Comparative molecular dynamics simulations identify a salt-sensitive loop responsible for the halotolerant activity of GH5 cellulases

Abstract

Halotolerant glycoside hydrolases (GH) have broad application potentials in biorefinery industries. Elucidating the structure-activity relationship underlying the halotolerant catalysis is essential to design superior biocatalysts. Here, we performed molecular dynamics simulations to investigate the structural dynamics of two GH5 cellulases, namely the halotolerant Cel5R and non-halotolerant TfCel5A. Through characterizing the physical properties at different salt concentrations, the results revealed that the overall structures of Cel5R and TfCel5A were marginally affected by the increase in salt concentrations. However, a salt-sensitive loop was identified from both Cel5R and TfCel5A based on its significantly increased flexibility at high salt concentrations. Importantly, compared to TfCel5A the salt-sensitive loop of Cel5R engaged more sodium ions and water molecules around the active site of the enzyme. Besides, the unique residue motif of the salt-sensitive loop in Cel5R formed more intramolecular hydrogen bonds, stabilizing the active architecture of Cel5R at high salt concentrations. Collectively, the structural and dynamic differences may contribute to the various catalytic halotolerance of Cel5R and TfCel5A. These findings provide mechanistic insight into the halotolerant catalysis and will guide the ration design of GH5 cellulases with improved catalytic properties.

Communicated by Ramaswamy H. Samy

Graphical Abstract

Keywords:

• Cellulase
• halotolerant catalysis
• MD simulations
• enzyme engineering
• biomass

Disclosure statement

No potential conflict of interest was reported by the authors.

Additional information

Funding

This research was supported by research grants from the National Key Research and Development Project (2016YFB0201702), National Natural Science Foundation of China (31770054) and Key Research and Development Project of Shandong Province (2020CXGC010601). The MD simulations were performed on the HPC Cloud Platform of Shandong University.

Notes on contributors

Yuxuan Song

YS performed the MD simulations. XW and XJ planed the work and analyzed the data. YZ offered the computational resources. LW supervised the whole project. All authors contributed to the writing and discussion of the manuscript.