Junmin Peng - US grants

DESCRIPTION (PROVIDED BY APPLICANT) Ubiquitin (Ub) is an essential signal molecule regulating protein degradation, localization and other activities. Generally the C-terminus of the Ub molecule is covalently conjugated to lysine residues of protein substrates by the E1/E2/E3 reaction cascade, and the modification is reversed by the action of deubiquitinating enzymes (DUBs). PolyUb chains can be further assembled on the substrates by the linkage between lysine groups of the first Ub molecule and the C-terminus of the next. Our current proteomic analysis revealed that all seven lysine groups on the Ub molecule can be utilized for the formation of polyUb chains, including Lys6, Lys11, Lys27, Lys29, Lys33, Lys48, and Lys63. We propose that the formation of functionally distinct polyUb chains is a regulatory step for ubiquitination and deubiquitination. To examine the function of these polyUb linkages, we will first develop a mass spectrometry technology for quantifying the abundance of all seven polyUb linkages, and then study the catalytic specificity between DUBs and polyUb chain topology. Moreover, we will focus on defining the function of Lys11 polyUb chains. Our studies will lead to the development of general proteomic tools for polyUb chain topology and better understanding of the diversity and function of polyUb chains.

The long-term goal of this research is to identify and validate the proteomic changes in the development of neurodegeneration. Alzheimer's disease (AD) and Parkinson's disease (PD) are the two most common neurodegenerative diseases. Although AD and PD are considered distinct disorders, significant overlap occurs. Mild cognitive impairment (MCI) is a transient state between healthy aging and dementia, often representing a very early stage of cognitive decline associated with a degenerative dementing illness. Histopathologically, accumulation of abnormal proteins has been recognized as hallmarks of neurodegeneration in both AD and PD, suggesting that shared molecular mechanisms may mediate the pathogenesis of neurodegeneration in AD, PD, and AD/PD overlap disorders. Using novel mass spectrometry-based technologies, we will test our central hypothesis: changes in the ubiquitinated proteome and the postsynaptic proteome will reveal molecular commonality among AD, PD, and AD/PD overlap syndromes, and changes in protein patterns will accompany the evolution of disease from MCI to AD. We will use clinically well-characterized human postmortem samples to evaluate protein pattern changes in the ubiquitinated proteome and in the postsynaptic density (PSD). Samples of MCI, AD, PD and AD/PD overlap disease will be analyzed and compared to discover shared protein patterns. These protein changes will be further confirmed in a large set of disease cases. The results will enable the identification of potential biomarkers and provide critical molecular maps for subsequent studies of neurodegeneration.

DESCRIPTION (provided by applicant): The goal of this research is to develop a proteomics approach to simultaneously quantify hundreds of proteins and their modifications in the postsynaptic density (PSD). PSD is a specialized membrane structure that is essential for neuronal communication, and dynamic protein changes in the PSD play a pivotal role in synapse plasticity. However, there is no method available to monitor the global protein changes in the structure under physiological and pathological conditions. Recently, we have made progress in developing novel mass spectrometry-based technologies to systematically identify protein elements in the PSD, and we propose to develop a quantitative approach for all proteins of interest. Basically, the approach will utilize an isotopic-labeled synthetic peptide for each protein. Hundreds of labeled peptides will be pooled together and serve as universal standards for PSD proteome. The strategy bypasses the requirement for antibodies and the measurements will be highly specific. In addition, the method provides absolute quantification of targeted proteins and protein modifications, enabling the stoichiometry analysis for protein complexes and protein modifications. This tool will allow quick evaluation of the PSD proteomic changes in various samples ranging from neuronal cell cultures to animal models of neurological disease and drug abuse.

[unreadable] DESCRIPTION (provided by applicant): [unreadable] The goal of this research is to develop a proteomics approach to isolate and quantify ubiquitinated proteome from tumor tissues based on high resolution mass spectrometry. Ubiquitin modification regulates a variety of cellular events in eukaryotic cells by covalently attaching ubiquitin to target substrates. The dysregulation of ubiquitin pathways has been involved in the pathogenesis of many types of cancers. However, there is no reliable method to globally analyze ubiquitinated proteins in cancer samples. Recently, we have made progress in developing novel mass spectrometry-based technologies to analyze ubiquitinated proteome in yeast. Here we propose to develop a generic method to capture and quantify ubiquitinated proteome from mammalian cells. The approach will utilize affinity chromatography composed of ubiquitin-binding domains. An array of fusion proteins with various ubiquitin-binding domains will be examined to optimize the binding affinity in order to improve the method with respect to the yield and purity of ubiquitin substrates. The isolated ubiquitinated proteins will be further analyzed by mass spectrometry for the determination of protein identity and ubiquitination sites. Quantitative mass spectrometry strategies will be implemented to investigate the dynamics of ubiquitinated proteome. Once established, the method will be highly useful for profiling ubiquitinated proteome in mammalian samples including clinical tumor tissues. [unreadable] [unreadable] [unreadable]

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