Mechanism Study on the Interaction Between Cefoxitin and Metal β-Lactamase BcⅡ Based on Spectroscopic Methods and Computional Simulations†

doi:10.7503/cjcu20170702

Abstract

Abstract:

The interaction mechanism between cefoxitin(CFX) and metal β-lactamase BcⅡ was studied by synchronous fluorescence spectroscopy, three-dimensional fluorescence spectroscopy and molecular dynamics simulation. The results of fluorescence spectra show that CFX could induce the conformation changes of BcⅡ during their binding. The simulation results show that the conformational change of BcⅡ is an induction-fit process. Under the induction of CFX, the loops near the binding pocket of BcⅡ match perfectly with the substrate by changing their conformation, and eventually form a cave-like hydrophobic pocket to facilitate the binding process and catalyze hydrolysis. This study may provide some valuable reference and inspiration for the development of new antibiotics to resist the hydrolysis of metal β-lactamases.

Key words: Metal β-lactamase;, Cefoxitin, Interaction, Fluorescence spectroscopy, Molecular dynamics simulation

CLC Number:

O641

TrendMD:

SHI Penghui,BIAN Liujiao. Mechanism Study on the Interaction Between Cefoxitin and Metal β-Lactamase BcⅡ Based on Spectroscopic Methods and Computional Simulations^†[J]. Chem. J. Chinese Universities, 2018, 39(5): 971.

Figures/Tables 9

Fig.1 Synchronous fluorescence spectra of BcⅡ-CFX complex Note：n(CFX)/n(BcⅡ): a—f. 0, 25, 50, 100, 150, 200; c(BcⅡ)=1.0×10-6 mol/L, Δλ=60 nm, T=277 K.

Fig.2 Three-dimensional fluorescence spectra of BcⅡ(A) and BcⅡ-CFX complex(B) Note：c(BcⅡ)=1.0×10-6 mol/L, c(CFX)=0 for (A) and 2×10-4 mol/L for (B), T=277 K.

Fig.3 RMSD of the backbone atoms of BcⅡ-CFX complex in 20 ns MD simulation

Fig.4 Snapshot of active site residues Note：Binding mode of BcⅡ-CFX complex obtained after MD simulation.

Fig.5 RMSF of the backbone atoms of apo BcⅡ and BcⅡ-CFX complex

Fig.6 RMSD of loop of BcⅡ-CFX complex in 20 ns MD simulation

Fig.7 Molecular surface of BcⅡ-CFX complex before(A) and after(B) dynamic equilibrium

Fig.8 Molecular surface of BcⅡ-CFX complex in 20 ns MD simulation Note：(A)—(J) correspond to average structure of BcⅡ-CFX complex in 0—2, 2—4, 4—6, 6—8, 8—10, 10—12, 12—14, 14—16, 16—18 and 18—20 ns, respectively; Loop 1: green; Loop 2: blue; CFX are not shown.

Fig.9 Distance of Phe28 to Asn174 along the simulation trajectories for BcⅡ-CFX complex

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