1
|
Wang J, Li Z. Electric field modulated configuration and orientation of aqueous molecule chains. J Chem Phys 2024; 161:094305. [PMID: 39230558 DOI: 10.1063/5.0222122] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2024] [Accepted: 08/22/2024] [Indexed: 09/05/2024] Open
Abstract
Understanding how external electric fields (EFs) impact the properties of aqueous molecules is crucial for various applications in chemistry, biology, and engineering. In this paper, we present a study utilizing molecular dynamics simulation to explore how direct-current (DC) and alternative-current (AC) EFs affect hydrophobic (n-triacontane) and hydrophilic (PEG-10) oligomer chains. Through a machine learning approach, we extract a 2-dimensional free energy (FE) landscape of these molecules, revealing that electric fields modulate the FE landscape to favor stretched configurations and enhance the alignment of the chain with the electric field. Our observations indicate that DC EFs have a more prominent impact on modulation compared to AC EFs and that EFs have a stronger effect on hydrophobic chains than on hydrophilic oligomers. We analyze the orientation of water dipole moments and hydrogen bonds, finding that EFs align water molecules and induce more directional hydrogen bond networks, forming 1D water structures. This favors the stretched configuration and alignment of the studied oligomers simultaneously, as it minimizes the disruption of 1D structures. This research deepens our understanding of the mechanisms by which electric fields modulate molecular properties and could guide the broader application of EFs to control other aqueous molecules, such as proteins or biomolecules.
Collapse
Affiliation(s)
- Jiang Wang
- College of Science, Guizhou Institute of Technology, Boshi Road, Dangwu Town, Gui'an New District, Guizhou 550025, China
| | - Zhiling Li
- College of Science, Guizhou Institute of Technology, Boshi Road, Dangwu Town, Gui'an New District, Guizhou 550025, China
| |
Collapse
|
2
|
Borges-Araújo L, Borges-Araújo AC, Ozturk TN, Ramirez-Echemendia DP, Fábián B, Carpenter TS, Thallmair S, Barnoud J, Ingólfsson HI, Hummer G, Tieleman DP, Marrink SJ, Souza PCT, Melo MN. Martini 3 Coarse-Grained Force Field for Cholesterol. J Chem Theory Comput 2023; 19:7387-7404. [PMID: 37796943 DOI: 10.1021/acs.jctc.3c00547] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/07/2023]
Abstract
Cholesterol plays a crucial role in biomembranes by regulating various properties, such as fluidity, rigidity, permeability, and organization of lipid bilayers. The latest version of the Martini model, Martini 3, offers significant improvements in interaction balance, molecular packing, and inclusion of new bead types and sizes. However, the release of the new model resulted in the need to reparameterize many core molecules, including cholesterol. Here, we describe the development and validation of a Martini 3 cholesterol model, addressing issues related to its bonded setup, shape, volume, and hydrophobicity. The proposed model mitigates some limitations of its Martini 2 predecessor while maintaining or improving the overall behavior.
Collapse
Affiliation(s)
- Luís Borges-Araújo
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av. da República, 2780-157 Oeiras, Portugal
- Molecular Microbiology and Structural Biochemistry, UMR 5086 CNRS & University of Lyon, 7 Passage du Vercors, Lyon F-69367, France
| | - Ana C Borges-Araújo
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av. da República, 2780-157 Oeiras, Portugal
| | - Tugba Nur Ozturk
- Physical and Life Sciences (PLS) Directorate, Lawrence Livermore National Laboratory, Livermore, California 94550, United States
| | - Daniel P Ramirez-Echemendia
- Centre for Molecular Simulation and Department of Biological Sciences, University of Calgary, Calgary, Alberta, Canada, T2N 1N4
| | - Balázs Fábián
- Department of Theoretical Biophysics, Max Planck Institute of Biophysics, Max-von-Laue Straße 3, 60438 Frankfurt am Main, Germany
| | - Timothy S Carpenter
- Physical and Life Sciences (PLS) Directorate, Lawrence Livermore National Laboratory, Livermore, California 94550, United States
| | - Sebastian Thallmair
- Frankfurt Institute for Advanced Studies, Ruth-Moufang-Straße 1, 60438 Frankfurt am Main, Germany
| | - Jonathan Barnoud
- Centre for Computational Chemistry, School of Chemistry, University of Bristol, Cantock's Close, Bristol BS8 1TS, U.K
- CiTIUS Intelligent Technologies Research Centre, University of Santiago de Compostela, Rúa de Jenaro de la Fuente, 15705 Santiago de Compostela, Spain
| | - Helgi I Ingólfsson
- Physical and Life Sciences (PLS) Directorate, Lawrence Livermore National Laboratory, Livermore, California 94550, United States
| | - Gerhard Hummer
- Department of Theoretical Biophysics, Max Planck Institute of Biophysics, Max-von-Laue Straße 3, 60438 Frankfurt am Main, Germany
- Institute of Biophysics, Goethe University Frankfurt, 60438 Frankfurt am Main, Germany
| | - D Peter Tieleman
- Centre for Molecular Simulation and Department of Biological Sciences, University of Calgary, Calgary, Alberta, Canada, T2N 1N4
| | - Siewert J Marrink
- Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Nijenborgh 7, 9747 AG Groningen, The Netherlands
| | - Paulo C T Souza
- Molecular Microbiology and Structural Biochemistry, UMR 5086 CNRS & University of Lyon, 7 Passage du Vercors, Lyon F-69367, France
| | - Manuel N Melo
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av. da República, 2780-157 Oeiras, Portugal
| |
Collapse
|
3
|
Higuchi Y, Bohinc K, Reščič J, Shimokawa N, Ito H. Coarse-grained molecular dynamics simulation of cation distribution profiles on negatively charged lipid membranes during phase separation. SOFT MATTER 2023; 19:3640-3651. [PMID: 37162535 DOI: 10.1039/d3sm00222e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
Revealing the ion distributions on a charged lipid membrane in aqueous solution under the influence of long-range interactions is essential for understanding the origin of the stability of the bilayer structure and the interaction between biomembranes and various electrolytes. However, the ion distributions and their dynamics associated with the phase separation process of the lipid bilayer membrane are still unclear. We perform coarse-grained molecular dynamics simulations to reveal the Na+ and Cl- distributions on charged phospholipid bilayer membranes during phase separation. During the phase separation, cations closely follow the position of negatively charged lipids on a microsecond timescale and are rapidly redistributed parallel to the lipid bilayer. In the homogenous mixture of zwitterionic and negatively charged lipids, cations weakly follow negatively charged lipids, indicating the strong interaction between cations and negatively charged lipids. We also compare cation concentrations as a function of surface charge density obtained by our simulation with those obtained by a modified Poisson-Boltzmann theory. Including the ion finite size makes the statistical results consistent, suggesting the importance of the ion-ion interactions in aqueous solution. Our simulation results advance our understanding of ion distribution during phase separation.
Collapse
Affiliation(s)
- Yuji Higuchi
- Research Institute for Information Technology, Kyushu University, 744 Motooka, Nishi-ku, Fukuoka, 819-0395, Japan.
| | - Klemen Bohinc
- Faculty of Health Sciences, University of Ljubljana, Zdravstvena 5, SI 1000 Ljubljana, Slovenia
| | - Jurij Reščič
- Faculty of Chemistry and Chemical Technology, University of Ljubljana, Vecna pot 113, 1000 Ljubljana, Slovenia
| | - Naofumi Shimokawa
- School of Materials Science, Japan Advanced Institute of Science and Technology, Ishikawa 923-1292, Japan
| | - Hiroaki Ito
- Department of Physics, Graduate School of Science, Chiba University, Chiba 263-8522, Japan
| |
Collapse
|
4
|
A simple approach to re-engineering small extracellular vesicles to circumvent endosome entrapment. Int J Pharm 2022; 626:122153. [PMID: 36055444 DOI: 10.1016/j.ijpharm.2022.122153] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2022] [Revised: 08/15/2022] [Accepted: 08/26/2022] [Indexed: 11/22/2022]
Abstract
Small extracellular vesicles (sEVs) have emerged as attractive drug delivery systems. However, the intracellular release of their cargoes is restricted. This study aimed to develop an efficient approach to re-engineer sEVs by hybridisation with pH-sensitive liposomes (PSLs) and investigate their endosome escape potential. MIA PaCa-2 cell-derived sEVs and PSLs were fused via three methods, and fusion efficiency (FE) was measured using a fluorescence resonance energy transfer assay and nanoparticle tracking analysis. Cellular uptake, intracellular trafficking, and cytotoxicity of doxorubicin-loaded vesicles (Dox@hybrids, Dox@sEVs, and Dox@PSLs) were investigated on MIA PaCa-2 cells. Among the three methods, Ca2+-mediated fusion was the simplest and led to a comparable FE with freeze-thaw method, which was significantly higher than PEG8000-mediated fusion. sEVs were more stable after hybridisation with PSLs. Confocal microscopy revealed that the hybrids internalised more efficiently than natural sEVs. While the internalised Dox@sEVs were primarily co-localised with endo/lysosomes even after 8 h, Dox from Dox@hybrids was found to escape from endosomes by 2 h and homogenously distributed in the cytosol before accumulated at nucleus, corresponding to the in vitro pH-responsive release profile. Consequently, Dox@hybrids enhanced cytotoxicity compared with Dox@sEVs, Dox@PSLs, or free drugs. Overall, the biomimetic nanosystem generated by simple Ca2+-mediated fusion was more stable and demonstrated higher efficiencies of cellular uptake and endosome escape compared to natural sEVs.
Collapse
|
5
|
Marrink SJ, Monticelli L, Melo MN, Alessandri R, Tieleman DP, Souza PCT. Two decades of Martini: Better beads, broader scope. WIRES COMPUTATIONAL MOLECULAR SCIENCE 2022. [DOI: 10.1002/wcms.1620] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Siewert J. Marrink
- Groningen Biomolecular Sciences and Biotechnology Institute & Zernike Institute for Advanced Materials University of Groningen Groningen The Netherlands
| | - Luca Monticelli
- Molecular Microbiology and Structural Biochemistry (MMSB ‐ UMR 5086) CNRS & University of Lyon Lyon France
| | - Manuel N. Melo
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa Oeiras Portugal
| | - Riccardo Alessandri
- Pritzker School of Molecular Engineering University of Chicago Chicago Illinois USA
| | - D. Peter Tieleman
- Centre for Molecular Simulation and Department of Biological Sciences University of Calgary Alberta Canada
| | - Paulo C. T. Souza
- Molecular Microbiology and Structural Biochemistry (MMSB ‐ UMR 5086) CNRS & University of Lyon Lyon France
| |
Collapse
|
6
|
Lavagna E, Bochicchio D, De Marco AL, Güven ZP, Stellacci F, Rossi G. Ion-bridges and lipids drive aggregation of same-charge nanoparticles on lipid membranes. NANOSCALE 2022; 14:6912-6921. [PMID: 35451442 PMCID: PMC9109710 DOI: 10.1039/d1nr08543c] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/31/2021] [Accepted: 02/14/2022] [Indexed: 05/19/2023]
Abstract
The control of the aggregation of biomedical nanoparticles (NP) in physiological conditions is crucial as clustering may change completely the way they interact with the biological environment. Here we show that Au nanoparticles, functionalized by an anionic, amphiphilic shell, spontaneously aggregate in fluid zwitterionic lipid bilayers. We use molecular dynamics and enhanced sampling techniques to disentangle the short-range and long-range driving forces of aggregation. At short inter-particle distances, ion-mediated, charge-charge interactions (ion bridging) stabilize the formation of large NP aggregates, as confirmed by cryo-electron microscopy. Lipid depletion and membrane curvature are the main membrane deformations driving long-range NP-NP attraction. Ion bridging, lipid depletion, and membrane curvature stem from the configurational flexibility of the nanoparticle shell. Our simulations show, more in general, that the aggregation of same-charge membrane inclusions can be expected as a result of intrinsically nanoscale effects taking place at the NP-NP and NP-bilayer soft interfaces.
Collapse
Affiliation(s)
- Enrico Lavagna
- Physics Department, University of Genoa, Via Dodecaneso 33, 16146 Genoa, Italy. rossig.@fisica.unige.it
| | - Davide Bochicchio
- Physics Department, University of Genoa, Via Dodecaneso 33, 16146 Genoa, Italy. rossig.@fisica.unige.it
| | - Anna L De Marco
- Physics Department, University of Genoa, Via Dodecaneso 33, 16146 Genoa, Italy. rossig.@fisica.unige.it
| | - Zekiye P Güven
- Institute of Materials, École Polytechnique Fédérale de Lausanne, 1015 Lausanne, Switzerland
| | - Francesco Stellacci
- Institute of Materials, École Polytechnique Fédérale de Lausanne, 1015 Lausanne, Switzerland
- Bioengineering Institute, École Polytechnique Fédérale de Lausanne, 1015 Lausanne, Switzerland
| | - Giulia Rossi
- Physics Department, University of Genoa, Via Dodecaneso 33, 16146 Genoa, Italy. rossig.@fisica.unige.it
| |
Collapse
|
7
|
Prakash S, Krishna A, Sengupta D. Caveolin induced membrane curvature and lipid clustering: two sides of the same coin? Faraday Discuss 2021; 232:218-235. [PMID: 34545870 DOI: 10.1039/d0fd00062k] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Caveolin-1 (cav-1) is a multi-domain membrane protein that is a key player in cell signaling, endocytosis and mechanoprotection. It is the principle component of cholesterol-rich caveolar domains and has been reported to induce membrane curvature. The molecular mechanisms underlying the interactions of cav-1 with complex membranes, leading to modulation of membrane topology and the formation of cholesterol-rich domains, remain elusive. In this study, we aim to understand the effect of lipid composition by analyzing the interactions of cav-1 with complex membrane bilayers comprised of about sixty lipid types. We have performed a series of coarse-grain molecular dynamics simulations using the Martini force-field with a cav-1 protein construct (residue 82-136) that includes the membrane binding domains and a palmitoyl tail. We observe that cav-1 induces curvature in this complex membrane, though it is restricted to a nanometer length scale. Concurrently, we observe a clustering of cholesterol, sphingolipids and other lipid molecules leading to the formation of nanodomains. Direct microsecond timescale interactions are observed for specific lipids such as cholesterol, phosphatidylserine and phosphatidylethanolamine lipid types. The results indicate that there is an interplay between membrane topology and lipid species. Our work is a step toward understanding how lipid composition and organization regulate the formation of caveolae, in the context of endocytosis and cell signaling.
Collapse
Affiliation(s)
- Shikha Prakash
- National Chemical Laboratory, Council of Scientific and Industrial Research, Dr. Homi Bhabha Road, Pune 411008, India.
| | - Anjali Krishna
- National Chemical Laboratory, Council of Scientific and Industrial Research, Dr. Homi Bhabha Road, Pune 411008, India.
| | - Durba Sengupta
- National Chemical Laboratory, Council of Scientific and Industrial Research, Dr. Homi Bhabha Road, Pune 411008, India.
| |
Collapse
|
8
|
Schlich M, Palomba R, Costabile G, Mizrahy S, Pannuzzo M, Peer D, Decuzzi P. Cytosolic delivery of nucleic acids: The case of ionizable lipid nanoparticles. Bioeng Transl Med 2021; 6:e10213. [PMID: 33786376 PMCID: PMC7995196 DOI: 10.1002/btm2.10213] [Citation(s) in RCA: 138] [Impact Index Per Article: 46.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2020] [Revised: 01/22/2021] [Accepted: 01/25/2021] [Indexed: 12/14/2022] Open
Abstract
Ionizable lipid nanoparticles (LNPs) are the most clinically advanced nano-delivery system for therapeutic nucleic acids. The great effort put in the development of ionizable lipids with increased in vivo potency brought LNPs from the laboratory benches to the FDA approval of patisiran in 2018 and the ongoing clinical trials for mRNA-based vaccines against SARS-CoV-2. Despite these success stories, several challenges remain in RNA delivery, including what is known as "endosomal escape." Reaching the cytosol is mandatory for unleashing the therapeutic activity of RNA molecules, as their accumulation in other intracellular compartments would simply result in efficacy loss. In LNPs, the ability of ionizable lipids to form destabilizing non-bilayer structures at acidic pH is recognized as the key for endosomal escape and RNA cytosolic delivery. This is motivating a surge in studies aiming at designing novel ionizable lipids with improved biodegradation and safety profiles. In this work, we describe the journey of RNA-loaded LNPs across multiple intracellular barriers, from the extracellular space to the cytosol. In silico molecular dynamics modeling, in vitro high-resolution microscopy analyses, and in vivo imaging data are systematically reviewed to distill out the regulating mechanisms underlying the endosomal escape of RNA. Finally, a comparison with strategies employed by enveloped viruses to deliver their genetic material into cells is also presented. The combination of a multidisciplinary analytical toolkit for endosomal escape quantification and a nature-inspired design could foster the development of future LNPs with improved cytosolic delivery of nucleic acids.
Collapse
Affiliation(s)
- Michele Schlich
- Fondazione Istituto Italiano di TecnologiaLaboratory of Nanotechnology for Precision MedicineGenoaItaly
- Department of Life and Environmental SciencesUniversity of CagliariCagliariItaly
| | - Roberto Palomba
- Fondazione Istituto Italiano di TecnologiaLaboratory of Nanotechnology for Precision MedicineGenoaItaly
| | - Gabriella Costabile
- Fondazione Istituto Italiano di TecnologiaLaboratory of Nanotechnology for Precision MedicineGenoaItaly
| | - Shoshy Mizrahy
- Fondazione Istituto Italiano di TecnologiaLaboratory of Nanotechnology for Precision MedicineGenoaItaly
- Laboratory of Precision NanoMedicine, Shmunis School of Biomedicine and Cancer Research, George S. Wise Faculty of Life SciencesTel Aviv UniversityTel AvivIsrael
- Department of Materials Sciences and Engineering, Iby and Aladar Fleischman Faculty of EngineeringTel Aviv UniversityTel AvivIsrael
- Center for Nanoscience and NanotechnologyTel Aviv UniversityTel AvivIsrael
- Cancer Biology Research CenterTel Aviv UniversityTel AvivIsrael
| | - Martina Pannuzzo
- Fondazione Istituto Italiano di TecnologiaLaboratory of Nanotechnology for Precision MedicineGenoaItaly
| | - Dan Peer
- Laboratory of Precision NanoMedicine, Shmunis School of Biomedicine and Cancer Research, George S. Wise Faculty of Life SciencesTel Aviv UniversityTel AvivIsrael
- Department of Materials Sciences and Engineering, Iby and Aladar Fleischman Faculty of EngineeringTel Aviv UniversityTel AvivIsrael
- Center for Nanoscience and NanotechnologyTel Aviv UniversityTel AvivIsrael
- Cancer Biology Research CenterTel Aviv UniversityTel AvivIsrael
| | - Paolo Decuzzi
- Fondazione Istituto Italiano di TecnologiaLaboratory of Nanotechnology for Precision MedicineGenoaItaly
| |
Collapse
|
9
|
Chan C, Du S, Dong Y, Cheng X. Computational and Experimental Approaches to Investigate Lipid Nanoparticles as Drug and Gene Delivery Systems. Curr Top Med Chem 2021; 21:92-114. [PMID: 33243123 PMCID: PMC8191596 DOI: 10.2174/1568026620666201126162945] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2020] [Revised: 10/16/2020] [Accepted: 10/22/2020] [Indexed: 02/06/2023]
Abstract
Lipid nanoparticles (LNPs) have been widely applied in drug and gene delivery. More than twenty years ago, DoxilTM was the first LNPs-based drug approved by the US Food and Drug Administration (FDA). Since then, with decades of research and development, more and more LNP-based therapeutics have been used to treat diverse diseases, which often offer the benefits of reduced toxicity and/or enhanced efficacy compared to the active ingredients alone. Here, we provide a review of recent advances in the development of efficient and robust LNPs for drug/gene delivery. We emphasize the importance of rationally combining experimental and computational approaches, especially those providing multiscale structural and functional information of LNPs, to the design of novel and powerful LNP-based delivery systems.
Collapse
Affiliation(s)
- Chun Chan
- Division of Medicinal Chemistry and Pharmacognosy, College of Pharmacy, The Ohio State University, Columbus, OH 43210, USA
| | - Shi Du
- Division of Pharmaceutics and Pharmacology, College of Pharmacy, The Ohio State University, Columbus, OH 43210, USA
| | - Yizhou Dong
- Division of Pharmaceutics and Pharmacology, College of Pharmacy, The Ohio State University, Columbus, OH 43210, USA
- Department of Biomedical Engineering; The Center for Clinical and Translational Science; The Comprehensive Cancer Center; Dorothy M. Davis Heart & Lung Research Institute; Department of Radiation Oncology, The Ohio State University, Columbus, OH 43210, USA
| | - Xiaolin Cheng
- Division of Medicinal Chemistry and Pharmacognosy, College of Pharmacy, The Ohio State University, Columbus, OH 43210, USA
- Biophysics Graduate Program, Translational Data Analytics Institute, The Ohio State University, Columbus, OH 43210, USA
| |
Collapse
|
10
|
Light-induced lipid mixing implies a causal role of lipid splay in membrane fusion. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2020; 1862:183438. [PMID: 32781156 DOI: 10.1016/j.bbamem.2020.183438] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/15/2020] [Revised: 07/31/2020] [Accepted: 07/31/2020] [Indexed: 11/23/2022]
Abstract
The fusion of lipid membranes is central to many biological processes and requires substantial structural reorganization of lipids brought about by the action of fusogenic proteins. Previous molecular dynamics simulations have suggested that splayed lipids, whose tails transiently contact the headgroup region of the bilayer, initiate lipid mixing. Here, we explore the lipid splay hypothesis experimentally. We show that the light-induced trans/cis conversion of the azobenzene-based tail of a model lipid molecule enhances the probability by which its own acyl chains, or the acyl chains of the host lipid, transiently contact the lipid headgroup in a liposomal bilayer. At the same time, the trans/cis conversion triggers lipid mixing of sonicated or extruded liposomes, without requiring fusogenic proteins. This establishes a causal relationship between lipid splay and membrane fusion.
Collapse
|
11
|
Komorowski K, Schaeper J, Sztucki M, Sharpnack L, Brehm G, Köster S, Salditt T. Vesicle adhesion in the electrostatic strong-coupling regime studied by time-resolved small-angle X-ray scattering. SOFT MATTER 2020; 16:4142-4154. [PMID: 32319505 DOI: 10.1039/d0sm00259c] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
We have used time-resolved small-angle X-ray scattering (SAXS) to study the adhesion of lipid vesicles in the electrostatic strong-coupling regime induced by divalent ions. The bilayer structure and the interbilayer distance dw between adhered vesicles was studied for different DOPC:DOPS mixtures varying the surface charge density of the membrane, as well as for different divalent ions, such as Ca2+, Sr2+, and Zn2+. The results are in good agreement with the strong coupling theory predicting the adhesion state and the corresponding like-charge attraction based on ion-correlations. Using SAXS combined with the stopped-flow rapid mixing technique, we find that in highly charged bilayers the adhesion state is only of transient nature, and that the adhering vesicles subsequently transform to a phase of multilamellar vesicles, again with an inter-bilayer distance according to the theory of strong binding. Aside from the stopped-flow SAXS instrumentations used primarily for these results, we also evaluate microfluidic sample environments for vesicle SAXS in view of future extension of this work.
Collapse
Affiliation(s)
- Karlo Komorowski
- Institute for X-Ray Physics, University of Göttingen, Friedrich-Hund-Platz 1, 37077 Göttingen, Germany.
| | - Jannis Schaeper
- Institute for X-Ray Physics, University of Göttingen, Friedrich-Hund-Platz 1, 37077 Göttingen, Germany.
| | - Michael Sztucki
- European Synchrotron Radiation Facility, CS 40220, 38043 Grenoble Cedex 9, France
| | - Lewis Sharpnack
- European Synchrotron Radiation Facility, CS 40220, 38043 Grenoble Cedex 9, France
| | - Gerrit Brehm
- Institute for X-Ray Physics, University of Göttingen, Friedrich-Hund-Platz 1, 37077 Göttingen, Germany.
| | - Sarah Köster
- Institute for X-Ray Physics, University of Göttingen, Friedrich-Hund-Platz 1, 37077 Göttingen, Germany.
| | - Tim Salditt
- Institute for X-Ray Physics, University of Göttingen, Friedrich-Hund-Platz 1, 37077 Göttingen, Germany.
| |
Collapse
|
12
|
Bruininks BM, Souza PC, Ingolfsson H, Marrink SJ. A molecular view on the escape of lipoplexed DNA from the endosome. eLife 2020; 9:52012. [PMID: 32297853 PMCID: PMC7170654 DOI: 10.7554/elife.52012] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2019] [Accepted: 02/24/2020] [Indexed: 12/23/2022] Open
Abstract
The use of non-viral vectors for in vivo gene therapy could drastically increase safety, whilst reducing the cost of preparing the vectors. A promising approach to non-viral vectors makes use of DNA/cationic liposome complexes (lipoplexes) to deliver the genetic material. Here we use coarse-grained molecular dynamics simulations to investigate the molecular mechanism underlying efficient DNA transfer from lipoplexes. Our computational fusion experiments of lipoplexes with endosomal membrane models show two distinct modes of transfection: parallel and perpendicular. In the parallel fusion pathway, DNA aligns with the membrane surface, showing very quick release of genetic material shortly after the initial fusion pore is formed. The perpendicular pathway also leads to transfection, but release is slower. We further show that the composition and size of the lipoplex, as well as the lipid composition of the endosomal membrane, have a significant impact on fusion efficiency in our models.
Collapse
Affiliation(s)
- Bart Mh Bruininks
- Groningen Biomolecular Sciences and Biotechnology Institute and Zernike Institute for Advanced Materials, University of Groningen, Nijenborgh, Netherlands
| | - Paulo Ct Souza
- Groningen Biomolecular Sciences and Biotechnology Institute and Zernike Institute for Advanced Materials, University of Groningen, Nijenborgh, Netherlands
| | - Helgi Ingolfsson
- Groningen Biomolecular Sciences and Biotechnology Institute and Zernike Institute for Advanced Materials, University of Groningen, Nijenborgh, Netherlands
| | - Siewert J Marrink
- Groningen Biomolecular Sciences and Biotechnology Institute and Zernike Institute for Advanced Materials, University of Groningen, Nijenborgh, Netherlands
| |
Collapse
|
13
|
Shmilovich K, Mansbach RA, Sidky H, Dunne OE, Panda SS, Tovar JD, Ferguson AL. Discovery of Self-Assembling π-Conjugated Peptides by Active Learning-Directed Coarse-Grained Molecular Simulation. J Phys Chem B 2020; 124:3873-3891. [PMID: 32180410 DOI: 10.1021/acs.jpcb.0c00708] [Citation(s) in RCA: 54] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Electronically active organic molecules have demonstrated great promise as novel soft materials for energy harvesting and transport. Self-assembled nanoaggregates formed from π-conjugated oligopeptides composed of an aromatic core flanked by oligopeptide wings offer emergent optoelectronic properties within a water-soluble and biocompatible substrate. Nanoaggregate properties can be controlled by tuning core chemistry and peptide composition, but the sequence-structure-function relations remain poorly characterized. In this work, we employ coarse-grained molecular dynamics simulations within an active learning protocol employing deep representational learning and Bayesian optimization to efficiently identify molecules capable of assembling pseudo-1D nanoaggregates with good stacking of the electronically active π-cores. We consider the DXXX-OPV3-XXXD oligopeptide family, where D is an Asp residue and OPV3 is an oligophenylenevinylene oligomer (1,4-distyrylbenzene), to identify the top performing XXX tripeptides within all 203 = 8000 possible sequences. By direct simulation of only 2.3% of this space, we identify molecules predicted to exhibit superior assembly relative to those reported in prior work. Spectral clustering of the top candidates reveals new design rules governing assembly. This work establishes new understanding of DXXX-OPV3-XXXD assembly, identifies promising new candidates for experimental testing, and presents a computational design platform that can be generically extended to other peptide-based and peptide-like systems.
Collapse
Affiliation(s)
- Kirill Shmilovich
- Pritzker School of Molecular Engineering, University of Chicago, Chicago, Illinois 60637, United States
| | - Rachael A Mansbach
- Theoretical Biology and Biophysics Group, Los Alamos National Laboratory, Los Alamos, New Mexico 87545, United States
| | - Hythem Sidky
- Pritzker School of Molecular Engineering, University of Chicago, Chicago, Illinois 60637, United States
| | - Olivia E Dunne
- Pritzker School of Molecular Engineering, University of Chicago, Chicago, Illinois 60637, United States
| | - Sayak Subhra Panda
- Department of Chemistry, Johns Hopkins University, Baltimore, Maryland 21218, United States.,Institute of NanoBioTechnology, Johns Hopkins University, Baltimore, Maryland 21218, United States
| | - John D Tovar
- Department of Chemistry, Johns Hopkins University, Baltimore, Maryland 21218, United States.,Institute of NanoBioTechnology, Johns Hopkins University, Baltimore, Maryland 21218, United States.,Department of Materials Science and Engineering, Johns Hopkins University, Baltimore, Maryland 21218, United States
| | - Andrew L Ferguson
- Pritzker School of Molecular Engineering, University of Chicago, Chicago, Illinois 60637, United States
| |
Collapse
|
14
|
Schroer CFE, Baldauf L, van Buren L, Wassenaar TA, Melo MN, Koenderink GH, Marrink SJ. Charge-dependent interactions of monomeric and filamentous actin with lipid bilayers. Proc Natl Acad Sci U S A 2020; 117:5861-5872. [PMID: 32123101 PMCID: PMC7084070 DOI: 10.1073/pnas.1914884117] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
The cytoskeletal protein actin polymerizes into filaments that are essential for the mechanical stability of mammalian cells. In vitro experiments showed that direct interactions between actin filaments and lipid bilayers are possible and that the net charge of the bilayer as well as the presence of divalent ions in the buffer play an important role. In vivo, colocalization of actin filaments and divalent ions are suppressed, and cells rely on linker proteins to connect the plasma membrane to the actin network. Little is known, however, about why this is the case and what microscopic interactions are important. A deeper understanding is highly beneficial, first, to obtain understanding in the biological design of cells and, second, as a possible basis for the building of artificial cortices for the stabilization of synthetic cells. Here, we report the results of coarse-grained molecular dynamics simulations of monomeric and filamentous actin in the vicinity of differently charged lipid bilayers. We observe that charges on the lipid head groups strongly determine the ability of actin to adsorb to the bilayer. The inclusion of divalent ions leads to a reversal of the binding affinity. Our in silico results are validated experimentally by reconstitution assays with actin on lipid bilayer membranes and provide a molecular-level understanding of the actin-membrane interaction.
Collapse
Affiliation(s)
- Carsten F E Schroer
- Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, 9747 AG, Groningen, The Netherlands
- Zernike Institute for Advanced Materials, University of Groningen, 9747 AG, Groningen, The Netherlands
| | - Lucia Baldauf
- Department of Bionanoscience, Kavli Institute of Nanoscience Delft, Delft University of Technology, 2629 HZ Delft, The Netherlands
- Living Matter Department, AMOLF, 1098 XG Amsterdam, The Netherlands
| | - Lennard van Buren
- Department of Bionanoscience, Kavli Institute of Nanoscience Delft, Delft University of Technology, 2629 HZ Delft, The Netherlands
- Living Matter Department, AMOLF, 1098 XG Amsterdam, The Netherlands
| | - Tsjerk A Wassenaar
- Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, 9747 AG, Groningen, The Netherlands
- Zernike Institute for Advanced Materials, University of Groningen, 9747 AG, Groningen, The Netherlands
| | - Manuel N Melo
- Instituto de Tecnologia Química e Biológica, New University of Lisbon, 2780-157, Oeiras, Portugal
| | - Gijsje H Koenderink
- Department of Bionanoscience, Kavli Institute of Nanoscience Delft, Delft University of Technology, 2629 HZ Delft, The Netherlands;
- Living Matter Department, AMOLF, 1098 XG Amsterdam, The Netherlands
| | - Siewert J Marrink
- Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, 9747 AG, Groningen, The Netherlands;
- Zernike Institute for Advanced Materials, University of Groningen, 9747 AG, Groningen, The Netherlands
| |
Collapse
|
15
|
Lemaalem M, Hadrioui N, Derouiche A, Ridouane H. Structure and dynamics of liposomes designed for drug delivery: coarse-grained molecular dynamics simulations to reveal the role of lipopolymer incorporation. RSC Adv 2020; 10:3745-3755. [PMID: 35492626 PMCID: PMC9048902 DOI: 10.1039/c9ra08632c] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2019] [Accepted: 01/06/2020] [Indexed: 12/22/2022] Open
Abstract
In this work, coarse-grained molecular dynamics simulations are carried out in NPTH and NVTE statistical ensembles in order to study the structure and dynamics properties of liposomes coated with polyethylene glycol (PEG).
Collapse
Affiliation(s)
- Mohammed Lemaalem
- Laboratoire de Physique des Polymères et Phénomènes Critiques Sciences Faculty Ben M'Sik
- Hassan II University
- Casablanca
- Morocco
| | - Nourddine Hadrioui
- Laboratoire de Physique des Polymères et Phénomènes Critiques Sciences Faculty Ben M'Sik
- Hassan II University
- Casablanca
- Morocco
| | - Abdelali Derouiche
- Laboratoire de Physique des Polymères et Phénomènes Critiques Sciences Faculty Ben M'Sik
- Hassan II University
- Casablanca
- Morocco
| | - Hamid Ridouane
- Laboratoire de Physique des Polymères et Phénomènes Critiques Sciences Faculty Ben M'Sik
- Hassan II University
- Casablanca
- Morocco
| |
Collapse
|
16
|
Bandyopadhyay P, Gupta-Bhaya P. A comparative evaluation of pair correlation functions for a highly asymmetric electrolyte with mono and divalent counterions from integral equation theory in hypernetted chain (HNC) approximation and Monte Carlo simulation. Chem Phys Lett 2019. [DOI: 10.1016/j.cplett.2019.136664] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
|
17
|
Komorowski K, Salditt A, Xu Y, Yavuz H, Brennich M, Jahn R, Salditt T. Vesicle Adhesion and Fusion Studied by Small-Angle X-Ray Scattering. Biophys J 2019; 114:1908-1920. [PMID: 29694868 PMCID: PMC5936998 DOI: 10.1016/j.bpj.2018.02.040] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2017] [Revised: 02/19/2018] [Accepted: 02/28/2018] [Indexed: 12/02/2022] Open
Abstract
We have studied the adhesion state (also denoted by docking state) of lipid vesicles as induced by the divalent ions Ca2+ or Mg2+ at well-controlled ion concentration, lipid composition, and charge density. The bilayer structure and the interbilayer distance in the docking state were analyzed by small-angle x-ray scattering. A strong adhesion state was observed for DOPC:DOPS vesicles, indicating like-charge attraction resulting from ion correlations. The observed interbilayer separations of ∼1.6 nm agree quantitatively with the predictions of electrostatics in the strong coupling regime. Although this phenomenon was observed when mixing anionic and zwitterionic (or neutral) lipids, pure anionic membranes (DOPS) with highest charge density σ resulted in a direct phase transition to a multilamellar state, which must be accompanied by rupture and fusion of vesicles. To extend the structural assay toward protein-controlled docking and fusion, we have characterized reconstituted N-ethylmaleimide-sensitive factor attachment protein receptors in controlled proteoliposome suspensions by small-angle x-ray scattering.
Collapse
Affiliation(s)
- Karlo Komorowski
- Institut für Röntgenphysik, Georg-August-Universität Göttingen, Göttingen, Germany; Department of Neurobiology, Max-Planck-Institute for Biophysical Chemistry, Göttingen, Germany
| | - Annalena Salditt
- Institut für Röntgenphysik, Georg-August-Universität Göttingen, Göttingen, Germany
| | - Yihui Xu
- Institut für Röntgenphysik, Georg-August-Universität Göttingen, Göttingen, Germany
| | - Halenur Yavuz
- Department of Neurobiology, Max-Planck-Institute for Biophysical Chemistry, Göttingen, Germany
| | - Martha Brennich
- European Molecular Biology Laboratory, Grenoble Outstation, Grenoble, France
| | - Reinhard Jahn
- Department of Neurobiology, Max-Planck-Institute for Biophysical Chemistry, Göttingen, Germany
| | - Tim Salditt
- Institut für Röntgenphysik, Georg-August-Universität Göttingen, Göttingen, Germany.
| |
Collapse
|
18
|
Marrink SJ, Corradi V, Souza PC, Ingólfsson HI, Tieleman DP, Sansom MS. Computational Modeling of Realistic Cell Membranes. Chem Rev 2019; 119:6184-6226. [PMID: 30623647 PMCID: PMC6509646 DOI: 10.1021/acs.chemrev.8b00460] [Citation(s) in RCA: 422] [Impact Index Per Article: 84.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2018] [Indexed: 12/15/2022]
Abstract
Cell membranes contain a large variety of lipid types and are crowded with proteins, endowing them with the plasticity needed to fulfill their key roles in cell functioning. The compositional complexity of cellular membranes gives rise to a heterogeneous lateral organization, which is still poorly understood. Computational models, in particular molecular dynamics simulations and related techniques, have provided important insight into the organizational principles of cell membranes over the past decades. Now, we are witnessing a transition from simulations of simpler membrane models to multicomponent systems, culminating in realistic models of an increasing variety of cell types and organelles. Here, we review the state of the art in the field of realistic membrane simulations and discuss the current limitations and challenges ahead.
Collapse
Affiliation(s)
- Siewert J. Marrink
- Groningen
Biomolecular Sciences and Biotechnology Institute & Zernike Institute
for Advanced Materials, University of Groningen, Nijenborgh 7, 9747 AG Groningen, The Netherlands
| | - Valentina Corradi
- Centre
for Molecular Simulation and Department of Biological Sciences, University of Calgary, 2500 University Drive NW, Calgary, Alberta T2N 1N4, Canada
| | - Paulo C.T. Souza
- Groningen
Biomolecular Sciences and Biotechnology Institute & Zernike Institute
for Advanced Materials, University of Groningen, Nijenborgh 7, 9747 AG Groningen, The Netherlands
| | - Helgi I. Ingólfsson
- Biosciences
and Biotechnology Division, Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, 7000 East Avenue, Livermore, California 94550, United States
| | - D. Peter Tieleman
- Centre
for Molecular Simulation and Department of Biological Sciences, University of Calgary, 2500 University Drive NW, Calgary, Alberta T2N 1N4, Canada
| | - Mark S.P. Sansom
- Department
of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, U.K.
| |
Collapse
|
19
|
Messineo E, Pollins A, Thayer W. Optimization and evaluation of an in vitro model of PEG-mediated fusion of nerve cell bodies. J Clin Neurosci 2019; 63:189-195. [DOI: 10.1016/j.jocn.2019.01.037] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2018] [Revised: 01/20/2019] [Accepted: 01/28/2019] [Indexed: 01/27/2023]
|
20
|
Jefferys EE, Sansom MSP. Computational Virology: Molecular Simulations of Virus Dynamics and Interactions. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2019; 1215:201-233. [DOI: 10.1007/978-3-030-14741-9_10] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
|
21
|
Krishna A, Sengupta D. Interplay between Membrane Curvature and Cholesterol: Role of Palmitoylated Caveolin-1. Biophys J 2018; 116:69-78. [PMID: 30579563 DOI: 10.1016/j.bpj.2018.11.3127] [Citation(s) in RCA: 50] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2018] [Revised: 10/14/2018] [Accepted: 11/01/2018] [Indexed: 01/07/2023] Open
Abstract
Caveolin-1 (cav-1) is an important player in cell signaling and endocytosis that has been shown to colocalize with cholesterol-rich membrane domains. Experimental studies with varying cav-1 constructs have suggested that it can induce both cholesterol clustering and membrane curvature. Here, we probe the molecular origin of membrane curvature and cholesterol clustering by cav-1 by using coarse-grain molecular dynamics simulations. We have performed a series of simulations of a functionally important cav-1 construct, comprising the membrane-interacting domains and a C-terminal palmitoyl tail. Our results suggest that cav-1 is able to induce cholesterol clustering in the membrane leaflet to which it is bound as well as the opposing leaflet. A positive membrane curvature is observed upon cav-1 binding in cholesterol-containing bilayers. Interestingly, we observe an interplay between cholesterol clustering and membrane curvature such that cav-1 is able to induce higher membrane curvature in cholesterol-rich membranes. The role of the cav-1 palmitoyl tail is less clear and appears to increase the membrane contacts. Further, we address the importance of the secondary structure of cav-1 domains and show that it could play an important role in membrane curvature and cholesterol clustering. Our work is an important step toward a molecular picture of caveolae and vesicular endocytosis.
Collapse
Affiliation(s)
- Anjali Krishna
- CSIR-National Chemical Laboratory, Pune, Maharashtra, India
| | - Durba Sengupta
- CSIR-National Chemical Laboratory, Pune, Maharashtra, India.
| |
Collapse
|
22
|
Michalowsky J, Zeman J, Holm C, Smiatek J. A polarizable MARTINI model for monovalent ions in aqueous solution. J Chem Phys 2018; 149:163319. [PMID: 30384758 DOI: 10.1063/1.5028354] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
We present a new polarizable coarse-grained martini force field for monovalent ions, called refIon, which is developed mainly for the accurate reproduction of electrostatic properties in aqueous electrolyte solutions. The ion model relies on full long-range Coulomb interactions and introduces satellite charges around the central interaction site in order to model molecular polarization effects. All force field parameters are matched to reproduce the mass density and the static dielectric permittivity of aqueous NaCl solutions, such that experimental values are well-reproduced up to moderate salt concentrations of 2 m o l / l . In addition, an improved agreement with experimentally measured ionic conductivities is observed. Our model is validated with regard to analytic solutions for the ion distribution around highly charged rod-like polyelectrolytes in combination with atomistic simulations and experimental results concerning structural properties of lipid bilayers in the presence of distinct salt concentrations. Further results regarding the coordination numbers of counterions around dilute poly(styrene sulfonate) and poly(diallyldimethylammonium) polyelectrolyte chains also highlight the applicability of our approach. The introduction of our force field allows us to eliminate heuristic scaling factors, as reported for previous martini ion models in terms of effective salt concentrations, and in consequence provides a better agreement between simulation and experimental results. The presented approach is specifically useful for recent martini attempts that focus on highly charged systems-such as models of DNA, polyelectrolytes or polyelectrolyte complexes-where precise studies of electrostatic effects and charge transport processes are essential.
Collapse
Affiliation(s)
- Julian Michalowsky
- Institut für Computerphysik, Universität Stuttgart, Allmandring 3, D-70569 Stuttgart, Germany
| | - Johannes Zeman
- Institut für Computerphysik, Universität Stuttgart, Allmandring 3, D-70569 Stuttgart, Germany
| | - Christian Holm
- Institut für Computerphysik, Universität Stuttgart, Allmandring 3, D-70569 Stuttgart, Germany
| | - Jens Smiatek
- Institut für Computerphysik, Universität Stuttgart, Allmandring 3, D-70569 Stuttgart, Germany
| |
Collapse
|
23
|
Xue M, Cheng L, Faustino I, Guo W, Marrink SJ. Molecular Mechanism of Lipid Nanodisk Formation by Styrene-Maleic Acid Copolymers. Biophys J 2018; 115:494-502. [PMID: 29980293 PMCID: PMC6084417 DOI: 10.1016/j.bpj.2018.06.018] [Citation(s) in RCA: 60] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2018] [Revised: 05/02/2018] [Accepted: 06/11/2018] [Indexed: 01/06/2023] Open
Abstract
Experimental characterization of membrane proteins often requires solubilization. A recent approach is to use styrene-maleic acid (SMA) copolymers to isolate membrane proteins in nanometer-sized membrane disks, or so-called SMA lipid particles (SMALPs). The approach has the advantage of allowing direct extraction of proteins, keeping their native lipid environment. Despite the growing popularity of using SMALPs, the molecular mechanism behind the process remains poorly understood. Here, we unravel the molecular details of the nanodisk formation by using coarse-grained molecular dynamics simulations. We show how SMA copolymers bind to the lipid bilayer interface, driven by the hydrophobic effect. Due to the concerted action of multiple adsorbed copolymers, large membrane defects appear, including small, water-filled pores. The copolymers can stabilize the rim of these pores, leading to pore growth and membrane disruption. Although complete solubilization is not seen on the timescale of our simulations, self-assembly experiments show that small nanodisks are the thermodynamically preferred end state. Our findings shed light on the mechanism of SMALP formation and on their molecular structure. This can be an important step toward the design of optimized extraction tools for membrane protein research.
Collapse
Affiliation(s)
- Minmin Xue
- State Key Laboratory of Mechanics and Control of Mechanical Structures, Key Laboratory for Intelligent Nano Materials and Devices of the Ministry of Education, Institute of Nanoscience, Nanjing University of Aeronautics and Astronautics, Nanjing, People's Republic of China; Groningen Biomolecular Science and Biotechnology Institute, University of Groningen, Groningen, the Netherlands; Zernike Institute for Advanced Materials, University of Groningen, Groningen, the Netherlands
| | - Lisheng Cheng
- College of Mechanical and Electrical Engineering, Beijing University of Chemical Technology, Beijing, People's Republic of China
| | - Ignacio Faustino
- Groningen Biomolecular Science and Biotechnology Institute, University of Groningen, Groningen, the Netherlands; Zernike Institute for Advanced Materials, University of Groningen, Groningen, the Netherlands
| | - Wanlin Guo
- State Key Laboratory of Mechanics and Control of Mechanical Structures, Key Laboratory for Intelligent Nano Materials and Devices of the Ministry of Education, Institute of Nanoscience, Nanjing University of Aeronautics and Astronautics, Nanjing, People's Republic of China
| | - Siewert J Marrink
- Groningen Biomolecular Science and Biotechnology Institute, University of Groningen, Groningen, the Netherlands; Zernike Institute for Advanced Materials, University of Groningen, Groningen, the Netherlands.
| |
Collapse
|
24
|
Abstract
Background The management of peripheral nerve injuries remains a large challenge for plastic surgeons. With the inability to fuse axonal endings, results after microsurgical nerve repair have been inconsistent. Our current nerve repair strategies rely upon the slow and lengthy process of axonal regeneration (~1 mm/d). Polyethylene glycol (PEG) has been investigated as a potential axonal fusion agent; however, the percentage of axonal fusion has been inconsistent. The purpose of this study was to identify a PEG delivery device to standardize outcomes after attempted axonal fusion with PEG. Materials and Methods We used a rat sciatic nerve injury model in which we completely transected and repaired the left sciatic nerve to evaluate the efficacy of PEG fusion over a span of 12 weeks. In addition, we evaluated the effectiveness of a delivery device's ability to optimize results after PEG fusion. Results We found that PEG rapidly (within minutes) restores axonal continuity as assessed by electrophysiology, fluorescent retrograde tracer, and diffusion tensor imaging. Immunohistochemical analysis shows that motor axon counts are significantly increased at 1 week, 4 weeks, and 12 weeks postoperatively in PEG-treated animals. Furthermore, PEG restored behavioral functions up to 50% compared with animals that received the criterion standard epineurial repair (control animals). Conclusions The ability of PEG to rapidly restore nerve function after neurotmesis could have vast implications on the clinical management of traumatic injuries to peripheral nerves.
Collapse
|
25
|
Scheidt HA, Kolocaj K, Veje Kristensen J, Huster D, Langosch D. Transmembrane Helix Induces Membrane Fusion through Lipid Binding and Splay. J Phys Chem Lett 2018; 9:3181-3186. [PMID: 29799756 DOI: 10.1021/acs.jpclett.8b00859] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
The fusion of biological membranes may require splayed lipids whose tails transiently visit the headgroup region of the bilayer, a scenario suggested by molecular dynamics simulations. Here, we examined the lipid splay hypothesis experimentally by relating liposome fusion and lipid splay induced by model transmembrane domains (TMDs). Our results reveal that a conformationally flexible transmembrane helix promotes outer leaflet mixing and lipid splay more strongly than a conformationally rigid one. The lipid dependence of basal as well as of TMD-driven lipid mixing and splay suggests that the cone-shaped phosphatidylethanolamine stimulates basal fusion via enhancing lipid splay and that the negatively charged phosphatidylserine inhibits fusion via electrostatic repulsion. Phosphatidylserine also strongly differentiates basal and helix-driven fusion, which is related to its preferred interaction with the conformationally more flexible transmembrane helix. Thus, the contribution of a transmembrane helix to membrane fusion appears to depend on lipid binding, which results in lipid splay.
Collapse
Affiliation(s)
- Holger A Scheidt
- Institute for Medical Physics and Biophysics , Leipzig University , Härtelstrasse 16-18 , 04107 Leipzig , Germany
| | - Katja Kolocaj
- Lehrstuhl für Chemie der Biopolymere , Technische Universität München , Weihenstephaner Berg 3 , 85354 Freising , Germany
- Munich Center For Integrated Protein Science (CIPSM) , Butenandtstrasse 5 , 81377 München , Germany
| | - Julie Veje Kristensen
- Lehrstuhl für Chemie der Biopolymere , Technische Universität München , Weihenstephaner Berg 3 , 85354 Freising , Germany
- Munich Center For Integrated Protein Science (CIPSM) , Butenandtstrasse 5 , 81377 München , Germany
| | - Daniel Huster
- Institute for Medical Physics and Biophysics , Leipzig University , Härtelstrasse 16-18 , 04107 Leipzig , Germany
| | - Dieter Langosch
- Lehrstuhl für Chemie der Biopolymere , Technische Universität München , Weihenstephaner Berg 3 , 85354 Freising , Germany
- Munich Center For Integrated Protein Science (CIPSM) , Butenandtstrasse 5 , 81377 München , Germany
| |
Collapse
|
26
|
Danielsen EM, Hansen GH. Intestinal surfactant permeation enhancers and their interaction with enterocyte cell membranes in a mucosal explant system. Tissue Barriers 2018; 5:e1361900. [PMID: 28837408 DOI: 10.1080/21688370.2017.1361900] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Intestinal permeation enhancers (PEs) are agents aimed to improve oral delivery of therapeutic drugs with poor bioavailability. The main permeability barrier for oral delivery is the intestinal epithelium, and PEs act to increase the paracellular and/or transcellular passage of drugs. Transcellular passage can be achieved by cell membrane permeabilization and/or by endocytic uptake and subsequent transcytosis. One broad class of PEs is surfactants which act by inserting into the cell membrane, thereby perturbing its integrity, but little is known about how the dynamics of the membrane are affected. In the present work, the interaction of the surfactants lauroyl-L-carnitine, 1-decanoyl-rac-glycerol, and nonaethylene glycol monododecyl ether with the intestinal epithelium was studied in organ cultured pig jejunal mucosal explants. As expected, at 2 mM, these agents rapidly permeabilized the enterocytes for the fluorescent polar tracer lucifer yellow, but surprisingly, they all also blocked both constitutive -and receptor-mediated pathways of endocytosis from the brush border, indicating a complete arrest of apical membrane trafficking. At the ultrastructural level, the PEs caused longitudinal fusion of brush border microvilli. Such a membrane fusogenic activity could also explain the observed formation of vesicle-like structures and large vacuoles along the lateral cell membranes of the enterocytes induced by the PEs. We conclude that the surfactant action of the PEs selected in this study not only permeabilized the enterocytes, but profoundly changed the dynamic properties of their constituent cell membranes.
Collapse
Affiliation(s)
- E Michael Danielsen
- a Department of Cellular and Molecular Medicine, The Panum Institute, Faculty of Health Sciences , University of Copenhagen , Copenhagen , Denmark
| | - Gert H Hansen
- a Department of Cellular and Molecular Medicine, The Panum Institute, Faculty of Health Sciences , University of Copenhagen , Copenhagen , Denmark
| |
Collapse
|
27
|
Daskalakis V. Protein-protein interactions within photosystem II under photoprotection: the synergy between CP29 minor antenna, subunit S (PsbS) and zeaxanthin at all-atom resolution. Phys Chem Chem Phys 2018; 20:11843-11855. [PMID: 29658553 DOI: 10.1039/c8cp01226a] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
The assembly and disassembly of protein complexes within cells are crucial life-sustaining processes. In photosystem II (PSII) of higher plants, there is a delicate yet obscure balance between light harvesting and photo-protection under fluctuating light conditions, that involves protein-protein complexes. Recent breakthroughs in molecular dynamics (MD) simulations are combined with new approaches herein to provide structural and energetic insight into such a complex between the CP29 minor antenna and the PSII subunit S (PsbS). The microscopic model involves extensive sampling of bound and dissociated states at atomic resolution in the presence of photo-protective zeaxanthin (Zea), and reveals well defined protein-protein cross-sections. The complex is placed within PSII, and macroscopic connections are emerging (PsbS-CP29-CP24-CP47) along the energy transfer pathways from the antenna to the PSII core. These connections explain macroscopic observations in the literature, while the previously obscured atomic scale details are now revealed. The implications of these findings are discussed in the context of the Non-Photochemical Quenching (NPQ) of chlorophyll fluorescence, the down-regulatory mechanism of photosynthesis, that enables the protection of PSII against excess excitation load. Zea is found at the PsbS-CP29 cross-section and a pH-dependent equilibrium between PsbS dimer/monomers and the PsbS-CP29 dissociation/association is identified as the target for engineering tolerant plants with increased crop and biomass yields. Finally, the new MD based approaches can be used to probe protein-protein interactions in general, and the PSII structure provided can initiate large scale molecular simulations of the photosynthetic apparatus, under NPQ conditions.
Collapse
Affiliation(s)
- Vangelis Daskalakis
- Department of Environmental Science and Technology, Cyprus University of Technology (CUT), 30 Archbishop Kyprianou Str., 3603, Limassol, Cyprus.
| |
Collapse
|
28
|
Wang H, Tang X, Eike DM, Larson RG, Koenig PH. Scission Free Energies for Wormlike Surfactant Micelles: Development of a Simulation Protocol, Application, and Validation for Personal Care Formulations. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2018; 34:1564-1573. [PMID: 29244513 DOI: 10.1021/acs.langmuir.7b03552] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
We present a scheme to calculate wormlike micelle scission free energies from a potential of mean force (PMF) derived from a weighted histogram analysis method (WHAM) applied to coarse grained dissipative particle dynamics (DPD) simulations. In contrast to previous related work, we use a specially chosen external potential based on a reaction coordinate that reversibly drives surfactants out of the nascent scission location. For the application to a model body wash formulation, we predict how addition of NaCl and small molecules such as perfume raw materials (PRMs) affect scission energies. The results show qualitative agreement and correct trends compared to recently determined scission energies for the same system; however, a more rigorous parametrization of the underlying DPD potential is required for quantitative agreement.
Collapse
Affiliation(s)
- Huan Wang
- University of Cincinnati Simulation Center , 2728 Vine Street, Cincinnati, Ohio 45220, United States
| | - Xueming Tang
- Department of Chemical Engineering, 2800 Plymouth Road, University of Michigan , Ann Arbor, Michigan 48109, United States
| | - David M Eike
- Computational Chemistry, Modeling and Simulation, The Procter & Gamble Company , 8611 Beckett Road, West Chester, Ohio 45069, United States
| | - Ronald G Larson
- Department of Chemical Engineering, 2800 Plymouth Road, University of Michigan , Ann Arbor, Michigan 48109, United States
| | - Peter H Koenig
- Computational Chemistry, Modeling and Simulation, The Procter & Gamble Company , 8611 Beckett Road, West Chester, Ohio 45069, United States
| |
Collapse
|
29
|
Molina BG, Cianga L, Bendrea AD, Cianga I, del Valle LJ, Estrany F, Alemán C, Armelin E. Amphiphilic polypyrrole-poly(Schiff base) copolymers with poly(ethylene glycol) side chains: synthesis, properties and applications. Polym Chem 2018. [DOI: 10.1039/c8py00762d] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
New amphiphilic poly(ethylene glycol) (PEG)-grafted random intrinsically conducting copolymers which combine three different functionalities have been engineered, prepared and characterized.
Collapse
Affiliation(s)
- Brenda G. Molina
- Departament d'Enginyeria Química
- EEBE
- Universitat Politècnica de Catalunya
- Barcelona
- Spain
| | - Luminita Cianga
- “Petru Poni” Institute of Macromolecular Chemistry
- Iasi
- Romania
| | | | - Ioan Cianga
- “Petru Poni” Institute of Macromolecular Chemistry
- Iasi
- Romania
| | - Luis J. del Valle
- Departament d'Enginyeria Química
- EEBE
- Universitat Politècnica de Catalunya
- Barcelona
- Spain
| | - Francesc Estrany
- Departament d'Enginyeria Química
- EEBE
- Universitat Politècnica de Catalunya
- Barcelona
- Spain
| | - Carlos Alemán
- Departament d'Enginyeria Química
- EEBE
- Universitat Politècnica de Catalunya
- Barcelona
- Spain
| | - Elaine Armelin
- Departament d'Enginyeria Química
- EEBE
- Universitat Politècnica de Catalunya
- Barcelona
- Spain
| |
Collapse
|
30
|
Liu X, Tian F, Yue T, Zhang X, Zhong C. Pulling force and surface tension drive membrane fusion. J Chem Phys 2017; 147:194703. [PMID: 29166098 DOI: 10.1063/1.4997393] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Despite catalyzed by fusion proteins of quite different molecular architectures, intracellular, viral, and cell-to-cell fusions are found to have the essential common features and the nearly same nature of transition states. The similarity inspires us to find a more general catalysis mechanism for membrane fusion that minimally depends on the specific structures of fusion proteins. In this work, we built a minimal model for membrane fusion, and by using dissipative particle dynamics simulations, we propose a mechanism that the pulling force generated by fusion proteins initiates the fusion process and the membrane tension regulates the subsequent fusion stages. The model shows different features compared to previous computer simulation studies: the pulling force catalyzes membrane fusion through lipid head overcrowding in the contacting region, leading to an increase in the head-head repulsion and/or the unfavorable head-tail contacts from opposing membranes, both of which destabilize the contacting leaflets and thus promote membrane fusion or vesicle rupture. Our simulations produce a variety of shapes and intermediates, closely resembling cases seen experimentally. Our work strongly supports the view that the tight pulling mechanism is a conserved feature of fusion protein-mediated fusion and that the membrane tension plays an essential role in fusion.
Collapse
Affiliation(s)
- Xuejuan Liu
- State Key Laboratory of Organic-Inorganic Composites, Beijing University of Chemical Technology, Beijing 100029, People's Republic of China
| | - Falin Tian
- State Key Laboratory of Organic-Inorganic Composites, Beijing University of Chemical Technology, Beijing 100029, People's Republic of China
| | - Tongtao Yue
- State Key Laboratory of Heavy Oil Processing, Center for Bioengineering and Biotechnology, China University of Petroleum (East China), Qingdao 266580, People's Republic of China
| | - Xianren Zhang
- State Key Laboratory of Organic-Inorganic Composites, Beijing University of Chemical Technology, Beijing 100029, People's Republic of China
| | - Chongli Zhong
- State Key Laboratory of Organic-Inorganic Composites, Beijing University of Chemical Technology, Beijing 100029, People's Republic of China
| |
Collapse
|
31
|
Hsu PC, Bruininks BMH, Jefferies D, Cesar Telles de Souza P, Lee J, Patel DS, Marrink SJ, Qi Y, Khalid S, Im W. CHARMM-GUI Martini Maker for modeling and simulation of complex bacterial membranes with lipopolysaccharides. J Comput Chem 2017; 38:2354-2363. [PMID: 28776689 DOI: 10.1002/jcc.24895] [Citation(s) in RCA: 118] [Impact Index Per Article: 16.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2017] [Revised: 07/03/2017] [Accepted: 07/09/2017] [Indexed: 12/18/2022]
Abstract
A complex cell envelope, composed of a mixture of lipid types including lipopolysaccharides, protects bacteria from the external environment. Clearly, the proteins embedded within the various components of the cell envelope have an intricate relationship with their local environment. Therefore, to obtain meaningful results, molecular simulations need to mimic as far as possible this chemically heterogeneous system. However, setting up such systems for computational studies is far from trivial, and consequently the vast majority of simulations of outer membrane proteins still rely on oversimplified phospholipid membrane models. This work presents an update of CHARMM-GUI Martini Maker for coarse-grained modeling and simulation of complex bacterial membranes with lipopolysaccharides. The qualities of the outer membrane systems generated by Martini Maker are validated by simulating them in bilayer, vesicle, nanodisc, and micelle environments (with and without outer membrane proteins) using the Martini force field. We expect this new feature in Martini Maker to be a useful tool for modeling large, complicated bacterial outer membrane systems in a user-friendly manner. © 2017 Wiley Periodicals, Inc.
Collapse
Affiliation(s)
- Pin-Chia Hsu
- School of Chemistry, University of Southampton, Southampton, SO17 1BJ, United Kingdom
| | - Bart M H Bruininks
- Groningen Biomolecular Sciences and Biotechnology Institute and Zernike Institute for Advanced Materials, University of Groningen, Nijenborgh 7, Groningen, AG, 9747, The Netherlands
| | - Damien Jefferies
- School of Chemistry, University of Southampton, Southampton, SO17 1BJ, United Kingdom
| | - Paulo Cesar Telles de Souza
- Groningen Biomolecular Sciences and Biotechnology Institute and Zernike Institute for Advanced Materials, University of Groningen, Nijenborgh 7, Groningen, AG, 9747, The Netherlands
| | - Jumin Lee
- Departments of Biological Sciences and Bioengineering, Lehigh University, Pennsylvania
| | - Dhilon S Patel
- Departments of Biological Sciences and Bioengineering, Lehigh University, Pennsylvania
| | - Siewert J Marrink
- Groningen Biomolecular Sciences and Biotechnology Institute and Zernike Institute for Advanced Materials, University of Groningen, Nijenborgh 7, Groningen, AG, 9747, The Netherlands
| | - Yifei Qi
- College of Chemistry and Molecular Engineering, East China Normal University, Shanghai, 200062, China
| | - Syma Khalid
- School of Chemistry, University of Southampton, Southampton, SO17 1BJ, United Kingdom
| | - Wonpil Im
- Departments of Biological Sciences and Bioengineering, Lehigh University, Pennsylvania
| |
Collapse
|
32
|
Gong Z, Sun H. A Coarse-Grained Force Field Parameterized for MgCl2 and CaCl2 Aqueous Solutions. J Chem Inf Model 2017; 57:1599-1608. [DOI: 10.1021/acs.jcim.7b00206] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Affiliation(s)
- Zheng Gong
- School of Chemistry and Chemical
Engineering and Ministry of Education Key Laboratory of Scientific
and Engineering Computing, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Huai Sun
- School of Chemistry and Chemical
Engineering and Ministry of Education Key Laboratory of Scientific
and Engineering Computing, Shanghai Jiao Tong University, Shanghai, 200240, China
| |
Collapse
|
33
|
Mansbach RA, Ferguson AL. Coarse-Grained Molecular Simulation of the Hierarchical Self-Assembly of π-Conjugated Optoelectronic Peptides. J Phys Chem B 2017; 121:1684-1706. [DOI: 10.1021/acs.jpcb.6b10165] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Affiliation(s)
- Rachael A. Mansbach
- Department
of Physics, University of Illinois at Urbana-Champaign, 1110 W Green Street, Urbana, Illinois 61801, United States
| | - Andrew L. Ferguson
- Department
of Materials Science and Engineering, University of Illinois at Urbana-Champaign, 1304 W Green Street, Urbana, Illinois 61801, United States
- Department
of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, 600 South Mathews Avenue, Urbana, Illinois 61801, United States
| |
Collapse
|
34
|
Han J, Pluhackova K, Böckmann RA. The Multifaceted Role of SNARE Proteins in Membrane Fusion. Front Physiol 2017; 8:5. [PMID: 28163686 PMCID: PMC5247469 DOI: 10.3389/fphys.2017.00005] [Citation(s) in RCA: 178] [Impact Index Per Article: 25.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2016] [Accepted: 01/04/2017] [Indexed: 12/28/2022] Open
Abstract
Membrane fusion is a key process in all living organisms that contributes to a variety of biological processes including viral infection, cell fertilization, as well as intracellular transport, and neurotransmitter release. In particular, the various membrane-enclosed compartments in eukaryotic cells need to exchange their contents and communicate across membranes. Efficient and controllable fusion of biological membranes is known to be driven by cooperative action of SNARE proteins, which constitute the central components of the eukaryotic fusion machinery responsible for fusion of synaptic vesicles with the plasma membrane. During exocytosis, vesicle-associated v-SNARE (synaptobrevin) and target cell-associated t-SNAREs (syntaxin and SNAP-25) assemble into a core trans-SNARE complex. This complex plays a versatile role at various stages of exocytosis ranging from the priming to fusion pore formation and expansion, finally resulting in the release or exchange of the vesicle content. This review summarizes current knowledge on the intricate molecular mechanisms underlying exocytosis triggered and catalyzed by SNARE proteins. Particular attention is given to the function of the peptidic SNARE membrane anchors and the role of SNARE-lipid interactions in fusion. Moreover, the regulatory mechanisms by synaptic auxiliary proteins in SNARE-driven membrane fusion are briefly outlined.
Collapse
Affiliation(s)
- Jing Han
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Xi'an Jiaotong University Health Science CenterXi'an, China; Computational Biology, Department of Biology, Friedrich-Alexander Universität Erlangen-NürnbergErlangen, Germany
| | - Kristyna Pluhackova
- Computational Biology, Department of Biology, Friedrich-Alexander Universität Erlangen-Nürnberg Erlangen, Germany
| | - Rainer A Böckmann
- Computational Biology, Department of Biology, Friedrich-Alexander Universität Erlangen-Nürnberg Erlangen, Germany
| |
Collapse
|
35
|
Xu Y, Deng L, Ren H, Zhang X, Huang F, Yue T. Transport of nanoparticles across pulmonary surfactant monolayer: a molecular dynamics study. Phys Chem Chem Phys 2017. [DOI: 10.1039/c7cp02548c] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Three types of nanoparticles, including hydrophobic nanoparticles, hydrophilic nanoparticles, and hydrophilic nanoparticles coated with lipids, were found by our molecular dynamics simulations to be transported across the pulmonary surfactant monolayer, but via different pathways, which affect their subsequent interactions with target cell membranes.
Collapse
Affiliation(s)
- Yan Xu
- State Key Laboratory of Heavy Oil Processing
- China University of Petroleum (East China)
- Qingdao
- China
- Center for Bioengineering and Biotechnology
| | - Li Deng
- Center for Bioengineering and Biotechnology
- College of Chemical Engineering
- China University of Petroleum (East China)
- Qingdao
- China
| | - Hao Ren
- Center for Bioengineering and Biotechnology
- College of Chemical Engineering
- China University of Petroleum (East China)
- Qingdao
- China
| | - Xianren Zhang
- State Key Laboratory of Organic-Inorganic Composites
- Beijing University of Chemical Technology
- Beijing
- China
| | - Fang Huang
- State Key Laboratory of Heavy Oil Processing
- China University of Petroleum (East China)
- Qingdao
- China
- Center for Bioengineering and Biotechnology
| | - Tongtao Yue
- State Key Laboratory of Heavy Oil Processing
- China University of Petroleum (East China)
- Qingdao
- China
- Center for Bioengineering and Biotechnology
| |
Collapse
|
36
|
Zhdanov VP. Interpretation of amperometric kinetics of content release during contacts of vesicles with a lipid membrane. EUROPEAN BIOPHYSICS JOURNAL: EBJ 2016; 46:461-470. [PMID: 27942741 DOI: 10.1007/s00249-016-1189-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/14/2016] [Revised: 10/21/2016] [Accepted: 11/28/2016] [Indexed: 11/25/2022]
Abstract
The exocytotic pathway of secretion of molecules from cells includes transport by vesicles, tether-mediated fusion of vesicles with the plasma membrane accompanied by pore formation, and diffusion-mediated release of their contents via a pore to the outside. In related basic biophysical studies, vesicle-content release is tracked by measuring corresponding amperometric spikes. Although experiments of this type have a long history, the understanding of the underlying physics is still elusive. The present study elucidates the likely contribution of line energy, membrane tension and bending, osmotic pressure, hydration forces, and tethers to the potential energy for fusion-related pore formation and evolution. The overdamped Langevin equation is used to describe the pore dynamics, which are in turn employed to calculate the kinetics of content release and to interpret the shape of amperometric spikes.
Collapse
Affiliation(s)
- Vladimir P Zhdanov
- Section of Biological Physics, Department of Physics, Chalmers University of Technology, Göteborg, Sweden.
- Boreskov Institute of Catalysis, Russian Academy of Sciences, Novosibirsk, Russia.
| |
Collapse
|
37
|
Kawamoto S, Klein ML, Shinoda W. Coarse-grained molecular dynamics study of membrane fusion: Curvature effects on free energy barriers along the stalk mechanism. J Chem Phys 2016; 143:243112. [PMID: 26723597 DOI: 10.1063/1.4933087] [Citation(s) in RCA: 50] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The effects of membrane curvature on the free energy barrier for membrane fusion have been investigated using coarse-grained molecular dynamics (CG-MD) simulations, assuming that fusion takes place through a stalk intermediate. Free energy barriers were estimated for stalk formation as well as for fusion pore formation using the guiding potential method. Specifically, the three different geometries of two apposed membranes were considered: vesicle-vesicle, vesicle-planar, and planar-planar membranes. The free energy barriers for the resulting fusion were found to depend importantly on the fusing membrane geometries; the lowest barrier was obtained for vesicular membranes. Further, lipid sorting was observed in fusion of the mixed membranes of dimyristoyl phosphatidylcholine and dioleoyl phosphatidylethanolamine (DOPE). Specifically, DOPE molecules were found to assemble around the stalk to support the highly negative curved membrane surface. A consistent result for lipid sorting was observed when a simple continuum model (CM) was used, where the Helfrich energy and mixing entropy of the lipids were taken into account. However, the CM predicts a much higher free energy barrier than found using CG-MD. This discrepancy originates from the conformational changes of lipids, which were not considered in the CM. The results of the CG-MD simulations reveal that a large conformational change in the lipid takes place around the stalk region, which results in a reduction of free energy barriers along the stalk mechanism of membrane fusion.
Collapse
Affiliation(s)
- Shuhei Kawamoto
- Department of Applied Chemistry, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi 464-8603, Japan
| | - Michael L Klein
- Institute for Computational Molecular Science, Temple University, SERC Building 1925 North 12th Street, Philadelphia, Pennsylvania 19122, USA
| | - Wataru Shinoda
- Department of Applied Chemistry, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi 464-8603, Japan
| |
Collapse
|
38
|
Li X, Murthy NS, Becker ML, Latour RA. Multiscale approach for the construction of equilibrated all-atom models of a poly(ethylene glycol)-based hydrogel. Biointerphases 2016; 11:021002. [PMID: 27013229 PMCID: PMC4808066 DOI: 10.1116/1.4944829] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2016] [Revised: 03/09/2016] [Accepted: 03/15/2016] [Indexed: 11/17/2022] Open
Abstract
A multiscale modeling approach is presented for the efficient construction of an equilibrated all-atom model of a cross-linked poly(ethylene glycol) (PEG)-based hydrogel using the all-atom polymer consistent force field (PCFF). The final equilibrated all-atom model was built with a systematic simulation toolset consisting of three consecutive parts: (1) building a global cross-linked PEG-chain network at experimentally determined cross-link density using an on-lattice Monte Carlo method based on the bond fluctuation model, (2) recovering the local molecular structure of the network by transitioning from the lattice model to an off-lattice coarse-grained (CG) model parameterized from PCFF, followed by equilibration using high performance molecular dynamics methods, and (3) recovering the atomistic structure of the network by reverse mapping from the equilibrated CG structure, hydrating the structure with explicitly represented water, followed by final equilibration using PCFF parameterization. The developed three-stage modeling approach has application to a wide range of other complex macromolecular hydrogel systems, including the integration of peptide, protein, and/or drug molecules as side-chains within the hydrogel network for the incorporation of bioactivity for tissue engineering, regenerative medicine, and drug delivery applications.
Collapse
Affiliation(s)
- Xianfeng Li
- Department of Bioengineering, Clemson University, Clemson, South Carolina 29634
| | - N Sanjeeva Murthy
- New Jersey Center for Biomaterials, Rutgers University, Piscataway, New Jersey 08854
| | - Matthew L Becker
- Departments of Polymer Science and Biomedical Engineering, The University of Akron, Akron, Ohio 44325
| | - Robert A Latour
- Department of Bioengineering, Clemson University, Clemson, South Carolina 29634
| |
Collapse
|
39
|
Streifel BC, Parker JF, Giles SL, Williams SJ, Duncan JH, Wynne JH. Porosity control in high internal phase emulsion templated polyelectrolytes via ionic crosslinking. ACTA ACUST UNITED AC 2016. [DOI: 10.1002/pola.28125] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Affiliation(s)
- Benjamin C. Streifel
- Naval Research Laboratory; 4555 Overlook Ave Washington District of Columbia 20375
| | - Joseph F. Parker
- Naval Research Laboratory; 4555 Overlook Ave Washington District of Columbia 20375
| | - Spencer L. Giles
- Naval Research Laboratory; 4555 Overlook Ave Washington District of Columbia 20375
| | - Sierra J. Williams
- Naval Research Laboratory; 4555 Overlook Ave Washington District of Columbia 20375
| | - Jesse H. Duncan
- Naval Research Laboratory; 4555 Overlook Ave Washington District of Columbia 20375
| | - James H. Wynne
- Naval Research Laboratory; 4555 Overlook Ave Washington District of Columbia 20375
| |
Collapse
|
40
|
Ramezanpour M, Leung SSW, Delgado-Magnero KH, Bashe BYM, Thewalt J, Tieleman DP. Computational and experimental approaches for investigating nanoparticle-based drug delivery systems. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2016; 1858:1688-709. [PMID: 26930298 DOI: 10.1016/j.bbamem.2016.02.028] [Citation(s) in RCA: 105] [Impact Index Per Article: 13.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/23/2016] [Revised: 02/20/2016] [Accepted: 02/23/2016] [Indexed: 12/21/2022]
Abstract
Most therapeutic agents suffer from poor solubility, rapid clearance from the blood stream, a lack of targeting, and often poor translocation ability across cell membranes. Drug/gene delivery systems (DDSs) are capable of overcoming some of these barriers to enhance delivery of drugs to their right place of action, e.g. inside cancer cells. In this review, we focus on nanoparticles as DDSs. Complementary experimental and computational studies have enhanced our understanding of the mechanism of action of nanocarriers and their underlying interactions with drugs, biomembranes and other biological molecules. We review key biophysical aspects of DDSs and discuss how computer modeling can assist in rational design of DDSs with improved and optimized properties. We summarize commonly used experimental techniques for the study of DDSs. Then we review computational studies for several major categories of nanocarriers, including dendrimers and dendrons, polymer-, peptide-, nucleic acid-, lipid-, and carbon-based DDSs, and gold nanoparticles. This article is part of a Special Issue entitled: Membrane Proteins edited by J.C. Gumbart and Sergei Noskov.
Collapse
Affiliation(s)
- M Ramezanpour
- Centre for Molecular Simulation, Department of Biological Sciences, University of Calgary, Calgary, AB T2N 1N4, Canada
| | - S S W Leung
- Department of Physics, Simon Fraser University, Burnaby, BC V5A 1S6, Canada
| | - K H Delgado-Magnero
- Centre for Molecular Simulation, Department of Biological Sciences, University of Calgary, Calgary, AB T2N 1N4, Canada
| | - B Y M Bashe
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC V5A 1S6, Canada
| | - J Thewalt
- Department of Physics, Simon Fraser University, Burnaby, BC V5A 1S6, Canada; Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC V5A 1S6, Canada
| | - D P Tieleman
- Centre for Molecular Simulation, Department of Biological Sciences, University of Calgary, Calgary, AB T2N 1N4, Canada
| |
Collapse
|
41
|
Nukui LHN, Barbosa LRS, Petri DFS. Impact of Monovalent and Divalent Cations on the Colloidal Stability of Negatively Charged Latex Particles Decorated with Poly(ethylene glycol). Ind Eng Chem Res 2016. [DOI: 10.1021/acs.iecr.5b04103] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Larissa H. N. Nukui
- Instituto
de Química, Universidade de São Paulo, P.O. Box 26077, São
Paulo, SP 05513-970, Brazil
| | | | - Denise F. S. Petri
- Instituto
de Química, Universidade de São Paulo, P.O. Box 26077, São
Paulo, SP 05513-970, Brazil
| |
Collapse
|
42
|
Pluhackova K, Böckmann RA. Biomembranes in atomistic and coarse-grained simulations. JOURNAL OF PHYSICS. CONDENSED MATTER : AN INSTITUTE OF PHYSICS JOURNAL 2015. [PMID: 26194872 DOI: 10.1088/0953-8984/27/32/323103] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Abstract
The architecture of biological membranes is tightly coupled to the localization, organization, and function of membrane proteins. The organelle-specific distribution of lipids allows for the formation of functional microdomains (also called rafts) that facilitate the segregation and aggregation of membrane proteins and thus shape their function. Molecular dynamics simulations enable to directly access the formation, structure, and dynamics of membrane microdomains at the molecular scale and the specific interactions among lipids and proteins on timescales from picoseconds to microseconds. This review focuses on the latest developments of biomembrane force fields for both atomistic and coarse-grained molecular dynamics (MD) simulations, and the different levels of coarsening of biomolecular structures. It also briefly introduces scale-bridging methods applicable to biomembrane studies, and highlights selected recent applications.
Collapse
Affiliation(s)
- Kristyna Pluhackova
- Computational Biology, Department of Biology, Friedrich-Alexander Universität Erlangen-Nürnberg, Staudtstr. 5, 91058 Erlangen, Germany
| | | |
Collapse
|
43
|
Leman JK, Ulmschneider MB, Gray JJ. Computational modeling of membrane proteins. Proteins 2015; 83:1-24. [PMID: 25355688 PMCID: PMC4270820 DOI: 10.1002/prot.24703] [Citation(s) in RCA: 81] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2014] [Revised: 10/01/2014] [Accepted: 10/18/2014] [Indexed: 02/06/2023]
Abstract
The determination of membrane protein (MP) structures has always trailed that of soluble proteins due to difficulties in their overexpression, reconstitution into membrane mimetics, and subsequent structure determination. The percentage of MP structures in the protein databank (PDB) has been at a constant 1-2% for the last decade. In contrast, over half of all drugs target MPs, only highlighting how little we understand about drug-specific effects in the human body. To reduce this gap, researchers have attempted to predict structural features of MPs even before the first structure was experimentally elucidated. In this review, we present current computational methods to predict MP structure, starting with secondary structure prediction, prediction of trans-membrane spans, and topology. Even though these methods generate reliable predictions, challenges such as predicting kinks or precise beginnings and ends of secondary structure elements are still waiting to be addressed. We describe recent developments in the prediction of 3D structures of both α-helical MPs as well as β-barrels using comparative modeling techniques, de novo methods, and molecular dynamics (MD) simulations. The increase of MP structures has (1) facilitated comparative modeling due to availability of more and better templates, and (2) improved the statistics for knowledge-based scoring functions. Moreover, de novo methods have benefited from the use of correlated mutations as restraints. Finally, we outline current advances that will likely shape the field in the forthcoming decade.
Collapse
Affiliation(s)
- Julia Koehler Leman
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, MD 21218, USA
| | - Martin B. Ulmschneider
- Department of Materials Science and Engineering, Johns Hopkins University, Baltimore, MD 21218, USA
| | - Jeffrey J. Gray
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, MD 21218, USA
| |
Collapse
|