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Comprehensive Similarity Algorithm and Molecular Dynamics Simulation-Assisted Terahertz Spectroscopy for Intelligent

Lintong Zhang1, Xiangzeng Kong1, Fangfang Qu1

  • 1Center for Artificial Intelligence in Agriculture, Fujian Agriculture and Forestry University, Fuzhou 350002, China.

International Journal of Molecular Sciences
|February 10, 2024
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Summary

This study introduces a new method using terahertz spectroscopy to identify N-acyl-homoserine lactones (AHLs), crucial signaling molecules in aquatic pathogens. The technique accurately distinguishes between similar AHL structures, aiding in understanding bacterial communication.

Keywords:
Gram-negative pathogensmolecular dynamics simulationquorum signaling moleculesspectral similarity calculationterahertz spectroscopy

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Area of Science:

  • Microbiology
  • Spectroscopy
  • Computational Chemistry

Background:

  • Quorum sensing (QS) is vital for bacterial communication and virulence in aquatic pathogens.
  • N-acyl-homoserine lactones (AHLs) are key signaling molecules in Gram-negative bacterial QS.
  • Accurate identification of AHLs is crucial for understanding and controlling bacterial behavior.

Purpose of the Study:

  • To develop an intelligent method for identifying eight structurally similar AHL quorum signaling molecules.
  • To decode signal transmission mechanisms in aquatic Gram-negative pathogens.
  • To establish a high-throughput and automatic identification method for AHLs.

Main Methods:

  • Utilized terahertz (THz) spectroscopy for spectral fingerprinting of AHLs.
  • Employed density functional theory (DFT) for molecular dynamics simulation and spectral peak assignment.
  • Developed a comprehensive similarity calculation (CSC) method integrating weighted improved Jaccard similarity (IJS) and discrete Fréchet distance (DFD).

Main Results:

  • Successfully identified THz absorption spectral peaks for eight AHLs.
  • Achieved correct identification of all tested AHL molecular types.
  • Demonstrated an average quantization accuracy of 98.48% using the CSC method.

Conclusions:

  • The proposed THz spectroscopy combined with computational methods provides a robust approach for AHL identification.
  • This study offers a novel, accurate, and high-throughput method for automatic AHL identification.
  • The findings support a theoretical and data-driven foundation for AHL analysis in aquatic environments.