Predicting The Function Of A Putative Uncharacterized Hypothetical Protein From Leishmania Major

摘要

3M3I, a hypothetical protein from Leishmania Major was selected for functional studies using the Basic Local Alignment Search Tool (BLAST) to perform a similarity search through the National Center for Biotechnology Information (NCBI). Comparative analysis disclosed matches to the cupin family and purine nucleotide permease. To further elucidate the identity of 3M3I the STRING database was employed. STRING revealed protein interactions with glyoxalase II and adenosine deaminase. Based on the BLAST and STRING identifications 3M3I appears to be involved in nucleotide metabolism. In addition, analysis revealed possible participation in ATP-dependent protease activity and shuttling within metabolic pathways. This data has laid foundations for further studies to be accomplished linking 3M3I to the enzyme system responsible for the renewal of nucleic acids in Leishmania Major. Introduction Leishmania major is one of a few species of Leishmania, which is apart of the genus of Trypanosomatid protozoa. This intracellular pathogen is responsible for the disease Leishmaniasis, targeting dendritic cells and macrophages. Leishmaniasis has caused prominent morbidity and mortality to populations of more than 80 counties worldwide. Leishmania major infection is characterized by the presence of disfiguring cutaneous lesions. To better understand the pathogenic disease genome-wide and proteomic studies have been extensively underway. Studies have identified the genome of Leishmania as containing 8000 genes. The genes of the species have no introns and no alternative splicing thereby indicating that there should not be many more proteins than there are genes [1]. Proteomics can be defined as the study of global protein expression of biological samples [2]. This area of study employs qualitative and quantitative mass spectrometry approaches to examine global sample sets, which have provided a wealth of knowledge in the understanding of cellular function [3-6]. One of the key outcomes of global proteomic analysis is the identification of new proteins with unknown function. These hypothetical proteins are those having a predicted existence but no experimental data to define their function [7]. In order for a complete analysis and understanding of any proteome to take place we must unravel all pieces of the puzzle.In this paper we address the prediction of a hypothetical protein, 3M3I, from Leishmania Major. Elucidating the function and family classification of hypothetical proteins without experimental data involves the combined effort of a number of strategies [8,9]. These include, (1) identification of the sequence homology to proteins of known function, (2) phylogenetic analysis to show evolutionary relationships between biological species based upon similarities and differences in their DNA/protein sequence, and (3) comparative analysis for the identification of probable protein-protein interactions. One of the key points in identifying the function of hypothetical proteins will be to identify the domain(s) found and their organization in order to be able to classify these proteins into a family [10]. Materials and Methods A search of hypothetical proteins was performed at the Protein Data Bank (PDB) (http://www.rcsb.org/pdb) and a hypothetical protein of unknown function, 3M3I (225 residues in length), of Leishmania major was selected. Pair-wise AlignmentThe sequence of 3M3I was extracted in FASTA format from PDB. Through the National Center for Biotechnology Information (NCBI) (http://www.ncbi.nlm.nih.gov), a similarity search using the Basic Local Alignment Search Tool program, BLASTp, a protein-to-protein pair wise alignment was performed. Predicted Protein-Protein InteractionA search was carried out using the protein sequence of 3M3I in the Search Tool for the Retrieval of Interacting Genes/Proteins (STRING 9.0). The STRING 9.0 database allowed for the identification of predicted and known protein interactions, encompassing physical and fu