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Ahyayauch H, Masserini ME, Alonso A, Goñi FM. Understanding Aβ Peptide Binding to Lipid Membranes: A Biophysical Perspective. Int J Mol Sci 2024; 25:6401. [PMID: 38928107 PMCID: PMC11203662 DOI: 10.3390/ijms25126401] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2024] [Revised: 05/27/2024] [Accepted: 06/05/2024] [Indexed: 06/28/2024] Open
Abstract
Aβ peptides are known to bind neural plasma membranes in a process leading to the deposit of Aβ-enriched plaques. These extracellular structures are characteristic of Alzheimer's disease, the major cause of late-age dementia. The mechanisms of Aβ plaque formation and deposition are far from being understood. A vast number of studies in the literature describe the efforts to analyze those mechanisms using a variety of tools. The present review focuses on biophysical studies mostly carried out with model membranes or with computational tools. This review starts by describing basic physical aspects of lipid phases and commonly used model membranes (monolayers and bilayers). This is followed by a discussion of the biophysical techniques applied to these systems, mainly but not exclusively Langmuir monolayers, isothermal calorimetry, density-gradient ultracentrifugation, and molecular dynamics. The Methodological Section is followed by the core of the review, which includes a summary of important results obtained with each technique. The last section is devoted to an overall reflection and an effort to understand Aβ-bilayer binding. Concepts such as Aβ peptide membrane binding, adsorption, and insertion are defined and differentiated. The roles of membrane lipid order, nanodomain formation, and electrostatic forces in Aβ-membrane interaction are separately identified and discussed.
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Affiliation(s)
- Hasna Ahyayauch
- Departamento de Bioquímica, Instituto Biofisika (CSIC, UPV/EHU), Universidad del País Vasco, 48940 Leioa, Spain; (H.A.); (A.A.)
- Institut Supérieur des Professions Infirmières et Techniques de Santé, Rabat 60000, Morocco
- Laboratoire de Biologie et Santé, Unité Neurosciences, Neuroimmunologie et Comportement, Faculty of Sciences, Ibn Tofail University, Kénitra 14000, Morocco
| | - Massimo E. Masserini
- School of Medicine and Surgery, University of Milano-Bicocca, 20900 Monza, Italy;
| | - Alicia Alonso
- Departamento de Bioquímica, Instituto Biofisika (CSIC, UPV/EHU), Universidad del País Vasco, 48940 Leioa, Spain; (H.A.); (A.A.)
| | - Félix M. Goñi
- Departamento de Bioquímica, Instituto Biofisika (CSIC, UPV/EHU), Universidad del País Vasco, 48940 Leioa, Spain; (H.A.); (A.A.)
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2
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Zonta F, Mammano F, Pantano S. Molecular Dynamics Simulation of Permeation Through Connexin Channels. Methods Mol Biol 2024; 2801:45-56. [PMID: 38578412 DOI: 10.1007/978-1-0716-3842-2_4] [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] [Indexed: 04/06/2024]
Abstract
Molecular dynamics (MD) simulations are a collection of computational tools that can be used to trace intermolecular interactions at the sub-nanometer level. They offer possibilities that are often unavailable to experimental methods, making MD an ideal complementary technique for the understanding a plethora of biological processes. Thanks to significant efforts by many groups of developers around the world, setting up and running MD simulations has become progressively simpler. However, simulating ionic permeation through membrane channels still presents significant caveats.MD simulations of connexin (Cx) hemichannels (HCs) are particularly problematic because HCs create wide pores in the plasma membrane, and the lateral sizes of the extracellular and intracellular regions are quite different. In this chapter, we provide a detailed instruction to perform MD simulations aimed at computationally modeling the permeation of inorganic ions and larger molecules through Cx HCs.
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Affiliation(s)
- Francesco Zonta
- Department of Biological Sciences, School of Science, Xi'an Jiaotong-Liverpool University, Suzhou, China.
| | - Fabio Mammano
- Department of Physics and Astronomy "G. Galilei", University of Padova, Padova, Italy
- Institute of Biochemistry and Cell Biology, Italian National Research Council, Rome, Italy
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3
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Trofimenko E, Grasso G, Heulot M, Chevalier N, Deriu MA, Dubuis G, Arribat Y, Serulla M, Michel S, Vantomme G, Ory F, Dam LC, Puyal J, Amati F, Lüthi A, Danani A, Widmann C. Genetic, cellular, and structural characterization of the membrane potential-dependent cell-penetrating peptide translocation pore. eLife 2021; 10:69832. [PMID: 34713805 PMCID: PMC8639150 DOI: 10.7554/elife.69832] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2021] [Accepted: 10/28/2021] [Indexed: 12/11/2022] Open
Abstract
Cell-penetrating peptides (CPPs) allow intracellular delivery of bioactive cargo molecules. The mechanisms allowing CPPs to enter cells are ill-defined. Using a CRISPR/Cas9-based screening, we discovered that KCNQ5, KCNN4, and KCNK5 potassium channels positively modulate cationic CPP direct translocation into cells by decreasing the transmembrane potential (Vm). These findings provide the first unbiased genetic validation of the role of Vm in CPP translocation in cells. In silico modeling and live cell experiments indicate that CPPs, by bringing positive charges on the outer surface of the plasma membrane, decrease the Vm to very low values (–150 mV or less), a situation we have coined megapolarization that then triggers formation of water pores used by CPPs to enter cells. Megapolarization lowers the free energy barrier associated with CPP membrane translocation. Using dyes of varying dimensions in CPP co-entry experiments, the diameter of the water pores in living cells was estimated to be 2 (–5) nm, in accordance with the structural characteristics of the pores predicted by in silico modeling. Pharmacological manipulation to lower transmembrane potential boosted CPP cellular internalization in zebrafish and mouse models. Besides identifying the first proteins that regulate CPP translocation, this work characterized key mechanistic steps used by CPPs to cross cellular membranes. This opens the ground for strategies aimed at improving the ability of cells to capture CPP-linked cargos in vitro and in vivo. Before a drug can have its desired effect, it must reach its target tissue or organ, and enter its cells. This is not easy because cells are surrounded by the plasma membrane, a fat-based barrier that separates the cell from its external environment. The plasma membrane contains proteins that act as channels, shuttling specific molecules in and out of the cell, and it also holds charge, with its inside surface being more negatively charged than its outside surface. Cell-penetrating peptides are short sequences of amino acids (the building blocks that form proteins) that carry positive charges. These positive charges allow them to cross the membrane easily, but it is not well understood how. To find out how cell-penetrating peptides cross the membrane, Trofimenko et al. attached them to dyes of different sizes. This revealed that the cell-penetrating peptides enter the cell through temporary holes called water pores, which measure about two nanometres across. The water pores form when the membrane becomes ‘megapolarized’, this is, when the difference in charge between the inside and the outside of the membrane becomes greater than normal. This can happen when the negative charge on the inside surface or the positive charge on the outer surface of the membrane increase. Megapolarization depends on potassium channels, which transport positive potassium ions outside the cell, making the outside of the membrane positive. When cell-penetrating peptides arrive at the outer surface of the cell near potassium channels, they make it even more positive. This increases the charge difference between the inside and the outside of the cell, allowing water pores to form. Once the peptides pass through the pores, the charge difference between the inside and the outside of the cell membrane dissipates, and the pores collapse. Drug developers are experimenting with attaching cell-penetrating peptides to drugs to help them get inside their target cells. Currently there are several experimental medications of this kind in clinical trials. Understanding how these peptides gain entry, and what size of molecule they could carry with them, provides solid ground for further drug development.
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Affiliation(s)
- Evgeniya Trofimenko
- Department of Biomedical Sciences, University of Lausanne, Lausanne, Switzerland
| | - Gianvito Grasso
- Dalle Molle Institute for Artificial Intelligence Research, Università della Svizzera italiana, Scuola Universitaria Professionale della Svizzera Italiana, Lugano, Switzerland
| | - Mathieu Heulot
- Department of Biomedical Sciences, University of Lausanne, Lausanne, Switzerland
| | - Nadja Chevalier
- Department of Biomedical Sciences, University of Lausanne, Lausanne, Switzerland
| | - Marco A Deriu
- PolitoBIOMed Lab Department of Mechanical and Aerospace Engineering, Politecnico di Torino, Torino, Italy
| | - Gilles Dubuis
- Department of Biomedical Sciences, University of Lausanne, Lausanne, Switzerland
| | - Yoan Arribat
- Department of Biomedical Sciences, University of Lausanne, Lausanne, Switzerland
| | - Marc Serulla
- Department of Biomedical Sciences, University of Lausanne, Lausanne, Switzerland
| | - Sebastien Michel
- Department of Biomedical Sciences, University of Lausanne, Lausanne, Switzerland
| | - Gil Vantomme
- Department of Fundamental Neurosciences, University of Lausanne, Lausanne, Switzerland
| | - Florine Ory
- Department of Biomedical Sciences, University of Lausanne, Lausanne, Switzerland
| | - Linh Chi Dam
- Department of Biomedical Sciences, University of Lausanne, Lausanne, Switzerland
| | - Julien Puyal
- Department of Fundamental Neurosciences, University of Lausanne, Lausanne, Switzerland.,CURML (University Center of Legal Medicine), Lausanne University Hospital, Lausanne, Switzerland
| | - Francesca Amati
- Department of Biomedical Sciences, University of Lausanne, Lausanne, Switzerland
| | - Anita Lüthi
- Department of Fundamental Neurosciences, University of Lausanne, Lausanne, Switzerland
| | - Andrea Danani
- Dalle Molle Institute for Artificial Intelligence Research, Università della Svizzera italiana, Scuola Universitaria Professionale della Svizzera Italiana, Lugano, Switzerland
| | - Christian Widmann
- Department of Biomedical Sciences, University of Lausanne, Lausanne, Switzerland
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Hsu WS, Preet A, Lin TY, Lin TE. Miniaturized Salinity Gradient Energy Harvesting Devices. Molecules 2021; 26:molecules26185469. [PMID: 34576940 PMCID: PMC8466105 DOI: 10.3390/molecules26185469] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2021] [Revised: 08/28/2021] [Accepted: 08/30/2021] [Indexed: 11/16/2022] Open
Abstract
Harvesting salinity gradient energy, also known as "osmotic energy" or "blue energy", generated from the free energy mixing of seawater and fresh river water provides a renewable and sustainable alternative for circumventing the recent upsurge in global energy consumption. The osmotic pressure resulting from mixing water streams with different salinities can be converted into electrical energy driven by a potential difference or ionic gradients. Reversed-electrodialysis (RED) has become more prominent among the conventional membrane-based separation methodologies due to its higher energy efficiency and lesser susceptibility to membrane fouling than pressure-retarded osmosis (PRO). However, the ion-exchange membranes used for RED systems often encounter limitations while adapting to a real-world system due to their limited pore sizes and internal resistance. The worldwide demand for clean energy production has reinvigorated the interest in salinity gradient energy conversion. In addition to the large energy conversion devices, the miniaturized devices used for powering a portable or wearable micro-device have attracted much attention. This review provides insights into developing miniaturized salinity gradient energy harvesting devices and recent advances in the membranes designed for optimized osmotic power extraction. Furthermore, we present various applications utilizing the salinity gradient energy conversion.
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Affiliation(s)
- Wei-Shan Hsu
- Institute of Biomedical Engineering, College of Electrical and Computer Engineering, National Yang Ming Chiao Tung University, Hsinchu 30010, Taiwan; (W.-S.H.); or (A.P.)
| | - Anant Preet
- Institute of Biomedical Engineering, College of Electrical and Computer Engineering, National Yang Ming Chiao Tung University, Hsinchu 30010, Taiwan; (W.-S.H.); or (A.P.)
- Chemical Biology and Molecular Biophysics Program, Taiwan International Graduate Program, Institute of Biological Chemistry, Academia Sinica, Nankang, Taipei 115, Taiwan
- Department of Chemistry, College of Science, National Taiwan University, Taipei 10617, Taiwan
| | - Tung-Yi Lin
- Institute of Traditional Medicine, College of Medicine, National Yang Ming Chiao Tung University, Taipei 11221, Taiwan;
- Program in Molecular Medicine, College of Life Sciences, National Yang Ming Chiao Tung University, Taipei 11221, Taiwan
- Biomedical Industry Ph.D. Program, College of Life Sciences, National Yang Ming Chiao Tung University, Taipei 11221, Taiwan
| | - Tzu-En Lin
- Institute of Biomedical Engineering, College of Electrical and Computer Engineering, National Yang Ming Chiao Tung University, Hsinchu 30010, Taiwan; (W.-S.H.); or (A.P.)
- Correspondence: ; Tel.: +886-(03)-573-1750
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5
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Ivanova N, Ivanova A. Influence of the dimensionality of the periodic boundary conditions on the transport of a drug-peptide complex across model cell membranes. J Biomol Struct Dyn 2021; 40:5345-5356. [PMID: 33416039 DOI: 10.1080/07391102.2020.1870157] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Abstract
Many research efforts are devoted to improving the efficiency of chemotherapy. One of the aspects is to facilitate the transport of drugs across the cell membranes by attaching the therapeutics to a carrier molecule. The current study focuses on computational investigation of such a system with doxorubicin as the model drug, which is covalently bound to a cell-penetrating peptide. The correct description of its membrane translocation at the molecular level requires proper choice of the model membrane and of the simulation parameters. For the purpose, two phospholipid bilayers are built, one containing solely DPPC and another with mixed lipid content mimicking the composition of a human erythrocyte membrane. Atomistic molecular dynamics simulations are carried out in two types of periodic boundary conditions (2D and 3D PBC), in order to assess the effect of the periodicity dimensionality on the intermolecular interactions. The evolution of some basic characteristics of the bilayers and of the drug-peptide complex is tracked: mass density profiles, electrostatic potentials, lateral diffusion coefficients and areas per lipid, lipid-complex radial distribution functions, secondary structure of the peptide and orientation of the drug relative to the membrane. Thus, the influence of the periodic boundary conditions is quantified and it shows that the mixed system in 3D PBC is the most suitable for analysis of the translocation of the transporting moiety across cell membranes.
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Affiliation(s)
- Nikoleta Ivanova
- Department of Physical Chemistry, Laboratory of Quantum and Computational Chemistry, Faculty of Chemistry and Pharmacy, University of Sofia, Sofia, Bulgaria
| | - Anela Ivanova
- Department of Physical Chemistry, Laboratory of Quantum and Computational Chemistry, Faculty of Chemistry and Pharmacy, University of Sofia, Sofia, Bulgaria
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6
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Ahyayauch H, García-Arribas AB, Masserini ME, Pantano S, Goñi FM, Alonso A. β-Amyloid (1-42) peptide adsorbs but does not insert into ganglioside-containing phospholipid membranes in the liquid-disordered state: modelling and experimental studies. Int J Biol Macromol 2020; 164:2651-2658. [PMID: 32846182 DOI: 10.1016/j.ijbiomac.2020.08.165] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2020] [Revised: 08/09/2020] [Accepted: 08/21/2020] [Indexed: 12/14/2022]
Abstract
β-Amyloid (Aβ) is a 39-43 residue peptide involved in the pathogenesis of Alzheimer's disease. Aβ deposits onto the cells and gives rise to the plaques that are characteristic of the disease. In an effort to understand the molecular mechanism of plaque formation, we have examined the interaction of Aβ42, considered to be the most pathogenic of the peptides, with lipid bilayers consisting of 1-palmitoyl-2-oleoyl phosphatidylcholine (POPC) to which small amounts of GM1 ganglioside (1-5 mol%) were incorporated. POPC bilayers exist in the fluid, or liquid-disordered state at room temperature, mimicking the fluidity of cell membranes. An Aβ42 preparation consisting essentially of peptide monomers was used. A combination of molecular dynamics (MD), isothermal calorimetry and Langmuir balance measurements was applied. Our results show that Aβ binds POPC bilayers, and that binding increases (ΔG of binding decreases) with GM1, but only up to 3 mol% of the ganglioside, larger concentrations appearing to have a lower effect. MD and Langmuir balance measurements concur in showing that the peptide adsorbs onto the bilayer surface, but does not become inserted into it at surface pressures compatible with the cell membrane conditions. Thioflavin T measurements agree with MD in revealing a very low degree of peptide oligomerization/aggregation under our conditions. This is in contrast with previous studies showing peptide aggregation and insertion when interacting with membranes in the liquid-ordered state. The present contribution underlines the importance of bilayer lipid composition and properties for Aβ plaque formation.
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Affiliation(s)
- Hasna Ahyayauch
- Instituto Biofisika (CSIC, UPV/EHU) and Departamento de Bioquímica, Universidad del País Vasco, Bilbao, Spain; Institut Supérieur des Professions Infirmières et Techniques de Santé, Rabat, Morocco; Neuroendocrinology Unit, Laboratory of Genetics, Neuroendocrinology and Biotechnology, Faculty of Sciences, Ibn Tofail University, Kénitra, Morocco
| | - Aritz B García-Arribas
- Instituto Biofisika (CSIC, UPV/EHU) and Departamento de Bioquímica, Universidad del País Vasco, Bilbao, Spain
| | | | - Sergio Pantano
- Biomolecular Simulations Group, Institut Pasteur de Montevideo, Montevideo, Uruguay
| | - Félix M Goñi
- Instituto Biofisika (CSIC, UPV/EHU) and Departamento de Bioquímica, Universidad del País Vasco, Bilbao, Spain
| | - Alicia Alonso
- Instituto Biofisika (CSIC, UPV/EHU) and Departamento de Bioquímica, Universidad del País Vasco, Bilbao, Spain.
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7
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Barrera EE, Frigini EN, Porasso RD, Pantano S. Modeling DMPC lipid membranes with SIRAH force-field. J Mol Model 2017; 23:259. [PMID: 28799119 DOI: 10.1007/s00894-017-3426-5] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2017] [Accepted: 07/19/2017] [Indexed: 10/19/2022]
Abstract
Coarse-grained simulation schemes are increasingly gaining popularity in the scientific community because of the significant speed up granted, allowing a considerable expansion of the accessible time and size scales accessible to molecular simulations. However, the number of compatible force fields capable of representing ensembles containing different molecular species (i.e., Protein, DNA, etc) is still limited. Here, we present a set of parameters and simplified representation for lipids compatible with the SIRAH force field for coarse-grained simulations ( http://www.sirahff.com ). We show that the present model not only achieves a correct reproduction of structural parameters as area per lipid and thickness, but also dynamic descriptors such as diffusion coefficient, order parameters, and proper temperature driven variations. Adding phospholipid membranes to the existing aqueous solution, protein and DNA representations of the SIRAH force field permit considering the most common problems tackled by the biomolecular simulation community.
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Affiliation(s)
- Exequiel E Barrera
- Biomolecular Simulations Group, Institut Pasteur de Montevideo, Mataojo 2020, 11400, Montevideo, Uruguay.
| | - Ezequiel N Frigini
- Instituto de Matemática Aplicada San Luis (IMASL), CONICET, Facultad de Ciencias Físico Matemáticas y Naturales, Universidad Nacional de San Luis, Av. Ejército de los Andes 950, 5700, San Luis, Argentina
| | - Rodolfo D Porasso
- Instituto de Matemática Aplicada San Luis (IMASL), CONICET, Facultad de Ciencias Físico Matemáticas y Naturales, Universidad Nacional de San Luis, Av. Ejército de los Andes 950, 5700, San Luis, Argentina
| | - Sergio Pantano
- Biomolecular Simulations Group, Institut Pasteur de Montevideo, Mataojo 2020, 11400, Montevideo, Uruguay
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Kirsch SA, Böckmann RA. Membrane pore formation in atomistic and coarse-grained simulations. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2015; 1858:2266-2277. [PMID: 26748016 DOI: 10.1016/j.bbamem.2015.12.031] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/15/2015] [Revised: 12/23/2015] [Accepted: 12/24/2015] [Indexed: 12/26/2022]
Abstract
Biological cells and their organelles are protected by ultra thin membranes. These membranes accomplish a broad variety of important tasks like separating the cell content from the outer environment, they are the site for cell-cell interactions and many enzymatic reactions, and control the in- and efflux of metabolites. For certain physiological functions e.g. in the fusion of membranes and also in a number of biotechnological applications like gene transfection the membrane integrity needs to be compromised to allow for instance for the exchange of polar molecules across the membrane barrier. Mechanisms enabling the transport of molecules across the membrane involve membrane proteins that form specific pores or act as transporters, but also so-called lipid pores induced by external fields, stress, or peptides. Recent progress in the simulation field enabled to closely mimic pore formation as supposed to occur in vivo or in vitro. Here, we review different simulation-based approaches in the study of membrane pores with a focus on lipid pore properties such as their size and energetics, poration mechanisms based on the application of external fields, charge imbalances, or surface tension, and on pores that are induced by small molecules, peptides, and lipids. This article is part of a Special Issue entitled: Biosimulations edited by Ilpo Vattulainen and Tomasz Róg.
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Affiliation(s)
- Sonja A Kirsch
- 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.
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Abstract
Complex biological systems are intimately linked to their environment, a very crowded and equally complex solution compartmentalized by fluid membranes. Modeling such systems remains challenging and requires a suitable representation of these solutions and their interfaces. Here, we focus on particle-based modeling at an atomistic level using molecular dynamics (MD) simulations. As an example, we discuss important steps in modeling the solution chemistry of an ion channel of the ligand-gated ion channel receptor family, a major target of many drugs including anesthetics and addiction treatments. The bacterial pentameric ligand-gated ion channel (pLGIC) called GLIC provides clues about the functional importance of solvation, in particular for mechanisms such as permeation and gating. We present some current challenges along with promising novel modeling approaches.
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10
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Darré L, Tek A, Baaden M, Pantano S. Mixing Atomistic and Coarse Grain Solvation Models for MD Simulations: Let WT4 Handle the Bulk. J Chem Theory Comput 2012; 8:3880-94. [DOI: 10.1021/ct3001816] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Affiliation(s)
- Leonardo Darré
- Institut Pasteur de Montevideo,
Mataojo 2020, CP 11400, Uruguay
| | - Alex Tek
- Laboratoire de Biochimie Théorique,
CNRS, UPR9080, Univ Paris Diderot, Sorbonne Paris Cité. 13
rue Pierre et Marie Curie, 75005, Paris, France
- Université Pierre et Marie
Curie, UPMC Sorbonne Universités, 4 place Jussieu 75005 Paris,
France
| | - Marc Baaden
- Laboratoire de Biochimie Théorique,
CNRS, UPR9080, Univ Paris Diderot, Sorbonne Paris Cité. 13
rue Pierre et Marie Curie, 75005, Paris, France
| | - Sergio Pantano
- Institut Pasteur de Montevideo,
Mataojo 2020, CP 11400, Uruguay
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11
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Herrera FE, Bouchet A, Lairion F, Disalvo EA, Pantano S. Molecular Dynamics Study of the Interaction of Arginine with Phosphatidylcholine and Phosphatidylethanolamine Bilayers. J Phys Chem B 2012; 116:4476-83. [DOI: 10.1021/jp2096357] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Fernando E. Herrera
- Institut Pasteur de Montevideo, Calle Mataojo 2020. CP 11400 Montevideo,
Uruguay
- Consejo Nacional
de Investigaciones
Científicas y Técnicas (CONICET), Departamento de Física,
Facultad de Bioquímica y Ciencias Biológicas, Universidad Nacional del Litoral, C.C. 242, Ciudad
Universitaria, C.P. S3000ZAA, Santa Fe, Argentina
| | - Ana Bouchet
- Laboratorio de Fisicoquímica
de Membranas Lipídicas, Facultad de Farmacia y Bioquímica, Universidad de Buenos Aires, Junín 956 2°P
(1113), Buenos Aires, Argentina
| | - Fabiana Lairion
- Laboratorio de Fisicoquímica
de Membranas Lipídicas, Facultad de Farmacia y Bioquímica, Universidad de Buenos Aires, Junín 956 2°P
(1113), Buenos Aires, Argentina
| | - E. Aníbal Disalvo
- Laboratorio de Fisicoquímica
de Membranas Lipídicas, Facultad de Farmacia y Bioquímica, Universidad de Buenos Aires, Junín 956 2°P
(1113), Buenos Aires, Argentina
| | - Sergio Pantano
- Institut Pasteur de Montevideo, Calle Mataojo 2020. CP 11400 Montevideo,
Uruguay
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12
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Herrera FE, Pantano S. Structure and dynamics of nano-sized raft-like domains on the plasma membrane. J Chem Phys 2012; 136:015103. [DOI: 10.1063/1.3672704] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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13
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Yang H, Xu Y, Gao Z, Mao Y, Du Y, Jiang H. Effects of Na+, K+, and Ca2+ on the Structures of Anionic Lipid Bilayers and Biological Implication. J Phys Chem B 2010; 114:16978-88. [DOI: 10.1021/jp1091569] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Huaiyu Yang
- Drug Discovery and Design Center, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203, China
| | - Yechun Xu
- Drug Discovery and Design Center, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203, China
| | - Zhaobing Gao
- Drug Discovery and Design Center, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203, China
| | - Yanyan Mao
- Drug Discovery and Design Center, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203, China
| | - Yun Du
- Drug Discovery and Design Center, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203, China
| | - Hualiang Jiang
- Drug Discovery and Design Center, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203, China
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14
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Darré L, Machado MR, Dans PD, Herrera FE, Pantano S. Another Coarse Grain Model for Aqueous Solvation: WAT FOUR? J Chem Theory Comput 2010. [DOI: 10.1021/ct100379f] [Citation(s) in RCA: 94] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Leonardo Darré
- Institut Pasteur de Montevideo, Calle Mataojo 2020, CP 11400, Montevideo, Uruguay, and Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Avda. Rivadavia 1917 - CP C1033AAJ - Cdad. de Buenos Aires, Argentina
| | - Matías R. Machado
- Institut Pasteur de Montevideo, Calle Mataojo 2020, CP 11400, Montevideo, Uruguay, and Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Avda. Rivadavia 1917 - CP C1033AAJ - Cdad. de Buenos Aires, Argentina
| | - Pablo D. Dans
- Institut Pasteur de Montevideo, Calle Mataojo 2020, CP 11400, Montevideo, Uruguay, and Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Avda. Rivadavia 1917 - CP C1033AAJ - Cdad. de Buenos Aires, Argentina
| | - Fernando E. Herrera
- Institut Pasteur de Montevideo, Calle Mataojo 2020, CP 11400, Montevideo, Uruguay, and Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Avda. Rivadavia 1917 - CP C1033AAJ - Cdad. de Buenos Aires, Argentina
| | - Sergio Pantano
- Institut Pasteur de Montevideo, Calle Mataojo 2020, CP 11400, Montevideo, Uruguay, and Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Avda. Rivadavia 1917 - CP C1033AAJ - Cdad. de Buenos Aires, Argentina
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15
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Gurtovenko AA, Anwar J, Vattulainen I. Defect-Mediated Trafficking across Cell Membranes: Insights from in Silico Modeling. Chem Rev 2010; 110:6077-103. [DOI: 10.1021/cr1000783] [Citation(s) in RCA: 158] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
- Andrey A. Gurtovenko
- Institute of Macromolecular Compounds, Russian Academy of Sciences, Bolshoi Prospect 31, V.O., St. Petersburg, 199004 Russia, Computational Laboratory, Institute of Pharmaceutical Innovation, University of Bradford, Bradford, West Yorkshire BD7 1DP, U.K., Department of Physics, Tampere University of Technology, P.O. Box 692, FI-33101 Tampere, Finland, Aalto University, School of Science and Technology, Finland, and MEMPHYS—Center for Biomembrane Physics, University of Southern Denmark, Odense, Denmark
| | - Jamshed Anwar
- Institute of Macromolecular Compounds, Russian Academy of Sciences, Bolshoi Prospect 31, V.O., St. Petersburg, 199004 Russia, Computational Laboratory, Institute of Pharmaceutical Innovation, University of Bradford, Bradford, West Yorkshire BD7 1DP, U.K., Department of Physics, Tampere University of Technology, P.O. Box 692, FI-33101 Tampere, Finland, Aalto University, School of Science and Technology, Finland, and MEMPHYS—Center for Biomembrane Physics, University of Southern Denmark, Odense, Denmark
| | - Ilpo Vattulainen
- Institute of Macromolecular Compounds, Russian Academy of Sciences, Bolshoi Prospect 31, V.O., St. Petersburg, 199004 Russia, Computational Laboratory, Institute of Pharmaceutical Innovation, University of Bradford, Bradford, West Yorkshire BD7 1DP, U.K., Department of Physics, Tampere University of Technology, P.O. Box 692, FI-33101 Tampere, Finland, Aalto University, School of Science and Technology, Finland, and MEMPHYS—Center for Biomembrane Physics, University of Southern Denmark, Odense, Denmark
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