Dissertation Defense: Qi Huang

Candidate Name: Qi Huang

Major: Chemistry

Advisor: Toshiko Ichiye, Ph.D.

Title: Enzymes Under Pressure

One of the most interesting questions about piezophiles (pressure-loving) is why enzymes from piezophiles are active at much higher pressures than the homologous enzymes from mesophiles (normal-loving). To study pressure effects on enzymes and the adaptations of enzymes from piezophiles to high pressure, molecular dynamics simulations were performed for homologous enzymes from extremophiles and mesophiles at various temperatures and pressures including the growth temperature (TG) and pressure (PG) of the parent organisms. Most of the studies focus on dihydrofolate reductase (DHFR) from a piezophile Moritella profunda (MpDHFR) and a mesophile Escherichia coli (EcDHFR). Additional simulations compared homologous adenylate kinase (AK) from extremophiles and mesophiles.

The simulations of MpDHFR and EcDHFR show that while the average mean-square fluctuations (MSF) of the atomic coordinates on a sub-nanosec timescale increase with temperature, the MSF on a timescale greater than nanosec also increase with pressure. Moreover, the MSF are almost constant at the TG and PG of the parent organisms indicating they are “corresponding states” conditions for enzyme activity. A quasiharmonic approximation for energy landscapes analysis shows that increasing temperature makes the energy minima of the local effective potential energy less steep while increasing pressure steepens the energy minima, which is consistent with the sub-nanosec behavior of the MSF. Moreover, the underlying potential energy surface of MpDHFR appears inherently softer than that of EcDHFR. In addition, the underlying physical reason for the increased nanosec-plus timescale MSF of MpDHFR and EcDHFR appears to be that pressure, as well as temperature, shortens lifetimes of protein hydrogen bonds. A few sequence differences appear responsible for fewer hydrogen bonds in MpDHFR for flexibility at its lower TG, while EcDHFR has stronger hydrogen bonds to keep it stable at its higher TG. Moreover, a sequence difference is identified in MpDHFR that appeared to reduce over-correlation of collective motions at its higher PG.

Finally, the simulations of homologous AK from extremophiles show that the nanosec-plus timescale MSF of the CORE domain are similar to the results for DHFR. In particular, the MSF are almost constant at the TG and PG of the parent organisms, indicating they are corresponding states.