Improving the Thermostability and Activity of Transaminase From Aspergillus terreus by Charge-Charge Interaction

Transaminases that promote the amination of ketones into amines are an emerging class of biocatalysts for preparing a series of drugs and their intermediates. One of the main limitations of (R)-selective amine transaminase from Aspergillus terreus (At-ATA) is its weak thermostability, with a half-life (t1/2) of only 6.9 min at 40°C. To improve its thermostability, four important residue sites (E133, D224, E253, and E262) located on the surface of At-ATA were identified using the enzyme thermal stability system (ETSS). Subsequently, 13 mutants (E133A, E133H, E133K, E133R, E133Q, D224A, D224H, D224K, D224R, E253A, E253H, E253K, and E262A) were constructed by site-directed mutagenesis according to the principle of turning the residues into opposite charged ones. Among them, three substitutions, E133Q, D224K, and E253A, displayed higher thermal stability than the wild-type enzyme. Molecular dynamics simulations indicated that these three mutations limited the random vibration amplitude in the two α-helix regions of 130–135 and 148–158, thereby increasing the rigidity of the protein. Compared to the wild-type, the best mutant, D224K, showed improved thermostability with a 4.23-fold increase in t1/2 at 40°C, and 6.08°C increase in T5010. Exploring the three-dimensional structure of D224K at the atomic level, three strong hydrogen bonds were added to form a special “claw structure” of the α-helix 8, and the residues located at 151–156 also stabilized the α-helix 9 by interacting with each other alternately.

The Analysis of Hydrophobic Interaction on Aspergillus Niger Xylanase Enzyme Thermal Stability

Xylanase is a type of enzyme that has an important role in the industrial field. One measure that can be done to improve the thermostability of an enzyme is by protein engineering. The mutation of the protein can be done by studying protein structures through molecular dynamics simulation approach. In this research, thermal stability analysis on Aspergilus niger Wild Type Xylase (AnX) was performed which aims to study the thermal stability characteristics of xynalase enzyme from Aspergillus niger through molecular dynamics simulation approach. AnX molecular dynamics simulation was performed by NAMD (Not Just Another Molecular Dynamic) software at 300 – 500 K. The research was focused on the study of enzyme thermal stability characteristics in order to get the information of residues accountable for such characteristics. The selection of residues to be mutated was based on hydrophocic interaction analysis. Then from that, the design of xylanase enzyme mutant with better thermostability than wild type xynalase enzyme was made in order to provide design reference for more stable xylanase mutation design which can be implemented in wet experiments for of Aspergillus niger Xylanase enzyme genetic engineering. The enzyme was unfolded at 500 K at 9.5 ns. The residues responsible of the thermal stability were based on hydrophobic interaction analysis in Alanin at residue 60. This residue is located in segmen/chain 3. The best mutant is Alanin 60 residue mutant which is replaced by Methionin and ∆∆Gsolv of -21.10345 was obtained. Thus, Ala60Met is the most stable mutant which might increase the thermal stability of Aspergillus niger Xylanase Enzyme.

Comparing mutagenesis and simulations as tools for identifying functionally important sequence changes for protein thermal adaptation

Comparative studies of orthologous proteins of species evolved at different temperatures have revealed consistent patterns of temperature-related variation in thermal stabilities of structure and function. However, the precise mechanisms by which interspecific variations in sequence foster these adaptive changes remain largely unknown. Here, we compare orthologs of cytosolic malate dehydrogenase (cMDH) from marine molluscs adapted to temperatures ranging from −1.9 °C (Antarctica) to ∼55 °C (South China coast) and show how amino acid usage in different regions of the enzyme (surface, intermediate depth, and protein core) varies with adaptation temperature. This eukaryotic enzyme follows some but not all of the rules established in comparisons of archaeal and bacterial proteins. To link the effects of specific amino acid substitutions with adaptive variations in enzyme thermal stability, we combined site-directed mutagenesis (SDM) and in vitro protein experimentation with in silico mutagenesis using molecular dynamics simulation (MDS) techniques. SDM and MDS methods generally but not invariably yielded common effects on protein stability. MDS analysis is shown to provide insights into how specific amino acid substitutions affect the conformational flexibilities of mobile regions (MRs) of the enzyme that are essential for binding and catalysis. Whereas these substitutions invariably lie outside of the MRs, they effectively transmit their flexibility-modulating effects to the MRs through linked interactions among surface residues. This discovery illustrates that regions of the protein surface lying outside of the site of catalysis can help establish an enzyme’s thermal responses and foster evolutionary adaptation of function.

Enzyme Immobilization on Nanoporous Gold: A Review

Nanoporous gold (referred to as np-Au or NPG) has emerged over the past 10 years as a new support for enzyme immobilization. The material has appealing features of ease of preparation, tunability of pore size, high surface to volume ratio, and compatibility with multiple strategies for enzyme immobilization. The np-Au material is especially of interest for immobilization of redox enzymes for biosensor and biofuel cell applications given the ability to construct electrodes of high surface area and stability. Adjustment of the pore size of np-Au can yield enhancements in enzyme thermal stability. Glucose oxidase immobilization on np-Au has been a focus for development of glucose sensors. Immobilization of laccase and related enzymes has demonstrated the utility of np-Au for construction of biofuel cells. Np-Au has been used to immobilize other redox enzymes, enzyme conjugates for use in bioassays, and enzymes of interest for industrial processes.

Improvement in Thermostability of an Achaetomium sp. Strain Xz8 Endopolygalacturonase via the Optimization of Charge-Charge Interactions

ABSTRACTImproving enzyme thermostability is of importance for widening the spectrum of application of enzymes. In this study, a structure-based rational design approach was used to improve the thermostability of a highly active, wide-pH-range-adaptable, and stable endopolygalacturonase (PG8fn) fromAchaetomiumsp. strain Xz8 via the optimization of charge-charge interactions. By using the enzyme thermal stability system (ETSS), two residues—D244 and D299—were inferred to be crucial contributors to thermostability. Single (D244A and D299R) and double (D244A/D299R) mutants were then generated and compared with the wild type. All mutants showed improved thermal properties, in the order D244A < D299R < D244A/D299R. In comparison with PG8fn, D244A/D299R showed the most pronounced shifts in temperature of maximum enzymatic activity (Tmax), temperature at which 50% of the maximal activity of an enzyme is retained (T50), and melting temperature (Tm), of about 10, 17, and 10.2°C upward, respectively, with the half-life (t1/2) extended by 8.4 h at 50°C and 45 min at 55°C. Another distinguishing characteristic of the D244A/D299R mutant was its catalytic activity, which was comparable to that of the wild type (23,000 ± 130 U/mg versus 28,000 ± 293 U/mg); on the other hand, it showed more residual activity (8,400 ± 83 U/mg versus 1,400 ± 57 U/mg) after the feed pelleting process (80°C and 30 min). Molecular dynamics (MD) simulation studies indicated that mutations at sites D244 and D299 lowered the overall root mean square deviation (RMSD) and consequently increased the protein rigidity. This study reveals the importance of charge-charge interactions in protein conformation and provides a viable strategy for enhancing protein stability.