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The aim of this study was to obtain molecular insight into the deactivation of recombinant urate oxidase (uricase, UOX, EC (rUOX) from Aspergillus flavus. The enzyme is a tunnel-shaped homotetramer and has important clinical applications. By means of molecular dynamics simulations, multidimensional structural characterization and enzyme activity(More)
One challenge in protein refolding is to dissociate the non-native disulfide bonds and promote the formation of native ones. In this study, we present a coarse-grained off-lattice model protein containing disulfide bonds and simulate disulfide bond shuffling during the folding of this model protein. Introduction of disulfide bonds in the model protein led(More)
This paper presents a Langevin dynamics simulation that suggests a novel way to fold protein at high concentration, a fundamental issue in neurodegenerative diseases in vivo and the production of recombinant proteins in vitro. The simulation indicates that the folding of a coarse-grained beta-barrel protein at high concentration follows the(More)
Proteins fold in a confined space not only in vivo, i.e., folding assisted by molecular chaperons and chaperonins in a crowded cellular medium, but also in vitro as in production of recombinant proteins. Despite extensive work on protein folding in bulk, little is known about how and to what extent the thermodynamics and kinetics of protein folding are(More)
The changes in microbial ecology interpreted from taxonomic and functional genes and biological functions represented by urease and dehydrogenase activities were monitored in soil contaminated with different petroleum hydrocarbons including crude oil, diesel, n-hexadecane and poly-aromatic hydrocarbons (PAHs). It was shown that the presence of n-hexadecane(More)
A Gram-negative rod-shaped bacterium, previously shown to utilize alkanes and polycyclic aromatic hydrocarbons (PAHs), was identified as Enterobacter cloacae (GenBank accession number, GQ426323) by 16S rRNA sequence analysis and was designated as strain TU. During growing on n-hexadecane as the sole carbon source, the strain TU extracellularly released an(More)
Glycosylation is one of the most common post-translational modifications in the biosynthesis of protein, but its effect on the protein conformational transitions underpinning folding and stabilization is poorly understood. In this study, we present a coarse-grained off-lattice 46-β barrel model protein glycosylated by glycans with different hydrophobicity(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(More)
We describe an enzyme-responsive polymeric vehicle, which is of great interest in controlled drug delivery, biosensing, and other related areas. The polymer synthesized using lipase as catalyst in DMSO has a favorable molecular structure that is quickly hydrolyzed by lipase in aqueous phase, and allows a fast release of encapsulated molecules.
A two-step procedure to encapsulate a single bovine carbonic anhydrase (BCA) molecule into a spherical nanogel was proposed. BCA was reacted first with N-acryloxysuccinimide to introduce surface vinyl groups, followed by in-situ aqueous polymerization. Characterization of the nanogel by dynamic light scattering, transmission electron microscopy, and atomic(More)