Many recent studies have shown that the way nanoparticles interact with cells and biological molecules can vary greatly in the serum-containing or serum-free culture medium. However, the underlying molecular mechanisms of how the so-called “protein corona” formed in serum medium affects nanoparticles’ biological responses are still largely unresolved. Thus, it is critical to understand how absorbed proteins on the surfaces of nanoparticles alter their biological effects. In this work, we have demonstrated with both experimental and theoretical approaches that protein BSA coating can mitigate the cytotoxicity of graphene oxide (GO) by reducing its cell membrane penetration. Our cell viability and cellular uptake experiments showed that protein corona decreased cellular uptake of GO, thus significantly mitigating the potential cytotoxicity of GO. The electron microscopy images also confirmed that protein corona reduced the cellular morphological damage by limiting GO penetration into the cell membrane. Further molecular dynamics (MD) simulations validated the experimental results and revealed that the adsorbed BSA in effect weakened the interaction between the phospholipids and graphene surface due to a reduction of the available surface area plus an unfavorable steric effect, thus significantly reducing the graphene penetration and lipid bilayer damaging. These findings provide new insights into the underlying molecular mechanism of this important graphene protein corona interaction with cell membranes, and should have implications in future development of graphene-based biomedical applications.

Water self-diffusion and the dipolar response of the selectivity filter within human aquaporin 4 have been studied using molecular dynamics (MD) simulations in the absence and presence of pulses of external static and alternating electric fields. The pulses were approximately 50 and 100 ns in duration and 0.0065 V/Å in (r.m.s.) intensity and were either static or else 2.45 or 100 GHz in frequency and applied both along and perpendicular to the channels. In addition, the relaxation of the aquaporin, water self-diffusion and gating dynamics following cessation of the impulses was studied. In previous work it was determined that switches in the dihedral angle of the selectivity filter led to boosting of water permeation events within the channels, in the presence of identical external static and alternating electric fields, although applied continuously. Here the application of field impulses (and subsequently, upon removal) has shown that it is the dipolar orientation of the histidine-201 residue in the selectivity filter which governs the dihedral angle, and hence influences water self-diffusion; this constitutes an appropriate order parameter. The dipolar response of this residue to the applied field leads to the adoption of four distinct states, which we modelled as time-homogeneous Markov jump processes, and may be distinguished in the potential of mean force (PMF) as a function of the dipolar orientation of histidine-201. The observations of enhanced "dipolar flipping" of H201 serve to explain increased levels of water self-diffusion within aquaporin channels during, and immediately following, field impulses, although the level of statistical certainty here is lower. Given the appreciable size of the energy barriers evident in PMFs computed directly from deterministic MD (whether in the absence or presence of external fields), metadynamics calculations were undertaken to explore the free-energy landscape of histidine-201 orientation with greater accuracy and precision. These indicate that electric fields do alter the free-energy profile of the H201 side-chain orientation, wherein a perturbation of the symmetric bimodal state evident in the zero-field case is observed. These effects are dependent on the field intensities.

Recognition of the lipopolysaccharide (LPS), a major component of the outer membrane of Gram-negative bacteria, by the Toll-like receptor 4 (TLR4)-myeloid differentiation factor 2 (MD-2) complex is essential for the control of bacterial infection. A pro-inflammatory signaling cascade is initiated upon binding of membrane-associated portion of LPS, a glycophospholipid Lipid A, by a coreceptor protein MD-2, which results in a protective host innate immune response. However, activation of TLR4 signaling by LPS may lead to the dysregulated immune response resulting in a variety of inflammatory conditions including sepsis syndrome. Understanding of structural requirements for Lipid A endotoxicity would ensure the development of effective anti-inflammatory medications. Herein, we report on design, synthesis, and biological activities of a series of conformationally confined Lipid A mimetics based on β,α-trehalose-type scaffold. Replacement of the flexible three-bond β(1→6) linkage in diglucosamine backbone of Lipid A by a two-bond β,α(1↔1) glycosidic linkage afforded novel potent TLR4 antagonists. Synthetic tetraacylated bisphosphorylated Lipid A mimetics based on a β–GlcN(1↔1)α–GlcN scaffold selectively block the LPS binding site on both human and murine MD-2 and completely abolish lipopolysaccharide-induced pro-inflammatory signaling, thereby serving as antisepsis drug candidates. In contrast to their natural counterpart lipid IVa, conformationally constrained Lipid A mimetics do not activate mouse TLR4. The structural basis for high antagonistic activity of novel Lipid A mimetics was confirmed by molecular dynamics simulation. Our findings suggest that besides the chemical structure, also the three-dimensional arrangement of the diglucosamine backbone of MD-2-bound Lipid A determines endotoxic effects on TLR4.

Water self-diffusion within human aquaporin 4 has been studied using molecular dynamics (MD) simulations in the absence and presence of external ac and dc electric fields. The computed diffusive (pd) and osmotic (pf) permeabilities under zero-field conditions are (0.718 ± 0.24) × 10−14 cm3 s−1 and (2.94 ± 0.47) × 10−14 cm3 s−1, respectively; our pf agrees with the experimental value of (1.50 ± 0.6) × 10−14 cm3 s−1. A gating mechanism has been proposed in which side-chain dynamics of residue H201, located in the selectivity filter, play an essential role. In addition, for nonequilibrium MD in external fields, it was found that water dipole orientation within the constriction region of the channel is affected by electric fields (e-fields) and that this governs the permeability. It was also found that the rate of side-chain flipping motion of residue H201 is increased in the presence of e-fields, which influences water conductivity further.