A quantum mechanics/molecular mechanics study of the acylation reaction of TEM1 β-lactamase and penicillanate

Abstract

The acylation step in β-lactamase catalyzed hydrolysis of β-lactams has been explored by means of a quantum mechanics/molecular mechanics approach (AM1/CHARMM). The TEM1 enzyme, a class A β-lactamase, and the penicillanate constitute the system employed in our study. The entire molecular system is divided into a quantum and a classical region: the quantum part is composed by the substrate, the serine Ser70 and the essential moieties of key active site residues, Lys73, Ser130 and Glu166, as well as a water molecule present in the active site region, while the classical part is formed by the remaining residues and structural waters of the enzyme. In particular, the sequence of steps proposed by Strynadka et al. (Nature, 1992, 359, 700) for the acylation reaction is analyzed. Minimal and transition structures for the mechanism are reported and an energy activation of 18.29 kcal mol⁻¹ has been calculated for the rate-limiting step, the formation of an initial tetrahedral adduct. From this structure, two different mechanistic routes have been found to achieve the acyl–enzyme intermediate. In the first of them a simultaneous β-lactam ring opening and proton transfer from Ser130 to the β-lactam nitrogen atom occurs, presenting an energy barrier of 12.91 kcal mol⁻¹ with respect to the tetrahedral intermediate. In the second route, these processes take place in a sequential way. From an energetic point of view, the sequential mechanism is favored, requiring the ring opening step (7.66 kcal mol⁻¹) and the subsequent nitrogen protonation (2.76 kcal mol⁻¹). Some reflections arising from the preference of sequential processes in this system are exposed.