Molecular dynamics simulation of self-assembling process of ternary nanoparticle

Tao Feng, Ke Wang, Jinjie Zhou, Bhopatkar Deepak, Feng Chen, Osvaldo Campanella, Bruce R. Hamaker, Marcelo Carignano, Haining Zhuang

Research output: Contribution to journalArticle

1 Citation (Scopus)

Abstract

Ternary complex system of amylose/whey protein/free fatty acid has attracted significant interest in food nutraceuticals or functional compounds in food delivery systems due to the well-known low toxicity, excellent biocompatibility, and solubility. Maize amylose, β-lactoglobulin, α-linoleic acid were self-assembled and characterized by the TEM. Then, in order to understand the mechanism of the self-assembling actions of such a ternary system (interaction among amylose, β-lactoglobulin and α-linoleic acid) deeply, all-atom molecular dynamics simulations were performed to analyze the self-assembling of the 3 components by the Gromacs software. An amylose segment of 55 glucose residues was used to form a 6-fold left-handed helix with 55 nm inner diameter and 135 nm outer diameter approximately and a length of 738 nm. A β-lactoglobulin peptide segment was used on the basis of the three-dimensional (3D) structure determined from an NMR (nuclear magnetic resonance) analysis. The PDB (protein data bank) file for α-linoleic acid was obtained from the Heterocompound Information Centre in Uppsala, Sweden. The glucose force field was chosen and all simulations for the amylose-like molecule were carried out using the glucose force field. The Gromacs 4.6.1 MD package (ScalaLife Competence Center, European Research Council) was used for the simulation. The MD simulations were performed using the leapfrog motion routine with a 2×10-15 s time step. A total of 250 000 000 simulation steps (for a total of 500 ns simulation time) were performed to assess the progression of the self-assembly process. The LINCS algorithm was used to constrain all bond lengths. In the simulation, the temperature was set at 100 °C, necessary for the initial formation of the nanoparticle. This was performed using the modified Berendsen thermocouple between the different groups with a relaxation time of 0.1 ps, and the pressure was maintained at 1.0×105 Pa using the Parrinello-Rahman coupling to a pressure bath via an isotropic coordinate scaling with a relaxation time of 2×10-12 s. Non-chemical bond interactions were handled using a neighboring grid cell cutoff scheme. Within a neighboring molecules list's cutoff distance of 0.9 nm in a short range, the interactions were evaluated at every time step based on a pair list. A short-range electrostatic cutoff radius of 0.9 nm and a long-range Van der Waals' cutoff radius of 1.4 nm were evaluated simultaneously with each list updating. The binding order of the 3 components could be obtained through the self-assembly snapshot diagram of ternary nanoparticles within 500 ns. The TEM images showed that ternary nanoparticles had a rod-like conformation, which could be confirmed by the snapshot at 500 ns of ternary system from molecular dynamic simulation. Further analyses of their gyration radius and solvent accessible surface area showed that the ternary nanoparticles were highly hydrosoluble, which indicated that the nanoparticles could significantly enhance the aqueous solubility of some hydrophobic nutraceuticals or functional compounds. It also indicated that the formation of the ternary nanoparticles was a thermodynamically spontaneous process among amylose, β-lactoglobulin and α-linoleic acid interaction through the free energy curved-surface map of the ternary nanoparticle. The present work provides insights into the mechanism of the atomic structures of aqueous soluble self-assembled nanoparticles and presents new perspective for the design of nutraceuticals delivery systems with desirable properties.

Original languageEnglish
Pages (from-to)300-306
Number of pages7
JournalNongye Gongcheng Xuebao/Transactions of the Chinese Society of Agricultural Engineering
Volume33
Issue number3
DOIs
Publication statusPublished - 1 Feb 2017

Fingerprint

molecular dynamics
nanoparticles
Molecular Dynamics Simulation
Nanoparticles
Amylose
Molecular dynamics
lactoglobulins
amylose
Linoleic acid
Lactoglobulins
Computer simulation
Linoleic Acid
linoleic acid
Dietary Supplements
functional foods
Glucose
Ternary systems
Relaxation time
Solubility
Self assembly

Keywords

  • Amylose
  • Molecular dynamics
  • Nanoparticles
  • Self assembly
  • α-linoleic acid
  • β-lactoglobulin

ASJC Scopus subject areas

  • Agricultural and Biological Sciences(all)
  • Mechanical Engineering

Cite this

Molecular dynamics simulation of self-assembling process of ternary nanoparticle. / Feng, Tao; Wang, Ke; Zhou, Jinjie; Deepak, Bhopatkar; Chen, Feng; Campanella, Osvaldo; Hamaker, Bruce R.; Carignano, Marcelo; Zhuang, Haining.

In: Nongye Gongcheng Xuebao/Transactions of the Chinese Society of Agricultural Engineering, Vol. 33, No. 3, 01.02.2017, p. 300-306.

Research output: Contribution to journalArticle

Feng, Tao ; Wang, Ke ; Zhou, Jinjie ; Deepak, Bhopatkar ; Chen, Feng ; Campanella, Osvaldo ; Hamaker, Bruce R. ; Carignano, Marcelo ; Zhuang, Haining. / Molecular dynamics simulation of self-assembling process of ternary nanoparticle. In: Nongye Gongcheng Xuebao/Transactions of the Chinese Society of Agricultural Engineering. 2017 ; Vol. 33, No. 3. pp. 300-306.
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AU - Feng, Tao

AU - Wang, Ke

AU - Zhou, Jinjie

AU - Deepak, Bhopatkar

AU - Chen, Feng

AU - Campanella, Osvaldo

AU - Hamaker, Bruce R.

AU - Carignano, Marcelo

AU - Zhuang, Haining

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N2 - Ternary complex system of amylose/whey protein/free fatty acid has attracted significant interest in food nutraceuticals or functional compounds in food delivery systems due to the well-known low toxicity, excellent biocompatibility, and solubility. Maize amylose, β-lactoglobulin, α-linoleic acid were self-assembled and characterized by the TEM. Then, in order to understand the mechanism of the self-assembling actions of such a ternary system (interaction among amylose, β-lactoglobulin and α-linoleic acid) deeply, all-atom molecular dynamics simulations were performed to analyze the self-assembling of the 3 components by the Gromacs software. An amylose segment of 55 glucose residues was used to form a 6-fold left-handed helix with 55 nm inner diameter and 135 nm outer diameter approximately and a length of 738 nm. A β-lactoglobulin peptide segment was used on the basis of the three-dimensional (3D) structure determined from an NMR (nuclear magnetic resonance) analysis. The PDB (protein data bank) file for α-linoleic acid was obtained from the Heterocompound Information Centre in Uppsala, Sweden. The glucose force field was chosen and all simulations for the amylose-like molecule were carried out using the glucose force field. The Gromacs 4.6.1 MD package (ScalaLife Competence Center, European Research Council) was used for the simulation. The MD simulations were performed using the leapfrog motion routine with a 2×10-15 s time step. A total of 250 000 000 simulation steps (for a total of 500 ns simulation time) were performed to assess the progression of the self-assembly process. The LINCS algorithm was used to constrain all bond lengths. In the simulation, the temperature was set at 100 °C, necessary for the initial formation of the nanoparticle. This was performed using the modified Berendsen thermocouple between the different groups with a relaxation time of 0.1 ps, and the pressure was maintained at 1.0×105 Pa using the Parrinello-Rahman coupling to a pressure bath via an isotropic coordinate scaling with a relaxation time of 2×10-12 s. Non-chemical bond interactions were handled using a neighboring grid cell cutoff scheme. Within a neighboring molecules list's cutoff distance of 0.9 nm in a short range, the interactions were evaluated at every time step based on a pair list. A short-range electrostatic cutoff radius of 0.9 nm and a long-range Van der Waals' cutoff radius of 1.4 nm were evaluated simultaneously with each list updating. The binding order of the 3 components could be obtained through the self-assembly snapshot diagram of ternary nanoparticles within 500 ns. The TEM images showed that ternary nanoparticles had a rod-like conformation, which could be confirmed by the snapshot at 500 ns of ternary system from molecular dynamic simulation. Further analyses of their gyration radius and solvent accessible surface area showed that the ternary nanoparticles were highly hydrosoluble, which indicated that the nanoparticles could significantly enhance the aqueous solubility of some hydrophobic nutraceuticals or functional compounds. It also indicated that the formation of the ternary nanoparticles was a thermodynamically spontaneous process among amylose, β-lactoglobulin and α-linoleic acid interaction through the free energy curved-surface map of the ternary nanoparticle. The present work provides insights into the mechanism of the atomic structures of aqueous soluble self-assembled nanoparticles and presents new perspective for the design of nutraceuticals delivery systems with desirable properties.

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KW - Amylose

KW - Molecular dynamics

KW - Nanoparticles

KW - Self assembly

KW - α-linoleic acid

KW - β-lactoglobulin

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