Calculation of substrate binding affinities for a bacterial GH78 rhamnosidase through molecular dynamics simulations
•Structural model of rhamnosidase Ram2 of Pediococcus acidilactici.•Calculated binding free energies of rutinose and p-NPR agree with experiments.•Suggested binding poses of rutinose and p-NPR are distinctly different.•Different binding poses of rutinose and p-NPR are supported by experiments.•Activ...
| Main Authors: | , , , |
|---|---|
| Format: | Online |
| Language: | English |
| Published: |
Elsevier Science
2013
|
| Online Access: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3663046/ |
| Summary: | •Structural model of rhamnosidase Ram2 of Pediococcus acidilactici.•Calculated binding free energies of rutinose and p-NPR agree with experiments.•Suggested binding poses of rutinose and p-NPR are distinctly different.•Different binding poses of rutinose and p-NPR are supported by experiments.•Active site residues are proposed for further mutagenesis studies |
|---|