.2c00842] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/10/2022] [Accepted: 04/07/2022] [Indexed: 06/15/2023]
Abstract
Biosensors are of vital significance for healthcare by supporting the management of infectious diseases for preventing pandemics and the diagnosis of life-threatening conditions such as cancer. However, the advancement of the field can be limited by low sensing accuracy. Here, we altered the bioelectrical signatures of the cells using carbon nanotubes (CNTs) via structural loosening effects. Using an alternating current (AC) pulse under light irradiation, we developed a photo-assisted AC pulse sensor based on CNTs to differentiate between healthy breast epithelial cells (MCF-10A) and luminal breast cancer cells (MCF-7) within a heterogeneous cell population. We observed a previously undemonstrated increase in current contrast for MCF-7 cells with CNTs compared to MCF-10A cells with CNTs under light exposure. Moreover, we obtained a detection limit of ∼1.5 × 103 cells below a baseline of ∼1 × 104 cells for existing electrical-based sensors for an adherent, heterogeneous cell population. All-atom molecular dynamics (MD) simulations reveal that interactions between the embedded CNT and cancer cell membranes result in a less rigid lipid bilayer structure, which can facilitate CNT translocation for enhancing current. This as-yet unconsidered cancer cell-specific method based on the unique optoelectrical properties of CNTs represents a strategy for unlocking the detection of a small population of cancer cells and provides a promising route for the early diagnosis, monitoring, and staging of cancer.
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Affiliation(s)
- Sophia
S. Y. Chan
- Department
of Science, Mathematics and Technology, Singapore University of Technology and Design, Singapore487372, Singapore
| | - Denise Lee
- Department
of Science, Mathematics and Technology, Singapore University of Technology and Design, Singapore487372, Singapore
| | - Maria Prisca Meivita
- Department
of Science, Mathematics and Technology, Singapore University of Technology and Design, Singapore487372, Singapore
| | - Lunna Li
- Department
of Science, Mathematics and Technology, Singapore University of Technology and Design, Singapore487372, Singapore
- Thomas
Young Centre and Department of Chemical Engineering, University College London, LondonWC1E 6BT, U.K.
| | - Yaw Sing Tan
- Bioinformatics
Institute, Agency for Science, Technology
and Research (A*STAR), Singapore138671, Singapore
| | - Natasa Bajalovic
- Department
of Science, Mathematics and Technology, Singapore University of Technology and Design, Singapore487372, Singapore
| | - Desmond K. Loke
- Department
of Science, Mathematics and Technology, Singapore University of Technology and Design, Singapore487372, Singapore
- Office
of Innovation, Changi General Hospital, Singapore529889, Singapore
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9
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Huang J, Song W, Meng L, Shen Y, Zhou R. Role of polyplex charge density in lipopolyplexes. NANOSCALE 2022; 14:7174-7180. [PMID: 35535595 DOI: 10.1039/d1nr07897f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Lipopolyplexes have received extensive attention lately in gene therapy delivery. However, the interactions between the polyplex and the liposome and their underlying molecular mechanisms remain to be elucidated. Here, we adopted a simple model, mainly to illustrate the impact of polyplex charge density on the self-assembly of liposomes (containing DOPE and CHEMS lipids) using coarse-grained molecular dynamics simulations. Our simulation results show that when the charge density increases in the polyplex, more lipids, especially CHEMS (a negatively charged helper lipid) lipids, are attracted to the polyplex (positively charged) surface, and meanwhile nearby water molecules are driven away from the polyplex, resulting in a less spherical liposome. Energy decomposition analyses further reveal that, at higher charge densities, the polyplex exhibits much stronger interactions with CHEMS lipids than with water molecules, with the majority contribution from electrostatic interactions. In addition, the mobility of lipids, especially CHEMS, is reduced as the polyplex charge density increases, indicating a more rigid liposome. Overall, our molecular dynamics simulations elucidate the influence of polyplex charge density on the liposome self-assembly process at the atomic level, which provides a complementary approach to experiments for a better understanding of this promising gene therapy delivery system.
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Affiliation(s)
- Jianxiang Huang
- Institute of Quantitative Biology, College of Life Sciences, and Department of Physics, Zhejiang University, Hangzhou 310027, China.
| | - Wei Song
- Institute of Quantitative Biology, College of Life Sciences, and Department of Physics, Zhejiang University, Hangzhou 310027, China.
| | - Lijun Meng
- Institute of Quantitative Biology, College of Life Sciences, and Department of Physics, Zhejiang University, Hangzhou 310027, China.
| | - Youqing Shen
- College of Chemical and Biological Engineering, Zhejiang University, Hangzhou 310027, China
| | - Ruhong Zhou
- Institute of Quantitative Biology, College of Life Sciences, and Department of Physics, Zhejiang University, Hangzhou 310027, China.
- Department of Chemistry, Columbia University, New York, NY10027, USA
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10
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Blanco-González A, Piñeiro Á, García-Fandiño R. Unravelling hierarchical levels of structure in lipid membranes. Comput Struct Biotechnol J 2022; 20:2798-2806. [PMID: 35685357 PMCID: PMC9168047 DOI: 10.1016/j.csbj.2022.05.042] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2022] [Revised: 05/21/2022] [Accepted: 05/21/2022] [Indexed: 11/30/2022] Open
Abstract
A set of hierarchical levels of structure can be proposed for lipid bilayers. The composition of a lipid bilayer is identified as a fluid version of primary structure. The interaction between leaflets is taken as the secondary structure of lipid bilayers. A method to identify membrane domains and their interaction is proposed as a third level of structure. The highly specific lipid perturbation around embedded macromolecules is taken as the quaternary level of structure.
In analogy with the hierarchical levels typically used to describe the structure of nucleic acids or proteins and keeping in mind that lipid bilayers are not just mere envelopers for biological material but directly responsible for many important functions of life, it is discussed here how membrane models can also be interpreted in terms of different hierarchies in their structure. Namely, lipid composition, interaction between leaflets, existence and interaction of domains arising from the coordinate behavior of lipids and their properties, plus the manifest and specific perturbation of the lipid organization around macromolecules embedded in a membrane are hereby used to define the primary, secondary, tertiary and quaternary structures, respectively. Molecular Dynamics simulations are used to illustrate this proposal. Alternative levels of organization and methods to define domains can be proposed but the final aim is to highlight the paradigm arising from this description which is expected to have significant consequences on deciphering the underlying factors governing membranes and their interactions with other molecules.
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Affiliation(s)
- Alexandre Blanco-González
- Departamento de Física Aplicada, Facultade de Física, Universidade de Santiago de Compostela, E-15782 Santiago de Compostela, Spain
- Departamento de Química Orgánica, Centro Singular de Investigación en Química Biolóxica e Materiais Moleculares (CiQUS), Universidade de Santiago de Compostela, Campus Vida s/n, E-15782 Santiago de Compostela, Spain
- MD.USE Innovations SL, Edificio Emprendia, 15782 Santiago de Compostela, Spain
| | - Ángel Piñeiro
- Departamento de Física Aplicada, Facultade de Física, Universidade de Santiago de Compostela, E-15782 Santiago de Compostela, Spain
- Corresponding authors.
| | - Rebeca García-Fandiño
- Departamento de Química Orgánica, Centro Singular de Investigación en Química Biolóxica e Materiais Moleculares (CiQUS), Universidade de Santiago de Compostela, Campus Vida s/n, E-15782 Santiago de Compostela, Spain
- Corresponding authors.
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11
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Lanphere C, Ciccone J, Dorey A, Hagleitner-Ertuğrul N, Knyazev D, Haider S, Howorka S. Triggered Assembly of a DNA-Based Membrane Channel. J Am Chem Soc 2022; 144:4333-4344. [PMID: 35253434 PMCID: PMC8931747 DOI: 10.1021/jacs.1c06598] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2021] [Indexed: 01/01/2023]
Abstract
Chemistry is in a powerful position to synthetically replicate biomolecular structures. Adding functional complexity is key to increase the biomimetics' value for science and technology yet is difficult to achieve with poorly controlled building materials. Here, we use defined DNA blocks to rationally design a triggerable synthetic nanopore that integrates multiple functions of biological membrane proteins. Soluble triggers bind via molecular recognition to the nanopore components changing their structure and membrane position, which controls the assembly into a defined channel for efficient transmembrane cargo transport. Using ensemble, single-molecule, and simulation analysis, our activatable pore provides insight into the kinetics and structural dynamics of DNA assembly at the membrane interface. The triggered channel advances functional DNA nanotechnology and synthetic biology and will guide the design of controlled nanodevices for sensing, cell biological research, and drug delivery.
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Affiliation(s)
- Conor Lanphere
- Department
of Chemistry, Institute of Structural Molecular Biology, University College London, London WC1H 0AJ, United Kingdom
| | - Jonah Ciccone
- Department
of Chemistry, Institute of Structural Molecular Biology, University College London, London WC1H 0AJ, United Kingdom
| | - Adam Dorey
- Department
of Chemistry, Institute of Structural Molecular Biology, University College London, London WC1H 0AJ, United Kingdom
| | | | - Denis Knyazev
- Institute
of Applied Experimental Biophysics, Johannes
Kepler University, 4040 Linz, Austria
| | - Shozeb Haider
- Department
of Pharmaceutical and Biological Chemistry, University College London School of Pharmacy, London WC1N 1AX, United Kingdom
| | - Stefan Howorka
- Department
of Chemistry, Institute of Structural Molecular Biology, University College London, London WC1H 0AJ, United Kingdom
- Institute
of Applied Experimental Biophysics, Johannes
Kepler University, 4040 Linz, Austria
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12
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Conde D, Garrido PF, Calvelo M, Piñeiro Á, Garcia-Fandino R. Molecular Dynamics Simulations of Transmembrane Cyclic Peptide Nanotubes Using Classical Force Fields, Hydrogen Mass Repartitioning, and Hydrogen Isotope Exchange Methods: A Critical Comparison. Int J Mol Sci 2022; 23:3158. [PMID: 35328578 PMCID: PMC8951607 DOI: 10.3390/ijms23063158] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2022] [Revised: 03/06/2022] [Accepted: 03/07/2022] [Indexed: 12/04/2022] Open
Abstract
Self-assembled cyclic peptide nanotubes with alternating D- and L-amino acid residues in the sequence of each subunit have attracted a great deal of attention due to their potential for new nanotechnology and biomedical applications, mainly in the field of antimicrobial peptides. Molecular dynamics simulations can be used to characterize these systems with atomic resolution at different time scales, providing information that is difficult to obtain via wet lab experiments. However, the performance of classical force fields typically employed in the simulation of biomolecules has not yet been extensively tested with this kind of highly constrained peptide. Four different classical force fields (AMBER, CHARMM, OPLS, and GROMOS), using a nanotube formed by eight D,L-α-cyclic peptides inserted into a lipid bilayer as a model system, were employed here to fill this gap. Significant differences in the pseudo-cylindrical cavities formed by the nanotubes were observed, the most important being the diameter of the nanopores, the number and location of confined water molecules, and the density distribution of the solvent molecules. Furthermore, several modifications were performed on GROMOS54a7, aiming to explore acceleration strategies of the MD simulations. The hydrogen mass repartitioning (HMR) and hydrogen isotope exchange (HIE) methods were tested to slow down the fastest degrees of freedom. These approaches allowed a significant increase in the time step employed in the equation of the motion integration algorithm, from 2 fs up to 5-7 fs, with no serious changes in the structural and dynamical properties of the nanopores. Subtle differences with respect to the simulations with the unmodified force fields were observed in the concerted movements of the cyclic peptides, as well as in the lifetime of several H-bonds. All together, these results are expected to contribute to better understanding of the behavior of self-assembled cyclic peptide nanotubes, as well as to support the methods tested to speed up general MD simulations; additionally, they do provide a number of quantitative descriptors that are expected to be used as a reference to design new experiments intended to validate and complement computational studies of antimicrobial cyclic peptides.
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Affiliation(s)
- Daniel Conde
- Center for Research in Biological Chemistry and Molecular Materials, Departamento de Química Orgánica, Universidade de Santiago de Compostela, Campus Vida s/n, 15782 Santiago de Compostela, Spain; (D.C.); (M.C.)
- Departamento de Física Aplicada, Facultade de Física, Universidade de Santiago de Compostela, 15782 Santiago de Compostela, Spain;
| | - Pablo F. Garrido
- Departamento de Física Aplicada, Facultade de Física, Universidade de Santiago de Compostela, 15782 Santiago de Compostela, Spain;
| | - Martín Calvelo
- Center for Research in Biological Chemistry and Molecular Materials, Departamento de Química Orgánica, Universidade de Santiago de Compostela, Campus Vida s/n, 15782 Santiago de Compostela, Spain; (D.C.); (M.C.)
- Departament de Química Inorgánica i Orgànica and Institut de Química Teòrica i Computacional (IQTCUB), Universitat de Barcelona, 08028 Barcelona, Spain
| | - Ángel Piñeiro
- Departamento de Física Aplicada, Facultade de Física, Universidade de Santiago de Compostela, 15782 Santiago de Compostela, Spain;
| | - Rebeca Garcia-Fandino
- Center for Research in Biological Chemistry and Molecular Materials, Departamento de Química Orgánica, Universidade de Santiago de Compostela, Campus Vida s/n, 15782 Santiago de Compostela, Spain; (D.C.); (M.C.)
- CIQUP, Centro de Investigação em Química, Departamento de Química e Bioquímica, Faculdade de Ciências, Universidade do Porto, 4196-007 Porto, Portugal
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13
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Wu F, Jin X, Guan Z, Lin J, Cai C, Wang L, Li Y, Lin S, Xu P, Gao L. Membrane Nanopores Induced by Nanotoroids via an Insertion and Pore-Forming Pathway. NANO LETTERS 2021; 21:8545-8553. [PMID: 34623162 DOI: 10.1021/acs.nanolett.1c01331] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
The formation of membrane nanopores is one of the crucial activities of cells and has attracted considerable attention. However, the understanding of their types and mechanisms is still limited. Herein, we report a novel nanopore formation phenomenon achieved through the insertion of polymeric nanotoroids into the cellular membrane. As revealed by theoretical simulations, the nanotoroid can embed in the membrane, leaving a nanopore on the cell. The through-the-cavity wrapping of lipids is critical for the retention of the nanotoroid in the membrane, which is attributed to both a relatively large inner cavity of the nanotoroid and a moderate attraction between the nanotoroid and membrane lipids. Under the guidance of the simulation predictions, experiments using polypeptide toroids as pore-forming agents were performed, confirming the unique biophysical phenomenon. This work demonstrates a distinctive pore-forming pathway, deepens the understanding of the membrane nanopore phenomenon, and assists in the design of advanced pore-forming materials.
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Affiliation(s)
- Fangsheng Wu
- Shanghai Key Laboratory of Advanced Polymeric Materials, Key Laboratory for Ultrafine Materials of Ministry of Education, Frontiers Science Center for Materiobiology and Dynamic Chemistry, School of Materials Science and Engineering, East China University of Science and Technology, Shanghai 200237, People's Republic of China
| | - Xiao Jin
- Shanghai Key Laboratory of Advanced Polymeric Materials, Key Laboratory for Ultrafine Materials of Ministry of Education, Frontiers Science Center for Materiobiology and Dynamic Chemistry, School of Materials Science and Engineering, East China University of Science and Technology, Shanghai 200237, People's Republic of China
| | - Zhou Guan
- Shanghai Key Laboratory of Advanced Polymeric Materials, Key Laboratory for Ultrafine Materials of Ministry of Education, Frontiers Science Center for Materiobiology and Dynamic Chemistry, School of Materials Science and Engineering, East China University of Science and Technology, Shanghai 200237, People's Republic of China
| | - Jiaping Lin
- Shanghai Key Laboratory of Advanced Polymeric Materials, Key Laboratory for Ultrafine Materials of Ministry of Education, Frontiers Science Center for Materiobiology and Dynamic Chemistry, School of Materials Science and Engineering, East China University of Science and Technology, Shanghai 200237, People's Republic of China
| | - Chunhua Cai
- Shanghai Key Laboratory of Advanced Polymeric Materials, Key Laboratory for Ultrafine Materials of Ministry of Education, Frontiers Science Center for Materiobiology and Dynamic Chemistry, School of Materials Science and Engineering, East China University of Science and Technology, Shanghai 200237, People's Republic of China
| | - Liquan Wang
- Shanghai Key Laboratory of Advanced Polymeric Materials, Key Laboratory for Ultrafine Materials of Ministry of Education, Frontiers Science Center for Materiobiology and Dynamic Chemistry, School of Materials Science and Engineering, East China University of Science and Technology, Shanghai 200237, People's Republic of China
| | - Yongsheng Li
- Shanghai Key Laboratory of Advanced Polymeric Materials, Key Laboratory for Ultrafine Materials of Ministry of Education, Frontiers Science Center for Materiobiology and Dynamic Chemistry, School of Materials Science and Engineering, East China University of Science and Technology, Shanghai 200237, People's Republic of China
| | - Shaoliang Lin
- Shanghai Key Laboratory of Advanced Polymeric Materials, Key Laboratory for Ultrafine Materials of Ministry of Education, Frontiers Science Center for Materiobiology and Dynamic Chemistry, School of Materials Science and Engineering, East China University of Science and Technology, Shanghai 200237, People's Republic of China
| | - Pengfei Xu
- Shanghai Key Laboratory of Advanced Polymeric Materials, Key Laboratory for Ultrafine Materials of Ministry of Education, Frontiers Science Center for Materiobiology and Dynamic Chemistry, School of Materials Science and Engineering, East China University of Science and Technology, Shanghai 200237, People's Republic of China
| | - Liang Gao
- Shanghai Key Laboratory of Advanced Polymeric Materials, Key Laboratory for Ultrafine Materials of Ministry of Education, Frontiers Science Center for Materiobiology and Dynamic Chemistry, School of Materials Science and Engineering, East China University of Science and Technology, Shanghai 200237, People's Republic of China
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14
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Blanco-González A, Calvelo M, Garrido PF, Amorín M, Granja JR, Piñeiro Á, Garcia-Fandino R. Transmembrane Self-Assembled Cyclic Peptide Nanotubes Based on α-Residues and Cyclic δ-Amino Acids: A Computational Study. Front Chem 2021; 9:704160. [PMID: 34386480 PMCID: PMC8353252 DOI: 10.3389/fchem.2021.704160] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2021] [Accepted: 06/23/2021] [Indexed: 11/18/2022] Open
Abstract
Self-assembling cyclic peptide nanotubes have been shown to function as synthetic, integral transmembrane channels. The combination of natural and nonnatural aminoacids in the sequence of cyclic peptides enables the control not only of their outer surface but also of the inner cavity behavior and properties, affecting, for instance, their permeability to different molecules including water and ions. Here, a thorough computational study on a new class of self-assembling peptide motifs, in which δ-aminocycloalkanecarboxylic acids are alternated with natural α-amino acids, is presented. The presence of synthetic δ-residues creates hydrophobic regions in these α,δ-SCPNs, which makes them especially attractive for their potential implementation in the design of new drug or diagnostic agent carrier systems. Using molecular dynamics simulations, the behavior of water molecules, different ions (Li+, Na+, K+, Cs+, and Ca2+), and their correspondent counter Cl- anions is extensively investigated in the nanoconfined environment. The structure and dynamics are mutually combined in a diving immersion inside these transmembrane channels to discover a fascinating submarine nanoworld where star-shaped water channels guide the passage of cations and anions therethrough.
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Affiliation(s)
- Alexandre Blanco-González
- Departamento de Química Orgánica, Center for Research in Biological Chemistry and Molecular Materials, Universidade de Santiago de Compostela, Campus Vida s/n, Santiago de Compostela, Spain
- Departamento de Física Aplicada, Facultade de Física, Universidade de Santiago de Compostela, Santiago de Compostela, Spain
| | - Martín Calvelo
- Departamento de Química Orgánica, Center for Research in Biological Chemistry and Molecular Materials, Universidade de Santiago de Compostela, Campus Vida s/n, Santiago de Compostela, Spain
| | - Pablo F. Garrido
- Departamento de Física Aplicada, Facultade de Física, Universidade de Santiago de Compostela, Santiago de Compostela, Spain
| | - Manuel Amorín
- Departamento de Química Orgánica, Center for Research in Biological Chemistry and Molecular Materials, Universidade de Santiago de Compostela, Campus Vida s/n, Santiago de Compostela, Spain
| | - Juan R. Granja
- Departamento de Química Orgánica, Center for Research in Biological Chemistry and Molecular Materials, Universidade de Santiago de Compostela, Campus Vida s/n, Santiago de Compostela, Spain
| | - Ángel Piñeiro
- Departamento de Física Aplicada, Facultade de Física, Universidade de Santiago de Compostela, Santiago de Compostela, Spain
| | - Rebeca Garcia-Fandino
- Departamento de Química Orgánica, Center for Research in Biological Chemistry and Molecular Materials, Universidade de Santiago de Compostela, Campus Vida s/n, Santiago de Compostela, Spain
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15
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Calvelo M, Lynch CI, Granja JR, Sansom MSP, Garcia-Fandiño R. Effect of Water Models on Transmembrane Self-Assembled Cyclic Peptide Nanotubes. ACS NANO 2021; 15:7053-7064. [PMID: 33739081 PMCID: PMC8485350 DOI: 10.1021/acsnano.1c00155] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/06/2021] [Accepted: 03/15/2021] [Indexed: 05/23/2023]
Abstract
Self-assembling cyclic peptide nanotubes can form nanopores when they are inserted in lipid bilayers, acting as ion and/or water permeable channels. In order to improve the versatility of these systems, it is possible to specifically design cyclic peptides with a combination of natural and non-natural amino acids, enabling the control of the nature of the inner cavity of the channels. Here, the behavior of two types of self-assembling peptide motifs, alternating α-amino acids with γ- or δ-aminocycloalkanecarboxylic acids, is studied via molecular dynamics (MD) simulations. The behavior of water molecules in nanopores is expected to affect the properties of these channels and therefore merits detailed examination. A number of water models commonly used in MD simulations have been validated by how well they reproduce bulk water properties. However, it is less clear how these water models behave in the nanoconfined condition inside a channel. The behavior of four different water models-TIP3P, TIP4P, TIP4P/2005, and OPC-are evaluated in MD simulations of self-assembled cyclic peptide nanotubes of distinct composition and diameter. The dynamic behavior of the water molecules and ions in these designed artificial channels depends subtly on the water model used. TIP3P water molecules move faster than those of TIP4P, TIP4P/2005, and OPC. This demeanor is clearly observed in the filling of the nanotube, in water diffusion within the pore, and in the number and stability of hydrogen bonds of the peptides with water. It was also shown that the water model influences the simulated ion flux through the nanotubes, with TIP3P producing the greatest ion flux. Additionally, the two more recent models, TIP4P/2005 and OPC, which are known to reproduce the experimental self-diffusion coefficient of bulk water quite well, exhibit very similar results under the nanoconfined conditions studied here. Because none of these models have been parametrized specifically for waters confined in peptide nanotubes, this study provides a point of reference for further validation.
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Affiliation(s)
- Martin Calvelo
- Center
for Research in Biological Chemistry and Molecular Materials (CIQUS), University of Santiago de Compostela, 15782 Santiago
de Compostela, Spain
| | - Charlotte I. Lynch
- Department
of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, United Kingdom
| | - Juan R. Granja
- Center
for Research in Biological Chemistry and Molecular Materials (CIQUS), University of Santiago de Compostela, 15782 Santiago
de Compostela, Spain
| | - Mark S. P. Sansom
- Department
of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, United Kingdom
| | - Rebeca Garcia-Fandiño
- Center
for Research in Biological Chemistry and Molecular Materials (CIQUS), University of Santiago de Compostela, 15782 Santiago
de Compostela, Spain
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16
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Ma X, Zhu X, Huang C, Li Z, Fan J. Molecular mechanisms underlying the role of the puckered surface in the biocompatibility of black phosphorus. NANOSCALE 2021; 13:3790-3799. [PMID: 33565554 DOI: 10.1039/d0nr08480h] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
As a newly emerging two-dimensional material, black phosphorus (BP) has received broad attention in the field of biomedical applications. Prior to its clinical application, its cytotoxicity to cells should be carefully evaluated; however, this field is still in its infancy. Motivated by this, we performed molecular dynamics (MD) simulations to systematically investigate the potential mechanisms of the cytotoxicity of BP to the lipid membrane, including lipid extraction, penetration into the membrane, and the impacts of BP on the physical properties of the membrane. Surprisingly, we observed that BP could not extract lipid molecules from the membrane. The thermodynamic analyses suggested that the puckered surface structure could weaken the interactions between BP and lipid molecules, thus inhibiting the lipid extraction. Additionally, through simulating the spontaneous interaction modes between BP and the lipid membrane, we found that the "passivated" edges of BP prohibited it from penetrating into the membrane. As a result, BP could only spontaneously lie parallel on the surface of the membrane, in which manner BP exerted little influence on the properties of the lipid membrane. To comprehensively appraise the cytotoxicity, we even artificially inserted BP into the membrane and compared the effects of BP and graphene on the properties of the membrane. Simulation results showed that the influences of the inserted BP on the lipid properties were much milder than those of graphene. Overall, the present work suggests that BP possesses distinctive biocompatibility benefiting from its puckered surface structure. This work provides a better understanding of the interactions between BP and the membrane, which may offer some useful suggestions for exploring strategies to improve the biocompatibility of nanomaterials.
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Affiliation(s)
- Xinyao Ma
- Department of Materials Science and Engineering, City University of Hong Kong, Hong Kong, China.
| | - Xiaohong Zhu
- Department of Materials Science and Engineering, City University of Hong Kong, Hong Kong, China.
| | - Changxiong Huang
- Department of Materials Science and Engineering, City University of Hong Kong, Hong Kong, China.
| | - Zhen Li
- School of Materials Science and Engineering, China University of Petroleum (East China), Qingdao, 266580, China
| | - Jun Fan
- Department of Materials Science and Engineering, City University of Hong Kong, Hong Kong, China. and Center for Advanced Nuclear Safety and Sustainable Development, City University of Hong Kong, Hong Kong, China
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17
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Omori S, Tsugita M, Hoshikawa Y, Morita M, Ito F, Yamaguchi SI, Xie Q, Noyori O, Yamaguchi T, Takada A, Saitoh T, Toyokuni S, Akiba H, Nagata S, Kinoshita K, Nakayama M. Tim4 recognizes carbon nanotubes and mediates phagocytosis leading to granuloma formation. Cell Rep 2021; 34:108734. [PMID: 33567275 DOI: 10.1016/j.celrep.2021.108734] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2020] [Revised: 10/02/2020] [Accepted: 01/19/2021] [Indexed: 12/22/2022] Open
Abstract
Macrophage recognition and phagocytosis of crystals is critical for the associated fibrosis and cancer. Of note, multi-walled carbon nanotubes (MWCNTs), the highly representative products of nanotechnology, induce macrophage NLRP3 inflammasome activation and cause asbestosis-like pathogenesis. However, it remains largely unknown how macrophages efficiently recognize MWCNTs on their cell surfaces. Here, we identify by a targeted screening of phagocyte receptors the phosphatidylserine receptors T cell immunoglobulin mucin 4 (Tim4) and Tim1 as the pattern-recognition receptors for carbon crystals. Docking simulation studies reveal spatiotemporally stable interfaces between aromatic residues in the extracellular IgV domain of Tim4 and one-dimensional carbon crystals. Further, CRISPR-Cas9-mediated deletion of Tim4 and Tim1 reveals that Tim4, but not Tim1, critically contributes to the recognition of MWCNTs by peritoneal macrophages and to granuloma development in a mouse model of direct mesothelium exposure to MWCNTs. These results suggest that Tim4 recognizes MWCNTs through aromatic interactions and mediates phagocytosis leading to granulomas.
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Affiliation(s)
- Satoshi Omori
- Graduate School of Information Sciences, Tohoku University, Sendai, Japan
| | - Misato Tsugita
- Frontier Research Institute for Interdisciplinary Sciences, Tohoku University, Sendai, Japan
| | - Yasuto Hoshikawa
- Institute of Multidisciplinary Research for Advanced Materials (IMRAM), Tohoku University, Sendai, Japan
| | - Masanobu Morita
- Department of Environmental Medicine and Molecular Toxicology, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Fumiya Ito
- Department of Pathology and Biological Responses, Nagoya University Graduate School of Medicine, Nagoya, Japan; CREST, Japan Science and Technology Agency (JST), Kawaguchi, Japan
| | - Shin-Ichiro Yamaguchi
- Laboratory of Immunology and Microbiology, College of Pharmaceutical Sciences, Ritsumeikan University, Kusatsu, Japan
| | - Qilin Xie
- Laboratory of Immunology and Microbiology, College of Pharmaceutical Sciences, Ritsumeikan University, Kusatsu, Japan
| | - Osamu Noyori
- Laboratory of Immunology and Microbiology, College of Pharmaceutical Sciences, Ritsumeikan University, Kusatsu, Japan
| | - Tomoya Yamaguchi
- Department of Cancer Biology, Graduate School of Medical Sciences, Kumamoto University, Kumamoto, Japan; PRESTO, JST, Kawaguchi, Japan
| | - Ayato Takada
- Division of Global Epidemiology, Research Center for Zoonosis Control, Hokkaido University, Sapporo, Japan
| | - Tatsuya Saitoh
- Laboratory of Bioresponse Regulation, Graduate School of Pharmaceutical Sciences, Osaka University, Suita, Japan
| | - Shinya Toyokuni
- Department of Pathology and Biological Responses, Nagoya University Graduate School of Medicine, Nagoya, Japan; CREST, Japan Science and Technology Agency (JST), Kawaguchi, Japan; Center for Low-temperature Plasma Sciences, Nagoya University, Nagoya, Japan
| | - Hisaya Akiba
- Department of Immunology, Juntendo University School of Medicine, Tokyo, Japan
| | - Shigekazu Nagata
- Laboratory of Biochemistry and Immunology, Immunology Frontier Research Center, Osaka University, Suita, Japan
| | - Kengo Kinoshita
- Graduate School of Information Sciences, Tohoku University, Sendai, Japan; Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan.
| | - Masafumi Nakayama
- Frontier Research Institute for Interdisciplinary Sciences, Tohoku University, Sendai, Japan; Laboratory of Immunology and Microbiology, College of Pharmaceutical Sciences, Ritsumeikan University, Kusatsu, Japan; PRESTO, JST, Kawaguchi, Japan.
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18
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Lynch C, Rao S, Sansom MSP. Water in Nanopores and Biological Channels: A Molecular Simulation Perspective. Chem Rev 2020; 120:10298-10335. [PMID: 32841020 PMCID: PMC7517714 DOI: 10.1021/acs.chemrev.9b00830] [Citation(s) in RCA: 88] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2019] [Indexed: 12/18/2022]
Abstract
This Review explores the dynamic behavior of water within nanopores and biological channels in lipid bilayer membranes. We focus on molecular simulation studies, alongside selected structural and other experimental investigations. Structures of biological nanopores and channels are reviewed, emphasizing those high-resolution crystal structures, which reveal water molecules within the transmembrane pores, which can be used to aid the interpretation of simulation studies. Different levels of molecular simulations of water within nanopores are described, with a focus on molecular dynamics (MD). In particular, models of water for MD simulations are discussed in detail to provide an evaluation of their use in simulations of water in nanopores. Simulation studies of the behavior of water in idealized models of nanopores have revealed aspects of the organization and dynamics of nanoconfined water, including wetting/dewetting in narrow hydrophobic nanopores. A survey of simulation studies in a range of nonbiological nanopores is presented, including carbon nanotubes, synthetic nanopores, model peptide nanopores, track-etched nanopores in polymer membranes, and hydroxylated and functionalized nanoporous silica. These reveal a complex relationship between pore size/geometry, the nature of the pore lining, and rates of water transport. Wider nanopores with hydrophobic linings favor water flow whereas narrower hydrophobic pores may show dewetting. Simulation studies over the past decade of the behavior of water in a range of biological nanopores are described, including porins and β-barrel protein nanopores, aquaporins and related polar solute pores, and a number of different classes of ion channels. Water is shown to play a key role in proton transport in biological channels and in hydrophobic gating of ion channels. An overall picture emerges, whereby the behavior of water in a nanopore may be predicted as a function of its hydrophobicity and radius. This informs our understanding of the functions of diverse channel structures and will aid the design of novel nanopores. Thus, our current level of understanding allows for the design of a nanopore which promotes wetting over dewetting or vice versa. However, to design a novel nanopore, which enables fast, selective, and gated flow of water de novo would remain challenging, suggesting a need for further detailed simulations alongside experimental evaluation of more complex nanopore systems.
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Affiliation(s)
- Charlotte
I. Lynch
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU, U.K.
| | - Shanlin Rao
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU, U.K.
| | - Mark S. P. Sansom
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU, U.K.
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19
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Membrane interactions in drug delivery: Model cell membranes and orthogonal techniques. Adv Colloid Interface Sci 2020; 281:102177. [PMID: 32417568 DOI: 10.1016/j.cis.2020.102177] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2019] [Revised: 03/05/2020] [Accepted: 05/07/2020] [Indexed: 01/22/2023]
Abstract
To generate the desired effect in the human body, the active pharmaceutical ingredient usually needs to interact with a receptor located on the cell membrane or inside the cell. Thus, understanding membrane interactions is of great importance when it comes to the development and testing of new drug molecules or new drug delivery systems. Nowadays, there is a tremendous selection of both model cell membranes and of techniques that can be used to characterize interactions between selected model cell membranes and a drug molecule, an excipient, or a drug delivery system. Having such a wide selection of model cell membranes and techniques available makes it sometimes challenging to select the optimal combination for a specific study. Furthermore, it is difficult to compare results obtained using different model cell membranes and techniques, and not all in vitro studies translate as well to an estimation of the in vivo biological activity or understanding of mode of action. This review provides an overview of the available lipid bilayer-based model cell membranes and of the most widely employed techniques for studying membrane interactions. Finally, the need for employing complimentary characterization techniques in order to acquire more reliable and in-depth information is highlighted.
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20
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Calvelo M, Lamas A, Guerra A, Amorín M, Garcia-Fandino R, Granja JR. Parallel Versus Antiparallel β-Sheet Structure in Cyclic Peptide Hybrids Containing γ- or δ-Cyclic Amino Acids. Chemistry 2020; 26:5846-5858. [PMID: 31999874 DOI: 10.1002/chem.201905554] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2019] [Indexed: 11/07/2022]
Abstract
Cyclic peptides with disc-shaped structures have emerged as potent building blocks for the preparation of new biomaterials in fields ranging from biological to material science. In this work, we analyze in depth the self-assembling properties of a new type of cyclic peptides based on the alternation of α-residues and cyclic δ-amino acids (α,δ-CPs). To examine the preferred stacking properties adopted by cyclic peptides bearing this type of amino acids, we carried out a synergistic in vitro/in silico approximation by using simple dimeric models and then extended to nanotubes. Although these new cyclic peptides (α,δ-CPs) can interact either in a parallel or antiparallel fashion, our results confirm that although the parallel β-sheet is more stable, it can be switched to the antiparallel stacking by choosing residues that can establish favorable cross-strand interactions. Moreover, the subsequent comparison by using the same methodology but applied to α,γ-CPs models, up to the moment assumed as antiparallel-like d,l-α-CPs, led to unforeseen conclusions that put into question preliminary conjectures about these systems. Surprisingly, they tend to adopt a parallel β-sheet directed by the skeleton interactions. These results imply a change of paradigm with respect to cyclic peptide designs that should be considered for dimers and nanotubes.
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Affiliation(s)
- Martín Calvelo
- Centro Singular de Investigación en Química Biolóxica e, Materiais Moleculares (CIQUS), Departamento de Química Orgánica, Universidade de Santiago de Compostela, 15782, Santiago de Compostela, Spain
| | - Alejandro Lamas
- Centro Singular de Investigación en Química Biolóxica e, Materiais Moleculares (CIQUS), Departamento de Química Orgánica, Universidade de Santiago de Compostela, 15782, Santiago de Compostela, Spain
| | - Arcadio Guerra
- Centro Singular de Investigación en Química Biolóxica e, Materiais Moleculares (CIQUS), Departamento de Química Orgánica, Universidade de Santiago de Compostela, 15782, Santiago de Compostela, Spain
| | - Manuel Amorín
- Centro Singular de Investigación en Química Biolóxica e, Materiais Moleculares (CIQUS), Departamento de Química Orgánica, Universidade de Santiago de Compostela, 15782, Santiago de Compostela, Spain
| | - Rebeca Garcia-Fandino
- Centro Singular de Investigación en Química Biolóxica e, Materiais Moleculares (CIQUS), Departamento de Química Orgánica, Universidade de Santiago de Compostela, 15782, Santiago de Compostela, Spain
| | - Juan R Granja
- Centro Singular de Investigación en Química Biolóxica e, Materiais Moleculares (CIQUS), Departamento de Química Orgánica, Universidade de Santiago de Compostela, 15782, Santiago de Compostela, Spain
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21
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van Hilten N, Stroh KS, Risselada HJ. Membrane Thinning Induces Sorting of Lipids and the Amphipathic Lipid Packing Sensor (ALPS) Protein Motif. Front Physiol 2020; 11:250. [PMID: 32372966 PMCID: PMC7177014 DOI: 10.3389/fphys.2020.00250] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2020] [Accepted: 03/05/2020] [Indexed: 12/16/2022] Open
Abstract
Heterogeneities (e.g., membrane proteins and lipid domains) and deformations (e.g., highly curved membrane regions) in biological lipid membranes cause lipid packing defects that may trigger functional sorting of lipids and membrane-associated proteins. To study these phenomena in a controlled and efficient way within molecular simulations, we developed an external field protocol that artificially enhances packing defects in lipid membranes by enforcing local thinning of a flat membrane region. For varying lipid compositions, we observed strong thinning-induced depletion or enrichment, depending on the lipid's intrinsic shape and its effect on a membrane's elastic modulus. In particular, polyunsaturated and lysolipids are strongly attracted to regions high in packing defects, whereas phosphatidylethanolamine (PE) lipids and cholesterol are strongly repelled from it. Our results indicate that externally imposed changes in membrane thickness, area, and curvature are underpinned by shared membrane elastic principles. The observed sorting toward the thinner membrane region is in line with the sorting expected for a positively curved membrane region. Furthermore, we have demonstrated that the amphipathic lipid packing sensor (ALPS) protein motif, a known curvature and packing defect sensor, is effectively attracted to thinner membrane regions. By extracting the force that drives amphipathic molecules toward the thinner region, our thinning protocol can directly quantify and score the lipid packing sensing of different amphipathic molecules. In this way, our protocol paves the way toward high-throughput exploration of potential defect- and curvature-sensing motifs, making it a valuable addition to the molecular simulation toolbox.
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Affiliation(s)
- Niek van Hilten
- Leiden Institute of Chemistry, Leiden University, Leiden, Netherlands
| | - Kai Steffen Stroh
- Institute for Theoretical Physics, Georg August University Göttingen, Göttingen, Germany
| | - Herre Jelger Risselada
- Leiden Institute of Chemistry, Leiden University, Leiden, Netherlands.,Institute for Theoretical Physics, Georg August University Göttingen, Göttingen, Germany
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22
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F. Garrido P, Calvelo M, Garcia-Fandiño R, Piñeiro Á. Rings, Hexagons, Hetals, and Dipolar Moment Sink-Sources: The Fanciful Behavior of Water around Cyclodextrin Complexes. Biomolecules 2020; 10:E431. [PMID: 32164358 PMCID: PMC7175221 DOI: 10.3390/biom10030431] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2020] [Revised: 02/24/2020] [Accepted: 03/04/2020] [Indexed: 01/08/2023] Open
Abstract
The basket-like geometry of cyclodextrins (CDs), with a cavity able to host hydrophobic groups, makes these molecules well suited for a large number of fundamental and industrial applications. Most of the established CD-based applications rely on trial and error studies, often ignoring key information at the atomic level that could be employed to design new products and to optimize their use. Computational simulations are well suited to fill this gap, especially in the case of CD systems due to their low number of degrees of freedom compared with typical macromolecular systems. Thus, the design and validation of solid and efficient methods to simulate and analyze CD-based systems is key to contribute to this field. The behavior of supramolecular complexes critically depends on the media where they are embedded, so the detailed characterization of the solvent is required to fully understand these systems. In the present work, we use the inclusion complex formed by two α-CDs and one sodium dodecyl sulfate molecule to test eight different parameterizations of the GROMOS and AMBER force fields, including several methods aimed to increase the conformational sampling in computational molecular dynamics simulation trajectories. The system proved to be extremely sensitive to the employed force field, as well as to the presence of a water/air interface. In agreement with previous experiments and in contrast to the results obtained with AMBER, the analysis of the simulations using GROMOS showed a quick adsorption of the complex to the interface as well as an extremely exotic behavior of the water molecules surrounding the structure both in the bulk aqueous solution and at the water surface. The chirality of the CD molecule seems to play an important role in this behavior. All together, these results are expected to be useful to better understand the behavior of CD-based supramolecular complexes such as adsorption or aggregation driving forces, as well as to introduce new methods able to speed up general MD simulations.
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Affiliation(s)
- Pablo F. Garrido
- Departamento de Física de Aplicada, Facultade de Física, Universidade de Santiago de Compostela, E-15782 Santiago de Compostela, Spain;
| | - Martín Calvelo
- Departamento de Química Orgánica, Center for Research in Biological Chemistry and Molecular Materials, Universidade de Santiago de Compostela, Campus Vida s/n, E-15782 Santiago de Compostela, Spain;
| | - Rebeca Garcia-Fandiño
- Departamento de Química Orgánica, Center for Research in Biological Chemistry and Molecular Materials, Universidade de Santiago de Compostela, Campus Vida s/n, E-15782 Santiago de Compostela, Spain;
| | - Ángel Piñeiro
- Departamento de Física de Aplicada, Facultade de Física, Universidade de Santiago de Compostela, E-15782 Santiago de Compostela, Spain;
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23
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Guo Y, Werner M, Fleury JB, Baulin VA. Unexpected Cholesterol-Induced Destabilization of Lipid Membranes near Transmembrane Carbon Nanotubes. PHYSICAL REVIEW LETTERS 2020; 124:038001. [PMID: 32031854 DOI: 10.1103/physrevlett.124.038001] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/14/2019] [Indexed: 06/10/2023]
Abstract
Cholesterol is a crucial component of mammalian cell membranes that takes part in many vital processes. It is generally accepted that cholesterol stabilizes the membrane and induces transitions into ordered states. In contrast to expectations, we demonstrate that cholesterol can destabilize the membrane by creating a nanodomain around a perpendicularly embedded ultrashort carbon nanotube (CNT), and we show that cholesterol triggers the translocation of an ultrashort CNT through the cell membrane. Using atomistic simulations, we report the existence of a nanoscale domain around an ultrashort carbon nanotube within a crossover distance of 0.9 nm from the surface of the nanotube, where the properties of the bilayer are different from the bulk: the domain is characterized by increased fluctuations, increased thickness, and increased order of the lipids with respect to the bulk. Cholesterol decreases the thickness and order of lipids and increases the fluctuations with respect to a pure lipid bilayer. Experimentally, we confirm that cholesterol nanodomains provoke spontaneous translocation of nanotubes through a lipid bilayer even for low membrane tensions. A specially designed microfluidic device allows us to trace the kinetic pathway of the translocation process and establish the threshold cholesterol concentration of 20% for translocation. The reported nanoscale cholesterol-induced membrane restructuring near the ultrashort CNT in lipid membranes enables precise control and specific targeting of a membrane using cholesterol. As an example, it may allow for specific targeting between cholesterol-rich mammalian cells and cholesterol-poor bacterial cells.
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Affiliation(s)
- Yachong Guo
- Kuang Yaming Honors School, Nanjing University, Nanjing 210023, China
| | - Marco Werner
- Leibniz-Institut für Polymerforschung Dresden, Hohe Strasse 6, 01069 Dresden, Germany
| | - Jean Baptiste Fleury
- Universitat des Saarlandes, Experimental Physics and Center for Biophysics, 66123 Saarbruecken, Germany
| | - Vladimir A Baulin
- Departament d'Enginyeria Quimica, Universitat Rovira i Virgili, 26 Avinguda dels Paisos Catalans, 43007 Tarragona, Spain
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24
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Liu Y, Yang Y, Qu Y, Li YQ, Zhao M, Li W. Mild lipid extraction and anisotropic cell membrane penetration of α-phase phosphorene carbide nanoribbons by molecular dynamics simulation studies. Phys Chem Chem Phys 2020; 22:23268-23275. [DOI: 10.1039/d0cp04145a] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
α-PC penetrates the interior of membrane efficiently only along its zigzag direction rather than its armchair direction.
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Affiliation(s)
- Yang Liu
- School of Physics, State Key Laboratory of Crystal Materials
- Shandong University
- Jinan
- China
| | - Yanmei Yang
- College of Chemistry
- Chemical Engineering and Materials Science
- Collaborative Innovation Center of Functionalized Probes for Chemical Imaging in Universities of Shandong
- Key Laboratory of Molecular and Nano Probes, Ministry of Education
- Shandong Normal University
| | - Yuanyuan Qu
- School of Physics, State Key Laboratory of Crystal Materials
- Shandong University
- Jinan
- China
| | - Yong-Qiang Li
- School of Physics, State Key Laboratory of Crystal Materials
- Shandong University
- Jinan
- China
| | - Mingwen Zhao
- School of Physics, State Key Laboratory of Crystal Materials
- Shandong University
- Jinan
- China
| | - Weifeng Li
- School of Physics, State Key Laboratory of Crystal Materials
- Shandong University
- Jinan
- China
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25
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Liang L, Zhang Y, Kong Z, Liu F, Shen JW, He Z, Wang H. DNA fragment translocation through the lipid membrane assisted by carbon nanotube. Int J Pharm 2019; 574:118921. [PMID: 31812796 DOI: 10.1016/j.ijpharm.2019.118921] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2019] [Revised: 11/14/2019] [Accepted: 11/29/2019] [Indexed: 12/11/2022]
Abstract
DNA delivery through cell membrane is a fundamental step for efficiency gene therapy. As a potential DNA carrier, carbon nanotubes (CNTs) have been extensively studied due to its unique properties. However, the mechanism of DNA translocation with CNTs through cell membrane is still not well understood. In this study, the DNA translocation process through POPC (1-palmitoyl-2-oleoylphosphatidylcholine) membrane with the assistance of CNTs was explored by molecular dynamics (MD) simulation. Our simulation results demonstrated that the CNTs could insert steadily into the POPC membrane, and DNA molecules tends to insert into the inner space of CNTs. With the assistance of CNTs, the free energy of nucleotides passing through the POPC membrane decreases. Moreover, the free energy of nucleotides (DA (deoxyadenosine), DT (deoxythymidine), DC (deoxycytidine), and DG (deoxyguanosine)) passing through POPC membrane follows the order: DA (deoxyadenosine) > DG (deoxyguanosine) > DC (deoxycytidine) > DT (deoxythymidine). These results may promote the design and application of CNT-based gene delivery system.
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Affiliation(s)
- Lijun Liang
- College of Automation, College of Materials and Environmental Engineering, Hangzhou Dianzi University, Hangzhou 310018, People's Republic of China
| | - Yujin Zhang
- School of Electronic and Information Engineering (Department of Physics), Qilu University of Technology, Jinan, Shandong 250353, People's Republic of China
| | - Zhe Kong
- College of Automation, College of Materials and Environmental Engineering, Hangzhou Dianzi University, Hangzhou 310018, People's Republic of China
| | - Fei Liu
- College of Automation, College of Materials and Environmental Engineering, Hangzhou Dianzi University, Hangzhou 310018, People's Republic of China
| | - Jia-Wei Shen
- School of Medicine, Hangzhou Normal University, Hangzhou 311121, People's Republic of China.
| | - Zhiwei He
- College of Automation, College of Materials and Environmental Engineering, Hangzhou Dianzi University, Hangzhou 310018, People's Republic of China
| | - Hongbo Wang
- College of Automation, College of Materials and Environmental Engineering, Hangzhou Dianzi University, Hangzhou 310018, People's Republic of China.
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26
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Nangia S, Boyd KJ, May ER. Molecular dynamics study of membrane permeabilization by wild-type and mutant lytic peptides from the non-enveloped Flock House virus. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2019; 1862:183102. [PMID: 31678020 DOI: 10.1016/j.bbamem.2019.183102] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/27/2019] [Revised: 09/16/2019] [Accepted: 10/14/2019] [Indexed: 12/19/2022]
Abstract
Flock House virus (FHV) serves as a model system for understanding infection mechanisms utilized by non-enveloped viruses to transport across cellular membranes. During the infection cycle of FHV, a fundamental stage involves disruption of the endosomal membrane by membrane active peptides, following externalization of the peptides from the capsid interior. The FHV lytic agents are the 44 C-terminal amino acids residues of the capsid protein, which are auto-catalytically cleaved during the capsid maturation process. The cleaved peptides are termed γ peptides. In this study, we perform multi-scale molecular dynamics simulations including 40 μs all-atom molecular dynamics simulations to study the behavior of pre-inserted transmembrane lytic peptides at a high concentration in a neutral membrane. We study the dynamical organization among peptides to form oligomeric bundles in four systems including the wild-type γ peptide and three mutant forms; namely, a truncation mutant in which the 23 C-terminal residues are deleted (γ1), a construct where the 8 C-terminal residues of γ are fused to γ1 (Δ385-399 γ) and a single-point mutant (F402A γ), all of which have been experimentally shown to drastically affect infectivity and lytic activity compared to the wild-type γ. Our results shed light on the actions of varied forms of the FHV lytic peptide including membrane insertion, trans-membrane stability, peptide oligomerization, water permeation activity and dynamic pore formation. Findings from this study provide detailed structural information and rationale for the differences in lytic activity among variants of FHV γ.
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Affiliation(s)
- Shivangi Nangia
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, CT 06269, United States of America
| | - Kevin J Boyd
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, CT 06269, United States of America
| | - Eric R May
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, CT 06269, United States of America.
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27
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Liu Y, Vashisth H. Conformational dynamics and interfacial interactions of peptide-appended pillar[5]arene water channels in biomimetic membranes. Phys Chem Chem Phys 2019; 21:22711-22721. [PMID: 31454001 DOI: 10.1039/c9cp04408f] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Peptide appended pillar[5]arene (PAP) is an artificial water channel resembling biological water channel proteins, which has shown a significant potential for designing bioinspired water purification systems. Given that PAP channels need to be incorporated at a high density in membrane matrices, it is critical to examine the role of channel-channel and channel-membrane interactions in governing the structural and functional characteristics of channels. To resolve the atomic-scale details of these interactions, we have carried out atomistic molecular dynamics (MD) simulations of multiple PAP channels inserted in a lipid or a block-copolymer (BCP) membrane matrix. Classical MD simulations on a sub-microsecond timescale showed clustering of channels only in the lipid membrane, but enhanced sampling MD simulations showed thermodynamically-favorable dimerized states of channels in both lipid and BCP membranes. The dimerized configurations of channels, with an extensive buried surface area, were stabilized via interactions between the aromatic groups in the peptide arms of neighboring channels. The conformational metrics characterizing the orientational and structural changes in channels revealed a higher flexibility in the lipid membrane as opposed to the BCP membrane although hydrogen bonds between the channel and the membrane molecules were not a major contributor to the stability of channels in the BCP membrane. We also found that the channels undergo wetting/dewetting transitions in both lipid and BCP membranes with a marginally higher probability of undergoing a dewetting transition in the BCP membrane. Collectively, these results highlight the role of channel dynamics in governing channel-channel and channel-membrane interfacial interactions, and provide atomic-scale insights needed to design stable and functional biomimetic membranes for efficient separations.
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Affiliation(s)
- Yong Liu
- Department of Chemical Engineering, University of New Hampshire, 33 Academic Way, Durham, NH 03824, USA.
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28
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Pannuzzo M, Szała B, Raciti D, Raudino A, Ferrarini A. Helical Inclusions in Phospholipid Membranes: Lipid Adaptation and Chiral Order. J Phys Chem Lett 2019; 10:5629-5633. [PMID: 31487187 DOI: 10.1021/acs.jpclett.9b02252] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
The lipid bilayer is a flexible matrix that is able to adapt in response to the perturbation induced by inclusions, such as peptides and proteins. Here we use molecular dynamics simulations with a coarse-grained model to investigate the effect of a helical inclusion on a lipid bilayer in the liquid disordered phase. We show that the helical inclusion induces a collective tilt of acyl chains, with a small, yet unambiguous difference between a right- and a left-handed inclusion. This behavior is rationalized using the elastic continuum theory: The magnitude of the chiral (twist) deformation of the bilayer is determined by the interaction at the lipid/inclusion interface, and the decay length is controlled by the elastic properties of the bilayer. The lipid reorganization can thus be identified as a generic mechanism that, together with specific interactions, contributes to chiral recognition in phospholipid bilayers. An enhanced response is expected in highly ordered environments, such as rafts in biomembranes, with a potential impact on membrane-mediated interactions between inclusions.
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Affiliation(s)
- Martina Pannuzzo
- Laboratory of Nanotechnology for Precision Medicine , Fondazione Istituto Italiano di Tecnologia , via Morego, 30 , 16163 Genova , Italy
| | - Beata Szała
- Department of Chemical Sciences , University of Padova , via Marzolo 1 , 35131 Padova , Italy
- Faculty of Chemistry , Adam Mickiewicz University in Poznań , Umultowska 89b , 61-614 Poznań , Poland
| | - Domenica Raciti
- Department of Chemical Sciences , University of Catania , Viale A. Doria, 6 , 95125 Catania , Italy
| | - Antonio Raudino
- Department of Chemical Sciences , University of Catania , Viale A. Doria, 6 , 95125 Catania , Italy
| | - Alberta Ferrarini
- Department of Chemical Sciences , University of Padova , via Marzolo 1 , 35131 Padova , Italy
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29
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Wang Z, An HW, Hou D, Wang M, Zeng X, Zheng R, Wang L, Wang K, Wang H, Xu W. Addressable Peptide Self-Assembly on the Cancer Cell Membrane for Sensitizing Chemotherapy of Renal Cell Carcinoma. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2019; 31:e1807175. [PMID: 30663139 DOI: 10.1002/adma.201807175] [Citation(s) in RCA: 59] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/06/2018] [Revised: 01/02/2019] [Indexed: 05/06/2023]
Abstract
Chemotherapy has been validated unavailable for treatment of renal cell carcinoma (RCC) in clinic due to its intrinsic drug resistance. Sensitization of chemo-drug response plays a crucial role in RCC treatment and increase of patient survival. Herein, a recognition-reaction-aggregation (RRA) cascaded strategy is utilized to in situ construct peptide-based superstructures on the renal cancer cell membrane, enabling specifically perturbing the permeability of cell membranes and enhancing chemo-drug sensitivity in vitro and in vivo. First, P1-DBCO can specifically recognize renal cancer cells by targeting carbonic anhydrase IX. Subsequently, P2-N3 is introduced and efficiently reacts with P1-DBCO to form a peptide P3, which exhibits enhanced hydrophobicity and simultaneously aggregates into a superstructure. Interestingly, the superstructure retains on the cell membrane and perturbs its integrity/permeability, allowing more doxorubicin (DOX) uptaken by renal cancer cells. Owing to this increased influx, the IC50 is significantly reduced by nearly 3.5-fold compared with that treated with free DOX. Finally, RRA strategy significantly inhibits the tumor growth of xenografted mice with a 3.2-fold enhanced inhibition rate compared with that treated with free DOX. In summary, this newly developed RRA strategy will open a new avenue for chemically engineering cell membranes with diverse biomedical applications.
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Affiliation(s)
- Ziqi Wang
- Department of Urology, The Fourth Hospital of Harbin Medical University, Heilongjiang Key Laboratory of Scientific Research in Urology, Harbin, 150001, China
- CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety, CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology (NCNST), Beijing, 100190, China
| | - Hong-Wei An
- CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety, CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology (NCNST), Beijing, 100190, China
- CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety, Institute of High Energy Physics, Yuquan Road, Beijing, 100049, China
| | - Dayong Hou
- Department of Urology, The Fourth Hospital of Harbin Medical University, Heilongjiang Key Laboratory of Scientific Research in Urology, Harbin, 150001, China
- CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety, CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology (NCNST), Beijing, 100190, China
| | - Mandi Wang
- CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety, CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology (NCNST), Beijing, 100190, China
| | - Xiangzhong Zeng
- CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety, CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology (NCNST), Beijing, 100190, China
| | - Rui Zheng
- CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety, CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology (NCNST), Beijing, 100190, China
| | - Lu Wang
- Department of Urology, The Fourth Hospital of Harbin Medical University, Heilongjiang Key Laboratory of Scientific Research in Urology, Harbin, 150001, China
| | - Keliang Wang
- Department of Urology, The Fourth Hospital of Harbin Medical University, Heilongjiang Key Laboratory of Scientific Research in Urology, Harbin, 150001, China
| | - Hao Wang
- CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety, CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology (NCNST), Beijing, 100190, China
- Center of Materials Science and Optoelectronics Engineering, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Wanhai Xu
- Department of Urology, The Fourth Hospital of Harbin Medical University, Heilongjiang Key Laboratory of Scientific Research in Urology, Harbin, 150001, China
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30
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Song X, Guo H, Tao J, Zhao S, Han X, Liu H. Design of tunable-size 2D nanopore membranes from self-assembled amphiphilic nanosheets using dissipative particle dynamics simulations. Chem Eng Sci 2018. [DOI: 10.1016/j.ces.2018.05.023] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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31
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Zhang J, Li D, Yue X, Zhang M, Liu P, Li G. Colorimetric in situ assay of membrane-bound enzyme based on lipid bilayer inhibition of ion transport. Theranostics 2018; 8:3275-3283. [PMID: 29930729 PMCID: PMC6010988 DOI: 10.7150/thno.25123] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2018] [Accepted: 04/01/2018] [Indexed: 12/19/2022] Open
Abstract
Membrane-bound enzymes (MBEs), which make up a very high proportion of intracellular enzymes, catalyze a variety of activities that are currently analyzed by various techniques after purification. However, due to their amphipathic character, the purification of MBEs is difficult. Therefore, the most productive approach represents in situ analysis of MBEs in the cellular membrane. Methods: In this study, using membrane-bound α-glucosidase (α-Glu) as an example, we have developed a colorimetric in situ assay for MBEs based on the inhibitory effect of lipid bilayer on ion transport. The enzyme substrate could mediate the self-assembly of phospholipid PEG derivative around magnetic nanospheres that were modified with boronic acid. The formation of lipid bilayer could inhibit the leaking of iron ions under acidic conditions. However, the product of the catalytic reaction had no capability for self-assembly of the lipid bilayer, leading to the release of iron ions from the magnetic nanospheres under acidic pH. Results: The colorimetric in situ assay for MBEs could not only analyze the activity of membrane-bound α-Glu located on Caco-2 cells but could also evaluate the α-Glu inhibitors in cell medium. Conclusions: The simple, economic, and efficient method proposed here offers a potential application for high-throughput testing of α-Glu and its inhibitors. Our study also outlines a strategy for exploring the colorimetric method to detect the activities of MBEs in situ.
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Affiliation(s)
- Juan Zhang
- Center for Molecular Recognition and Biosensing, School of Life Sciences, Shanghai University, Shanghai 200444, P. R. China
| | - Defeng Li
- Center for Molecular Recognition and Biosensing, School of Life Sciences, Shanghai University, Shanghai 200444, P. R. China
- Shanghai Key Laboratory of Bio-Energy Crops, Shanghai University, Shanghai 200444, P. R. China
| | - Xiquan Yue
- Center for Molecular Recognition and Biosensing, School of Life Sciences, Shanghai University, Shanghai 200444, P. R. China
| | - Meiling Zhang
- Department of Oncology, the First Affiliated Hospital of Nanjing Medical University, Nanjing 210029, P. R. China
| | - Ping Liu
- Department of Oncology, the First Affiliated Hospital of Nanjing Medical University, Nanjing 210029, P. R. China
| | - Genxi Li
- Center for Molecular Recognition and Biosensing, School of Life Sciences, Shanghai University, Shanghai 200444, P. R. China
- State Key Laboratory of Pharmaceutical Biotechnology, Department of Biochemistry, Nanjing University, Nanjing 210093, P. R. China
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32
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Zhang Y, Tunuguntla RH, Choi PO, Noy A. Real-time dynamics of carbon nanotube porins in supported lipid membranes visualized by high-speed atomic force microscopy. Philos Trans R Soc Lond B Biol Sci 2018. [PMID: 28630162 DOI: 10.1098/rstb.2016.0226] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
In-plane mobility of proteins in lipid membranes is one of the fundamental mechanisms supporting biological functionality. Here we use high-speed atomic force microscopy (HS-AFM) to show that a novel type of biomimetic channel-carbon nanotube porins (CNTPs)-is also laterally mobile in supported lipid membranes, mimicking biological protein behaviour. HS-AFM can capture real-time dynamics of CNTP motion in the supported lipid bilayer membrane, build long-term trajectories of the CNTP motion and determine the diffusion coefficients associated with this motion. Our analysis shows that diffusion coefficients of CNTPs fall into the same range as those of proteins in supported lipid membranes. CNTPs in HS-AFM experiments often exhibit 'directed' diffusion behaviour, which is common for proteins in live cell membranes.This article is part of the themed issue 'Membrane pores: from structure and assembly, to medicine and technology'.
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Affiliation(s)
- Yuliang Zhang
- Biology and Biotechnology Division, Physics and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA 94550, USA
| | - Ramya H Tunuguntla
- Biology and Biotechnology Division, Physics and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA 94550, USA
| | - Pyung-On Choi
- Biology and Biotechnology Division, Physics and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA 94550, USA
| | - Aleksandr Noy
- Biology and Biotechnology Division, Physics and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA 94550, USA .,School of Natural Sciences, University of California Merced, Merced, CA 95343, USA
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33
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Shearer J, Khalid S. Communication between the leaflets of asymmetric membranes revealed from coarse-grain molecular dynamics simulations. Sci Rep 2018; 8:1805. [PMID: 29379141 PMCID: PMC5789016 DOI: 10.1038/s41598-018-20227-1] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2017] [Accepted: 01/04/2018] [Indexed: 01/09/2023] Open
Abstract
We use coarse-grain molecular simulations to investigate the structural and dynamics differences between an asymmetric and a symmetrical membrane, both containing beta barrel transmembrane proteins. We find in where the dynamics of the two leaflets differ greatly, the slowest leaflet dominates the structural effects and importance of protein-lipid interactions.
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Affiliation(s)
- Jonathan Shearer
- University of Southampton, Southampton, SO17 1BJ, United Kingdom
| | - Syma Khalid
- University of Southampton, Southampton, SO17 1BJ, United Kingdom.
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34
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Otero-Mato JM, Montes-Campos H, Calvelo M, García-Fandiño R, Gallego LJ, Piñeiro Á, Varela LM. GADDLE Maps: General Algorithm for Discrete Object Deformations Based on Local Exchange Maps. J Chem Theory Comput 2018; 14:466-478. [DOI: 10.1021/acs.jctc.7b00861] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Affiliation(s)
- J. Manuel Otero-Mato
- Nanomaterials,
Photonics and Soft Matter Group, Departamento de Física de
Partículas y Departamento de Física Aplicada, Facultade
de Física, Universidade de Santiago de Compostela, Campus Vida s/n, E-15782 Santiago de Compostela, Spain
| | - Hadrián Montes-Campos
- Nanomaterials,
Photonics and Soft Matter Group, Departamento de Física de
Partículas y Departamento de Física Aplicada, Facultade
de Física, Universidade de Santiago de Compostela, Campus Vida s/n, E-15782 Santiago de Compostela, Spain
| | - Martín Calvelo
- Department
of Organic Chemistry, Center for Research in Biological Chemistry
and Molecular Materials, University of Santiago de Compostela, Campus
Vida s/n, E-15782 Santiago de Compostela, Spain
| | - Rebeca García-Fandiño
- CIQUP,
Department of Chemistry and Biochemistry, Faculty of Sciences, University of Porto, R. Campo alegre, 687, P-4169-007 Porto, Portugal
| | - Luis J. Gallego
- Nanomaterials,
Photonics and Soft Matter Group, Departamento de Física de
Partículas y Departamento de Física Aplicada, Facultade
de Física, Universidade de Santiago de Compostela, Campus Vida s/n, E-15782 Santiago de Compostela, Spain
| | - Ángel Piñeiro
- Soft
Matter and Molecular Biophysics Group, Departamento de Física
Aplicada, Facultade de Física, Universidade de Santiago de Compostela, Campus Vida s/n, E-15782 Santiago de Compostela, Spain
| | - Luis M. Varela
- Nanomaterials,
Photonics and Soft Matter Group, Departamento de Física de
Partículas y Departamento de Física Aplicada, Facultade
de Física, Universidade de Santiago de Compostela, Campus Vida s/n, E-15782 Santiago de Compostela, Spain
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35
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Vögele M, Köfinger J, Hummer G. Molecular dynamics simulations of carbon nanotube porins in lipid bilayers. Faraday Discuss 2018; 209:341-358. [DOI: 10.1039/c8fd00011e] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
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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36
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Park S, Lansac Y, Jang YH. Sub-nanometer pore formation in single-molecule-thick polyurea molecular-sieving membrane: a computational study. Phys Chem Chem Phys 2018; 20:16463-16468. [DOI: 10.1039/c8cp01580e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The surprisingly narrow sub-nm-pore-size distribution and urea-versus-glucose selectivity of a single-molecule-thick polyurea membrane are explained by Monte Carlo simulations on simple molecular models.
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Affiliation(s)
- Seongjin Park
- Department of Energy Science and Engineering
- DGIST
- Daegu 42988
- Korea
| | - Yves Lansac
- GREMAN
- UMR 7347
- CNRS
- Université de Tours
- 37200 Tours
| | - Yun Hee Jang
- Department of Energy Science and Engineering
- DGIST
- Daegu 42988
- Korea
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37
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Zhang Y, Li Z, Chan C, Ma J, Zhi C, Cheng X, Fan J. Ordering of lipid membranes altered by boron nitride nanosheets. Phys Chem Chem Phys 2018; 20:3903-3910. [DOI: 10.1039/c7cp07136a] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
Boron nitride nanosheets are novel promising nanomaterials with a lower cytotoxicity than graphene making them a better candidate for biomedical applications.
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Affiliation(s)
- Yonghui Zhang
- Department of Materials Science and Engineering
- City University of Hong Kong
- Hong Kong
- China
| | - Zhen Li
- Department of Materials Science and Engineering
- City University of Hong Kong
- Hong Kong
- China
| | - Chun Chan
- Department of Materials Science and Engineering
- City University of Hong Kong
- Hong Kong
- China
| | - Jiale Ma
- Department of Materials Science and Engineering
- City University of Hong Kong
- Hong Kong
- China
| | - Chunyi Zhi
- Department of Materials Science and Engineering
- City University of Hong Kong
- Hong Kong
- China
| | - Xiaolin Cheng
- Division of Medicinal Chemistry and Pharmacognosy
- College of Pharmacy
- The Ohio State University
- Columbus
- USA
| | - Jun Fan
- Department of Materials Science and Engineering
- City University of Hong Kong
- Hong Kong
- China
- Center for Advanced Nuclear Safety and Sustainable Development
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38
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Fu Y, Yan T, Xu X. Insight of Transmembrane Processes of Self-Assembling Nanotubes Based on a Cyclic Peptide Using Coarse Grained Molecular Dynamics Simulation. J Phys Chem B 2017; 121:9006-9012. [PMID: 28872323 DOI: 10.1021/acs.jpcb.7b05948] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Transmembrane self-assembling cyclic peptide (SCP) nanotubes are promising candidates for delivering specific molecules through cell membranes. The detailed mechanisms behind the transmembrane processes, as well as stabilization factors of transmembrane structures, are difficult to elucidate through experiments. In this study, the effects of peptide sequence and oligomeric state on the transmembrane capabilities of SCP nanotubes and the perturbation of embedded SCP nanotubes acting on the membrane were investigated based on coarse grained molecular dynamics simulation. The simulation results reveal that hydrophilic SCP oligomers result in the elevation of the energy barrier while the oligomerization of hydrophobic SCPs causes the reduction of the energy barrier, further leading to membrane insertion. Once SCP nanotubes are embedded, membrane properties such as density, thickness, ordering state and lateral mobility are adjusted along the radial direction. This study provides insight into the transmembrane strategy of SCP nanotubes and sheds light on designing novel transport systems.
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Affiliation(s)
- Yankai Fu
- State Key Laboratory of Biochemical Engineering, Institute of Process Engineering, Chinese Academy of Sciences , Beijing 100190, P.R. China
- University of Chinese Academy of Sciences , Beijing 100049, P.R. China
| | - Tingxuan Yan
- School of Chemistry and Chemical Engineering, Anhui University of Technology , Ma'anshan, Anhui 243002, P.R. China
| | - Xia Xu
- School of Chemistry and Chemical Engineering, Anhui University of Technology , Ma'anshan, Anhui 243002, P.R. China
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39
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Yousefpour A, Modarress H, Goharpey F, Amjad-Iranagh S. Combination of anti-hypertensive drugs: a molecular dynamics simulation study. J Mol Model 2017; 23:158. [DOI: 10.1007/s00894-017-3333-9] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2016] [Accepted: 03/27/2017] [Indexed: 01/03/2023]
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40
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Yue T, Xu Y, Li S, Luo Z, Zhang X, Huang F. Ultrashort Single-Walled Carbon Nanotubes Insert into a Pulmonary Surfactant Monolayer via Self-Rotation: Poration and Mechanical Inhibition. J Phys Chem B 2017; 121:2797-2807. [DOI: 10.1021/acs.jpcb.7b00297] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
| | | | | | | | - Xianren Zhang
- State Key Laboratory of Organic-Inorganic
Composites, Beijing University of Chemical Technology, Beijing 100029, China
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