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Updated: Nov 12, 2025

Identification of Protein Complexes in Escherichia coli using Sequential Peptide Affinity Purification in Combination with Tandem Mass Spectrometry

Identification of Protein Complexes in Escherichia coli using Sequential Peptide Affinity Purification in Combination with Tandem Mass Spectrometry

Published on: November 12, 2012

Integrating Multimeric Threading With High-throughput Experiments for Structural Interactome of Escherichia coli.

Weikang Gong¹, Aysam Guerler², Chengxin Zhang²

¹Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI 48109, USA; Faculty of Environmental and Life Sciences, Beijing University of Technology, Beijing 100124, China.

Journal of Molecular Biology

|March 20, 2021

Summary

We developed Threpp, a computational pipeline to accurately predict protein-protein interactions (PPIs) and their structures. Threpp enhances genome-wide PPI network analysis and structural modeling, improving upon traditional methods.

Keywords:

Escherichia coli genome multiple-chain threading network centrality protein-protein interaction networks structural interactome

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Last Updated: Nov 12, 2025

Identification of Protein Complexes in Escherichia coli using Sequential Peptide Affinity Purification in Combination with Tandem Mass Spectrometry

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Published on: November 12, 2012

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Published on: February 5, 2015

Area of Science:

Structural Biology
Computational Biology
Bioinformatics

Background:

Genome-wide determination of protein-protein interactions (PPIs) is challenging due to high false-positive rates in high-throughput experiments (HTEs).
Solving PPI quaternary structures is more difficult than tertiary structures using conventional techniques.

Purpose of the Study:

To introduce Threpp, a uniform computational pipeline designed to address limitations in PPI detection and structural determination.
To improve the accuracy and scope of genome-wide PPI network analysis and complex structure modeling.

Main Methods:

Threpp utilizes sequence threading through a complex structure library, integrating alignment scores with HTE data via a naive Bayesian classifier.
Quaternary complex structures are built by reassembling monomeric alignments with dimeric threading frameworks using interface-specific structural alignments.

Main Results:

Applied to E. coli, Threpp identified 35,125 confident PPIs, a 4.5-fold increase over HTE alone.
Constructed complex structure models for predicted PPIs, with 6,771 achieving high confidence (TM-score >0.5) and 39 showing strong consistency with experimental structures (avg. TM-score = 0.73).

Conclusions:

Threpp significantly enhances genome-wide PPI network detection and complex structural construction.
Threading-based homologous modeling proves effective for both PPI network discovery and structural prediction.