On the spontaneous encapsulation of proteins in carbon nanotubes

Kang, Yu; Liu, Yingchun; Wang, Qi; Shen, Jia-Wei; Wu, Tao; Guan, Wenjun

doi:10.1016/j.biomaterials.2009.01.024

Cited by 112 publications

(106 citation statements)

References 51 publications

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“…The beginning distance between the mass-center of L-leucine and the graphene layer was 25 Å, at which the potential energy is defined as zero. This separation is large enough compared to the bond length in L-leucine molecule and graphene layer, and there is no interaction between two molecules separated by that distance [5]. Three different temperature conditions were use to conduct MD simulations under the pressure of 1 Â10 3 kPa, results of which were plotted in Fig.…”

Section: Potential Energy For Adsorption Of L-leucine Through MDmentioning

confidence: 99%

“…It is well-known that carbon nanotubes (CNTs), owing to their excellent geometrical, physical, and chemical properties, carbon nanotubes have attracted a great deal of interest in biomedicine, biomaterials, (bio) sensors, catalysts, and so on [1][2][3][4][5]. However, in comparison with CNTs, graphene as a singlelayer two-dimensional material composed of layers of carbon atoms forming sixmembered rings, presents long and reactive edges which make it not only notably more accessible to doping and chemical modification but also more susceptible to structural defects and impurities, which becomes more exciting materials being investigated today.…”

Section: Introductionmentioning

confidence: 99%

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Density functional theory calculations and molecular dynamics simulations of the adsorption of biomolecules on graphene surfaces

Bian

et al. 2010

Biomaterials

158

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Section: Potential Energy For Adsorption Of L-leucine Through MDmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Density functional theory calculations and molecular dynamics simulations of the adsorption of biomolecules on graphene surfaces

Bian

et al. 2010

Biomaterials

158

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“…Indeed, their ability to cross cell membranes [2] opens innumerable possibilities for biomedical applications [3,4]. Their large surface area allows attachment (of chemical or physical nature) of drug molecules [5][6][7] and the empty core of the CNTs provides an opportunity to exploit them as nano-containers for drug [8,9] or any desired biologically active molecule encapsulation [10,11]. For this reason, several experimental studies have been performed in order to understand the pathways of internalization [12][13][14][15][16][17][18][19].…”

Section: Introductionmentioning

confidence: 99%

Spontaneous insertion of carbon nanotube bundles inside biomembranes: A hybrid particle-field coarse-grained molecular dynamics study

Sarukhanyan¹,

Roccatano²,

Kawakatsu³

et al. 2014

Chemical Physics Letters

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The processes of CNTs bundle formation and insertion/rearrangement inside lipid bilayers, as models of cellular membranes, is described and analyzed in details using simulations on the microsecond scale. Molecular Dynamics simulations employing hybrid particle-field models (MD-SCF) show that during the insertion process lipid molecules coat bundles surfaces The distortions of bilayers are more pronounced for systems undergoing to insertion of bundles made of longer CNTs. Interestingly, in this case, for the insertion of bundles in perpendicular orientation, it has been possible to observe, for the first time, a transient poration of the bilayer and a subsequent water percolation through it.

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“…The electrostatic and van der Waals interaction energies were calculated in the same way. E int ( t ) is the quantitative indicator of the instantaneous interaction between the two molecules corresponding to each simulation moment, which is different from the interaction energy in general sense [44]. …”

Section: Methodsmentioning

confidence: 99%

Trastuzumab-Peptide Interactions: Mechanism and Application in Structure-Based Ligand Design

Sun

Wang

Zhang

et al. 2013

IJMS

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Understanding of protein-ligand interactions and its influences on protein stability is necessary in the research on all biological processes and correlative applications, for instance, the appropriate affinity ligand design for the purification of bio-drugs. In this study, computational methods were applied to identify binding site interaction details between trastuzumab and its natural receptor. Trastuzumab is an approved antibody used in the treatment of human breast cancer for patients whose tumors overexpress the HER2 (human epidermal growth factor receptor 2) protein. However, rational design of affinity ligands to keep the stability of protein during the binding process is still a challenge. Herein, molecular simulations and quantum mechanics were used on protein-ligand interaction analysis and protein ligand design. We analyzed the structure of the HER2-trastuzumab complex by molecular dynamics (MD) simulations. The interaction energies of the mutated peptides indicate that trastuzumab binds to ligand through electrostatic and hydrophobic interactions. Quantitative investigation of interactions shows that electrostatic interactions play the most important role in the binding of the peptide ligand. Prime/MM-GBSA calculations were carried out to predict the binding affinity of the designed peptide ligands. A high binding affinity and specificity peptide ligand is designed rationally with equivalent interaction energy to the wild-type octadecapeptide. The results offer new insights into affinity ligand design.

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On the spontaneous encapsulation of proteins in carbon nanotubes

Cited by 112 publications

References 51 publications

Density functional theory calculations and molecular dynamics simulations of the adsorption of biomolecules on graphene surfaces

Density functional theory calculations and molecular dynamics simulations of the adsorption of biomolecules on graphene surfaces

Spontaneous insertion of carbon nanotube bundles inside biomembranes: A hybrid particle-field coarse-grained molecular dynamics study

Trastuzumab-Peptide Interactions: Mechanism and Application in Structure-Based Ligand Design

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