Cooperative Effect in Receptor-Mediated Endocytosis of Multiple Nanoparticles

The uptake of nanoparticles (NPs) by a cellular membrane is known to be NP size dependent, but the pathway and kinetics for the endocytosis of multiple NPs still remain ambiguous. With the aid of computer simulation techniques, we show that the internalization of multiple NPs is in fact a cooperative process. The cooperative effect, which in this work is interpreted as a result of membrane curvature mediated NP interaction, is found to depend on NP size, membrane tension, and NP concentration on the membranes. While small NPs generally cluster into a close packed aggregate on the membrane and internalize, as a whole, NPs with intermediate size tend to aggregate into a linear pearl-chain-like arrangement, and large NPs are apt to separate from each other and internalize independently. The cooperative wrapping process is also affected by the size difference between neighboring NPs. Depending on the size difference of neighboring NPs and inter-NP distance, four different internalization pathways, namely, synchronous internalization, asynchronous internalization, pinocytosis-like internalization, and independent internalization, are observed

Phosphatidylinositol 4,5-Bisphosphate Sensing Lipid Raft via Inter-Leaflet Coupling Regulated by Acyl Chain Length of Sphingomyelin

Phosphatidylinositol 4,5-bisphosphate (PIP2) is an important molecule located at the inner leaflet of cell membrane, where it serves as anchoring sites for a cohort of membrane-associated molecules and as a broad-reaching signaling intermediate. The lipid raft is thought as the major platform recruiting proteins for signal transduction and also known to mediate PIP2 accumulation across the membrane. While the significance of this cross-membrane coupling is increasingly appreciated, it remains unclear whether and how PIP2 senses the dynamic change of the ordered lipid domains over the packed hydrophobic core of the bilayer. Herein, by means of molecular dynamic simulation, we reveal that inner PIP2 molecules can sense the outer lipid domain via inter-leaflet coupling, and the coupling manner is dictated by the acyl chain length of sphingomyelin (SM) partitioned to the lipid domain. Shorter SM promotes membrane domain registration, whereby PIP2 accumulates beneath the domain across the membrane. In contrast, the anti-registration is thermodynamically preferred if the lipid domain has longer SM due to the hydrophobic mismatch between the corresponding acyl chains in SM and PIP2. In this case, PIP2 is expelled by the domain with a higher diffusivity. These results provide molecular insights into the regulatory mechanism of correlation between the outer lipid domain and inner PIP2, both of which are critical components for cell signal transduction

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

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

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

Precisely Tailoring Bubble Morphology in Microchannel by Nanoparticles Self-assembly

Precisely tailoring bubble morphology is always a long-standing great challenge. In this work, a facile and scalable method to generate nonspherical bubbles with long-term stability is proposed. Taking advantage of the electrostatic interaction between silica nanoparticles (SNPs) and cationic surfactants, the SNPs are decorated with surfactants and endowed with interfacial activity. Due to the rearrangement of surfactants, the decorated SNPs transform to a kind of Janus particles at the gas–liquid interface. By precisely manipulating the surface activity, packing density, and jamming of Janus SNPs at the bubble surface, four different shapes such as oblaten-like, bullet-like, tadpole-like, and worm-like bubble were obtained continuously in the microchannel. Herein, our method to generate bubbles with a prescribed shape poses opportunities for gas microreactor, cavity material, gas storage, and provide a platform to study the applicable scope of the Young–Laplace equation

Supramolecular Construction of Biohybrid Nanozymes Based on the Molecular Chaperone GroEL as a Promiscuous Scaffold

The study of enzymatic reactions in a confined space can provide valuable insight into the natural selection of nanocompartments for biocatalytic processes. Design of nanozyme capsules with the barrel-shaped protein cage of GroEL has been proposed as a promising means to constrain chemical reactions in a spatiotemporally controllable manner. Herein, we further demonstrate with hemin that the open GroEL cavity can provide a favorable microenvironment for shielding hydrophobic catalytically active species. Meanwhile, it is shown that the GroEL-caged hemin nanozyme not only has a significantly higher catalytic activity than merely dispersed hemin but also exhibits substrate specificity in the model oxidation reactions, which is a merit lacking in natural hemoproteins. To understand the underlying mechanism behind this supramolecular assembly, molecular docking and molecular dynamics simulations were performed to study the detailed interactions of hemin with the protein cage. This revealed the most likely binding mode and preferred binding residues in the paired hydrophobic α-helices lining the GroEL cavity which are genetically encoded for substrate capture. Finally, we demonstrate that the hemin-GroEL nanozyme has great potential in label-free fluorometric molecular detection when combined with suitable substrates such as homovanillic acid. We believe that our strategy is an advantageous tool for studying confined biocatalytic kinetics as simple mimics of protein-based organelles found in nature and for designing diverse nanozymes or bio-nanoreactors with the promiscuous GroEL binding cavity

Revealing Cooperation between Knotted Conformation and Dimerization in Protein Stabilization by Molecular Dynamics Simulations

The topological knot is thought to play a stabilizing role in maintaining the global fold and nature of proteins with the underlying mechanism yet to be elucidated. Given that most proteins containing trefoil knots exist and function as homodimers with a large part of the dimer interface occupied by the knotted region, we reason that the knotted conformation cooperates with dimerization in protein stabilization. Here, we take YbeA from Escherichia coli as the knotted protein model, using molecular dynamics (MD) simulations to compare the stability of two pairs of dimeric proteins having the same sequence and secondary structures but differing in the presence or absence of a trefoil knot in each subunit. The dimer interface of YbeA is identified to involve favorable contacts among three α-helices (α1, α3, and α5), one of which (α5) is threaded through a loop connected with α3 to form the knot. Upon removal of the knot by appropriate change of the knot-making crossing of the polypeptide chain, relevant domains are less constrained and exhibit enhanced fluctuations to decrease contacts at the interface. Unknotted subunits are less compact and undergo structural changes to ease the dimer separation. Such a stabilizing effect is evidenced by steered MD simulations, showing that the mechanical force required for dimer separation is significantly reduced by removing the knot. In addition to the knotted conformation, dimerization further improves the protein stability by restricting the α1−α5 separation, which is defined as a leading step for protein unfolding. These results provide important insights into the structure–function relationship of dimerization in knotted proteins

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 < <i>l</i> < 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

Size‑, Aggregation‑, and Oxidization-Dependent Perturbation of Methane Hydrate by Graphene Nanosheets Revealed by Molecular Dynamics Simulations

Understanding and control of the methane hydrate formation are of central importance for applications ranging from natural gas exploitation to transportation. Fabricated carbon nanomaterials, owing to their outstanding physicochemical properties, are increasingly considered as additives to manipulate the hydrate formation, whereas little is known about the underlying molecular mechanism. Here, we investigate the methane hydrate formation in the presence of graphene nanosheets (GNs) using molecular dynamics simulations. Particular attention is placed on the effects of size, aggregation, and oxidation of GNs. Individual GNs are found to play roles in a size-dependent manner, as sharp corners of GNs are preferentially anchored into cavities at the hydrate surface, exposing other segment in a solvent to disturb the local hydrate structure. Once GNs form aggregates exceeding a critical size, methane molecules can be recruited to promote formation of nanobubbles, thus retarding the hydrate formation due to depletion of methane in the aqueous phase. Graphene oxide forms hydrogen bonds with water both in the aqueous phase and at the hydrate surface, thus reducing the water activity to obstruct the hydrate growth. Our results have important consequences for regulating the methane hydrate formation and open up new avenues for the energy application of graphene family nanomaterials