Molecular dynamics insights into urease stability under reservoir conditions: Implications for sustainable bio-cementation

Sand production is a major challenge in oil and gas extraction, leading to equipment damage, operational inefficiencies, and elevated costs. Conventional sand control techniques are associated with environmental concerns and high economic costs. Microbially induced precipitation (MICP), driven by urease, provides an eco-friendly approach to stabilize unconsolidated formations by catalyzing urea hydrolysis to produce CaCO₃. However, urease's structural resilience under harsh reservoir conditions remains poorly understood. To address this, we conducted large-scale molecular dynamics simulations to probe the enzyme's structural and thermodynamic stability under subsurface conditions. Our simulations over 1.5 μs reveal that urease retains remarkable structural integrity under extreme reservoir conditions, preserving its secondary structure and active-site architecture. Notably, these harsh conditions enhance conformational stability and promote dynamics beneficial to substrate binding. Specifically, the active site flap samples wide-open conformations more frequently under reservoir conditions, facilitating optimal urea access, a key determinant of catalytic efficiency. Furthermore, Ca²⁺ and Cl⁻ ions in the simulated brine stabilize the protein surface through enhanced electrostatic interactions, while the catalytic Ni²⁺ coordination site remains structurally intact with no interference from competing divalent cations (e.g., Ca²⁺, Mg²⁺). Density functional theory calculations on a truncated active-site model further confirm the strong binding preference for Ni²⁺ over other divalent cations. These findings reveal the molecular basis of urease robustness in high-salinity environments, providing essential insights for optimizing MICP processes. The study establishes a computational framework for engineering enhanced enzymes or refining protocols, advancing sustainable bio-cementation technologies for reliable sand control in upstream petroleum operations.