Identifying the Sulfate Ion Binding Residues in Proteins

Many proteins function execution depends on the process of protein and ligand interact with each other. The identification of ligand binding residues is important for the research of the protein function. The 4442 protein chains with <25% sequence identity and resolution <3.0 Å were analyzed using Ligand Protein Contact database. Our final dataset contained 8112 sulfate ion binding residues (SIBR). We did a statistical analysis on window size as 7 amino acids. Using the amino acid composition, hydropathy information, correlation information and predicted structure information as the characteristic parameter, a Support Vector Machine algorithm for identifying sulphate ion binding residues was proposed. The overall accuracy and Matthew's correlation coefficient achieved 78.5% and 0.571 using the 5 fold cross validation. The Acc and MCC achieved 72.7% and 0.455 by using independent test. In addition, an online web server was established. http://202.207. 30.72:7321/ Introduction The purpose of research protein is to understand and annotate the function of protein. In recent years, it is a hot issue to research protein function by using theoretical calculation methods in bioinformatics field. The sulphate ion binding site is a basic form for protein functional annotation. Therefore, the study of sulphate ion binding residue (SIBR) is important [1, 2]. The sulphate ion is an important matter in biological cells, and it takes part in several major processes of cell metabolism [3-5]: the synthesis process of Cysteine, the sulfation process after protein translation, the synthesis process of proteoglycan, the sulfate absorption and decomposition process of plant and others. For example, the sulfation process occurs in the Golgi apparatus, and the sulfate radical is transferred into hydroxyl of tyrosine in peptide chain by catalyzing of enzyme, so it can make many proteins to have certain activity [5]. The identification of SIBR is helpful to study protein cell metabolism processes, and it has very important meaning to design medicine molecules [6]. In 1966, Pardee has researched sulfate-binding protein of salmonella typhimurium by using experimental method observing the interactional mechanism of binding sites with sulfate ion [7]. Richard et al. have tested sulphate ion binding site of proteoglycan in 2002, and they fixed the sites that is interaction with heparan sulfate [8]. In 2003, Tamada has researched sulfation of protein, and modified sulfated silk fibroin by concentrated sulfuric acid. They got silk fibroin sulfated efficiency, and found that the reaction efficiency is not high and is very susceptible to decomposition of the sample [9]. Monigatti et al. have done a statistical analysis on Tyrosine which may be sulfated in 5 proteins, and given the analysis regularity of Tyrosine sulfation in 2002[4]. The previous study of sulphate ion binding site used experimental method or statistical analysis on few proteins. At present, in the post-genomic era, with more 209 This is an open access article under the CC BY-NC license (http://creativecommons.org/licenses/by-nc/4.0/). Copyright © 2017, the Authors. Published by Atlantis Press. 2nd International Conference on Biomedical and Biological Engineering 2017 (BBE 2017) Advances in Biological Sciences Research (ABSR), volume 4