Root mean square deviation analysis. Root mean square deviation (RMSD) analysis was carried out for the molecular dynamics simulations of each system. Simulations with mannohexaose and cellohexaose were repeated three times with slightly different initial configurations leading to similar results (data not shown). A. RMSD of Man5B without substrates (black), with cellohexaose (red) and mannohexaose substrate (green). The binding of a substrate reduces thermal fluctuation as reflected in a reduced RMSD value of the enzyme. The two abrupt changes in the RMSD value seen in the case of the simulations with substrates are related to the equilibration protocol, where the entire protein backbone had its position constrained initially, but in a second step only the atoms of the protein backbone close to the substrate remained constrained. B. Separate RMSD of carbohydrate monomers. An analysis of the RMSD per carbohydrate monomer shows that the peak RMSD values are due to unbound carbohydrates at the end of the chain. Carbohydrates in position -1 and 1 are extremely stable in the pocket (data not shown). Red: cellohexaose; green: mannohexaose.