Charge clusters signatures in prokaryotic proteomes: Temperature-dependence and distribution

Area of Science:

• Proteomics
• Bioinformatics
• Structural Biology

Background:

• Charged Clusters (CCs) are crucial for understanding protein structure-function relationships.
• Identifying CCs aids in quantitative structure-function correlation analysis.

Purpose of the Study:

• To perform a proteome-wide scan for CCs in 99,292 proteins.
• To develop and utilize a new tool, Finding Clusters Charge in Protein Sequences Program (FCCP), for CC identification.
• To create a repository of identified CCs.

Main Methods:

• A proteome-wide scan was conducted using the FCCP tool.
• The analysis covered 35 prokaryotic proteomes, including psychrophiles, mesophiles, thermophiles, and hyperthermophiles.
• A new repository of 855 CCs was established.

Main Results:

• Proteins with CCs are predominantly transmembrane proteins.
• Conserved CCs within proteomes are associated with DNA binding, integration, and transposase functions.
• Negative charged clusters correlate significantly with bacterial growth temperature, serving as a core protein signature.

Conclusions:

• The study successfully identified and cataloged CCs across diverse prokaryotic proteomes.
• CCs play significant roles in protein function, particularly in transmembrane proteins and DNA-related processes.
• The association of negative charged clusters with growth temperature provides insights into protein adaptation and function.