Abstract
BackgroundIn many important life activities, the execution of protein function depends on the interaction between proteins and ligands. As an important protein binding ligand, the identification of the binding site of the ion ligands plays an important role in the study of the protein function.ResultsIn this study, four acid radical ion ligands (NO2−,CO32−,SO42−,PO43−) and ten metal ion ligands (Zn2+,Cu2+,Fe2+,Fe3+,Ca2+,Mg2+,Mn2+,Na+,K+,Co2+) are selected as the research object, and the Sequential minimal optimization (SMO) algorithm based on sequence information was proposed, better prediction results were obtained by 5-fold cross validation.ConclusionsAn efficient method for predicting ion ligand binding sites was presented.
Highlights
The binding protein chains, including four acid radical ion ligands (NO2−, CO32−, SO42−,PO43−) and ten metal ion ligands (Zn2+, Cu2+, Fe2+, Fe3+, Ca2+, Mg2+, Mn2+, Na+, K+, Co2+), were downloaded from the BioLip database, wherein the sequence length is greater than 50 residues, the resolution is less than 3 Å, and the sequence identity threshold is less than 30%
The following calculations were made under the optimal window sizes and the 5-fold cross validation commonly used in the literature [33,34,35]
The results under component information parameters Under the optimal window size, amino acid component information, hydropathy component information, charge component information, secondary structure component information, and relative solvent accessibility component information were collectively used as characteristic parameters and input to the Sequential minimal optimization (SMO) algorithm
Summary
Ions play an important role in the structure and function of proteins: for example, the SO42− participate in the synthesis process of Cysteine [1], the sulfation process after protein translation [2], the synthesis process of proteoglycan, the sulfate absorption and decomposition process of plant and others [3]; the PO43− is an important component of bones and teeth which can maintain the neutrality of body fluids; alkali metal K+and Na+ control the charge balance in cells, tissue fluids and blood, which plays an important role in maintaining the normal circulation of body fluids and controlling the acid-base balance in the body; alkaline earth metal Ca2+ plays a regulatory role in nerve conduction and blood coagulation; transition metal Fe3+ plays an important role in the oxidative damage process of proteins, lipids, sugars and nucleic acids [4]. In 2017, Cao et al [17] used the SVM algorithm to identify ten metal ion binding sites based on amino acid sequences, which obtained a good result by 5fold cross validation.
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