Sequence identification, structure prediction and validation of tannase from Aspergillusniger N5-5

Tannases produced by filamentous fungi are in a family of important hydrolases of gallotannins and have broad industry applications.But until now,the 3-D structures of fungi tannases have not been reported.The protein sequence deduced from the cDNA sequence obtained using RT-PCR amplification was identified as tannase through sequence alignment and phylogenetic analysis.Structure models based on the tannase sequence were collected using I-TASSER,and the model with the best match to the surface charge density-pH titration profile was selected as the final structure for tannase from Aspergillusniger N5-5.This work provides an effective method for protein structure research.The structure constructed in this work should be very important to understand the enzyme bioactivities and further developments of fungi tannases.

Evolution of Conformation and Dynamics of Solvents in Hydration Shell along the Urea-induced Unfolding of Ubiquitin

A clear diagram for the unfolding of protein induced by denaturant is a classical but still unsolved challenge. To explore the unfolded conformations of ubiquitin under different urea concentrations, we performed hybrid Monte Carlo-molecular dynamics simulations (MC-MD) guided by small angle X-ray scattering (SAXS) structural information. Conformational ensembles sampled by the hybrid MC-MD algorithm exhibited typical 3D structures at different urea concentrations. These typical structures suggested that ubiquitin was subjected to a sequential unfolding, where the native contacts between adjacent β-sheets at first were disrupted together with the exposure of hydrophobic core, followed by the conversion of remaining β-strands and helices into random coils. Ubiquitin in 8 mol·L?1 urea is almost a random coil. With the disruption of native structure, urea molecules are enriched at protein hydrated layer to stabilize newly exposed residues. Compared with water, urea molecules prefer to form hydrogen bonds with the backbone of ubiquitin, thus occupying nodes of the hydrogen bonding network that construct the secondary structure of proteins. Meanwhile, we also found that the slow dynamics of urea molecules was almost unchanged while the dynamics of water was accelerated in the hydration shell when more residues were unfolded and exposed. The former was also responsible for the stabilization of unfolded structures.

Conformational and Dynamical Evolution of Block Copolymers in Shear Flow

Conformation and dynamical evolution of block copolymers in shear flow is an important topic in polymer physics that underscores the forming process of various materials.We explored deformation and dynamics of copolymers composed of rigid or flexible blocks in simple shear flow by employing multiparticle collision dynamics integrated with molecular dynamics simulations.We found that compared with the proportion between rigid and flexible blocks,the type of the central blocks plays more important role in the conformational and dynamical evolution of copolymers.That is,if the central block is a coil,the copolymer chain takes end-over-end tumbling motion,while if the central block is a rod,the copolymer chain undergoes U-shape or S-shape deformation at mid shear rate.As the shear strength increases,all copolymers behave similar to flexible polymers at high shear rate.This can be attributed to the fact that shear flow is strong enough to overcome the buckling force of the rigid blocks.These results provide a deeper understanding of the roles played by rod and coil blocks in copolymers for phase interface during forming processing.