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A Molecular Dynamics Study of the Ligand Release Path in Yeast Cytosine Deaminase

Lishan Yao ^* , Honggao Yan   and Robert I. Cukier ^* 

^* Department of Chemistry, Department of Biochemistry and Molecular Biology, and Michigan State University Center for Biological Modeling, Michigan State University, East Lansing, Michigan 48824

Correspondence: Address reprint requests to Professor Honggao Yan, Dept. of Biochemistry and Molecular Biology, Michigan State University, E. Lansing, MI 48224-1322. Tel.: 517-353-5282; Fax 517-353-9334; E-mail: yanh{at}msu.edu; or Professor R. I. Cukier, Dept. of Chemistry, Michigan State University, E. Lansing, MI 48224-1322. Tel.: 517-355-9715 x 263; Fax: 517-353-1793; E-mail: cukier{at}cem.msu.edu.

Yeast cytosine deaminase, a zinc metalloenzyme, catalyzes the deamination of cytosine to uracil. Experimental and computational evidence indicates that the rate-limiting step is product release, instead of the chemical reaction step. In this work, we use molecular dynamics to suggest ligand exit paths. Simulation at 300 K shows that the active site is well protected by the C-terminal helix (residues 150–158) and F-114 loop (residues 111–117) and that on the molecular dynamics timescale water does not flow in or out of the active site. In contrast, simulation at 320 K shows a significant increase in flexibility of the C-terminal helix and F-114 loop. The motions of these two regions at 320 K open the active site and permit water molecules to diffuse into and out of the active site through two paths with one much more favored than the other. Cytosine is pushed out of the active site by a restraint method in two directions specified by these two paths. In path 1 the required motion of the protein is local—involving only the C-terminal helix and F-114 loop—and two residues, F-114 and I-156, are identified that have to be moved away to let cytosine out; whereas in path 2, the protein has to rearrange itself much more extensively, and the changes are also much larger compared to the path 1 simulation.