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A Coarse-Grained Molecular Dynamics Simulation Using NAMD Package to Reveal Aggregation Profile of Phospholipids Self-Assembly in Water

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A Coarse-Grained Molecular Dynamics Simulation Using NAMD Package to Reveal Aggregation Profile of Phospholipids Self-Assembly in Water Hindawi Publishing Corporation Journal of Chemistry Volume 2014, Article ID 273084, 6 pages http://dx.doi.org/10.1155/2014/273084 Research Article A Coarse-Grained Molecular Dynamics Simulation Using NAMD Package to Reveal Aggregation Profile of Phospholipids Self-Assembly in Water Dwi Hudiyanti,1 Muhammad Radifar,2 Tri Joko Raharjo,3 Narsito Narsito,3 and Sri Noegrohati4 1 Department of Chemistry, Diponegoro University, Jl. Prof. Sudharto, SH., Semarang 50257, Indonesia 2 Graduate School, Gadjah Mada University, Sekip Utara, Yogyakarta 55281, Indonesia 3 Department of Chemistry, FMIPA, Gadjah Mada University, Sekip Utara, Yogyakarta 55281, Indonesia 4 Faculty of Pharmacy, Gadjah Mada University, Sekip Utara, Yogyakarta 55281, Indonesia Correspondence should be addressed to Dwi Hudiyanti; dwi [email protected] Received 21 May 2014; Revised 11 July 2014; Accepted 14 July 2014; Published 4 August 2014 Academic Editor: Hugo Verli Copyright © 2014 Dwi Hudiyanti 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. The energy profile of self-assembly process of DLPE, DLPS, DOPE, DOPS, DLiPE, and DLiPS in water was investigated by a coarse-grained molecular dynamics simulation using NAMD package. The self-assembly process was initiated from random configurations. The simulation was carried out for 160 ns. This study presented proof that there were three major self-assembled arrangements which became visible for a certain duration when the simulation took place, that is, liposome, deformed liposome, and planar bilayer. The energy profile that shows plateau at the time of these structures emerge confirmed their stability therein. Our findings have highlighted the idea that liposomes and deformed liposomes are metastable phases which eventually will turn into planar bilayer, the stable one. 1. Introduction Itdemandsalongtimetoequilibratearealphysicalsys- tem. Hence a coarse-grained molecular dynamics (CGMD) Solution of phospholipid molecules can demonstrate more method was built as a simplified model to carry out molecular thanonemicellarstructures,namely,sphericalmicelles,rod- dynamics. The CGMD models have been used to explore a like structures, liposomes, bilayers, and others due to their variety of structural and dynamic properties in large molec- surfactant-like features [1–4]. These structures play important ular systems. The CGMD method has offered significant role in drug delivery systems as well as in biological systems outcome when exploring time and length scales further than [5, 6]. Micellar structures rely on the molecular species, com- what is viable with conventional MD. While CGMD has position, and also on the self-assembly pathways affected by brought important findings for understanding the phospho- the initial configuration7 [ –10]. A great deal of experimental lipid self-assembly [12, 14, 15],thereisstilllimitedinforma- research has been done to study self-assembly of phospholi- tion accessible for a theoretical perceptive of phospholipid pid molecules. Nevertheless the dynamics information about self-assembly pathway. the liposome formation is still hard to achieve experimentally. An all atomic simulation on phospholipid aggregation by Molecular dynamics computer simulation has the ability Marrink and coworkers [13]hasshownatypicalpathwayfor to deliver more detailed information. It is an impressive bilayer formation. However, it did not state the formation of device to investigate the mechanism of self-assembly [11– liposomes during the course of aggregation. Applying CGMD 14]. Conventional molecular dynamics (MD) uncovers max- method on DLPE, DLPS, DOPE, DOPS, DLiPE, and DLiPS imum features however they are limited to small time scales. we demonstrate for the first time the aggregation profile of 2 Journal of Chemistry O O O − O O H O P P O O O O O − O + − + O H O NH3 O H O NH3 + Na O O (a) 1,2-Dilauroyl-sn-glycero-3-phosphoethanolamine (DLPE) (b) 1,2-Dilauroyl-sn-glycero-3-phosphoserine (DLPS) O O O O − O H O O O P + P −O O O O + O H O NH3 H − NH3 O O + Na O O (c) 1,2-Dioleoyl-sn-glycero-3-phosphoethanolamine (DOPE) (d) 1,2-Dioleoyl-sn-glycero-3-phosphoserine (DOPS) O O O O O H − P P O O O O + O O O + H − NH3 H − O O O O + NH3 Na O O (e) 1,2-Dilinoleoyl-sn-glycero-3-phosphoethanolamine (DLiPE) (f) 1,2-Dilinoleoyl-sn-glycero-3-phosphoserine (DLiPS) O O P + O O −O O H O N O (g) 1,2-Dilinoleoyl-sn-glycero-3-phosphocholine (DLiPC) Figure 1: The molecular structure of phospholipids in the simulation. phospholipid molecules which clearly show the formation reduce the steric clashes that might occur in the system. This ofliposomeasthemetastablephase.Thesephospholipids phase provided the system with the lowest energy to do the have been reported as the main phospholipid component simulation. It had been marked by the achievement of energy of coconut, sesame, and candlenut endosperm [16]which convergency at the end of minimization, 0.6 ns. produced liposomes and planar bilayer during aggregation After the minimization simulations were performed with [2]. 40 fs time step integration during the effective time of 160 ns. Simulations were conducted on periodic boundary condi- 2. Methodology tions (PBC). The duration of liposome formation and the total energy systems were analyzed from the simulation The structure of all phospholipids used in the simulation is results. Visualization during the simulation process was also presented in Figure 1. The model molecule was prepared done by VMD. The simulation was also undertaken for larger using the Open Babel package [17]. In this study, 256 phos- systems, that is, 1500 phospholipid molecules. pholipid molecules were placed randomly in a cube-shaped To evaluate our system, before running the simulation on box with a size of 8 nm using Packmol package [18]. Residue- the phospholipids we conducted the simulation on DLiPC based coarse-graining was applied on the system based on which has been recognized to form liposome [23]. Martini Force Field ver.2.0 [15, 19] using VMD package [20]. The force field was parameterized to reproduce accurate thermodynamic properties [21]. Each phospholipid molecule 3. Results and Discussion was represented as 10–14 beads. Water molecules were mod- eled by hydrophilic beads; each one represented four real Molecular dynamics simulation of phospholipid molecules water molecules. Figure 2 presents coarse-grained structure was able to provide an overview of the mechanism of the of all phospholipids used in the simulation. In Martini Force aggregation process and the relationship between aggregate Field each bead interacts with the pair wise Lennard-Jones structureandthetotalenergyofthesystem.Simulationwas performed on a system with 256 molecules of phospholipids potential (LJ). Screen Coulomb interaction is used to model 3 the electrostatic interaction between the zwitter ionic head in aqueous medium with density of 0.00609 atom/A using groups of phospholipids. NAMD package. For all molecules used in this report the Molecular dynamics simulations of phospholipid system simulation began with a random position. In general the began with energy minimization using NAMD package [22]. molecules then started to form various clusters of phospho- Energy minimization was done to adjust the structure to lipids with hydrocarbon tails directed to their interior. After the force field, the distribution of solvents, and especially to that they began to form liposomes or half-liposomes which Journal of Chemistry 3 1,2-Dilauroyl-sn-glycero-3-phospho- 1,2-Dilauroyl-sn-glycero-3-phospho- ethanolamine (DLPE) serine (DLPS) 1,2-Dioleoyl-sn-glycero-3-phospho- 1,2-Dioleoyl-sn-glycero-3-phospho- ethanolamine (DOPE) serine (DOPS) 1,2-Dilinoleoyl-sn-glycero-3-phospho- 1,2-Dilinoleoyl-sn-glycero-3-phospho- ethanolamine (DLiPE) serine (DLiPS) 1,2-Dilinoleoyl-sn-glycero-3-phospho- choline (DLiPC) Figure 2: Coarse-grained structures of phospholipids in the simulation. Bead of atoms are presented by colored beads. Ethanolamine head group are blue bead, brown for phosphate, glycerol backbone pink, green for hydrocarbon tail groups, and purple for the double bonds. were followed by deformed liposomes or planar bilayer for- structures observed in the aggregation process are presented mation at the end. We think the formation of half-liposome as snapshots on Figure 3. is due to shortage of phospholipid molecules supplies in the Observation of the total energy changes during the aggre- system. gation process showed that the process was accompanied To examine the influence of the number of molecules by a decrease in the total energy of the system. The energy the simulation was also performed on the system with 1500 decrease occurred in stages before reaching a minimum when molecules with the same density. These simulations have the simulation was terminated. This means that metastable shown the aggregation process better. It was preceded by the structure is formed which is subsequently followed by a formation of small clusters of phospholipids which then was stable structure with minimum energy state. The simulations followedbymergersintolargeraggregates,intheformof show that liposome and deformed liposome are metastable worm-like, cup-like, tube-like, and other structures, leading structures while a planar bilayer is a stable structure. This toformationofliposomeorplanarbilayer.Forsomephos- finding supports the views
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