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

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.

The emerging era of genomic data integration for analyzing splice isoform function

“…Prior to the recent accumulation of RNA-seq data, protein structure methods [69–75], based on the assumption that structural differences may predispose isoforms to functional diversification, had been the main route for predicting isoform functions. These methods are based on amino acid sequences, protein domains, and 3D conformational structures (Figure 2).…”

Novel function discovery through sequence and structural data mining

“…Structure-based function prediction approaches include docking and template-based structural modelling [71 ,72], detection of geometric and physicochemical similarities among functional sites [73][74][75][76], and structural alignment. These approaches have been successful in predicting a wide range of new protein functions/interactions including enzymatic functions [69,70 ,77], binding sites [78,79], protein-DNA interactions [76,80], and protein-protein complexes [68,71 ].…”

“…These approaches have been successful in predicting a wide range of new protein functions/interactions including enzymatic functions [69,70 ,77], binding sites [78,79], protein-DNA interactions [76,80], and protein-protein complexes [68,71 ]. In an exciting recent example of structure-based function prediction, Zhang et al…”

Parallel‐ProBiS: Fast parallel algorithm for local structural comparison of protein structures and binding sites

“…Possible interactions of a protein with ligands are thus taken into account. A structural similarity search algorithm, which uses a fast maximum clique algorithm [20] and operates independently of fold and sequence, performs a local, surface-oriented comparison of the proteins represented as graphs. All possible similar regions between two compared proteins are identified.…”

“…Particularly, we plan to parallelize the maximum clique algorithm, [20] which is the essential building block of the proposed protein structural comparisons. We will explore the efficiency of many-core and graphic processing unit (GPU) platforms in further parallelization approaches.…”