Prediction of the Three-Dimensional Structures of Complexes of Lysozyme with Cell Wall Substrates

The conformational energies of complexes of alternating copolymers of A-acetylglucosamine (GlcNAc) and A-acetylmuramic acid (MurNAc) with hen egg white lysozyme have been computed. This involved a complete search of the conformational space at the active site of the enzyme available to these substrates and minimization of the conformational energies of the noncovalent complexes. As with the homopolymer (GlcNAc)6, the hexasaccharide (GlcNAc-MurNAc)₂-(GlcNAc)² binds preferentially on the “left” side of the active-site cleft, involving residues such as Arg-45, Asn-46, and Thr-47. The alternating copolymer (GlcNAc-MurNAc)₃, however, binds with its F-site residue preferentially on the “right” side of the active-site cleft, involving residues such as Phe-34 and Arg-114. The lactic acid side chain prevents good binding to the F site on the left side. This result can explain the higher rate of catalysis for the cell wall substrate (the alternating copolymer). The relative affinities of the disaccharide GlcNAc-MurNAc for all sequential pairs of sites A-F (including E and F sites on both sides of the cleft) are determined. It is found that the highest affinity of this disaccharide is for sites C and D and “right-side” sites E and F, in good agreement with experimental results of Sarma & Bott [Sarma, R., & Bott, R. (1977) J. Mol. Biol. 113, 555]. The energy of the recently determined X-ray crystallographic structure of MurNAc-GlcNAc-MurNAc bound to the B, C, and D sites of hen egg white lysozyme has been minimized and found to lead to a conformation quite similar to one which we predicted previously for the trisaccharide (GlcNAc)3. The D ring is undistorted and binds close to the surface of the active-site cleft. The structure can be extended into sites E and F by addition of two GlcNAc residues, but only on the left side of the active-site cleft. This indicates that polymers bound with their D-site residues near the surface of the cleft must bind to sites E and F on the left side of the cleft, as we also predicted previously.