Supported lipid bilayers (SLBs) are able to accommodate membrane proteins useful for diverse biomimetic applications. Although liposome spreading represents a common procedure for preparation of SLBs, the underlying mechanism is not yet fully understood, particularly from a molecular perspective. The present study examines the effects of the substrate charge on unilamellar liposome spreading on the basis of molecular dynamics simulations for a coarse-grained model of the solvent and lipid molecules. Liposome transformation into a lipid bilayer of different microscopic structures suggests three types of kinetic pathways depending on the substrate charge density, that is, top-receding, parachute, and parachute with wormholes. Each pathway leads to a unique distribution of the lipid molecules and thereby distinctive properties of SLBs. An increase of the substrate charge density results in a magnified asymmetry of the SLBs in terms of the ratio of charged lipids, parallel surface movements, and the distribution of lipid molecules. While the lipid mobility in the proximal layer is strongly correlated with the substrate potential, the dynamics of lipid molecules in the distal monolayer is similar to that of a freestanding lipid bilayer. For liposome spreading on a highly charged surface, wormhole formation promotes lipid exchange between the SLB monolayers thus reduces the asymmetry on the number density of lipid molecules, the lipid order parameter, and the monolayer thickness. The simulation results reveal the important regulatory role of electrostatic interactions on liposome spreading and the properties of SLBs.

Supported lipid bilayers (SLBs) have been widely used in drug delivery, biosensors and biomimetic membranes. The microscopic mechanism of SLB formation and stability depends on a number of factors underlying solvent-mediated lipid–lipid and lipid–substrate interactions. Whereas recent years have witnessed remarkable progress in understanding the kinetics of SLB formation, relatively little is known about the lipid phase behavior controlling the SLB stability under diverse solution conditions. In this work, we examine the structure of SLBs using classical density functional theory (CDFT) in the context of a coarse-grained model that accounts for ion-explicit electrostatic interactions, surface hydrophobicity, as well as the molecular characteristics of the lipid tails. A morphological phase diagram is constructed in terms of various intrinsic properties of lipid molecules (such as the lipid tail length, size and charge of the lipid head segments), substrate conditions (such as the surface charge density and hydrophobicity), and solution parameters (such as the ion concentration and ion type). The morphological phase diagram provides useful insights into the rational design and broader application of SLB membranes as different types of nano-devices.

Molecular dynamics (MD) simulations, in combination with the Markov-state model (MSM), were applied to probe CO2 diffusion from an aqueous solution into the active site of human carbonic anhydrase II (hCA-II), an enzyme useful for enhanced CO2 capture and utilization. The diffusion process in the hydrophobic pocket of hCA-II was illustrated in terms of a two-dimensional free-energy landscape. We found that CO2 diffusion in hCA-II is a rate-limiting step in the CO2 diffusion-binding-reaction process. The equilibrium distribution of CO2 shows its preferential accumulation within a hydrophobic domain in the protein core region. An analysis of the committors and reactive fluxes indicates that the main pathway for CO2 diffusion into the active site of hCA-II is through a binding pocket where residue Gln136 contributes to the maximal flux. The simulation results offer a new perspective on the CO2 hydration kinetics and useful insights toward the development of novel biochemical processes for more efficient CO2 sequestration and utilization.

The capability of silencing genes makes small interfering RNA (siRNA) appealing for curing fatal diseases such as cancer and viral infections. In the present work, we chose a novel amphiphilic polymer, PMAL (poly(maleic anhydride-alt-1-decene) substituted with 3-(dimethylamino) propylamine), as the siRNA carrier, and conducted steered molecular dynamics simulations, together with traditional molecular dynamics simulations, to explore how PMAL facilitates the delivery of siRNA. It was shown that the use of PMAL reduced the energy barrier for siRNA to penetrate lipid bilayer membranes, as confirmed by the experimental work. The simulation of the transmembrane process revealed that PMAL can punch a hole in the lipid bilayer and form a channel for siRNA delivery. Monitoring of the structural transition further showed the targeting of siRNA through the attachment of PMAL encapsulating siRNA to a lipid membrane. The delivery of siRNA was facilitated by the hydrophobic interaction between PMAL and the lipid membrane, which favored the dissociation of the siRNA–PMAL complex. The above simulation established a molecular insight of the interaction between siRNA and PMAL and was helpful for the design and applications of new carriers for siRNA delivery.

While the preferential movement of water inside carbon nanotube is appealing for water purification, our understanding of the water transport mechanism through carbon nanotube (CNT)-based membrane is far from adequate. Here we conducted molecular dynamics simulations to study how the alignment of the CNTs in the membrane affects the water transport through the CNT membrane. It was shown that compared to the conventional CNT membrane where the alignment of CNTs was vertical to membrane surface, the “italicized CNT membrane” in which the contact angel between membrane surface and the CNT alignment is not 90° offered a higher transmembrane flux of water. The expanded exposure of more carbon atoms to water molecules reduced the energy barrier near the entrance of this italicized CNT membrane, compared to the vertical one. For water flows through the italicized CNT membrane, the Lennard-Jones interaction between water and nanotube as function of central path of the CNT changes from “U” to “V” pattern, which significantly lowers energy barrier for filling water into the CNT, favoring the water transport inside carbon nanotube. Above simulation indicates new opportunities for applying CNT in water purification or related fields in which water transport matters.

We synthesized a novel hydrophilic, negatively charged block polymer composed of polyethylene glycol (PEG) and poly(methacrylic acid) (PMAA) using atom-transfer radical polymerization (ATRP). The encapsulation of a positively charged protein, represented by hen-egg white lysozyme, by mPEG-b-PMAA micelles was achieved using a pH or salt-concentration swing, as shown by both structural characterization using dynamic light scattering and transmission electron microscopy and an activity assay. All-atom molecular dynamics simulations showed that using an acidic pH gave a more compact polymer–micelle assembly than did using a basic pH. As a result, this compact structure had less solvent-accessible surface area (SASA), indicating that lysozyme was encapsulated by mPEG-b-PMAA and that the active site was shielded by the polymer. This made the active site less accessible to the substrate. These accounted for the low apparent activity at an acidic pH in our experiments. A neutral or basic pH intensified the electrostatic repulsive interaction, which prevented the formation of polymer–lysozyme complex. The molecular simulation indicated that encapsulation of lysozyme by the polymer micelles could be divided into two consecutive steps. The first step involved the attachment of the negatively charged polymer chain to the positively charged portion of lysozyme, driven by electrostatic attractive force. Then, the hydrophobic interaction between the polymer and lysozyme became dominant and led to a more compact assembly with a reduced energy state. These simulations agreed with our experimental observations and provided molecular insight helpful for the design, fabrication, and application of protein-incorporated polymer micelles.

A lipase nanogel has been prepared by aqueous in situ polymerization, with initial acryloylation to introduce vinyl groups onto the lipase surface for subsequent polymerization with acrylamide monomers. Activation of lipase was observed using glycidyl methacrylate (GMA) as the acryloylation agent, leading to an increase of activity yield from 78 ± 4% (obtained using NAS for acryloylation) to 122 ± 14%. The acryloylation ratio was also improved, from 8 ± 5% to 20 ± 8%, which favored the subsequent polymerization. In addition, the overall activity yield of the lipase nanogel was increased from 44 ± 3% to 105 ± 2%. The lipase nanogel prepared with GMA for acryloylation displayed a lower Km and a higher kcat in comparison to its native counterpart, as well as the nanogel obtained using NAS for acryloylation. The half-life of the lipase nanogel at 60 °C was extended from 1.63 h (using NAS for acryloylation) to 5.61 h, while the half-life of the native lipase was 1.41 h. Molecular dynamics simulations and experiments further suggested that the activation effect was due in part to interactions between the lipase and the GMA, which reinforced the ‘open’ configuration of the lipase, thereby facilitating mass transport to and from the modified lipase in the free and encapsulated forms. The above mentioned activation effect of the enzyme nanogel illustrated the power of chemical modification by tailored design of the nanostructure of the enzyme catalyst, potentially expanding the applications of enzyme catalysis.

•Both TUAH-1 cell and its crude enzymes have capacity of CTN degradation in both aqueous and soil.•After treatment with 21.3 mg dry cells, the degradation efficiency was 97.4% for 20 mg L-1 CTN in the aqueous phase.•Treatment with crude enzyme solution containing 2.0 mg mL-1 protein led to complete degradation of 20.0 mg L-1 CTN within 10 h, which is significantly faster than that of TUAH-1.•According to degradation products detected by HPLC-MS, degradation pathways of CTN by TUAH-1 were proposed.•The mechanism of CTN degradation by TUAH-1 is multi-enzymatic catalysis.The long-term excessive use of chlorothalonil (CTN) can lead to serious environmental pollution, which presents a cause for concern. Here, we investigated the degradation of CTN by using an effective strain, TUAH-1, which was identified as Enterobacter cloacae according to the morphological approach, 16S rDNA gene sequence and phylogenetic tree analysis. Treatment with TUAH-1 demonstrated that the maximum processing capability was 74 mg CTN per gram dry cells in 48 h under optimum conditions (30 °C–35 °C, pH 7.0). After treatment with 21.3 mg dry cells, the degradation efficiency was 97.4% for 20 mg l-1 CTN in the aqueous phase. Meanwhile, treatment with crude enzyme solution containing 2.0 mg ml-1 protein led to complete degradation of 20.0 mg l-1 CTN within 10 h, which is significantly faster than that of TUAH-1. The results also showed that CTN could not be detected after treatment with 5.68 g TUAH-1 per kg soil for 48 h when the original CTN content in the soil was 10 mg kg-1. After treatment with THAH-1 or its crude proteins, many degradation products were detected by HPLC-MS, suggesting two possible degradation pathways. The mechanism of CTN degradation by TUAH-1 was noted to be multienzymatic catalysis comprising glyceraldehyde-3-phosphate dehydrogenase and glutathione S-transferase.

Molecular dynamics (MD) simulations, in combination with the Markov-state model (MSM), were applied to probe CO2 diffusion from an aqueous solution into the active site of human carbonic anhydrase II (hCA-II), an enzyme useful for enhanced CO2 capture and utilization. The diffusion process in the hydrophobic pocket of hCA-II was illustrated in terms of a two-dimensional free-energy landscape. We found that CO2 diffusion in hCA-II is a rate-limiting step in the CO2 diffusion-binding-reaction process. The equilibrium distribution of CO2 shows its preferential accumulation within a hydrophobic domain in the protein core region. An analysis of the committors and reactive fluxes indicates that the main pathway for CO2 diffusion into the active site of hCA-II is through a binding pocket where residue Gln136 contributes to the maximal flux. The simulation results offer a new perspective on the CO2 hydration kinetics and useful insights toward the development of novel biochemical processes for more efficient CO2 sequestration and utilization.

Supported lipid bilayers (SLBs) have been widely used in drug delivery, biosensors and biomimetic membranes. The microscopic mechanism of SLB formation and stability depends on a number of factors underlying solvent-mediated lipid–lipid and lipid–substrate interactions. Whereas recent years have witnessed remarkable progress in understanding the kinetics of SLB formation, relatively little is known about the lipid phase behavior controlling the SLB stability under diverse solution conditions. In this work, we examine the structure of SLBs using classical density functional theory (CDFT) in the context of a coarse-grained model that accounts for ion-explicit electrostatic interactions, surface hydrophobicity, as well as the molecular characteristics of the lipid tails. A morphological phase diagram is constructed in terms of various intrinsic properties of lipid molecules (such as the lipid tail length, size and charge of the lipid head segments), substrate conditions (such as the surface charge density and hydrophobicity), and solution parameters (such as the ion concentration and ion type). The morphological phase diagram provides useful insights into the rational design and broader application of SLB membranes as different types of nano-devices.