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Molecular & Cellular Proteomics 4:84-96, 2005.
© 2005 by The American Society for Biochemistry and Molecular Biology, Inc.

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Research

Rapid Purification and Mass Spectrometric Characterization of Mitochondrial NADH Dehydrogenase (Complex I) from Rodent Brain and a Dopaminergic Neuronal Cell Line^*,S

Birgit Schilling^,, Srinivas Bharath M.M.^,, Richard H. Row, James Murray^¶, Michael P. Cusack, Roderick A. Capaldi^¶, Curt R. Freed^||, Kedar N. Prasad^**, Julie K. Andersen and Bradford W. Gibson^,,

From the Buck Institute for Age Research, Novato, CA 94945; ^¶ Department of Molecular Biology, University of Oregon, Eugene, OR 97403; ^|| Division of Clinical Pharmacology, Departments of Medicine and Pharmacology, and the Neuroscience Program, University of Colorado Health Sciences Center, Denver, CO 80262; ^** Center for Vitamins and Cancer Research, Department of Radiology, University of Colorado Health Sciences Center, Denver, CO 80262; Department of Pharmaceutical Chemistry, University of California, San Francisco, CA 94143

Oxidative stress and mitochondrial dysfunction signify important biochemical events associated with the loss of dopaminergic neurons in Parkinson’s disease (PD). Studies using in vitro and in vivo PD models or tissues from diseased patients have demonstrated a selective inhibition of mitochondrial NADH dehydrogenase (Complex I of the OXPHOS electron transport chain) that affects normal mitochondrial physiology leading to neuronal death. In an earlier study, we demonstrated that oxidative stress due to glutathione depletion in dopaminergic cells, a hallmark of PD, leads to Complex I inhibition via cysteine thiol oxidation (Jha et al. (2000) J. Biol. Chem. 275, 26096–26101). Complex I is a 980-kDa multimeric enzyme spanning the inner mitochondrial membrane comprising at least 45 protein subunits. As a prerequisite to investigating modifications to Complex I using a rodent disease model for PD, we developed two independent rapid and mild isolation procedures based on sucrose gradient fractionation and immunoprecipitation to isolate Complex I from mouse brain and a cultured rat mesencephalic dopaminergic neuronal cell line. Both protocols are capable of purifying Complex I from small amounts of rodent tissue and cell cultures. Blue Native gel electrophoresis, one-dimensional and two-dimensional SDS-PAGE were employed to assess the purity and composition of isolated Complex I followed by extensive mass spectrometric characterization. Altogether, 41 of 45 rodent Complex I subunits achieved MS/MS sequence coverage. To our knowledge, this study provides the first detailed mass spectrometric analysis of neuronal Complex I proteins and provides a means to investigate the role of cysteine oxidation and other posttranslational modifications in pathologies associated with mitochondrial dysfunction.

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