Hydrogen
bonds or salt bridges are usually formed to stabilize
the buried ionizable residues. However, such interactions do not exist
for two buried residues D271 and E305 of Trichoderma
reesei Cel5A, an endoglucanase. Mutating D271 to alanine
or leucine improves the enzyme thermostability quantified by the temperature <i>T</i><sub>50</sub> due to the elimination of the desolvation
penalty of the aspartic acid. However, the same mutations for E305
decrease the enzyme thermostability. Free energy calculations based
on the molecular dynamics simulation predict the thermostability of
D271A, D271L, and E305A (compared to WT) in line with the experimental
observation but overestimate the thermostability of E305L. Quantum
mechanical calculations suggest that the carboxyl–peptide plane
stacking interactions occurring to E305 but not D271 are important
for the carboxyl group stabilization. For the protonated carboxyl
group, the interaction energy can be as much as about −4 kcal/mol
for parallel stacking and about −7 kcal/mol for T-shaped stacking.
For the deprotonated carboxyl group, the largest interaction energies
for parallel stacking and T-shaped stacking are comparable, about
−7 kcal/mol. The solvation effect generally weakens the interaction,
especially for the charged system. A search of the carboxyl–peptide
plane stacking in the PDB databank indicates that parallel stacking
but not T-shaped stacking is quite common, and the most probable distance
between the two stacking fragments is close to the value predicted
by the QM calculations. This work highlights the potential role of
carboxyl amide π–π stacking in the stabilization
of aspartic acid and glutamic acid in proteins
