Michael J. Sweredoski

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Intrinsically disordered regions in proteins are relatively frequent and important for our understanding of molecular recognition and assembly, and protein structure and function. From an algorithmic standpoint, flagging large disordered regions is also imortant for ab inito protein structure prediction methods. Here we first extract a curated,(More)
Parkin, an E3 ubiquitin ligase implicated in Parkinson's disease, promotes degradation of dysfunctional mitochondria by autophagy. Using proteomic and cellular approaches, we show that upon translocation to mitochondria, Parkin activates the ubiquitin-proteasome system (UPS) for widespread degradation of outer membrane proteins. This is evidenced by an(More)
MOTIVATION Accurate prediction of B-cell epitopes is an important goal of computational immunology. Up to 90% of B-cell epitopes are discontinuous in nature, yet most predictors focus on linear epitopes. Even when the tertiary structure of the antigen is available, the accurate prediction of B-cell epitopes remains challenging. RESULTS Our predictor,(More)
Protein domains are the structural and functional units of proteins. The ability to parse protein chains into different domains is important for protein classification and for understanding protein structure, function, and evolution. Here we use machine learning algorithms, in the form of recursive neural networks, to develop a protein domain predictor(More)
  • Colleen A. McHugh, Chun-Kan Chen, Amy Chow, Christine F. Surka, Christina Tran, Patrick McDonel +11 others
  • 2015
Many long non-coding RNAs (lncRNAs) affect gene expression 1 , but the mechanisms by which they act are still largely unknown 2. One of the best-studied lncRNAs is Xist, which is required for transcriptional silencing of one X-chromosome during development in female mammals 3,4. Despite extensive efforts to define the mechanism of Xist-mediated(More)
Accurate prediction of B-cell epitopes has remained a challenging task in computational immunology despite several decades of research. Only 10% of the known B-cell epitopes are estimated to be continuous, yet they are often the targets of predictors because a solved tertiary structure is not required and they are integral to the development of peptide(More)
MOTIVATION Transmembrane beta-barrel (TMB) proteins are embedded in the outer membranes of mitochondria, Gram-negative bacteria and chloroplasts. These proteins perform critical functions, including active ion-transport and passive nutrient intake. Therefore, there is a need for accurate prediction of secondary and tertiary structure of TMB proteins.(More)
Local protein synthesis and its activity-dependent modulation via dopamine receptor stimulation play an important role in synaptic plasticity - allowing synapses to respond dynamically to changes in their activity patterns. We describe here the metabolic labeling, enrichment, and MS-based identification of candidate proteins specifically translated in(More)
The human genome encodes 69 different F-box proteins (FBPs), each of which can potentially assemble with Skp1-Cul1-RING to serve as the substrate specificity subunit of an SCF ubiquitin ligase complex. SCF activity is switched on by conjugation of the ubiquitin-like protein Nedd8 to Cul1. Cycles of Nedd8 conjugation and deconjugation acting in conjunction(More)
BACKGROUND The proteasome is a multi-subunit protein machine that is the final destination for cellular proteins that have been marked for degradation via an ubiquitin (Ub) chain appendage. These ubiquitylated proteins either bind directly to the intrinsic proteasome ubiqutin chain receptors Rpn10, Rpn13, or Rpt5, or are shuttled to the proteasome by Rad23,(More)