Abstract
BackgroundThe notion of heme as a regulator of many physiological processes via transient binding to proteins is one that is recently being acknowledged. The broad spectrum of the effects of heme makes it important to identify further heme-regulated proteins to understand physiological and pathological processes. Moreover, several proteins were shown to be functionally regulated by interaction with heme, yet, for some of them the heme-binding site(s) remain unknown. The presented application HeMoQuest enables identification and qualitative evaluation of such heme-binding motifs from protein sequences.ResultsWe present HeMoQuest, an online interface (http://bit.ly/hemoquest) to algorithms that provide the user with two distinct qualitative benefits. First, our implementation rapidly detects transient heme binding to nonapeptide motifs from protein sequences provided as input. Additionally, the potential of each predicted motif to bind heme is qualitatively gauged by assigning binding affinities predicted by an ensemble learning implementation, trained on experimentally determined binding affinity data. Extensive testing of our implementation on both existing and new manually curated datasets reveal that our method produces an unprecedented level of accuracy (92%) in identifying those residues assigned “heme binding” in all of the datasets used. Next, the machine learning implementation for the prediction and qualitative assignment of binding affinities to the predicted motifs achieved 71% accuracy on our data.ConclusionsHeme plays a crucial role as a regulatory molecule exerting functional consequences via transient binding to surfaces of target proteins. HeMoQuest is designed to address this imperative need for a computational approach that enables rapid detection of heme-binding motifs from protein datasets. While most existing implementations attempt to predict sites of permanent heme binding, this application is to the best of our knowledge, the first of its kind to address the significance of predicting transient heme binding to proteins.
Highlights
The notion of heme as a regulator of many physiological processes via transient binding to proteins is one that is recently being acknowledged
Recent reports have expanded the knowledge on transient heme binding
The overarching aim of this work is to provide a computational tool exclusively developed for the prediction and qualitative evaluation of transient heme binding to protein surfaces based on our recently established SeqD-HBM algorithm [6]
Summary
The notion of heme as a regulator of many physiological processes via transient binding to proteins is one that is recently being acknowledged. The presented application HeMoQuest enables identification and qualitative evaluation of such heme-binding motifs from protein sequences. Paul George et al BMC Bioinformatics (2020) 21:124 transient heme binding have been reviewed extensively [1,2,3,4,5,6] (Additional Table 1, supplementary data 3). Well-known representatives are δ-aminolevulinic acid synthase 1 (ALAS1) and transcription regulator protein Bach, which bind heme via CP-containing motifs [1, 7, 8]. In this work we highlight the need for an exclusive computational method that is able to pinpoint heme-binding residues in protein sequences
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