title: Simulating the catalytic effect of a designed mononuclear zinc metalloenzyme that catalyzes the hydrolysis of phosphate triesters.
abstract: One of the greatest challenges in biotechnology and in biochemistry is the ability to design efficient enzymes. In fact, such an ability would be one of the most convincing manifestations of a full understanding of the origin of enzyme catalysis. Despite some progress on this front, most of the advances have been made by placing the reacting fragments in the proper places rather than by optimizing the preorganization of the environment, which is the key factor in enzyme catalysis. A rational improvement of the preorganization and a consistent assessment of the effectiveness of different design options require approaches capable of evaluating reliably the actual catalytic effect. In this work we examine the ability of the empirical valence bond (EVB) to reproduce the results of directed evolution improvements of the catalysis of diethyl 7-hydroxycoumarinyl by a designed mononuclear zinc metalloenzyme. Encouragingly, our study reproduced the catalytic effect obtained by directed evolution and offers a good start for further studies of this system.
authors.affiliation: Department of Chemistry, University of Southern California , SGM 418, 3620 McClintock Avenue, Los Angeles, California 90089, United States.
authors.forename: Manoj Kumar
authors.initials: MK
authors.lastname: Singh
authors.forename: Zhen T
authors.initials: ZT
authors.lastname: Chu
authors.forename: Arieh
authors.initials: A
authors.lastname: Warshel
mesh_terms: D055162:Biocatalysis; D004952:Esters; D006868:Hydrolysis; D008667:Metalloproteins / Q000737:chemistry* / Q000378:metabolism*; D008958:Models, Molecular; D010710:Phosphates / Q000737:chemistry* / Q000378:metabolism*; D011487:Protein Conformation; D011789:Quantum Theory; D013816:Thermodynamics; D014468:Umbelliferones / Q000378:metabolism; D015032:Zinc
chemical_list: D004952:Esters; D008667:Metalloproteins; D010710:Phosphates; D014468:Umbelliferones; D015032:Zinc