PH-Dependent conformational stability of SpeB from Thermus thermophilus HB8: insights from molecular dynamics simulation

Abstract

ABSTRACT N(1)-aminopropyl agmatine ureohydrolase (SpeB) is considered an essential enzyme for the growth and survival of thermophiles, it is involved in the biosynthesis of polyamines. The present study investigates the conformational stability and flexibility of Thermus thermophilus HB8 SpeB and its interactions with substrate, N1-aminopropyl agmatine at different physiological conditions to probe the optimal conditions that provide insights on biotechnological applications. As the 3D structure of SpeB is yet to be crystallized, it was modelled and validated using structural bioinformatics methods. To understand the conformational dynamics and also to assess the impact of pH and temperature variables on the tertiary structure of SpeB , atomistic molecular dynamics simulation (MDS) was employed. The MD investigation revealed that 300 K is not optimal for SpeB (apo form) at both acidic pH 4.5, and alkaline pH 8.5, since it exhibited decreased stability and compactness with higher residual flexibility. Further, the stable and strong binding of N1-aminopropyl agmatine with SpeB was observed at following conditions, neutral pH 7 at 353.15 K and alkaline pH 11 at 300 K. Thus, this in silico study provides significant insights into the structural investigations on SpeB along with optimal pH as well as temperature for its ideal enzymatic function. Highlights Structural and dynamic characteristics of T. thermophilus SpeB have been explored in detail Comparative Molecular dynamics simulations were performed to evaluate the effects of both pH and temperature on the structural stability of SpeB SpeB showed pH and temperature-dependent conformational changes that potentially affect substrate binding Structural stability of apo form of SpeB is not optimal at high temperature (363.15 K) in both acidic (pH 5.5) and neutral pH Stable and strong binding affinity of substrate molecule was observed in a neutral pH 7 at 353 K and alkaline pH 11 at 300K