Identification of metal ion binding sites based on amino acid sequences

Abstract

The identification of metal ion binding sites is important for protein function annotation and the design of new drug molecules. This study presents an effective method of analyzing and identifying the binding residues of metal ions based solely on sequence information. Ten metal ions were extracted from the BioLip database: Zn2+, Cu2+, Fe2+, Fe3+, Ca2+, Mg2+, Mn2+, Na+, K+ and Co2+. The analysis showed that Zn2+, Cu2+, Fe2+, Fe3+, and Co2+ were sensitive to the conservation of amino acids at binding sites, and promising results can be achieved using the Position Weight Scoring Matrix algorithm, with an accuracy of over 79.9% and a Matthews correlation coefficient of over 0.6. The binding sites of other metals can also be accurately identified using the Support Vector Machine algorithm with multifeature parameters as input. In addition, we found that Ca2+ was insensitive to hydrophobicity and hydrophilicity information and Mn2+ was insensitive to polarization charge information. An online server was constructed based on the framework of the proposed method and is freely available at http://60.31.198.140:8081/metal/HomePage/HomePage.html.

Fig 1. Schematic diagram of the proposed method.

Fig 2. Illustration of position-specific conservation of amino acid residues in the binding and non-binding sequence segments for ions of (A) Ca²⁺, (B) Mg²⁺, (C) K⁺, (D) Na⁺, (E) Zn²⁺ and (F) Cu²⁺.

The larger residues are more conserved than the smaller ones. Each subfigure of (A), (B), (C), (D), (E), and (F) contains two figures, where the left one indicates the position-specific conservation in positive sequence segments and the right one indicates the position-specific conservation in negative sequence segments.

Fig 3. Statistical analysis of the amino acid composition in positive and negative segments for Na⁺, K⁺, Mg²⁺, Ca²⁺, Zn²⁺, and Cu²⁺.

Fig 4. The distribution of relative solvent accessibilities for binding and non-binding residues of (A) Fe³⁺ ligand and (B) Mn²⁺ ligand.