Semi-rational evolution of ω-transaminase from Aspergillus terreus for enhancing the thermostability / 生物工程学报

ω-transaminase (ω-TA) is a natural biocatalyst that has good application potential in the synthesis of chiral amines. However, the poor stability and low activity of ω-TA in the process of catalyzing unnatural substrates greatly hampers its application. To overcome these shortcomings, the thermostability of (R)-ω-TA (AtTA) from Aspergillus terreus was engineered by combining molecular dynamics simulation assisted computer-aided design with random and combinatorial mutation. An optimal mutant AtTA-E104D/A246V/R266Q (M3) with synchronously enhanced thermostability and activity was obtained. Compared with the wild- type (WT) enzyme, the half-life t1/2 (35 ℃) of M3 was prolonged by 4.8-time (from 17.8 min to 102.7 min), and the half deactivation temperature (T1050) was increased from 38.1 ℃ to 40.3 ℃. The catalytic efficiencies toward pyruvate and 1-(R)-phenylethylamine of M3 were 1.59- and 1.56-fold that of WT. Molecular dynamics simulation and molecular docking showed that the reinforced stability of α-helix caused by the increase of hydrogen bond and hydrophobic interaction in molecules was the main reason for the improvement of enzyme thermostability. The enhanced hydrogen bond of substrate with surrounding amino acid residues and the enlarged substrate binding pocket contributed to the increased catalytic efficiency of M3. Substrate spectrum analysis revealed that the catalytic performance of M3 on 11 aromatic ketones were higher than that of WT, which further showed the application potential of M3 in the synthesis of chiral amines.

Local helix parameters fitting of proteins based on dual quaternions registration method / 生物医学工程学杂志

A fitting method of calculating local helix parameters of proteins based on dual quaternions registration fitting (DQRFit) is proposed in this paper. First, the C and N atom coordinates of each residue in the protein structure data are extracted. Then the unregistered data and reference data are constructed using the sliding windows. The square sum of the distance of the data points before and after registration is regarded as an optimization goal. We calculate the optimal rotation matrix and the translation vector using the dual quaternion registration algorithm, and get the helix parameters of the secondary structure which contain the number of residues per turn( ), helix radius( )and helix pitch( ). Furthermore, we can achieve the fitting of three-helix parameters of , , simultaneously with the dual quaternion registration, and can adjust the sliding windows to adapt to different error levels. Compared with the traditional helix fitting method, DQRFit has some advantages such as low computational complexity, strong anti-interference, and high fitting accuracy. It is proven that the precision of proposed DQRFit for α helix detection is comparable to that of the dictionary of secondary structure of proteins (DSSP), and is better than that of other traditional methods. This is of great significance for the protein structure classification and functional prediction, drug design, protein structure visualization and other fields in the future.

A study on detection of α-helix protein in posttraumatic epileptogenic focus by FTIR-mapping / 中国法医学杂志

Objective The article is to study on the detection of α-helix proteins in post-traumatic epileptogenic focus by FTIR-mapping. Methods Fourier transform infrared spectroscopy-mapping were applied to identifying α-helix by point-by-point scanning in post-traumatic epileptogenic focus sections and to develop FTIR-mapping profiles. Result The high absorbance of α-helix is accord with post-traumatic epilepsy, there are some significant differences between high absorbance and low absorbance. Conclusion α-helix proteins are distributed in post-traumatic epileptogenic focus widely, thus α-helix protein are involved in post-traumatic epilepsy.

Predicted secondary structure of maltodextrin Phosphorylase from Escherichia coli as deduced using Chou-Fasman model.

Secondary structure of maltodextrin Phosphorylase from Escherichia coli has been predicted using Chou-Fasman model. The enzyme protein contains 28% α-helix, 27% ß-pleated sheets and 20% reverse β-turns. The secondary structure predicted 4 regions showing Rossman-fold super secondary structure. Two regions, one from residue 268–361 and the another from residue 606–684, having 4 consecutive strands of parallel β-pleated sheets and 3 joining α-helix, are predicted. Two regions, one from residue 379–434 and the another from residue 496–573, having 3 consecutive strands of parallel ß-pleated sheets and two joining α-helix, are predicted.

Filamentous bacterial viruses.

The filamentous bacterial virus is a simple and well-characterized model system for studying how genetic information is transformed into molecular machines. The viral DNA is a single-stranded circle coding for about 10 proteins. The major viral coat protein is largely α- helical, with about 46 amino acid residues. Several thousand identical copies of this protein in a helical array form a hollow cylindrical tube 1–2 μm long, of outer diameter 60 Å and inner diameter 20 Å, with the twisted circular DNA extending down the core of the tube. Before assembly, the viral coat protein spans the cell membrane, and assembly involves extrusion of the coat from the membrane. X-ray fibre diffraction patterns of the Pf1 species of virus at 4°C, oriented in a strong magnetic field, give three-dimensional data to 4 Å resolution. An electron density map calculated from native virus and a single iodine derivative, using the maximum entropy technique, shows a helix pitch of 5·9 Å. This may indicate a stretched α-helix, or it may indicate a partially 310 helix conformation, resulting from the fact that the coat protein is an integral membrane protein before assembly, and is still in the hydrophobic environment of other coat proteins after assembly.