Model and molecular dynamic simulations of active and inactive endo-beta-1,4-mannanase in tomato fruit

Endo-beta-mannanase is a hemicellulase that is present in tomato fruit, and plays a role in its ripening. This enzyme protein is detectable in the cultivar Walter, but it is inactive due to the absence of the terminal four amino acids from its carboxyl-end. To elucidate why this deletion eliminates the activity of endo-beta-mannanase, a molecular dynamics (MD) study was conducted on the conformation of the enzyme at normal and elevated temperatures. The root mean square deviations, root mean square fluctuations per residue, and secondary structural evolution during MD simulations were analyzed. Differences in stability and dynamics between the active and inactive endo-beta-mannanases were documented; the inactive form has a lower stability than the active one. The loss of key amino acids from the C-terminal end of the protein indirectly affects the conformation of the catalytic Glu318 and stability of active site because of interactions between residues at the C-terminus and the rest of protein.