Characterisation of the hydrophobic collapse of polystyrene in water using free energy techniques

<p>We characterise the hydrophobic collapse of single polystyrene chains in water using molecular dynamics simulations. Specifically, we calculate the potential of mean force for the collapse of a single polystyrene chain in water using metadynamics, comparing the results between all atomistic with coarse-grained (CG) molecular simulation. We next explore the scaling behaviour of the collapsed globular shape at the minimum energy configuration, characterised by the radius of gyration, as a function of chain length. The exponent is close to one third, consistent with that predicted for a polymer chain in bad solvent. We also explore the scaling behaviour of the solvent accessible surface area (SASA) as a function of chain length, finding a similar exponent for both all atomistic and CG simulations. Furthermore, calculation of the local water density as a function of chain length near the minimum energy configuration suggests that intermediate chain lengths are more likely to form dewetted states, as compared to shorter or longer chain lengths.</p

Molecular Simulation of the Concentration-Dependent Interaction of Hydrophobic Drugs with Model Cellular Membranes

We report here the interactions between a hydrophobic drug and a model cellular membrane at the molecular level using all-atom molecular dynamics simulations of paclitaxel, a hydrophobic cancer drug. The calculated free energy of a single drug across the bilayer interface displays a minimum in the outer hydrophobic zone of the membrane. The transfer free energy shows excellent agreement with reported experimental data. In two sets of long-time simulations of high concentrations of drug in the membrane (12 and 11 mol %), the drugs display substantial clustering and rotation with significant directional preference in their diffusion. The main taxane ring partitions in the outer hydrophobic zone, while the three phenyl rings prefer to be closer to the hydrophobic core of the membrane. The clustering of the drug molecules, order parameters of the lipid tails, and water penetration suggest that the fluidity and permeability of the membrane are affected by the concentration of drugs that it contains. Furthermore, at the high-concentration limit, the free energy minimum shifts closer to the hydrophobic core and the central barrier to cross the membrane decreases. Moreover, the transfer free energy change substantially increases, suggesting that increasing concentration facilitates drug partitioning into the membrane

Molecular Dynamics Simulations of Supramolecular Anticancer Nanotubes

We report here on long-time all-atomistic molecular dynamics simulations of functional supramolecular nanotubes composed by the self-assembly of peptide-drug amphiphiles (DAs). These DAs have been shown to possess an inherently high drug loading of the hydrophobic anticancer drug camptothecin. We probe the self-assembly mechanism from random with ∼0.4 μs molecular dynamics simulations. Furthermore, we also computationally characterize the interfacial structure, directionality of π–π stacking, and water dynamics within several peptide-drug nanotubes with diameters consistent with the reported experimental nanotube diameter. Insight gained should inform the future design of these novel anticancer drug delivery systems

Molecular Dynamics Simulations of Polyelectrolyte Complexes

Polyelectrolyte complexes (PECs) are currently of great interest due to their applications toward developing new adaptive materials and their relevance in membraneless organelles. These complexes emerge during phase separation when oppositely charged polymers are mixed in aqueous media. Peptide-based PECs are particularly useful toward developing new drug delivery methods due to their inherent biocompatibility. The underlying peptide sequence can be tuned to optimize specific material properties of the complex, such as interfacial tension and viscosity. Given their applicability, it would be advantageous to understand the underlying sequence-dependent phase behavior of oppositely charged peptides. Here, we report microsecond molecular dynamic simulations to characterize the effect of hydrophobicity on the sequence-dependent peptide conformation for model polypeptide sequences that were previously reported by Tabandeh et al. These sequences are designed with alternating chirality of the peptide backbone. We present microsecond simulations of six oppositely charged peptide pairs, characterizing the sequence-dependent effect on peptide size, degree of hydrogen bonding, secondary structure, and conformation. This analysis recapitulates sensible trends in peptide conformation and degree of hydrogen bonding, consistent with experimentally reported results. Ramachandran plots reveal that backbone conformation at the single amino acid level is highly influenced by the neighboring sequence in the chain. These results give insight into how subtle changes in hydrophobic side chain size and chirality influence the strength of hydrogen bonding between the chains and, ultimately, the secondary structure. Furthermore, principal component analysis reveals that the minimum energy structures may be subtly modulated by the underlying sequence

π–π Stacking Mediated Chirality in Functional Supramolecular Filaments

While a great diversity of peptide-based supramolecular filaments have been reported, the impact of an auxiliary segment on the chiral assembly of peptides remains poorly understood. Herein we report on the formation of chiral filaments by the self-assembly of a peptide-drug conjugate containing an aromatic drug camptothecin (CPT) in a computational study. We find that the chirality of the filament is mediated by the π–π stacking between CPTs, not only by the well-expected intermolecular hydrogen bonding between peptide segments. Our simulations show that π–π stacking of CPTs governs the early stages of the self-assembly process, while a hydrogen bonding network starts at a relatively later stage to contribute to the eventual morphology of the filament. Our results also show the possible presence of water within the core of the CPT filament. These results provide very useful guiding principles for the rational design of supramolecular assemblies of peptide conjugates with aromatic segments

Effect of Nucleotide State on the Protofilament Conformation of Tubulin Octamers

At the molecular level, the dynamic instability (random growth and shrinkage) of the microtubule (MT) is driven by the nucleotide state (GTP vs GDP) in the β subunit of the tubulin dimers at the MT cap. Here, we use large-scale molecular dynamics (MD) simulations and normal-mode analysis (NMA) to characterize the effect of a single GTP cap layer on tubulin octamers composed of two neighboring protofilaments (PFs). We utilize recently reported high-resolution structures of dynamic MTs to simulate a GDP octamer both with and without a single GTP cap layer. We perform multiple replicas of long-time atomistic MD simulations (3 replicas, 0.3 μs for each replica, 0.9 μs for each octamer system, and 1.8 μs total) of both octamers. We observe that a single GTP cap layer induces structural differences in neighboring PFs, finding that one PF possesses a gradual curvature, compared to the second PF which possesses a kinked conformation. This results in either curling or splaying between these PFs. We suggest that this is due to asymmetric strengths of longitudinal contacts between the two PFs. Furthermore, using NMA, we calculate mechanical properties of these octamer systems and find that octamer system with a single GTP cap layer possesses a lower flexural rigidity

TCR Triggering by pMHC Ligands Tethered on Surfaces via Poly(Ethylene Glycol) Depends on Polymer Length

<div><p>Antigen recognition by T cells relies on the interaction between T cell receptor (TCR) and peptide-major histocompatibility complex (pMHC) at the interface between the T cell and the antigen presenting cell (APC). The pMHC-TCR interaction is two-dimensional (2D), in that both the ligand and receptor are membrane-anchored and their movement is limited to 2D diffusion. The 2D nature of the interaction is critical for the ability of pMHC ligands to trigger TCR. The exact properties of the 2D pMHC-TCR interaction that enable TCR triggering, however, are not fully understood. Here, we altered the 2D pMHC-TCR interaction by tethering pMHC ligands to a rigid plastic surface with flexible poly(ethylene glycol) (PEG) polymers of different lengths, thereby gradually increasing the ligands’ range of motion in the third dimension. We found that pMHC ligands tethered by PEG linkers with long contour length were capable of activating T cells. Shorter PEG linkers, however, triggered TCR more efficiently. Molecular dynamics simulation suggested that shorter PEGs exhibit faster TCR binding on-rates and off-rates. Our findings indicate that TCR signaling can be triggered by surface-tethered pMHC ligands within a defined 3D range of motion, and that fast binding rates lead to higher TCR triggering efficiency. These observations are consistent with a model of TCR triggering that incorporates the dynamic interaction between T cell and antigen-presenting cell.</p></div

FRET between streptavidin on plastic plates and IEkMCC tethered with PEG polymers.

<p>(A) Measured FRET efficiencies of IEkMCC tethered with six different PEG polymers. The intensity of DyLight 549 was captured before and after DyLight 649 was photobleached. The measured FRET efficiency () was calculated using the intensity of DyLight 549 before () and after () DyLight 649 photobleaching ( ). The averaged values of two measurements were plotted with standard deviations. (B) After normalization, the measured FRET efficiencies match those calculated based on the Flory radius () of the PEG polymers. The of the PEG polymer of subunits and unit length was calculated using , where is 0.28 nm <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0112292#pone.0112292-Oesterhelt1" target="_blank">[32]</a>. Theoretical FRET efficiency () was calculated using the equation , where the Förster distance () of the DyLight 549-DyLight 649 donor-acceptor pair is 5 nm and the distance between the pMHC ligand and streptavidin is of the PEG polymer plus the pMHC radius of 2 nm. The FRET efficiencies were normalized by dividing the FRET efficiencies by the FRET efficiency of PEG 88.</p

PEG linkers and properties.

1<p>PEG contour length is calculated based on the PEO unit length of 0.28 nm in water <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0112292#pone.0112292-Oesterhelt1" target="_blank">[32]</a>.</p>2<p>The Flory radius () of the PEG polymer of subunits and unit length was calculated using , where is 0.28 nm.</p><p>PEG linkers and properties.</p

T cell activation by IEkMCC tethered with PEG polymers of different lengths.

<p>(A) T cell IL2 production in response to IEkMCC-PEG ligands of varying coating densities after 6 hours of stimulation. Data are representative of three independent experiments. The percent of T cells producing IL2 was determined by intracellular staining and flow cytometry. Three experiments using T cells from three different mice were performed (see <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0112292#pone.0112292.s008" target="_blank">Fig. S8</a> for flow cytometry plots). The percent of T cells producing IL2 was normalized to the highest value in each experiment. The data points are averages of the normalized values with standard errors of the means. (B) The rate of T cell response to IEkMCC ligands tethered with PEG polymers of different lengths. T cell IL2 production in response to stimulation on 96 well plates coated with 110 pM IEkMC-PEG ligands. T cells were harvested every hour for 6 hours and levels of IL2 expression were assayed by flow cytometry. Three experiments using T cells from three different mice were performed (see <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0112292#pone.0112292.s009" target="_blank">Fig. S9</a> for flow cytometry plots). The percent of T cells producing IL2 was normalized to the highest value in each experiment. The data points are averages of the normalized values with standard errors of the means. (C) The rates of T cell IL2 responses to IEkMCC ligands tethered with PEG polymers were extracted from the slope of linear fitting curves in Fig. 4B and plotted against the Flory radius of the polymers. The linear regressions and equations for deriving the rates are shown in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0112292#pone.0112292.s007" target="_blank">Fig. S7</a>.</p