Carnegie Mellon University

Gordon Rule

Gordon Rule

Professor of Biological Sciences


Projects in the Rule lab are directed at understanding the relationship between protein dynamics and enzyme function using combined tools of molecular biology, NMR spectroscopy, and X-ray crystallography. Our past research efforts have been directed at enzyme-substrate interactions, protein-lipid interactions, antibody-antigen interactions, RNA structure, and protein-nucleic acid interactions.  Current areas of research are briefly described below.

1) Changes in Protein Dynamics due to sequence specific recognition by DNA binding proteins (Collaboration with Dr. L. Jen-Jacobson, University of Pittsburgh). A thermodynamic signature associated with the recognition of specific DNA sequences by DNA binding proteins is a very large decrease in heat capacity of the system.  The origin of this heat capacity change is currently unknown. Our hypothesis is that the heat capacity change is due to significant changes in the dynamics of the both the protein and the DNA.  We are currently using NMR methods to measure changes in the dynamics of both the protein and DNA to address this question.

2) Design of Inhibitors and Activators of Thymidylate Kinase. Thymidylate kinase is found in all organisms and this enzyme is required for the production of TTP, an essential component in DNA replication.  Consequently, this enzyme is a target for antibiotics. We are currently developing inhibitors of the thymidylate kinase from Plasmodium falciparum which can be used to treat malaria. In addition to the production of TTP, the human thymidylate kinase is responsible for activation of the HIV pro-drug, AZT.  AZT is a poor substrate for the enzyme, thus toxic levels of the pro-drug limit the amount of AZT that can be safely given to HIV patients. We are currently searching for activators of the human enzyme, which would increase the conversion of the AZT pro-drug to its active form, thus increasing the effectiveness of AZT.


Senutovitch, N.; Stanfield, R.L.; Bhattacharyya, S.; Rule, G.S.; Wilson, I.A.; Armitage, B.A.; Waggoner, A.S.; Berget, P.B. A variable light domain fluorogen activating protein homodimerizes to activate dimethylindole red. Biochemistry 2012, 51(12):2471-85. Epub 2012 Mar 14.

Sinha, K.; Jen-Jacobson, L.; Rule, G.S. Specific labeling of threonine methyl groups for NMR studies of protein-nucleic acid complexes. Biochemistry 2011, 50(47):10189-91. Epub 2011 Nov 3.

Hitchens, T.K.; Zhan, Y.; Richardson, L.V.; Richardson, J.P., Rule, G.S. Sequence-specific interactions in the RNA-binding domain of Escherichia coli transcription termination factor. Rho. J Biol Chem. 2006,  281:33697-703.

Zhan, Y; Rule, G.S. Stable triplet of uracil-uracil basepairs in a small antisense RNA. J Am Chem Soc. 2005, 127:15714-5.

Zhan, Y; Rule, G.S. Glutathione induces helical formation in the carboxy terminus of human glutathione transferase A1-1. Biochemistry 2004, 43:7244-54.

Hitchens, T.K.; Lukin, J.A.; Zhan, Y.; McCallum, S.A.; Rule, G.S. MONTE: An automated Monte Carlo based approach to nuclear magnetic resonance assignment of proteins. J Biomol NMR 2003, 25:1-9.

McCallum, S.A.; Hitchens, T.K.; Torborg, C. Rule, G.S. Ligand-induced changes in the structure and dynamics of a human class Mu glutathione S-transferase. Biochemistry 2000, 39:7343-56.