A Molecular Dynamics Study to Assess the Positive Ion Distribution and the Effects of Protonation on the N-terminus Region of a Xylanase

Kewalin Posansee, Pongsak Khunrae, Thana Sutthibutpong
2018 Journal of Physics, Conference Series  
Xylanase enzyme families play an important role in many industries due to its ability to digest the hemicellulose within plant cell walls. Developing the enzyme that can withstand a highly acidic environment in a stomach requires an extended information in molecular scale for further protein engineering. In this study, an atomistic molecular dynamics simulation was performed to assess the positive ion distribution pattern on the N-terminus region of a Xylanase enzyme molecule. Then, another
more » ... . Then, another series of simulations were performed for the enzyme protonated at the aspartate residues 11 and/or 32 identified by the previous calculation. Conformational analysis showed that ASP32 protonation caused a significant disruption at the N-terminus region, as the nearby arginine residue 31 (ARG31) became free from the Coulomb interaction with the negatively charged ASP32 sidechain and cause the N-terminus region to misfold.
doi:10.1088/1742-6596/1144/1/012011 fatcat:vccyo2zmzvabhoaokoah7c5a6q