Dr. Karl Clodfelter

Dr. Karl Clodfelter

Sequence, structure, and function are the three aspects of protein analysis. While no one aspect can fully describe a protein, all three aspects do share a great amount of information between them to describe a protein. On an abstract level, it is the analysis of the relationships between these aspects in which I am interested. Specifically, I have chosen the Cytochrome P450 protein family to study these relationships. This family provides a useful set of data for heavily conserved sequences within sub-families of the P450 superfamily. Beyond that, the function of the superfamily as a monooxygenase has been heavily conserved although sub-families may differ in sequence on average by 75% with each other. Finally, the crystal structures of a growing number of different sub-families of these proteins have been determined.

I am also interested in the cancer research benefits that knowing more about mammalian and human P450s provides. Almost every medication utilizes the monooxygenase activities of hepatic P450s for activation from their pro-drug form. This is the case of cyclophosphamide (CPA) and I-fosphamide (IFA), two pro-drugs used in chemotherapy.

My work in the Structural Bioinformatics Lab is to examine the structure of the P450s which are involved in the activation of CPA and IFA. Unfortunately, the structures of these P450s are not any of those directly determined by crystallography. Therefore, my research will involve the development of homology models and the refinement of these models. Through structure and function data obtained by work in Dr. David Waxman's experimental laboratory, the homology models I create can be refined to better demonstrate the interaction between P450 and chemotherapeutic substrates.

Once these models are refined through the use of structure and function information gained in the experimental lab, the structural representation should be strong enough to predict specific changes to the enzyme which will create a better active site for the activation of CPA. This provides a method for future directed evolution as well as a deeper understanding of the relationships between sequence, structure, and function.