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Protein Networks

Protein Networks

An organism can have thousands of different proteins, and these proteins must cooperate to ensure the health of an organism. Proteins bind to other proteins and form complexes to carry out their functions. Many proteins interact with multiple other proteins creating a complex network of protein interactions.
These interactions can be represented through maps depicting protein-protein interaction networks, represented as nodes and edges. Nodes are circles that are representative of a protein,...

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Updated: Sep 15, 2025

Mass Spectrometry-Guided Genome Mining as a Tool to Uncover Novel Natural Products

Mass Spectrometry-Guided Genome Mining as a Tool to Uncover Novel Natural Products

Published on: March 12, 2020

Genome mining with hypothetical proteins.

Grace E Kenney¹

¹University of Pittsburgh, Pittsburgh, PA, United States.

Methods in Enzymology

|July 12, 2025

Summary

This summary is machine-generated.

Exploring novel natural product pathways is crucial for discovering new antibiotics and anticancer drugs. This chapter details methods to uncover these challenging biosynthetic pathways, even those involving hypothetical proteins.

Keywords:

Bioinformatics Biosynthetic gene clusters Domains of unknown function Genome mining Hypothetical proteins Natural products Predicted proteins Secondary metabolites

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Last Updated: Sep 15, 2025

Mass Spectrometry-Guided Genome Mining as a Tool to Uncover Novel Natural Products

Mass Spectrometry-Guided Genome Mining as a Tool to Uncover Novel Natural Products

Published on: March 12, 2020

Modified Yeast-Two-Hybrid System to Identify Proteins Interacting with the Growth Factor Progranulin

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Published on: January 17, 2012

A Comparative Approach to Characterize the Landscape of Host-Pathogen Protein-Protein Interactions

A Comparative Approach to Characterize the Landscape of Host-Pathogen Protein-Protein Interactions

Published on: July 18, 2013

Area of Science:

Biochemistry
Genomics
Drug Discovery

Background:

Bioactive natural products from bacteria, fungi, and plants are vital drug candidates.
Genome mining tools like antiSMASH aid in identifying natural product biosynthetic genes.
Current tools often miss novel pathways or those with hypothetical proteins.

Purpose of the Study:

To present approaches for exploring and developing biosynthetic hypotheses for difficult-to-detect natural product pathways.
To address limitations in current genome mining tools for novel compound discovery.

Main Methods:

Utilizing genome mining tools to identify gene clusters.
Developing strategies to investigate pathways with hypothetical proteins.
Hypothesizing biosynthetic routes for uncharacterized compounds.

Main Results:

Identification of potential novel natural product pathways.
Development of methods to overcome limitations of existing tools.
Facilitation of the discovery of compounds with antibiotic and anticancer potential.

Conclusions:

Novel approaches are needed to expand the discovery of natural products.
Understanding unusual biosynthetic pathways is key to finding new therapeutics.
This work provides a framework for exploring uncharted natural product chemical space.