Biological and Environmental Research

DOE’s Office of Biological and Environmental Research is a major supporter of computational biological research and global climate studies using NERSC resources. This year’s accomplishments include the first report on the structure of a carcinogenic heterocyclic amine, in a study combining nuclear magnetic resonance (NMR) imaging and molecular mechanics computation. A poster presentation of this study at the Pasteur Institute in Paris in February 2002 received a Certificate of Merit Award from the Sixth International Symposium on Predictive Oncology and Intervention Strategies.

In other studies, comparison of the Fugu and human genomes enabled researchers to discover almost 1,000 human putative genes that have so far not been described in public annotation databases. And computational studies are increasing our understanding of how an enzyme called TIM speeds up the breakdown of carbohydrates. Climate research highlights include the first study of tropopause height as an indicator of climate change, and an analysis of the complex effects of aerosols on clouds.

Determining the Structure of a Carcinogenic Heterocyclic Amine

Consumption of foods containing heterocyclic amines (HA) has been implicated in the etiology of human cancers, including cancer of the colon, lung, and breast. The mutagen 2-amino-1-methyl-6-phenylimidazo[4,5-b]pyridine (PhIP) is the most abundant of the HAs, which are formed in meat and fish during cooking. PhIP has been shown to induce tumors in several organs in rodents and to form DNA adducts, which are considered initiating events in chemical carcinogenesis.

Because of difficulties in synthesizing the large quantities of highly purified samples needed, no structural studies of HA-DNA adducts had been reported until the work of Brown et al., who optimized the synthesis of the C8-dG-PhIP adduct in an 11-mer DNA sequence and determined its structure through a combination of NMR imaging and molecular mechanics computation. Restrained conformational searches were carried out with DUPLEX, a molecular mechanics program for nucleic acids that performs potential energy minimization in the reduced variable domain of torsional angle space.

	Figure 1   Comparison of the [PhIP]dG·dC and [AF]dG·dC 11-mer adduct duplexes with [PhIP]dG6 in blue, dC17 in green, and PhIP and AF ligands in red. The PhIP and AF structures are shown at the bottom.

The covalent binding of bulky carcinogens such as PhIP to DNA can alter biological processing of the DNA by cellular proteins governing replication, transcription, and repair, and thereby cause mutations and ultimately cancer, especially if the lesion is located in an oncogene or tumor-suppressor gene. Consequently, considerable efforts are being made to understand how adduct conformation affects cellular responses to DNA damage.

This study shows that the [PhIP]dGzdC 11-mer adduct duplex undergoes a conformational exchange between a major base-displaced intercalative structure and a minor external groove-binding structure. The subtle differences in the structural details and in the population ratios of each conformer of the C8-dG-PhIP-DNA adduct reveal the importance of the chemical structure of the PhIP molecule in governing its DNA adduct conformation. A comparison of the structures of the major conformers of the C8-dG-PhIP and C8-dG-AF (31) 11mer duplexes (Figure 1) shows that although both DNA adducts adopt overall similar structural motifs, several important differences are observed that would directly influence how cellular proteins interact with this type of damaged DNA substrate. Determination of the structure of this adduct is an important first step in elucidating the mechanisms by which DNA damage by PhIP can lead to cancer.

INVESTIGATORS
B. E. Hingerty, Oak Ridge National Laboratory; S. Broyde, New York University; K. Brown, M. Cosman, E. A. Guenther, V. V. Krishnan, and K. W. Turteltaub, Lawrence Livermore National Laboratory; L. Wang, New York University; M. Minkoff, Argonne National Laboratory; R. Wagner, Duke University.

PUBLICATION
K. Brown, B. E. Hingerty, E. A. Guenther, V. V. Krishnan, S. Broyde, K. W. Turteltaub, and M. Cosman, “Solution structure of the 2-amino-1-methyl-6-phenylimidazo[4,5-b]pyridine C8-deoxyguanosine adduct in duplex DNA,” PNAS 98, 8507 (2001).

URL
http://bio.lsd.ornl.gov/gst/newresearch/r1.html