Protein-water network dynamics during metalloenzyme hydrolysis observed by kinetic THz absorption (KITA)

For long, the contribution of water network motions to enzymatic reactions was enigmatic due to the complexity of biological systems and to experimental limitations. Thanks to the development of new powerful THz emitters and detectors in the last decades, it is now possible to probe dynamics on the timescale of the fast hydrogen bond rearrangements during biochemical reactions. For this purpose, we developed a kinetic terahertz absorption (KITA) spectrometer which combines the strength of THz radiation (∼10¹² Hz = 1 ps) to directly probe collective picosecond protein-water dynamics with the fast mixing properties of a stopped-flow apparatus which initializes a biochemical reaction within milliseconds. With KITA, we analyzed the collective water dynamics during substrate hydrolyses by a human matrix-metalloproteinase. In addition, we studied the reorganization and electrostatic changes at the catalytic zinc-ion from the enzyme active site and performed molecular dynamics simulations of the enzyme-substrate-water system. Our results revealed a systematic gradient of water network motions: From the active site to the bulk water hydrogen bond dynamics increased from 7 ps (active site) to 1ps (bulk water) prior to substrate binding and hydrolysis. The approaching substrate perturbs the dynamic water gradient resulting in an overshoot of KITA signal which then relaxes back during onset of substrate hydrolyses. Our findings suggest that collective water dynamics may contribute to effective substrate binding to enzyme active sites and could be induced by the charge of the catalytic zinc-ion residing at the active site.