Modulating the distribution of various states in protein ensembles through distal sites may be pr... more Modulating the distribution of various states in protein ensembles through distal sites may be promising in the evolution of enzymes in desired directions.
The 24-mer iron-storage protein, ferritin cage assembly plays important role in nanomaterials syn... more The 24-mer iron-storage protein, ferritin cage assembly plays important role in nanomaterials synthesis and drug delivery. Herein we explored the disassembly process of the cage by high-speed AFM in combination with all-atom MD simulations.
The development of a sensitive, quick-responding, and robust glucose sensor is consistently pursu... more The development of a sensitive, quick-responding, and robust glucose sensor is consistently pursued for use in numerous applications. Here, we propose a new method for preparing a Cu2O electrode for the electrochemical detection of glucose concentration. The Cu2O glucose electrode was prepared by in situ electrical oxidation in an alkaline solution, in which Cu2O nanoparticles were deposited on the electrode surface to form a thin film, followed by the growth of Cu(OH)2 nanorods or nanotubes. The morphology and electrocatalytic activity of a Cu2O glucose electrode can be tuned by the current density, reaction time, and NaOH concentration. The results from XRD, SEM, and a Raman spectrum show that the electrode surface was coated with cubic Cu2O nanoparticles with diameters ranging from 50 to 150 nm. The electrode exhibited a detection limit of 0.0275 mM, a peak sensitivity of 2524.9 μA·cm−2·mM−1, and a linear response range from 0.1 to 1 mM. The presence of high concentrations of asc...
Pressure significantly affects thermodynamic and diffusion properties of water confined in differ... more Pressure significantly affects thermodynamic and diffusion properties of water confined in different nanoslits. This difference is caused by the competition of interaction between water–water and water–wall.
Spherical protein cages with highly symmetrical structures provide unique environments for conjug... more Spherical protein cages with highly symmetrical structures provide unique environments for conjugation of metal ions and metal nanoparticles. Ferritin has been widely studied as a template for coordination of metal...
Quinclorac, a highly selective auxin herbicide, is widely used for controlling weeds in rice fiel... more Quinclorac, a highly selective auxin herbicide, is widely used for controlling weeds in rice field. However, the residual quinclorac is toxic to many crops, vegetables, and aquatic animals, resulting in one of the major problems in crop rotation. Here, we investigated the degradation of quinclorac by strain AH-B, which was isolated from long-term quinclorac-contaminated soil using continuous circulating fluidized bed reactor and subjected to atmospheric and room temperature plasma mutation. Morphological examination, 16S rRNA gene sequencing, and phylogenetic analysis revealed that strain AH-B was Streptomyces sp. The quinclorac degradation efficiency of AH-B in liquid medium was 97.2% after 18 days when the initial quinclorac concentration was 20 mg L. The degradation products were 3-chloro-7-methoxy-8-quinoline-carboxylic, 3-chloro-7-methyl-8-quinoline-carboxylic, 3-chloro-7-oxyethyl-8-quinoline-carboxylic, and 3,7-dichloro-6-methyl-8-quinoline-carboxylic. The inoculum size, initi...
The classical density functional theory is incorporated with the Stokes equation to examine the t... more The classical density functional theory is incorporated with the Stokes equation to examine the thermodynamic efficiency of pressure-driven electrokinetic energy conversion in slit nanochannels. Different from previous mean-field predictions, but in good agreement with recent experiments, the molecular theory indicates that the thermodynamic efficiency may not be linearly correlated with the channel size or the electrolyte concentration. For a given electrolyte, an optimal slit nanochannel size and ion concentration can be identified to maximize both the electrical current and the thermodynamic efficiency. The optimal conditions are sensitive to a large number of parameters including ion diameters, valences, electrolyte concentration, channel size, and the valence- and size-asymmetry of oppositely charged ionic species. The theoretical results offer fresh insights into pressure-driven current generation processes and are helpful guidelines for the design of apparatus for the electro...
While the effectiveness of PEGylation in enhancing the stability and potency of protein pharmaceu... more While the effectiveness of PEGylation in enhancing the stability and potency of protein pharmaceuticals has been validated for years, the underlying mechanism remains poorly understood, particularly at the molecular level. A molecular dynamics simulation was developed using an annealing procedure that allowed an all-atom level examination of the interaction between PEG polymers of different chain lengths and a conjugated protein represented by insulin. It was shown that PEG became entangled around the protein surface through hydrophobic interaction and concurrently formed hydrogen bonds with the surrounding water molecules. In addition to enhancing its structural stability, as indicated by the root-mean-square difference (rmsd) and secondary structure analyses, conjugation increased the size of the protein drug while decreasing the solvent accessible surface area of the protein. All these thus led to prolonged circulation life despite kidney filtration, proteolysis, and immunogenic side effects, as experimentally demonstrated elsewhere. Moreover, the simulation results indicated that an optimal chain length exists that would maximize drug potency underpinned by the parameters mentioned above. The simulation provided molecular insight into the interaction between PEG and the conjugated protein at the all-atom level and offered a tool that would allow for the design of PEGylated protein pharmaceuticals for given applications.
Urate oxidase (UOX, EC 1.7.3.3) is effective for the treatment of gout and hyperuricaemia associa... more Urate oxidase (UOX, EC 1.7.3.3) is effective for the treatment of gout and hyperuricaemia associated with tumor lysis syndrome. The inherent poor stability of UOX to temperature, proteolysis, and acidic environments is known to limit its efficacy. Herein, we encapsulated UOX into spherical and porous nanogels with diameters of 20-40 nm via a two-step in situ polymerization in the presence of oxonic acid potassium salt, an inhibitor of UOX. The UOX nanogel retained 70% of the initial activity but showed an expanded pH spectrum from pH 6-10 to 3-10 and an extended half-life at 37 °C from 5 min to 3 h. The enhanced pH stability, thermal stability, and enzyme resistance of the UOX nanogels were also confirmed by using fluorescence spectroscopy and enzymatic digestion. A molecular dynamics simulation was performed as a way to probe the mechanism underlying the formation of UOX nanogels as well as the strengthened stability against harsh conditions. It was shown that the encapsulation into the polyacrylamide network reinforced the intersubunit hydrogen bonding, shielded the hydrolytic reaction site, and thus protected the tertiary and quaternary structure of UOX. The UOX nanogel with enhanced stability provided a stable enzyme model that enables the exploration of UOX in the diagnosis and therapy of disorders associated with altered purine metabolism.
Langmuir : the ACS journal of surfaces and colloids, Jan 28, 2016
Supported lipid bilayers (SLBs) are able to accommodate membrane proteins useful for diverse biom... more 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, i.e., 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 movement...
Modulating the distribution of various states in protein ensembles through distal sites may be pr... more Modulating the distribution of various states in protein ensembles through distal sites may be promising in the evolution of enzymes in desired directions.
The 24-mer iron-storage protein, ferritin cage assembly plays important role in nanomaterials syn... more The 24-mer iron-storage protein, ferritin cage assembly plays important role in nanomaterials synthesis and drug delivery. Herein we explored the disassembly process of the cage by high-speed AFM in combination with all-atom MD simulations.
The development of a sensitive, quick-responding, and robust glucose sensor is consistently pursu... more The development of a sensitive, quick-responding, and robust glucose sensor is consistently pursued for use in numerous applications. Here, we propose a new method for preparing a Cu2O electrode for the electrochemical detection of glucose concentration. The Cu2O glucose electrode was prepared by in situ electrical oxidation in an alkaline solution, in which Cu2O nanoparticles were deposited on the electrode surface to form a thin film, followed by the growth of Cu(OH)2 nanorods or nanotubes. The morphology and electrocatalytic activity of a Cu2O glucose electrode can be tuned by the current density, reaction time, and NaOH concentration. The results from XRD, SEM, and a Raman spectrum show that the electrode surface was coated with cubic Cu2O nanoparticles with diameters ranging from 50 to 150 nm. The electrode exhibited a detection limit of 0.0275 mM, a peak sensitivity of 2524.9 μA·cm−2·mM−1, and a linear response range from 0.1 to 1 mM. The presence of high concentrations of asc...
Pressure significantly affects thermodynamic and diffusion properties of water confined in differ... more Pressure significantly affects thermodynamic and diffusion properties of water confined in different nanoslits. This difference is caused by the competition of interaction between water–water and water–wall.
Spherical protein cages with highly symmetrical structures provide unique environments for conjug... more Spherical protein cages with highly symmetrical structures provide unique environments for conjugation of metal ions and metal nanoparticles. Ferritin has been widely studied as a template for coordination of metal...
Quinclorac, a highly selective auxin herbicide, is widely used for controlling weeds in rice fiel... more Quinclorac, a highly selective auxin herbicide, is widely used for controlling weeds in rice field. However, the residual quinclorac is toxic to many crops, vegetables, and aquatic animals, resulting in one of the major problems in crop rotation. Here, we investigated the degradation of quinclorac by strain AH-B, which was isolated from long-term quinclorac-contaminated soil using continuous circulating fluidized bed reactor and subjected to atmospheric and room temperature plasma mutation. Morphological examination, 16S rRNA gene sequencing, and phylogenetic analysis revealed that strain AH-B was Streptomyces sp. The quinclorac degradation efficiency of AH-B in liquid medium was 97.2% after 18 days when the initial quinclorac concentration was 20 mg L. The degradation products were 3-chloro-7-methoxy-8-quinoline-carboxylic, 3-chloro-7-methyl-8-quinoline-carboxylic, 3-chloro-7-oxyethyl-8-quinoline-carboxylic, and 3,7-dichloro-6-methyl-8-quinoline-carboxylic. The inoculum size, initi...
The classical density functional theory is incorporated with the Stokes equation to examine the t... more The classical density functional theory is incorporated with the Stokes equation to examine the thermodynamic efficiency of pressure-driven electrokinetic energy conversion in slit nanochannels. Different from previous mean-field predictions, but in good agreement with recent experiments, the molecular theory indicates that the thermodynamic efficiency may not be linearly correlated with the channel size or the electrolyte concentration. For a given electrolyte, an optimal slit nanochannel size and ion concentration can be identified to maximize both the electrical current and the thermodynamic efficiency. The optimal conditions are sensitive to a large number of parameters including ion diameters, valences, electrolyte concentration, channel size, and the valence- and size-asymmetry of oppositely charged ionic species. The theoretical results offer fresh insights into pressure-driven current generation processes and are helpful guidelines for the design of apparatus for the electro...
While the effectiveness of PEGylation in enhancing the stability and potency of protein pharmaceu... more While the effectiveness of PEGylation in enhancing the stability and potency of protein pharmaceuticals has been validated for years, the underlying mechanism remains poorly understood, particularly at the molecular level. A molecular dynamics simulation was developed using an annealing procedure that allowed an all-atom level examination of the interaction between PEG polymers of different chain lengths and a conjugated protein represented by insulin. It was shown that PEG became entangled around the protein surface through hydrophobic interaction and concurrently formed hydrogen bonds with the surrounding water molecules. In addition to enhancing its structural stability, as indicated by the root-mean-square difference (rmsd) and secondary structure analyses, conjugation increased the size of the protein drug while decreasing the solvent accessible surface area of the protein. All these thus led to prolonged circulation life despite kidney filtration, proteolysis, and immunogenic side effects, as experimentally demonstrated elsewhere. Moreover, the simulation results indicated that an optimal chain length exists that would maximize drug potency underpinned by the parameters mentioned above. The simulation provided molecular insight into the interaction between PEG and the conjugated protein at the all-atom level and offered a tool that would allow for the design of PEGylated protein pharmaceuticals for given applications.
Urate oxidase (UOX, EC 1.7.3.3) is effective for the treatment of gout and hyperuricaemia associa... more Urate oxidase (UOX, EC 1.7.3.3) is effective for the treatment of gout and hyperuricaemia associated with tumor lysis syndrome. The inherent poor stability of UOX to temperature, proteolysis, and acidic environments is known to limit its efficacy. Herein, we encapsulated UOX into spherical and porous nanogels with diameters of 20-40 nm via a two-step in situ polymerization in the presence of oxonic acid potassium salt, an inhibitor of UOX. The UOX nanogel retained 70% of the initial activity but showed an expanded pH spectrum from pH 6-10 to 3-10 and an extended half-life at 37 °C from 5 min to 3 h. The enhanced pH stability, thermal stability, and enzyme resistance of the UOX nanogels were also confirmed by using fluorescence spectroscopy and enzymatic digestion. A molecular dynamics simulation was performed as a way to probe the mechanism underlying the formation of UOX nanogels as well as the strengthened stability against harsh conditions. It was shown that the encapsulation into the polyacrylamide network reinforced the intersubunit hydrogen bonding, shielded the hydrolytic reaction site, and thus protected the tertiary and quaternary structure of UOX. The UOX nanogel with enhanced stability provided a stable enzyme model that enables the exploration of UOX in the diagnosis and therapy of disorders associated with altered purine metabolism.
Langmuir : the ACS journal of surfaces and colloids, Jan 28, 2016
Supported lipid bilayers (SLBs) are able to accommodate membrane proteins useful for diverse biom... more 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, i.e., 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 movement...
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Papers by Diannan Lu