Dynamics of Antimicrobial Peptide Encapsulation in Carbon Nanotubes: The Role of Hydroxylation (original) (raw)
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Peptide encapsulation regulated by the geometry of carbon nanotubes
Biomaterials, 2014
In this work the encapsulation of an α-helical peptide in single carbon nanotubes (CNTs) with similar diameter and length but different geometry (armchair and zigzag) was investigated through molecular dynamics simulations and free energy calculations. Our simulation results showed that in vacuo it makes no evident difference whether the investigated peptide is encapsulated in armchair or zigzag CNTs; however, in aqueous solution the armchair CNT encapsulates the peptide remarkably easier than the zigzag CNT does. A detailed analysis revealed that the equilibrium conformation of the water molecules inside the CNTs with varying geometry mediates the peptide encapsulation. It suggests that the water molecules play an important role in regulating behaviors of biomolecules in bio-systems. Then the impact of the CNT geometry on the conformational changes of the confined peptide was studied. Analyses of secondary structures showed the α-helix of the peptide could be better maintained in t...
Computational analysis of binding free energies between peptides and single-walled carbon nanotubes
Physica A: Statistical Mechanics and its Applications, 2006
Coating carbon nanotubes (CNTs) with peptides can solubilize the nanotubes in water solvent. To explore the utilization of CNTs in solvent and the affinities of CNTs for different peptides, binding free energies of peptides to single-walled carbon nanotubes (SWCNTs) are calculated and analyzed. The interactions between different peptides and SWCNTs are simulated using molecular dynamics (MD) methods. The binding free energies of peptides onto the outer-surface of the SWCNTs are then estimated based on thermodynamics theory. The estimated results of binding free energies are qualitatively comparable to binding affinities observed in experiments. Furthermore, the conformations of the binding peptides, as well as the energetic contributions to total binding free energies are analyzed to reveal the physical mechanisms of the interactions, which would be difficult to observe using experimental approaches. The van der Waals interaction is found to play a key role in binding of peptides to SWCNTs. Other effects such as hydrophobicity and aromatic rings of peptides are also examined. The findings of this study provide better understanding of the binding strength between proteins and CNTs, and therefore have potential applications in both scientific research and in industry for controlling CNT self-assembly, designing bio-functionalized CNTs as biosensors, and drug and gene delivery devices.
The dispersion and manipulation of carbon nanotubes (CNTs) are of great importance if we are to utilise the unique properties of CNTs in a range of biological, electrical and mechanical applications. Recently, a designed amphiphilic peptide helix termed nano-1 has been shown to solubilise CNTs in aqueous solution. Furthermore, the peptide is capable of assembling these coated tubes into fibres. We use a multiscale molecular dynamics approach to study the adsorption profile of nano-1 on a CNT surface. We find that nano-1 interacts with a CNT in a preferred orientation, such that its hydrophobic surface is in contact with the tube. The adsorption profile is unchanged upon increasing the number of peptides on the CNT. Interestingly, when few peptides are adsorbed onto the CNT surface we find that the secondary structure of the peptide is unstable. However, the helical secondary structure is stabilised upon increasing the number of peptides on the CNT surface. This study sheds light on the adsorption of peptides on CNTs, and may be exploitable to enhance the selective solubilisation and manipulation of CNTs. +44 (0)1865 613238; Tel: +44 (0)1865 613306 † Electronic supplementary information (ESI) available: Details of the OPLS simulations and peptide a-helicity. See
Factors Governing Helix Formation in Peptides Confined to Carbon Nanotubes
Nano Letters, 2008
The effect of confinement on the stability and dynamics of peptides and proteins is relevant in the context of a number of problems in biology and biotechnology. We have examined the stability of different helix-forming sequences upon confinement to a carbon nanotube using Langevin dynamics simulations of a coarse-grained representation of the polypeptide chain. We show that the interplay of several factors that include sequence, solvent conditions, strength (λ) of nanotube-peptide interactions, and the nanotube diameter (D) determines confinement-induced stability of helicies. In agreement with predictions based on polymer theory, the helical state is entropically stabilized for all sequences when the interaction between the peptide and the nanotube is weakly hydrophobic and D is small. However, there is a strong sequence dependence as the strength of the λ increases. For an amphiphilic sequence, the helical stability increases with λ, whereas for polyalanine the diagram of states is a complex function of λ and D. In addition, decreasing the size of the 'hydrophobic patch' lining the nanotube, which mimics the chemical heterogeneity of the ribosome tunnel, increases the helical stability of the polyalanine sequence. Our results provide a framework for interpreting a number of experiments involving the structure formation of peptides in the ribosome tunnel as well as transport of biopolymers across nanotubes.
Microscopy and Microanalysis, 2007
Production of stable polymer-nanotube composites depends on good wetting interaction between polymer and nanotube, which is polymer specific, and depends in particular on chain conformation. In this paper, we examine this interaction for a conjugated, semiconducting polymer by a range of microscopic and spectroscopic techniques, to gain a greater understanding of the binding. Several interesting effects are observed, including an order to the interaction between the polymer and nanotube, the tendency of defects in the nanotube structure to nucleate crystal growth, and substantial changes in the spectroscopic behavior of the polymer due to the effect of the nanotubes on polymer conformation. This is substantiated by computational modeling, which demonstrates that these conformational modifications are due to the interaction with the nanotubes.
Colloids and Surfaces A: Physicochemical and Engineering Aspects, 2019
A detailed adsorption thermodynamic study of two nisin variants (nisA and nisZ) on multi-walled carbon nanotubes (MWCNT) was conducted, and the antimicrobial properties of biofunctionalized MWCNT were evaluated. The MWCNT adsorption capacity for peptides (q p) increased with pH increase, with greater values for nisZ (q p up to 250 mg g −1) than for nisA (q p up to 180 mg g −1) for all studied conditions. Zeta potential measurements (ζ) showed that the electrostatic repulsion between the MWCNT-peptide complexes determined the dispersion features that were stable at pH 2.0 and 3.0, with ζ reaching 45.0 mV at the lowest pH. Despite the similar ζ values for both peptides, slightly greater stabilization of MWCNT dispersions was exhibited in presence of nisZ at pH 3. At pH 4 and 5, peptide adsorption was not able to promote MWCNT dispersibility. Isothermal titration calorimetry revealed that the adsorption process was driven by enthalpy for both peptides, as the adsorption enthalpy changes (H ads) were less negative than −99.7 kJ mol −1. Despite the large dependence of H ads on the pH andq p values, indicating the important role of electrostatic interactions on the adsorption process, a change in only one amino acid residue in the nisin structure promoted intense changes in the adsorption thermodynamic parameters. We have suggested that the more hydrophobic character of nisZ at the lower pH values caused this peptide to interact with the MWCNT surface through its two domains. Interesting, the antimicrobial properties of
Encapsulation of a Chloroform Molecule in a Peptide Nanotube
Advances in Bioscience and Biotechnology, 2014
We determine the encapsulation of a chloroform molecule into a D,L-Ala cyclopeptide nanotube by investigating the interaction energy between the two molecular structures. We employ the Lennard-Jones potential and a continuum approach which assumes that the atoms are evenly distributed over the molecules providing average atomic densities. Our result demonstrates that the encapsulation depends on the size of the molecule and the internal diameter of the peptide nantube. In particular, the on-axis chloroform molecule is only accepted into a peptide nanotube whose internal radius is greater than 5 Å. If located near the edge of the nanotube, then it is unlikely that the chloroform molecule will enter the nanotube. This is due to the energy valley that the molecule will need to overcome to move past the edge into the open end of the nanotube.
Modeling the binding of peptides on carbon nanotubes and their use as protein and DNA carriers
Journal of Nanoparticle Research, 2012
An in deep study of the functionalization of carbon nanotubes for their application as peptides and DNA carriers is presented. Designed amphiphilic polypeptides are used to study the dispersion properties of single-walled carbon nanotubes (SWCNTs) and to measure the properties of the carbon nanotube-polypeptide complexes. These properties allow the design of methods for using carbon nanotubes as platforms for protein and DNA binding. First, a model that characterizes the adsorption of natural peptides onto SWCNTs is developed which allows the design of functionalization methods of SWCNTs with proteins. This model was based on properties that describe the protein structure and composition. Second, the binding of cationic amphiphilic polypeptides to SWCNTs is studied for subsequent and efficient binding of DNA to carbon nanotubes by a bilayer approach. These functionalization methods for the development of protein and DNA carriers have potential applications in using SWCNTs in important fields such as biosensing and delivery systems design.