Structure-Based Function Prediction of Uncharacterized Protein Using Binding Sites Comparison

Janez Konc,Milan Hodošček,Joanna Trykowska Konc,Dušanka Janežič,Mitja Ogrizek,Alexander Donald Mackerell

doi:10.1371/journal.pcbi.1003341

Janez Konc, Milan Hodošček + Show 4 more

Open Access

https://doi.org/10.1371/journal.pcbi.1003341

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Abstract

A challenge in structural genomics is prediction of the function of uncharacterized proteins. When proteins cannot be related to other proteins of known activity, identification of function based on sequence or structural homology is impossible and in such cases it would be useful to assess structurally conserved binding sites in connection with the protein's function. In this paper, we propose the function of a protein of unknown activity, the Tm1631 protein from Thermotoga maritima, by comparing its predicted binding site to a library containing thousands of candidate structures. The comparison revealed numerous similarities with nucleotide binding sites including specifically, a DNA-binding site of endonuclease IV. We constructed a model of this Tm1631 protein with a DNA-ligand from the newly found similar binding site using ProBiS, and validated this model by molecular dynamics. The interactions predicted by the Tm1631-DNA model corresponded to those known to be important in endonuclease IV-DNA complex model and the corresponding binding free energies, calculated from these models were in close agreement. We thus propose that Tm1631 is a DNA binding enzyme with endonuclease activity that recognizes DNA lesions in which at least two consecutive nucleotides are unpaired. Our approach is general, and can be applied to any protein of unknown function. It might also be useful to guide experimental determination of function of uncharacterized proteins.

Highlights

Experimental determination of protein function is the most reliable way to characterize proteins of unknown activity but it is difficult to prioritize functional experiments amongst the many possible functions a protein could perform
We investigate a new strategy to predict protein function employing ProBiS enhanced by molecular dynamics (MD) simulation (Figure 1), to find structurally evolutionarily conserved binding sites
Based on the prediction of its binding site, and comparison of this predicted binding site with the protein structures in the Protein Data Bank [14] (PDB), we propose a DNA-repair function for Tm1631, the protein of unknown activity

Summary

Introduction

Experimental determination of protein function is the most reliable way to characterize proteins of unknown activity but it is difficult to prioritize functional experiments amongst the many possible functions a protein could perform. Web portals have been created that allow sharing information about protein structures [3,4]. In spite of these efforts, the gap between proteins with experimentally determined function and those with unknown function is growing [5,6]. In 2013, some 3000 proteins of unknown function in the PDB await characterization of their function, and for about one third of these proteins, including Tm1631, there is little hope that their function will be discovered using conventional methods based on sequence or structure homology [6].

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