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A case study comparing quantitative stability-flexibility relationships across five metallo-β-lactamases highlighting

Matthew C Brown1, Deeptak Verma, Christian Russell

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The Distance Constraint Model reveals conserved and varied protein flexibility. Metallo-β-lactamases show unique rigidity in NDM-1, impacting drug resistance in Klebsiella pneumoniae.

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Area of Science:

  • Biophysics
  • Structural Biology
  • Computational Biology

Background:

  • Protein structure-function relationships are key to understanding biological processes.
  • Metallo-β-lactamases (MBLs) are clinically significant enzymes conferring antibiotic resistance.
  • Quantified Stability-Flexibility Relationships (QSFR) provide insights into protein dynamics.

Purpose of the Study:

  • To investigate conserved and varied QSFR across protein families using MBLs as a model.
  • To identify specific structural differences in the NDM-1 enzyme.
  • To explore the implications of altered flexibility on protein function and drug resistance.

Main Methods:

  • Utilizing the Distance Constraint Model (DCM), an ensemble-based biophysical approach.
  • Integrating thermodynamic and mechanical perspectives for protein structure analysis.
  • Characterizing backbone flexibility and intramolecular couplings in five MBLs.

Main Results:

  • Overall backbone flexibility is conserved across the studied MBLs.
  • NDM-1 exhibits increased rigidity in specific regions compared to other MBLs.
  • NDM-1 displays atypical intramolecular couplings, with limited correlated flexibility isolated to active site loops.

Conclusions:

  • QSFR analysis reveals both conserved and distinct dynamic properties across protein families.
  • NDM-1's unique structural rigidity and limited correlated flexibility may contribute to its high activity and spread.
  • Understanding these dynamic differences is crucial for developing strategies against antibiotic resistance.