Deamidation reaction in pentapeptides and the enzyme Trio-sephosphate isomerase (TPI) is investigated by molecular dynamics. For TPI, simulations based on classical AMBER force field are performed in 60 to 90 ns timescale for six distinct samples. Conformational changes, desolvation effects, and hydrogen bond networks are analyzed to interpret the experimental findings. Results that are based on desolvation analysis clarify the experimental results about the different behavior of the two deamidating sites in TPI. Conformational analysis points out that the most favorable reaction mechanism is the one that yields succinimide intermediate via one or two steps as suggested by previous QM studies for peptides.