Impact of Mutation on the Structural Stability and
the Conformational Landscape of Inhibitor-Resistant TEM β‑Lactamase:
A High-Performance Molecular Dynamics Simulation Study
posted on 2021-10-05, 16:05authored bySandip
K. Mukherjee, Mandira Mukherjee, Padmaja P. Mishra
Gain-of-function
mutations and structural adjustment toward β-lactamase
inhibitors in the TEM-type β-lactamases among the uropathogenic E. coli (UPEC) culminate in treatment complications
and demands detailed investigation. In this study, uncharacterized
amino acid substitutions, M69L/I84V/W165G/V184A/V262I/N276S, in inhibitor-resistant
TEM (IRT) β-lactamase isolated from clinical UPEC were subjected
to extensive molecular dynamics (EMD) simulations for 100 ns to estimate
parameters such as root-mean-square deviation (RMSD), root-mean-square
fluctuation (RMSF), the radius of gyration (Rg), contour plot (Rg/RMSD), secondary
structure element (SSE), etc. Residue interaction networks, principal
component analysis (PCA), and correlation heatmaps were generated
to predict the relation between functionally important atomic motions
to uncover the structural stability of the mutants. To avoid the false
positive conclusion of the simulation study, we performed three identically
parameterize replicas of 100 ns each. Alterations in hydrophobic interactions
resulted in conformation changes exhibited as comparable residue interaction
networks. Besides, PCA and porcupine plot analysis based on the ensemble
of structure from molecular dynamics trajectories revealed the collective
atomic motions of the IRT variants that impart structural flexibility
to their active site loop. This study conducted on IRT mutants that
delineate intricate protein motions contributes to their stability
and folding, which is an absolute necessity for designing candidate
molecules owing to the clinical threat of emerging resistance against
potent β-lactam antibiotics.