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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

Structure-based function prediction of uncharacterized protein using binding sites comparison.

Janez Konc¹, Milan Hodošček, Mitja Ogrizek

¹National Institute of Chemistry, Ljubljana, Slovenia.

Plos Computational Biology

|November 19, 2013

Summary

Predicting protein function is challenging. Researchers identified the Tm1631 protein

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Area of Science:

Structural genomics
Protein function prediction
Bioinformatics

Background:

Predicting the function of uncharacterized proteins is a significant challenge in structural genomics.
Sequence or structural homology is often insufficient for function identification when proteins lack known relatives.

Purpose of the Study:

To determine the function of the uncharacterized Tm1631 protein from Thermotoga maritima.
To demonstrate a general approach for predicting protein function using binding site analysis.

Main Methods:

Comparison of the predicted binding site of Tm1631 against a library of known structures.
Utilizing the ProBiS tool to model the Tm1631-DNA complex.
Validation of the model using molecular dynamics simulations.

Main Results:

Tm1631's binding site showed similarities to nucleotide binding sites, particularly the DNA-binding site of endonuclease IV.
The Tm1631-DNA model exhibited interactions consistent with endonuclease IV-DNA complexes.
Calculated binding free energies for the Tm1631-DNA model were in close agreement with known endonuclease IV-DNA interactions.

Conclusions:

Tm1631 is proposed to be a DNA-binding enzyme with endonuclease activity.
Tm1631 likely recognizes DNA lesions involving at least two unpaired nucleotides.
The binding site comparison method can guide experimental function determination for uncharacterized proteins.