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Lado-Touriño I, Cerpa-Naranjo A. Coarse-Grained Molecular Dynamics of pH-Sensitive Lipids. Int J Mol Sci 2023; 24:ijms24054632. [PMID: 36902063 PMCID: PMC10003205 DOI: 10.3390/ijms24054632] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2023] [Revised: 02/20/2023] [Accepted: 02/25/2023] [Indexed: 03/06/2023] Open
Abstract
pH-sensitive lipids represent a class of lipids that can be protonated and destabilized in acidic environments, as they become positively charged in response to low-pH conditions. They can be incorporated into lipidic nanoparticles such as liposomes, which are able to change their properties and allow specific drug delivery at the acidic conditions encountered in some pathological microenvironments. In this work, we used coarse-grained molecular-dynamic simulations to study the stability of neutral and charged lipid bilayers containing POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine) and various kinds of ISUCA ((F)2-(imidazol-1-yl)succinic acid)-derived lipids, which can act as pH-sensitive molecules. In order to explore such systems, we used a MARTINI-derived forcefield, previously parameterized using all-atom simulation results. We calculated the average area per lipid, the second-rank order parameter and the lipid diffusion coefficient of both lipid bilayers made of pure components and mixtures of lipids in different proportions, under neutral or acidic conditions. The results show that the use of ISUCA-derived lipids disturbs the lipid bilayer structure, with the effect being particularly marked under acidic conditions. Although more-in depth studies on these systems must be carried out, these initial results are encouraging and the lipids designed in this research could be a good basis for developing new pH-sensitive liposomes.
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Kahana A, Lancet D. Protobiotic Systems Chemistry Analyzed by Molecular Dynamics. Life (Basel) 2019; 9:E38. [PMID: 31083329 PMCID: PMC6617412 DOI: 10.3390/life9020038] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2019] [Revised: 05/06/2019] [Accepted: 05/08/2019] [Indexed: 12/16/2022] Open
Abstract
Systems chemistry has been a key component of origin of life research, invoking models of life's inception based on evolving molecular networks. One such model is the graded autocatalysis replication domain (GARD) formalism embodied in a lipid world scenario, which offers rigorous computer simulation based on defined chemical kinetics equations. GARD suggests that the first pre-RNA life-like entities could have been homeostatically-growing assemblies of amphiphiles, undergoing compositional replication and mutations, as well as rudimentary selection and evolution. Recent progress in molecular dynamics has provided an experimental tool to study complex biological phenomena such as protein folding, ligand-receptor interactions, and micellar formation, growth, and fission. The detailed molecular definition of GARD and its inter-molecular catalytic interactions make it highly compatible with molecular dynamics analyses. We present a roadmap for simulating GARD's kinetic and thermodynamic behavior using various molecular dynamics methodologies. We review different approaches for testing the validity of the GARD model by following micellar accretion and fission events and examining compositional changes over time. Near-future computational advances could provide empirical delineation for further system complexification, from simple compositional non-covalent assemblies towards more life-like protocellular entities with covalent chemistry that underlies metabolism and genetic encoding.
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Affiliation(s)
- Amit Kahana
- Dept. Molecular Genetics, The Weizmann Institute of Science, Rehovot 7610010, Israel.
| | - Doron Lancet
- Dept. Molecular Genetics, The Weizmann Institute of Science, Rehovot 7610010, Israel.
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Stano P. Is Research on "Synthetic Cells" Moving to the Next Level? Life (Basel) 2018; 9:E3. [PMID: 30587790 PMCID: PMC6463193 DOI: 10.3390/life9010003] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2018] [Revised: 12/20/2018] [Accepted: 12/21/2018] [Indexed: 12/15/2022] Open
Abstract
"Synthetic cells" research focuses on the construction of cell-like models by using solute-filled artificial microcompartments with a biomimetic structure. In recent years this bottom-up synthetic biology area has considerably progressed, and the field is currently experiencing a rapid expansion. Here we summarize some technical and theoretical aspects of synthetic cells based on gene expression and other enzymatic reactions inside liposomes, and comment on the most recent trends. Such a tour will be an occasion for asking whether times are ripe for a sort of qualitative jump toward novel SC prototypes: is research on "synthetic cells" moving to a next level?
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Affiliation(s)
- Pasquale Stano
- Department of Biological and Environmental Sciences and Technologies (DiSTeBA), University of Salento; Ecotekne-S.P. Lecce-Monteroni, I-73100 Lecce, Italy.
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Altamura E, Carrara P, D'Angelo F, Mavelli F, Stano P. Extrinsic stochastic factors (solute partition) in gene expression inside lipid vesicles and lipid-stabilized water-in-oil droplets: a review. Synth Biol (Oxf) 2018; 3:ysy011. [PMID: 32995519 PMCID: PMC7445889 DOI: 10.1093/synbio/ysy011] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2017] [Revised: 06/18/2018] [Accepted: 06/21/2018] [Indexed: 11/13/2022] Open
Abstract
The encapsulation of transcription-translation (TX-TL) machinery inside lipid vesicles and water-in-oil droplets leads to the construction of cytomimetic systems (often called 'synthetic cells') for synthetic biology and origins-of-life research. A number of recent reports have shown that protein synthesis inside these microcompartments is highly diverse in terms of rate and amount of synthesized protein. Here, we discuss the role of extrinsic stochastic effects (i.e. solute partition phenomena) as relevant factors contributing to this pattern. We evidence and discuss cases where between-compartment diversity seems to exceed the expected theoretical values. The need of accurate determination of solute content inside individual vesicles or droplets is emphasized, aiming at validating or rejecting the predictions calculated from the standard fluctuations theory. At the same time, we promote the integration of experiments and stochastic modeling to reveal the details of solute encapsulation and intra-compartment reactions.
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Affiliation(s)
- Emiliano Altamura
- Chemistry Department, University of Bari, Via E. Orabona 4, I-70126, Bari, Italy
| | - Paolo Carrara
- Department of Sciences, Roma Tre University, Viale G. Marconi 446, I-00146, Rome, Italy
| | - Francesca D'Angelo
- Department of Sciences, Roma Tre University, Viale G. Marconi 446, I-00146, Rome, Italy
| | - Fabio Mavelli
- Chemistry Department, University of Bari, Via E. Orabona 4, I-70126, Bari, Italy
| | - Pasquale Stano
- Department of Biological and Environmental Sciences and Technologies (DiSTeBA), University of Salento, Ecotekne, I-73100, Lecce, Italy
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Bunker A, Magarkar A, Viitala T. Rational design of liposomal drug delivery systems, a review: Combined experimental and computational studies of lipid membranes, liposomes and their PEGylation. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2016; 1858:2334-2352. [DOI: 10.1016/j.bbamem.2016.02.025] [Citation(s) in RCA: 103] [Impact Index Per Article: 12.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/21/2015] [Revised: 02/09/2016] [Accepted: 02/10/2016] [Indexed: 01/22/2023]
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Smeijers A, Markvoort A, Pieterse K, Hilbers P. Coarse-grained modelling of urea-adamantyl functionalised poly(propylene imine) dendrimers. MOLECULAR SIMULATION 2015. [DOI: 10.1080/08927022.2015.1096359] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Affiliation(s)
- A.F. Smeijers
- Computational Biology, Department of Biomedical Engineering, Technische Universiteit Eindhoven, Eindhoven, the Netherlands
| | - A.J. Markvoort
- Computational Biology, Department of Biomedical Engineering, Technische Universiteit Eindhoven, Eindhoven, the Netherlands
- Institute for Complex Molecular Systems, Technische Universiteit Eindhoven, Eindhoven, the Netherlands
| | - K. Pieterse
- Computational Biology, Department of Biomedical Engineering, Technische Universiteit Eindhoven, Eindhoven, the Netherlands
- Institute for Complex Molecular Systems, Technische Universiteit Eindhoven, Eindhoven, the Netherlands
| | - P.A.J. Hilbers
- Computational Biology, Department of Biomedical Engineering, Technische Universiteit Eindhoven, Eindhoven, the Netherlands
- Institute for Complex Molecular Systems, Technische Universiteit Eindhoven, Eindhoven, the Netherlands
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D'Aguanno E, Altamura E, Mavelli F, Fahr A, Stano P, Luisi PL. Physical Routes to Primitive Cells: An Experimental Model Based on the Spontaneous Entrapment of Enzymes inside Micrometer-Sized Liposomes. Life (Basel) 2015; 5:969-96. [PMID: 25793278 PMCID: PMC4390888 DOI: 10.3390/life5010969] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2015] [Accepted: 03/10/2015] [Indexed: 01/18/2023] Open
Abstract
How did primitive living cells originate? The formation of early cells, which were probably solute-filled vesicles capable of performing a rudimentary metabolism (and possibly self-reproduction), is still one of the big unsolved questions in origin of life. We have recently used lipid vesicles (liposomes) as primitive cell models, aiming at the study of the physical mechanisms for macromolecules encapsulation. We have reported that proteins and ribosomes can be encapsulated very efficiently, against statistical expectations, inside a small number of liposomes. Moreover the transcription-translation mixture, which realistically mimics a sort of minimal metabolic network, can be functionally reconstituted in liposomes owing to a self-concentration mechanism. Here we firstly summarize the recent advancements in this research line, highlighting how these results open a new vista on the phenomena that could have been important for the formation of functional primitive cells. Then, we present new evidences on the non-random entrapment of macromolecules (proteins, dextrans) in phospholipid vesicle, and in particular we show how enzymatic reactions can be accelerated because of the enhancement of their concentration inside liposomes.
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Affiliation(s)
- Erica D'Aguanno
- Science Department, Roma Tre University, Viale G. Marconi 446, I-00146 Rome, Italy.
- Institut für Pharmazie, Friedrich-Schiller-Universität Jena, Lessingstraße 8, D-07743 Jena, Germany.
| | - Emiliano Altamura
- Science Department, Roma Tre University, Viale G. Marconi 446, I-00146 Rome, Italy.
- Chemistry Department, University of Bari, Via E. Orabona 4, I-70125 Bari, Italy.
| | - Fabio Mavelli
- Chemistry Department, University of Bari, Via E. Orabona 4, I-70125 Bari, Italy.
| | - Alfred Fahr
- Institut für Pharmazie, Friedrich-Schiller-Universität Jena, Lessingstraße 8, D-07743 Jena, Germany.
| | - Pasquale Stano
- Science Department, Roma Tre University, Viale G. Marconi 446, I-00146 Rome, Italy.
| | - Pier Luigi Luisi
- Science Department, Roma Tre University, Viale G. Marconi 446, I-00146 Rome, Italy.
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de Souza TP, Fahr A, Luisi PL, Stano P. Spontaneous Encapsulation and Concentration of Biological Macromolecules in Liposomes: An Intriguing Phenomenon and Its Relevance in Origins of Life. J Mol Evol 2014; 79:179-92. [DOI: 10.1007/s00239-014-9655-7] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2014] [Accepted: 11/10/2014] [Indexed: 12/31/2022]
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van Hoof B, Markvoort AJ, van Santen RA, Hilbers PAJ. Molecular Simulation of Protein Encapsulation in Vesicle Formation. J Phys Chem B 2014; 118:3346-54. [DOI: 10.1021/jp410612k] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Bram van Hoof
- Department of Biomedical Engineering, ‡Institute for Complex
Molecular
Systems, and §Department of Chemical Engineering and Chemistry, Eindhoven University of Technology,
P. O. Box 513, 5600 MB Eindhoven, The Netherlands
| | - Albert J. Markvoort
- Department of Biomedical Engineering, ‡Institute for Complex
Molecular
Systems, and §Department of Chemical Engineering and Chemistry, Eindhoven University of Technology,
P. O. Box 513, 5600 MB Eindhoven, The Netherlands
| | - Rutger A. van Santen
- Department of Biomedical Engineering, ‡Institute for Complex
Molecular
Systems, and §Department of Chemical Engineering and Chemistry, Eindhoven University of Technology,
P. O. Box 513, 5600 MB Eindhoven, The Netherlands
| | - Peter A. J. Hilbers
- Department of Biomedical Engineering, ‡Institute for Complex
Molecular
Systems, and §Department of Chemical Engineering and Chemistry, Eindhoven University of Technology,
P. O. Box 513, 5600 MB Eindhoven, The Netherlands
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Olasagasti F, Maurel MC, Deamer D. Physico-chemical interactions between compartment-forming lipids and other prebiotically relevant biomolecules. BIO WEB OF CONFERENCES 2014. [DOI: 10.1051/bioconf/20140205001] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
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