Abstract
BackgroundOne of the major challenges in post-genomic era is to provide functional annotations for large number of proteins arising from genome sequencing projects. The function of many proteins depends on their interaction with small molecules or ligands. ATP is one such important ligand that plays critical role as a coenzyme in the functionality of many proteins. There is a need to develop method for identifying ATP interacting residues in a ATP binding proteins (ABPs), in order to understand mechanism of protein-ligands interaction.ResultsWe have compared the amino acid composition of ATP interacting and non-interacting regions of proteins and observed that certain residues are preferred for interaction with ATP. This study describes few models that have been developed for identifying ATP interacting residues in a protein. All these models were trained and tested on 168 non-redundant ABPs chains. First we have developed a Support Vector Machine (SVM) based model using primary sequence of proteins and obtained maximum MCC 0.33 with accuracy of 66.25%. Secondly, another SVM based model was developed using position specific scoring matrix (PSSM) generated by PSI-BLAST. The performance of this model was improved significantly (MCC 0.5) from the previous one, where only the primary sequence of the proteins were used.ConclusionThis study demonstrates that it is possible to predict 'ATP interacting residues' in a protein with moderate accuracy using its sequence. The evolutionary information is important for the identification of 'ATP interacting residues', as it provides more information compared to the primary sequence. This method will be useful for researchers studying ATP-binding proteins. Based on this study, a web server has been developed for predicting 'ATP interacting residues' in a protein http://www.imtech.res.in/raghava/atpint/.
Highlights
One of the major challenges in post-genomic era is to provide functional annotations for large number of proteins arising from genome sequencing projects
After removing the redundant sequences using the program CD-HIT, a total of 267 nonredundant PDB chains were obtained where no two sequences have more than 40% identity. We examined these proteins using software Ligand Protein Contact (LPC) [19] and remove those proteins, which are not ATP binding proteins according to LPC
In order to evaluate the performance of BLAST on dataset used in this study, we have searched each ATP binding protein chain against remaining ATP binding protein chains
Summary
One of the major challenges in post-genomic era is to provide functional annotations for large number of proteins arising from genome sequencing projects. Adenosine-5'-triphosphate (ATP) is an important molecule in cell biology as an energy molecule and coenzyme This molecule interacts with large number of proteins during cellular activities and plays a crucial role in various biological reactions. ATP binding proteins (ABPs) have a binding site that allows ATP molecule to interact This binding sites is a micro-environment where ATP is captured and hydrolyzed to ADP, releasing energy which is utilized by the protein to "do work" by changing the shape of the protein and/or making the enzyme catalytically active. These proteins are powered by the hydrolysis of ATP and convert this chemical energy for mechanical work [1]. Many ATP Binding proteins are transmembrane (page number not for citation purposes)
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