Confined Nystatin Polyenes in Nanopore Induce Biologic Ionic Selectivity

Hindawi Publishing Corporation Journal of Nanomaterials Volume 2016, Article ID 2671383, 9 pages http://dx.doi.org/10.1155/2016/2671383 Research Article Confined Nystatin Polyenes in Nanopore Induce Biologic Ionic Selectivity Khaoula Boukari,1,2 Guillaume Paris,1 Tijani Gharbi,1 Sébastien Balme,3 Jean-Marc Janot,3 and Fabien Picaud1 1 Laboratoire de Nanomédecine, Imagerie et Thérapeutique, EA 4662, Université de Bourgogne-Franche-Comté, Centre Hospitalier Universitaire de Besançon, 16 route de Gray, 25030 Besançon Cedex, France 2 CINaM, CNRS UMR 7325, Aix-Marseille University, Campus de Luminy, 13288 Marseille Cedex 9, France 3 Institut Européen des Membranes, ENSCM, CNRS UMR 5635, Université de Montpellier, Place Eugène Bataillon, 34095 Montpellier Cedex 5, France Correspondence should be addressed to Fabien Picaud; Received 29 March 2016; Accepted 22 May 2016 Academic Editor: David Cornu Copyright © 2016 Khaoula Boukari et al. This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. Antifungal polyenes such as nystatin (or amphotericin B) molecules play an important role in regulating ions permeability through membrane cell. The creation of self-assembled nanopores into the fungal lipid membranes permits the leakage and the selectivity of ions (i.e., blockage of divalent cations) that cause the cell death. These abilities are thus of first interest to promote new biomimetic membranes with improved ionic properties. In the present work, we will use molecular dynamic simulations to interpret recent experimental data that showed the transfer of the nystatin action inside artificial nanopore in terms of ion permeability and selectivity. We will demonstrate that nystatin polyenes can be stabilized in a hydrophobic carbon nanotube, even at high concentration. The high potential interaction between the polyenes and the hydrophobic pore wall ensures the apparition of a hole inside the biomimetic nanopore that changes its intrinsic properties. The probability ratios of cation versus anion show interesting reproducibility of experimental measurements and, to a certain extent, opened the way for transferring biological properties in synthetic membranes. 1. Introduction Nystatin (NYS) is a membrane-active polyene produced by Streptomyces noursei strains [1]. These antifungal molecules are amphiphilic [2, 3]. They are composed of a polar head, a hydrophilic chain, and a hydrophobic chain. This amphiphilic character leads to their self-assembly in biological membranes. Indeed, polyenes can incorporate inside the lipid membrane and form a barrel [4] where all hydrophobic chains are turned on the external part of the barrel and face the lipids, while the hydrophilic chains form the inner part of the channel [3, 5]. This configuration allows the barrel intercalation inside the lipid membrane (depending on the sterol molecules [6]) and plays an important role in the ion permeability and selectivity (especially to monovalent ions [2, 5]). The mechanism responsible for the barrel formation is still under discussion but may follow the diagram illustrated in Figure 1. However, its ionic properties are involved in the antifungal action of the polyenes [7, 8]. Solid state nanopores appear now as excellent tools to mimic biological channel properties because of their combined well defined geometries (shape and dimensions) and mechanical robustness. But controlling the inner nanopore diameter is still very challenging since it necessitates controlling diameter range from subnanometers’ to hundreds of nanometers’ scale, depending on the applications. As already mentioned, solid state nanopores do not exhibit selectivity or activity without functionalization. Both the stability and the property of the solid state nanopores are highly dependent on the experimental conditions of formation (e.g., track etched nanopore) as well as used material. For several years, some applications were developed using solid state nanopores such 2 Journal of Nanomaterials Nystatin molecule Polar head Phospholipid molecule Polar head Amphiphilic domain OH group Hydrophobic carbon domain Figure 1: Schematic formation of the nystatin pore inside lipid membrane. as DNA sensing [9], control of the molecular transport, or fabrication of performing nanofluidic devices [10–13]. Some precise chemical treatments allow now controlling the diameter range of nanopores [14, 15] and the properties [16]. However, if we want to combine the high selectivity of biological channel and the robustness of solid state nanopore, one route is the development of hybrid biological/solid state nanopores. This proof of concept was done with 𝛼-hemolysin for DNA sensing application [14, 17] and with gramicidin A for higher ionic permeability and selectivity devices. The transfer of the biological properties of polyene to artificial membranes which could thus exhibit the same behavior as in the cell could be envisaged but still remains an important challenge. This transfer could find applications in water desalination [18] or dialysis [19, 20] with low energy cost. Recently, Balme et al. demonstrated experimentally that insertion of NYS polyenes inside solid state nanopore leads to very interesting ionic selective properties. We will try here to understand using molecular dynamic simulations the formation and the properties of such experimental systems [20, 21]. After a short description of the simulation method, we will present the progressive filling of the nanopore and the consequence to the properties of the polyenes in terms of geometry and energy. Then, we will analyze conductance of the hybrid nanopore and the role of the dipole moment, created after the polyenes incorporation in the ionic selectivity. 2. Computational Method and Model The model for nystatin (NYS) was carried out using the 3D structure of the DB00681 model in the DrugBank database (Figure 2). To obtain the missing potential parameters, we have followed the protocol described by Norrby and Brandt [22] by constructing the Hessian matrix for further use in the force field parametrization. This matrix was obtained via ab initio quantum calculations using Gaussian 09 package software [23]. In order to check the stability of polyene, nystatin 3 was equilibrated for 2 nS in a water box of 40 × 30 × 30 Å (Figure 2). Then, NYS was transferred into a solid nanopore modeled by a carbon nanotube and denoted by CNT. Its diameter was chosen to be sufficient to be compared with experiments [20, 21], that is, 7 nm, while its length was equal to 5 nm. The nanopore was filled progressively by 50 polyenes, water, and K+ and Cl− ions at 0.1 M concentration. The final system contained 43702 atoms in a periodic box of 80 × 75 × 3 80 Å with 10914 water molecules and 28 KCl ions in order to conserve the neutrality o (...truncated)