A comparative molecular dynamics study of thermophilic and mesophilic β-fructosidase enzymes

Abstract

Arabidopsis thaliana cell wall invertase 1 (AtcwINV1) and Thermotoga maritima β-fructosidase (BfrA) are among the best structurally studied members of the glycoside hydrolase family 32. Both enzymes hydrolyze sucrose as the main substrate but differ strongly in their thermal stability. Mesophilic AtcwINV1 and thermophilic BfrA have divergent sequence similarities in the N-terminal five bladed β-propeller catalytic domain (31 %) and the C-terminal β-sandwich domain (15 %) of unknown function. The two enzymes were subjected to 200 ns molecular dynamics simulations at 300 K (27 °C) and 353 K (80 °C). Regular secondary structure regions, but not loops, in AtcwINV1 and BfrA showed no significant fluctuation differences at both temperatures. BfrA was more rigid than AtcwINV1 at 300 K. The simulation at 353 K did not alter the structural stability of BfrA, but did increase the overall flexibility of AtcwINV1 exhibiting the most fluctuating regions in the β-propeller domain. The simulated heat treatment also increased the gyration radius and hydrophobic solvent accessible surface area of the plant enzyme, consistent with the initial steps of an unfolding process. The preservation of the conformational rigidity of BfrA at 353 K is linked to the shorter size of the protein loops. Shortening of BfrA loops appears to be a key mechanism for thermostability.

Heat-resistant cytosolic malate dehydrogenases (cMDHs) of thermophilic intertidal snails (genus Echinolittorina): protein underpinnings of tolerance to body temperatures reaching 55°C

“…The RMSD and RMSF values of EmcMDH were highly preserved during simulation at different temperatures, whereas the values for more heat-sensitive ErcMDH increased with temperature. The difference in structural thermal sensitivity between the EmcMDH and ErcMDH orthologs is consistent with the temperature adaptation observed in β-fructosidase of T. maritima (Mazola et al, 2015). The active site geometry of this thermophilic β-fructosidase was strongly conserved during simulations at different temperatures, whereas an increase in RMSD value was observed for a mesophilic ortholog at elevated temperature.…”

“…Previous studies of proteins of thermophilic organisms have shown that these species' proteins are characterized by high thermal stability and low levels of structural fluctuation in MD simulation studies (Li et al, 2005). For example, the equilibrium RMSD value of thermophilic isopropylmalate dehydrogenase from Thermus thermophilus was 3.5 Å at 64°C (Sharma and Sastry, 2015); the thermophilic β-fructosidase from Thermotoga maritima reached the stable state with a value of 1.97 Å at 80°C (Mazola et al, 2015). The hyperthermophilic amylase from Bacillus licheniformis is thermostable at very high temperature; the native state of the protein and enzymatic activity is strongly conserved at temperature below 90°C, whereas 50% of the molecules are unfolded at 103°C (Fitter et al, 2001;Fitter and Haber-Pohlmeier, 2004;Fitter, 2005).…”

Seed Extract of Psoralea corylifolia and Its Constituent Bakuchiol Impairs AHL-Based Quorum Sensing and Biofilm Formation in Food- and Human-Related Pathogens

“…Solvent-accessible surface area (SASA) is the surface area of a molecule that interacts with the solvent molecules (Mazola et al, 2015 ). The average SASA values for the LasR, LasR–bakuchiol, Rh1R, and Rh1R–bakuchiol complexes were calculated using the gmx sasa module of GROMACS.…”

Identification of High-Affinity Inhibitors of Cyclin-Dependent Kinase 2 Towards Anticancer Therapy

“…Solvent accessible surface area (SASA) of a protein is the area that directly interacts with its surrounding solvent [38,39]. The SASA of a protein is directly interrelated to its R g .…”