Shixin Li

Ultrashort Single-Walled Carbon Nanotubes Insert into a Pulmonary Surfactant Monolayer via Self-Rotation: Poration and Mechanical Inhibition

It has been widely accepted that longer single-walled carbon nanotubes (SWCNTs) exhibit higher toxicity by causing severe pneumonia once inhaled, yet relatively little is known regarding the potential toxicity of ultrashort SWCNTs, which are of central importance to the development of suitable vehicles for biomedical applications. Here, by combining coarse-grained molecular dynamics (CGMD), pulling simulations, and scaling analysis, we demonstrate that the inhalation toxicity of ultrashort SWCNTs (1.5 nm < l < 5.5 nm) can be derived from the unique behaviors on interaction with the pulmonary surfactant monolayer (PSM), which is located at the air-water interface of alveoli and forms the frontline of the lung host defense. Molecular dynamics (MD) simulations suggest that ultrashort SWCNTs spontaneously insert into the PSM via fast self-rotation. Further translocation toward the water or air phase involves overcoming a high free-energy barrier, indicating that removal of inhaled ultrashort SWCNTs from the PSM is difficult, possibly leading to the accumulation of SWCNTs in the PSM, with prolonged retention and increased inflammation potentials. Under certain conditions, the inserted SWCNTs are found to open hydrophilic pores in the PSM via a mechanism that mimics that of the antimicrobial peptide. Besides, the mechanical property of the PSM is inhibited by the deposited ultrashort SWCNTs through segregation of the inner lipid molecules from the outer phase. Our results bring to the forefront the concern of the inhalation toxicity of ultrashort SWCNTs and provide guidelines for future design of inhaled nanodrug carriers with minimized side effects.

Interplay Between Nanoparticle Wrapping and Clustering of Inner Anchored Membrane Proteins.

The receptor-mediated endocytosis of nanoparticles (NPs) is known to be size and shape dependent but regulated by membrane properties, like tension, rigidity, and especially membrane proteins. Compared with transmembrane receptors, which directly bind ligands coated on NPs to provide the driving force for passive endocytosis, the hidden role of inner anchored membrane proteins (IAMPs), however, has been grossly neglected. Here, by applying the N-varied dissipative particle dynamics (DPD) techniques, we present the first simulation study on the interplay between wrapping of NPs and clustering of IAMPs. Our results suggest that the wrapping dynamics of NPs can be regulated by clustering of IAMPs, but in a competitive way. In the early stage, the dispersed IAMPs rigidify the membrane and thus restrain NP wrapping by increasing the membrane bending energy. However, once the clustering completes, the rigidifying effect is reduced. Interestingly, the clustering of longer IAMPs can sense NP wrapping. They are found to locate preferentially at the boundary region of NP wrapping. More importantly, the adjacent IAMP clustering produces a late membrane monolayer protrusion, which finally wraps the NP from the top side. Our findings regarding the competitive effects of IAMP clustering on NP wrapping facilitate the molecular understanding of endocytosis and establish fundamental principles for design of NPs for widespread biomedical applications.

The role of nanoparticle shape in translocation across the pulmonary surfactant layer revealed by molecular dynamics simulations

Airborne nanoparticles (NPs), which vary widely in both shape and size, can be inhaled and deposit in the alveolar region, where they first interact with the pulmonary surfactant (PS) layer to cause toxicological effects and impact the subsequent fate of NPs inside the body. Previous studies on NP–PS interactions have been conducted focusing on spherical NPs, thereby overlooking the role of NP shape. Here, we demonstrate by molecular dynamics simulations the translocation of NPs across the PS layer being influenced by the NP shape. It was found that hydrophilic NPs with all dimensions smaller than 5 nm can rapidly penetrate through the PS layer, being barely affected by the NP shape, while the shape matters for larger NPs in both translocation and PS perturbation. For hydrophobic NPs with at least one dimension smaller than the PS layer thickness, they prefer to be immersed into but hardly transported across the PS layer. If at least one dimension is larger than the PS layer thickness, they can be readily wrapped by the layer under compression, with the steady wrapping state being dominated by the shape-dependent NP rotation. During transport, PS molecules can be recruited by NPs, acting as a corona to influence the biological identity of NPs. Adversely, PS depletion can be induced, together with the perturbed PS arrangement around sharp NP edges to cause destructive PS layer rupture. Our results suggest that all studies of inhalation toxicity and pulmonary drug delivery should consider first the interactions of target NPs with the PS layer, where the shape significantly matters.

Surface patterning of single-walled carbon nanotubes enhances their perturbation on a pulmonary surfactant monolayer: frustrated translocation and bilayer vesiculation

The pulmonary surfactant monolayer (PSM) is a complex material lining the air–water interface of lung alveoli to avoid its collapse by reducing surface tension. Once external particles are inhaled and captured by the PSM, this property might be perturbed to induce inhalation toxicity. However, relatively little is known regarding the detailed interaction between inhaled particles and the PSM. Here, by applying the coarse-grained molecular dynamics simulation method, we probe how inhaled single-walled carbon nanotubes (SWCNTs) interact with the PSM. For pristine SWCNTs, they are found to insert into or be wrapped by the PSM, depending on the tube size and the PSM tension. For hydrophilic tubes, they spontaneously translocate across the PSM, regardless of the tension. In contrast to SWCNTs with unique surface properties, the surface patterning of SWCNTs enhances their perturbation on the PSM. Under expansion, the PSM translocation is frustrated via inducing the ordered or disordered lipid arrangement adhering to the patterned tube surface. Under compression, the lipid rearrangements further self-adjust and grow into bilayers, which protrude along the tube surface and finally develop into vesicles. The stripe width and stripe orientation, among other factors, are found to be the most important factors that determine whether and how the vesiculation takes place.

Interaction pathways between soft lipid nanodiscs and plasma membranes: A molecular modeling study

Lipid nanodisc, a model membrane platform originally synthesized for study of membrane proteins, has recently been used as the carrier to deliver amphiphilic drugs into target tumor cells. However, the central question of how cells interact with such emerging nanomaterials remains unclear and deserves our research for both improving the delivery efficiency and reducing the side effect. In this work, a binary lipid nanodisc is designed as the minimum model to investigate its interactions with plasma membranes by using the dissipative particle dynamics method. Three typical interaction pathways, including the membrane attachment with lipid domain exchange of nanodiscs, the partial membrane wrapping with nanodisc vesiculation, and the receptor-mediated endocytosis, are discovered. For the first pathway, the boundary normal lipids acting as ligands diffuse along the nanodisc rim to gather at the membrane interface, repelling the central bola lipids to reach a stable membrane attachment. If bola lipids are positioned at the periphery and act as ligands, they diffuse to form a large aggregate being wrapped by the membrane, leaving the normal lipids exposed on the membrane exterior by assembling into a vesicle. Finally, by setting both central normal lipids and boundary bola lipids as ligands, the receptor-mediated endocytosis occurs via both deformation and self-rotation of the nanodiscs. All above pathways for soft lipid nanodiscs are quite different from those for rigid nanoparticles, which may provide useful guidelines for design of soft lipid nanodiscs in widespread biomedical applications.

Role of Lipid Coating in the Transport of Nanodroplets across the Pulmonary Surfactant Layer Revealed by Molecular Dynamics Simulations

Hydrophilic drugs can be delivered into lungs via nebulization for both local and systemic therapies. Once inhaled, ultrafine nanodroplets preferentially deposit in the alveolar region, where they first interact with the pulmonary surfactant (PS) layer, with nature of the interaction determining both efficiency of the pulmonary drug delivery and extent of the PS perturbation. Here, we demonstrate by molecular dynamics simulations the transport of nanodroplets across the PS layer being improved by lipid coating. In the absence of lipids, bare nanodroplets deposit at the PS layer to release drugs that can be directly translocated across the PS layer. The translocation is quicker under higher surface tensions but at the cost of opening pores that disrupt the ultrastructure of the PS layer. When the PS layer is compressed to lower surface tensions, the nanodroplet prompts collapse of the PS layer to induce severe PS perturbation. By coating the nanodroplet with lipids, the disturbance of the nanodroplet on the PS layer can be reduced. Moreover, the lipid-coated nanodroplet can be readily wrapped by the PS layer to form vesicular structures, which are expected to fuse with the cell membrane to release drugs into secondary organs. Properties of drug bioavailability, controlled drug release, and enzymatic tolerance in real systems could be improved by lipid coating on nanodroplets. Our results provide useful guidelines for the molecular design of nanodroplets as carriers for the pulmonary drug delivery.

Stabilizing Effect of Inherent Knots on Proteins Revealed by Molecular Dynamics Simulations

A growing number of proteins have been identified as knotted in their native structures, with such entangled topological features being expected to play stabilizing roles maintaining both the global fold and the nature of proteins. However, the molecular mechanism underlying the stabilizing effect is ambiguous. Here, we combine unbiased and mechanical atomistic molecular dynamics simulations to investigate how a protein is stabilized by an inherent knot by directly comparing chemical, thermal, and mechanical denaturing properties of two proteins having the same sequence and secondary structures but differing in the presence or absence of an inherent knot. One protein is YbeA from Escherichia coli, containing a deep trefoil knot within the sequence, and the other is the modified protein with the knot of YbeA being removed. Under certain chemical denaturing conditions, the unknotted protein fully unfolds whereas the knotted protein does not, suggesting a higher intrinsic stability for the protein having a knot. Both proteins unfold under enhanced thermal fluctuations but at different rates and with distinct pathways. Opening the hydrophobic core via separation between two α-helices is identified as a crucial step initiating the protein unfolding, which, however, is restrained for the knotted protein by topological and geometrical frustrations. Energy barriers for denaturing the protein are reduced by removing the knot, as evidenced by mechanical unfolding simulations. Finally, yet importantly, no obvious change in size or location of the knot was observed during denaturing processes, indicating that YbeA may remain knotted for a relatively long time during and after denaturation.

Combined thermodynamic and kinetic analysis of GroEL interacting with CXCR4 transmembrane peptides

GroEL along with ATP and its co-chaperonin GroES has been demonstrated to significantly enhance the folding of newly translated G-protein-coupled receptors (GPCRs). This work extends the previous studies to explore the guest capture and release processes in GroEL-assisted folding of GPCRs, by the reduced approach of employing CXCR4 transmembrane peptides as model substrates. Each of the CXCR4-derived peptides exhibited high affinity for GroEL with a binding stoichiometry near seven. It is found that the peptides interact with the paired α helices in the apical domain of the chaperonin which are similar with the binding sites of SBP (strongly binding peptide: SWMTTPWGFLHP). Complementary binding study with a single-ring version of GroEL indicates that each of the two chaperonin rings is competent for accommodating all the seven CXCR4 peptides bound to GroEL under saturation condition. Meanwhile, the binding kinetics of CXCR4 peptides with GroEL was also examined; ATP alone, or in combination of GroES evidently promoted the release of the peptide substrates from the chaperonin. The results obtained would be beneficial to understand the thermodynamic and kinetic nature of GroEL-GPCRs interaction which is the central molecular event in the assisted folding process.