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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.
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Optimization of Synthetic Proteins: Identification of Interpositional Dependencies Indicating Structurally and/or Functionally Linked Residues

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Published on: July 14, 2015

Computational Identification of Functional Centers in Complex Proteins: A Step-by-Step Guide With Examples.

Wei Zhou¹, Wei Chi¹, Wanting Shen¹

¹Department of Biology, College of Science and Technology, Wenzhou-Kean University, Wenzhou, China.

Frontiers in Bioinformatics

|October 28, 2022

Summary

We developed a computational protocol to discover hidden functional centers in proteins. This method uses sequence motifs and structural analysis to identify key amino acids essential for protein function.

Keywords:

H-NOX abscisic acid receptor adenylyl cyclase functional centers guanylate cyclase hidden domains moonlighting proteins nitric oxide sensors

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Last Updated: Aug 23, 2025

Optimization of Synthetic Proteins: Identification of Interpositional Dependencies Indicating Structurally and/or Functionally Linked Residues

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Published on: July 14, 2015

A Protocol for Computer-Based Protein Structure and Function Prediction

A Protocol for Computer-Based Protein Structure and Function Prediction

Published on: November 3, 2011

Identification of Functional Protein Regions Through Chimeric Protein Construction

Identification of Functional Protein Regions Through Chimeric Protein Construction

Published on: January 8, 2019

Area of Science:

Proteomics
Structural Biology
Bioinformatics

Background:

Functional centers in proteins, comprising key amino acids, are crucial for molecular functions like catalysis and ligand-binding.
These centers are often within complex multi-domain proteins and regulate cellular signaling pathways.

Purpose of the Study:

To present a robust, widely applicable computational protocol for discovering novel, hidden functional centers in proteins.
To provide a step-by-step guide detailing the workflow, including recommendations and cautions.

Main Methods:

Assembling a search motif based on key amino acids of a functional center.
Querying proteomes with the motif and performing structural assessments of identified proteins.
Utilizing computational tools for data analysis and biological interpretation of results.

Main Results:

The protocol has successfully uncovered several novel functional centers in complex proteins.
The approach integrates computational analysis of public data with biological interpretation.

Conclusions:

This protocol offers a systematic approach to identify previously undiscovered functional centers.
It enhances our understanding of protein function and cellular signaling regulation.