Dendrimer assisted dispersion of carbon nanotubes: a molecular dynamics study

Influence of DNA Sequences on the Thermodynamic and Structural Stability of the ZTA Transcription Factor─DNA Complex: An All-Atom Molecular Dynamics Study

The Epstein-Barr virus (EBV) is one of the cancer-causing gamma-type viruses. Although more than 90% of people are infected by this virus at some point, it remains in the body in a latent state, typically causing only minor symptoms. Our current understanding is that a known transcription factor (TF), the ZTA protein, binds with dsDNA (double-stranded DNA) and plays a crucial role in mediating the viral latent-to-lytic cycle through binding of specific ZTA-responsive elements (ZREs). However, there is no clear understanding of the effect of DNA sequences on the structural stability and quantitative estimation of the binding affinity between ZTA TF and DNA, along with their mechanistic details. In this study, we employed classical all-atom molecular dynamics and enhanced sampling simulations to study the ZTA-dsDNA structural properties, thermodynamics, and mechanistic details for the ZTA protein and for two different dsDNA systems: the core motif and the core motif with flanking end sequences. We conducted residue-level and nucleic acid-level analyses to assess the important protein residues and DNA bases forming interactions between the ZTA and dsDNA systems. We also explored the effect of adding flanking end sequences to the core motif on DNA groove lengths and interstrand hydrogen bonds. Our results indicate that the flanking sequences surrounding the core motif significantly influence the structural stability and binding affinity of the ZTA-dsDNA complex. Among ZRE 1, ZRE 2, and ZRE 3, particularly when paired with their naturally occurring flanking ends, ZRE 3 exhibits higher stability and binding affinity. These findings provide insights into the molecular mechanisms underlying EBV pathogenesis and may indicate potential targets for therapeutic intervention. A detailed explanation of the binding mechanisms will allow for the design of better-targeted therapies against EBV-associated cancers. This study will serve as a holistic benchmark for future studies of these viral protein interactions.

Probing the Molecular Interactions of A22 with Prokaryotic Actin MreB and Eukaryotic Actin: A Computational and Experimental Study

Actin is a major cytoskeletal system that mediates the intricate organization of macromolecules within cells. The bacterial cytoskeletal protein MreB is a prokaryotic actin-like protein governing the cell shape and intracellular organization in many rod-shaped bacteria, including pathogens. MreB stands as a target for antibiotic development, and compounds like A22 and its analogue, MP265, are identified as potent inhibitors of MreB. The bacterial actin MreB shares structural homology with eukaryotic actin despite lacking sequence similarity. It is currently not clear whether small molecules that inhibit MreB can act on eukaryotic actin due to their structural similarity. In this study, we investigate the molecular interactions between A22 and its analogue MP265 with MreB and eukaryotic actin through a molecular dynamics approach. Employing MD simulations and free energy calculations with an all-atom model, we unveil the robust interaction of A22 and MP265 with MreB, and substantial binding affinity is observed for A22 and MP265 with eukaryotic actin. Experimental assays reveal A22's toxicity to eukaryotic cells, including yeast and human glioblastoma cells. Microscopy analysis demonstrates the profound effects of A22 on actin organization in human glioblastoma cells. This integrative computational and experimental study provides new insights into A22's mode of action, highlighting its potential as a versatile tool for probing the dynamics of both prokaryotic and eukaryotic actins.

Phase Behavior of Pure PSPC and PEGylated Multicomponent Lipid and Their Interaction with Paclitaxel: An All-Atom MD Study

Exploring structural behavior of pure 1-palmitoyl-2-stearoyl-sn-glycero-3-phosphocholine (PSPC) and multicomponent PSPC and 1,2-distearoyl-sn-glycero-3-phosphoethanolamine-N[amino(poly(ethylene glycol))-2000] (DSPE-PEG₂₀₀₀) membranes and their interaction with pharmaceutically important drugs carry huge importance in drug delivery. Using all-atom molecular dynamics (MD) simulations, we investigated the phase behavior of pure and PEGylated membranes at the temperature range of 280-360 K. We observe a gel-to-liquid crystalline phase transition for pure PSPC between 320 and 330 K, and in the case of multicomponent membranes, at 320 K, a coexistence of order-disorder phases is observed, which gradually transform to a complete liquid crystalline to gel phase between 320 and 310 K. We further studied the interaction of Paclitaxel with pure PSPC and PEGylated bilayers and elucidated the interaction behavior of Paclitaxel at the bilayer interfaces. Understanding of structural and interaction behaviors of the PEGylated bilayers with Paclitaxel will help to explore Paclitaxel-based drug applications in the future.

Disentangling the liquid phase exfoliation of two-dimensional materials: an "in silico" perspective

Liquid Phase Exfoliation (LPE) is one of the most successful synthetic roots for the preparation of two-dimensional (2D) materials from their bulk counterparts. In recent years, significant progress has been accomplished for the development and modification of LPE techniques. However, precise identification of the hierarchical steps of the molecular mechanism of LPE remains to some extent elusive. Additionally, the a priori choice of suitable solvents for successful exfoliation and dispersion of various layered materials poses a challenge for both academia and industry. Computational methods, particularly Molecular Dynamics (MD) simulations with classical force-fields have contributed a great deal towards the understanding of the underlying mechanism of LPE, providing remarkable insights into the molecular-level details of the solvent-material interactions at the nanoscale and predicting "good" and "bad" solvents for exfoliation as well as stabilization of the dispersed state. With an intention to build up a unified understanding, in this perspective article, we summarize the recent advancements of molecular simulation techniques employed to decipher the mechanism of LPE, pointing out the key features of molecular interactions and identifying several thermodynamic parameters governing the phenomena. In addition, we outline the necessary characteristics of solvent molecules, essential for their use as "good" solvents towards LPE. Also, we highlight the limitations of simulation methods for the modelling of LPE. We believe that this article will be beneficial for the selection of solvents for the synthesis of novel 2D materials via LPE and will also provide a comprehensive view to computational material scientists towards the development of novel simulation protocols for investigating and analysing such complex molecular events.

Modulating Interdendrimer Interactions through Surface Adsorption

Physical confinement of polymers not only affects their structure but also modifies their effective interaction profiles. In this article, we investigate the nature of graphene-adsorbed poly(amidoamine) (PAMAM) dendrimers' interactions using fully atomistic molecular dynamics simulations. Using the umbrella sampling technique, we calculate the potential of mean force (PMF) profiles for the interaction between two graphene-adsorbed PAMAM dendrimers of generations 3 and 4 as a function of their protonation levels. We find that the attractive PMF profile observed for the interaction between two nonprotonated (high pH) PAMAM dendrimers in bulk becomes repulsive upon adsorption. Also, the repulsive interdendrimer interactions known in bulk for the protonated dendrimers become enhanced for the adsorbed case. We further explain these weakened interactions by explicitly showing that the dendrimer-graphene interaction is an order of magnitude larger than the dendrimer-dendrimer bulk interaction. Using the force integration method, we obtain the contributions from various subinteractions present in the system, that is, dendrimer-water, dendrimer-ions, dendrimer-graphene, and dendrimer-dendrimer to the total PMF. From these contributions, we conclude that the reduced dendrimer-dendrimer interactions in the adsorbed case, as compared to those in bulk, lead to the enhanced repulsive effective interdendrimer interactions. Our PMF profiles fit well with the sum of exponential and Gaussian functions, proposed in the bulk interdendrimer interaction study. We hope the current results provide the microscopic origin of how adsorption weakens the interpolymer interactions in general.

Simultaneous Improvement on Strength, Modulus, and Elongation of Carbon Nanotube Films Functionalized by Hyperbranched Polymers

Carbon nanotube (CNT) buckypapers, or films, have the potential for wide applications because of their unique properties. Neat buckypapers or pristine CNT (PCNT) films have relatively large elongation but low strength and low modulus due to the weak interaction between CNTs. Chemical modifications of PCNT films can significantly strengthen the interaction between CNTs, resulting in high strength and high modulus but usually accompanied by low elongation. Here, we report the functionalization of pristine CNT films by thiol-ended hyperbranched polymers (THBP-n) via a thiol-ene click reaction that can introduce simultaneous improvements on the strength, modulus, and elongation to the PCNT film by 689, 812, and 32.4%, respectively. The high thiol content of THBP-n enables the formation of a network with a high degree of cross-linking between carbon nanotubes, which provides high-efficiency load transfer that increases the tensile strength and modulus of the resulting films and at the same time a compressible hyperbranched structure that allows for deformation and slip between CNTs and consequently improved elongation. The main factors affecting the mechanical performance of the functionalized CNT film are also investigated.

Understanding the Thermodynamics of the Binding of PAMAM Dendrimers to Graphene: A Combined Analytical and Simulation Study

We investigate the thermodynamics of the binding of a poly(amidoamine) dendrimer to an uncharged graphene sheet as a function of the pH level using umbrella sampling simulations and a mean-field theory for generations three and four. We find that the dendrimer strongly binds to the graphene sheet ( O (100) kcal/mol) from our potential of mean force (PMF) calculations. In specific, we find that the dendrimer binds the most at neutral pH (∼7) and the least at low pH (∼4). We explain this nonmonotonic nature of the dendrimer's adsorption by studying the interactions contributing to the PMF, i.e., the dendrimer-graphene, dendrimer-water, and dendrimer-ion interactions. We also corroborate our PMF calculations with molecular mechanics generalized Born surface area analysis and free energies obtained from a mean-field theory of Flory-Huggins-Debye-Hückel type [ Muthukumar , M. , J. Chem. Phys. 2010 , 132 , 084901 ], including electrostatic interactions. We find that the van der Waals interactions between the dendrimer and the graphene alone cannot capture the accurate trends in the binding free energies (BEs) as a function of pH. The solvent and the counterions present in the system are also found to have a major influence on these trends. We demonstrate that the dendrimer-graphene and dendrimer-water interactions become favorable, whereas the dendrimer-ion interaction becomes unfavorable, as the dendrimer binds to graphene. These opposing effects lead to the observed nonmonotonicity in the BE trends. Our theoretical model also reproduces these trends in the subinteractions contributing to the PMF. To the best of our knowledge, this is a novel attempt where an equivalence between theory and simulations is made in the context of the dendrimer's adsorption.

A coarse grained molecular dynamics simulation study on the structural properties of carbon nanotube-dendrimer composites

By employing coarse grained (CG) molecular dynamics (MD) simulation, the effect of the size and hydrophilic/hydrophobic properties of the interior/exterior structures of the dendrimers in carbon nanotube (CNT)-dendrimer composites has been studied, to find a stable composite with high solubility in water and the capability to be used in drug delivery applications. For this purpose, composites consisting of core-shell dendrimer complexes including: [PPI{core}-PAMAM{shell}], [PAMAM{core}-polyethyleneglycol (PEG){shell}] and [PAMAM{core}-fattyacid (FTA){shell}] were constructed. A new CG model for the fatty acid (FTA) molecules as functionalized to the dendrimer was developed, which, unlike the previous models, could generate the structural conformations of the FTA properly. The obtained results indicated that the dendrimer complexes with short FTA chains can form stable composites with the CNT. Also, it was found that the pristine PAMAM and PPI-PAMAM with small PPI, and PAMAM-PEG dendrimers with short PEG chains, can distribute their chains into the water medium and interact with the CNT efficiently, to form a stable water-soluble CNT-dendrimer composite. The results demonstrated that the structural difference between the interior and exterior of a core-shell dendrimer complex can prevent the core and the interior layers of the dendrimer complex from interacting with the CNT. An overall analysis of the results manifested that the CNT-PAMAM:4-PEG:4 is the most stable composite, due to strong binding of the dendrimer with the CNT while also having high solubility in water, and its core retains its structure properly and unchanged, suitable for encapsulating drugs in the targeted delivery applications.

Translocation of Bioactive Molecules through Carbon Nanotubes Embedded in the Lipid Membrane

One of the major challenges of nanomedicine and gene therapy is the effective translocation of drugs and genes across cell membranes. In this study, we describe a systematic procedure that could be useful for efficient drug and gene delivery into the cell. Using fully atomistic molecular dynamics (MD) simulations, we show that molecules of various shapes, sizes, and chemistries can be spontaneously encapsulated in a single-walled carbon nanotube (SWCNT) embedded in a 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (POPC) lipid bilayer, as we have exemplified with dendrimers, asiRNA, ssDNA, and ubiquitin protein. We compute the free energy gain by the molecules upon their entry inside the SWCNT channel to quantify the stability of these molecules inside the channel as well as to understand the spontaneity of the process. The free energy profiles suggest that all molecules can enter the channel without facing any energy barrier but experience a strong energy barrier (≫k_BT) to translocate across the channel. We propose a theoretical model for the estimation of encapsulation and translocation times of the molecules. Whereas the model predicts the encapsulation time to be of the order of few nanoseconds, which match reasonably well with those obtained from the simulations, it predicts the translocation time to be astronomically large for each molecule considered in this study. This eliminates the possibility of passive diffusion of the molecules through the CNT-nanopore spanning across the membrane. To counter this, we put forward a mechanical method of ejecting the encapsulated molecules by pushing them with other free-floating SWCNTs of diameter smaller than the pore diameter. The feasibility of the proposed method is also demonstrated by performing MD simulations. The generic strategy described here should work for other molecules as well and hence could be potentially useful for drug- and gene-delivery applications.

DNA-Assisted Dispersion of Carbon Nanotubes and Comparison with Other Dispersing Agents

Separation and sorting of pristine carbon nanotubes (CNTs) from bundle geometry is a very challenging task due to the insoluble and nondispersive nature of CNTs in aqueous medium. Recently, many studies have been performed to address this problem using various organic and inorganic solutions, surfactant molecules, and biomolecules as dispersing agents. Recent experimental studies have reported the DNA to be highly efficient in dispersing CNTs from bundle geometry. However, there is no microscopic study and also quantitative estimation of the dispersion efficiency of the DNA. Using all-atom molecular dynamics simulation, we study the structure and stability of single-stranded DNA (ssDNA)-single-walled carbon nanotube (SWNT) (6,5) complex. To quantify the dispersion efficiency of various DNA sequences, we perform potential of mean forces (PMF) calculation between two bare SWNTs as well ssDNA-wrapped CNTs for different base sequences. From the PMF calculation, we find the PMF between two bare (6,5) SWNTs to be approximately -29 kcal/mol. For the ssDNA-wrapped SWNTs, the PMF reduces significantly and becomes repulsive. In the presence of ssDNA of different polynucleotide bases (A, T, G, and C), we present a microscopic picture of the ssDNA-SWNT (6,5) complex and also a quantitative estimate of the interaction strength between nanotubes from PMF calculation. From PMF, we show the sequence of dispersion efficiency for four different nucleic bases to be T > A > C > G. We have also presented a comparison of the dispersion efficiencies of ssDNA, flavin mononucleotide surfactant, and poly(amidoamine) (PAMAM) dendrimer by comparing their respective PMF values.