Investigation into Structural Changes of the Copper Binding Site in Lysyl Oxidase upon Substrate and Inhibitor Docking

The present paper reports a computational investigation of potential communication between the lysine tyrosylquinone (LTQ) and copper cofactors within lysyl oxidase (LOX). Various substrates and inhibitors of LOX were docked into the active site in our computer generated model of the enzyme. Conformational changes in the vicinity of the copper site as well as changes in the electrostatic environment were identified. The appearance of a canal-like structure involving tyrosine 35 (TYR35) and glutamine 104 (GLN104) residues was shown to be consistent upon docking of a variety of different compounds. Interactions between LOX and its natural substrate, collagen, were also explored through molecular dynamic simulations. The possibility of communication between the organic and inorganic cofactors in LOX was proposed, aiding the ongoing debate regarding the role of copper in the catalytic mechanism of this important enzyme. 1. Introduction Lysyl oxidase (LOX) is a copper containing amine oxidase (EC 1.4.3.13) that catalyzes the oxidation of lysine resulting in the formation of peptidyl α-aminoadipic-δ-semialdehyde. Once formed, this product can spontaneously condense to form intra- and inter-chain cross-links in connective tissue matrices [1, 2]. LOX is synthesized as a 50？kDa proenzyme, secreted into the extracellular environment, and then processed by proteolytic cleavage, resulting in a functional 32？kDa enzyme [3]. Within the LOX structure, two cofactors are of particular interest: a lysine tyrosylquinone (LTQ) and a bound Cu(II) ion. The copper site has been partially characterized and copper was shown to be coordinated with three specific histidines [4], while LTQ was shown to be formed in a self-processing, copper catalyzed reaction between specific sequential tyrosine and lysine residues in the presence of molecular oxygen [5–7]. Recent research shows developing evidence that the biological role of LOX may extend far beyond that of the structural maturation of elastin and collagen [8–12], demonstrating connections between LOX activity and cancer cell mobility and tumorgenesis [13–15]. Many aspects of LOX function are the subject of continuing investigations. Although it has been shown that Cu(II) is essential for the posttranslational formation of the LTQ cofactor during protein folding prior to proteolytic cleavage [5], whether or not it is imperative to the enzymes functionality has been debated. The first rational, supported by Gacheru et al. [16], presented evidence of copper playing a catalytic role in LOX. It was also reported there that upon