In our Facility, we use mass spectrometry to analyze and characterize biomolecules such as proteins and DNA. We also maintain a small molecule unit that analyzes chemical drug candidates synthesized by various researchers. We provide scientific and technical support in these areas. Furthermore, we successfully promote collaborations to increase our understanding of fundamental biological processes, mostly related but not limited to diabetes, digestive and kidney diseases. We concluded and published our investigations of the secretory proteome of adipocytes: A total of 84 proteins was identified as secreted adipokines. This large number of secretory proteins comprise multiple functional categories. Comparative proteomics of 18O proteolytic labeling allows the detection of different levels of many secreted proteins as exemplified by the difference between basal and insulin treatment of adipose cells. Our proteomic approach is able to identify and quantify the comprehensive secretory proteome of adipose cells. Thus, our data support the endocrine role of adipose cells in pathophysiological states through the secretion of signaling molecules. This successful approach is currently being adapted to investigate the secretory proteome of podocytes from kidneys. As for the adipocytes, we expect to gain further insights in the fundamentals of podocyte secretion. We also concluded a study on the cerebrospinal fluid proteome associated with chronic fatigue and related syndromes, which yielded the first predictive biomarkers for these syndromes. Using a logisitic model, we found that detection of >1 of a select set of 5 CFS-related proteins predicted CFS status with 80% concordance. We also expanded on our previously established protein-ligand interaction studies using HIV integrase as an important target for antiviral therapies. We found that pyridoxal-5-phosphate binds to a unique lysine (K244), located in the C-terminal domain, which signifantly impairs the formation of IN-DNA complex. Using a similar footprinting method, we also studied the hyperphosphorylation-induced conformational changes of full length native and hyperphosphorylated hRPA (human replication protein A). We found that three residues in the DNA binding domain B (K343, R335 and R382) were significantly shielded by hyperphosphorylation when compared to native hRPA. This led us to conclude that significant conformational changes involving the ssDNA binding cleft are induced after hyperphosphorylation. We provided analyses to more than 50 principal investigators of our Institute. Some of them, like the identification of a novel protein that forms complexes with MATER (Maternal Antigen That Embryos Require) are considered significant contributions. Many of these analyses are considered to be service and do not result in any publication.
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