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Technology Center for Networks & Pathways

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In Memoriam:  Professor Robert "Bob" J. Cotter  passed away unexpectedly in November (2012). A memorial symposium was held at the JHU Medical School Campus on Wednesday, November 20, 2013. Please see TCNP News for more details.

View TCNP news.

The amino acid lysine is emerging as important in a wide range of biological processes, from control of gene expression to recycling of proteins. Lysine is unique among the amino acids because it can be modified in many ways, ranging from the addition of small functional groups to entire proteins, and these modifications have profound biological effects. For example, protein modification of lysines found on DNA-coiling histones is critical for epigenetic control of gene expression, which itself dictates the expression of the proteome in all cells. Other lysine modifications include acetylation, methylation, ubiquitylation and sumoylation. Among these, ubiquitylation is most well-understood; it controls proteins' life, death and trafficking, among other roles.

In general, these modifications and the pathways regulating their interplay are poorly understood. Studying these networks is no small task -- many lysine-modifying proteins have multiple substrates and are encoded by multi-gene families with redundant activities.

Through the TCNP project, these signaling networks and pathways have been dissected by developing and applying genetic and computational approaches, proteomics technologies, mass spectrometry technologies, single-cell profiling and other novel methods to detect, quantify and monitor lysine modifications.

Among the specific technologies that were developed and used are: innovative proteomics technology, protein microarrays, and a new affinity ligand technology for identifying novel acetyltransferases; innovative mass spectrometry technologies, including ones to quantify the dynamics of lysine modification in response to biological stimuli; a unique instrumentation system to profile lysine modification in single cells. These experimental approaches may permit dynamic assessment of epigenetic changes that occur in individual cells as they develop or age, or as cancer progresses. The TCNP project integrated "driving biological projects" centered on lysine acetylation, methylation, and ubiquitylation, training and technology dissemination efforts, and technology development. Because lysine modification is intertwined with human health, aging and disease at many levels, what we learn will have far-reaching implications.

For more information, please contact Joel Bader and Heng Zhu.