Insights into the pH-dependent catalytic mechanism of Sulfolobus solfataricus β-glycosidase: A molecular dynamics study

Sulfolobus solfataricus beta-glycosidase (SS-beta Gly) belongs to Glycosyl Hydrolase family1 (GH1) with broad substrate specificity. SS-beta Gly catalyzes both hydrolysis and transglycosylation reactions. SS-beta Gly is commonly used to synthesize variety of galacto-oligosaccharides. A comparison of SS-beta Gly with bacterial and eukaryotic homologs, using DALI search, revealed unique inserts. Free enzyme molecular dynamics (MD) simulation was performed under two different pH conditions (pH 6.5 and 2.5) at a constant temperature of 65 degrees C using GROMACS. A probable active-site loop (residues 331-364) in SS-beta Gly was identified. Dynamics of substrate binding cavity revealed that it was buried and inaccessible during most timeframes at pH 6.5 whereas open and accessible at pH 2.5. New cavities identified during both simulations may act as probable water channel or product egress path. Analyses of docked complexes of 3D structures obtained at every 1 ns interval with compounds, involved in hydrolysis and tranglycosylation reactions, demonstrated that conformational states sampled by SS-beta Gly during free enzyme dynamics mimic the stages in enzyme catalysis thereby providing a mechanistic perspective. Current study revealed that conformational changes were conducive for hydrolysis at pH 6.5 and multiple cycles of transglycosylation at pH 2.5. Probable role of salt-bridge interactions in determining the type of reaction mechanism was also explored.