The Skaggs Institute
for Chemical Biology

Scientific Report 2007

Chemistry, Biology, and Disease

P. Wentworth, Jr., J.Y. Chang, Y.P. Chen, J. Dambacher, R.K. Grover, J. Nieva, M. Puga, B.D. Song, M.M.R. Peram, J. Rogel, S.R. Troseth, H. Wang, A.D. Wentworth

During the past year, we made significant progress toward understanding the structural basis of the antibody-catalyzed water oxidation pathway, expanded our discovery that inflammatory aldehydes can cause misfolding of disease-related proteins, and discovered a new biological target for parasite therapy.

Our discovery that all antibody molecules, regardless of source or antigenic specificity, can catalyze the reaction between singlet oxygen and water to give hydrogen peroxide is causing a revision of the axiom that antibodies are the classical adapter molecules of the immune system, linking recognition and killing of foreign pathogens. We have cloned and expressed soluble individual domains (V_HV_L, C_H1C_L,V_H, V_L, C_H1, C_L) of the murine Fab 4C6. All the domains have been successfully purified to homogeneity from the periplasm of Escherichia coli transformed with plasmids encoding individual domains. All the domains are folded, as indicted by far ultraviolet circular dichroism. These findings indicate that all these immunoglobulin domains can perform the antibody-catalyzed water oxidation pathway when activated with singlet dioxygen.

We have shown that the inflammation-derived cholesterol seco-sterols atheronal-A and atheronal-B (Fig. 1) trigger a deformation in the secondary structure of the normally folded low-density lipoprotein apoB-100 into a proamyloidogenic form. More recently, using mutated synthetic sequences of amyloid β-peptide_1-40, we found that the accelerated aggregation of this protein occurs only when a particular lysine of the sequence is modified. We have also shown that atheronals and other lipid aldehydes accelerate the aggregation of several wild-type amyloidogenic proteins, including immunoglobulin light chains, mouse prions, and the tumor suppressor protein p53. The generality and specificity of this process suggest that inflammatory aldehydes and their posttranslational modification of amyloidogenic peptides may be the chemical link between the known associations of inflammation, oxidative damage, and various misfolding disease states.

Fig. 1. The cholesterol seco-sterols atheronal-A (top) and atheronal-B (bottom).

Current treatments of parasitic infections such as leishmaniasis (cutaneous or visceral, Leishmania species), African trypanosomiasis (sleeping sickness, Trypanosoma brucei), and American trypanosomiasis (Chagas disease, Trypanosoma cruzi) have limited effectiveness, increasing drug resistance and the inherent toxic effects of the drugs. Thus, an elucidation of new parasite-specific biological targets for therapeutic agents is needed.

DNA from members of the order Kinetoplastida, but not from other eukaryotes, contains an unusual modified base, β-D-glucosyl
(hydroxymethyl)uracil, called base J. Extracts of several kinetoplastids contain a J-binding protein, JBP-1, that specifically binds to J-containing duplex DNA. As a drug target, JBP-1 has merit. The protein shares little homology with other proteins in the Protein Data Bank, and it has a unique ligand, J-DNA containing telomeric stretches of double-stranded DNA, that does not occur in other eukaryotes. We have studied the molecular recognition that underlies JBP-1 recognition of glycosylated DNA. In collaboration with D.P. Millar and D.A. Case, Scripps Research, we found that JBP-1 interacts with J-containing DNA only when a critical conformation of the glucose within the major groove is established (Fig. 2).

Fig. 2. Surface rendering of a molecular dynamics snapshot of the critical edge-on conformation of glucose (stick representation) within the major groove essential for recognition of J-DNA by JBP-1.

Our interdisciplinary research focus involves aspects of bioorganic, biophysical, physical organic, synthetic, and analytical chemistry coupled with biochemical techniques, cell-based assays, and animal models. Ongoing projects include studies on atherosclerosis, neurodegenerative diseases, ischemia-reperfusion injury, macular degeneration, cancer, inflammation, and infectious diseases.

Publications

Bieschke, J., Zhang, Q., Bosco, D.A., Lerner, R.A., Powers, E.T., Wentworth, P., Jr., Kelly, J.W. Small molecule oxidation products trigger disease-associated protein misfolding. Acc. Chem. Res. 39:611, 2006.

Bosco, D.A., Fowler, D.M., Zhang, Q., Nieva, J., Powers, E.T., Wentworth, P., Jr., Lerner, R.A., Kelly, J.W. Elevated levels of oxidized cholesterol metabolites in Lewy body disease accelerate α-synuclein fibrilization [published correction appears in Nat. Chem. Biol. 2:346, 2006]. Nat. Chem. Biol. 2:249, 2006.

Grover, R.K., Pond, S.J., Cui, Q., Subramanian, P., Case, D.A., Miller, D.P., Wentworth, P., Jr. O-Glycoside orientation is an essential aspect of base J recognition by the kinetoplastid DNA-binding protein JBP1. Angew. Chem. Int. Ed. 46:2839, 2007.

Takeuchi, C., Galvé, R., Nieva, J., Witter, D.P., Wentworth, A.D., Troseth, R.P., Lerner, R.A., Wentworth, P., Jr. Proatherogenic effects of the cholesterol ozonolysis products, atheronal-A and atheronal-B. Biochemistry 45:7162, 2006.

Witter, D., Wentworth, P., Jr. The antibody-catalyzed water-oxidation pathway from discovery to an emerging role in health and disease. Antioxid. Redox Signal., in press.

Xu, Y., Hixon, M.S., Yamamoto, N., McAllister, L.A., Wentworth, A.D., Wentworth, P., Jr., Janda, K.D. Antibody-catalyzed anaerobic destruction of methamphetamine. Proc. Natl. Acad. Sci. U. S. A. 104:3681, 2007.