Ethanol binding sites on proteins

Abstract

This study is on the analysis of ethanol binding sites on 3D structures of nonredundant proteins from the Protein Data Bank. The only one amino acid residue that is significantly overrepresented around ethanol molecules is Tyr. There are usually two or more Tyr residues in the same ethanol binding site, while residues of Thr, Asp and Gln are underrepresented around them. Residues of Ala and Pro are significantly underrepresented in ethanol binding surfaces. Several residues (Phe, Val, Pro, Ala, Arg, His, Ser, Asp) bind ethanol significantly more frequent if they are not included in beta strands. Residues of Ala, Ile and Arg preferably bind ethanol when they are included in an alpha helix. Ethanol molecules often make hydrogen bonds with oxygen and nitrogen atoms from the main chain of a protein. Because of this reason, the binding of ethanol may be associated with the decrease of the length of alpha helices and the disappearance of 3/10 helices. Obtained data should be useful for studies on new targets of the direct action of ethanol on enzymes, receptors, and transcription factors.