Molecular modeling of heme proteins using MOE: Bio-inorganic and structure-function activity for undergraduates*S

A biochemical molecular modeling project on heme proteins suitable for an introductory Biochemistry I class has been designed with a 2-fold objective: i) to reinforce the correlation between protein three-dimensional structure and function through a discovery oriented project, and ii) to introduce students to the fields of bioinorganic and coordination chemistry. Students are asked to identify several unknown heme proteins based on a careful analysis of covalent and noncovalent interactions at the active site of each protein, focusing on amino acid reactivity and H-bonding networks. Starting with the three-dimensional crystal structures of four unknown proteins, students isolate and examine the coordination environment of the iron center in order to predict the relative reactivity toward dioxygen (O(2) ) or hydrogen peroxide (H(2) O(2) ). The central question of the project is to determine how the same iron protoporphyrin IX cofactor can be used by four different proteins to carry out diverse reactions, from electron transfer, to reversible oxygen binding to hydrogen peroxide activation. Pedagogical reasons for implementation of this biomolecular discovery-based activity and student evaluations are discussed. In addition to developing many of the three-dimensional visualization skills needed to successfully learn biochemistry, students also learn to use the versatile MOE molecular modeling program (Molecular Operating Environment), become familiar with metalloprotein reactivity, and are introduced to computational biochemistry research.