|Robert C.A.M. van Waardenburg, Ph.D.|
Contact Dr. van Waardenburg;
Phone Office: (205) 934 4572, Phone Lab: (205) 934 4513, Fax: (205) 934 8240
B.Sc., Biotechnology, H.L.O. Delft, The Netherlands.
M.Sc., Biotechnology, Department of Chemistry, University of Groningen,
Ph.D., Department of Medical Oncology, University of Groningen, TheNetherlands.
- Structure-Function analysis DNA repair and post-translational modification enzymes
- Mechanism of Action of proteins and drugs (chemotherapeutics)
- Drug development for novel therapeutic targets
- Post-translational modification by Ubiquitin and SUMO (Small Ubiquitin-like MOdifier)
- Protein-Protein interactions
We are interested in the response of cells to treatment with chemotherapeutics, specifically DNA damaging agents. To investigate this response, we use yeast genetics, biochemistry, and RNAi technology in human cells, and collaborate with Structural Biologists to analyze the structure-function relations and mechanisms of action of proteins and anti-cancer drugs.
The lab studies the eukaryotic DNA repair enzyme Tyrosyl-DNA phosphodiesterase I (Tdp1), which belongs to the phospholipase D superfamily.Tdp1 comprisesa very interesting catalytic cycle that consists of two active site histidines, one that functions as nucleophile and the other one as general acid/base. Using this histidine couple, Tdp1 is able to remove DNA adducts from the 3’- and 5’-end of a DNA strand break. The interaction between Tdp1 and its substratesneeds to be very adaptable since Tdp1 hydrolyses a wide variety of substrates that differ in size and complexity, e.g. from a small and simple damage nucleotide to a large and complex protein-DNA adduct. We use two clinically relevant model substrates;DNA topoisomerase I (Top1) to study 3’DNA-adducts and DNA topoisomerase II (Top2) for 5’ DNA- adducts. Using these substrates, we are able to study Tdp1 function in vivo/cell. We are interested in the structure-function analysis of catalytic residue substitutions to investigate their catalytic function, determine mechanism of action (induction of cellular toxicity), and study Tdp1 cellular function/interaction with substrates and other proteins. In addition, we study the effects of post-translational modification,such asSUMOylation (SUMO conjugation),of Tdp1 on catalytic activity and protein-protein interactions, in both the yeast and human cell model. These studies will reveal Tdp1 physiological function, and identified Tdp1 as a therapeutic target for drug studies, which are ongoing in the lab and are in part supported by the Alabama Drug Discovery Alliance (ADDA).
Besides DNA repair, Tdp1 is also involved in neurodegeneration, as a substitution of the general acid/base histidine to arginine was identified in patients with the autosomal recessive disease spinocerebellar ataxia with axonal neuropathy (SCAN1). The mechanism by which this substitution only affects cerebellar neuronal cells is unknown.We are interested in elucidating this interesting phenotype by studying the role of Tdp1 in genome stability. Interestingly, these SCAN1 patients are not prone to other genetic disease, such as cancer or immune-deficiencies, suggesting that the cellular conditions of these cerebellar neurons play an important role in disease development
Another subject the lab is interested in is the role of post-translational modification of proteins by ubiquitin and ubiquitin-like proteins, specifically SUMO (small ubiquitin-like modifier) in response to DNA damage. We focus on the effects of SUMOylation of proteins stimulated by SUMO E3-ligase and the effects of SUMO modification on protein-protein. Unlike the ubiquitin pathway, the SUMO pathway only uses a limited amount (10 to 20) of E3-ligases, which specifically stimulates SUMO conjugation to a sub-set of proteins (substrates). We are interested in identifying those proteins that are modified and play a role in the response to DNA damage in human cells.