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Full-Text Articles in Computational Biology
Structural Characterization Of Human Uch37, E. S. Burgie, C. Bingman, Ameet Soni, G. N. Phillips Jr.
Structural Characterization Of Human Uch37, E. S. Burgie, C. Bingman, Ameet Soni, G. N. Phillips Jr.
Computer Science Faculty Works
Uch37 is a de-ubiquitylating enzyme that is functionally linked with the 26S proteasome via Rpn13, and is essential for metazoan development. Here, we report the X-ray crystal structure of full-length human Uch37 at 2.95 Å resolution. Uch37's catalytic domain is similar to those of all UCH enzymes characterized to date. The C-terminal extension is elongated, predominantly helical and contains coiled coil interactions. Additionally, we provide an initial characterization of Uch37's oligomeric state and identify a systematic error in previous analyses of Uch37 activity. Taken together, these data provide a strong foundation for further analysis of Uch37's several functions.
Probabilistic Ensembles For Improved Inference In Protein-Structure Determination, Ameet Soni, J. Shavlik
Probabilistic Ensembles For Improved Inference In Protein-Structure Determination, Ameet Soni, J. Shavlik
Computer Science Faculty Works
Protein X-ray crystallography — the most popular method for determining protein structures — remains a laborious process requiring a great deal of manual crystallographer effort to interpret low-quality protein images. Automating this process is critical in creating a high-throughput protein-structure determination pipeline. Previously, our group developed ACMI, a probabilistic framework for producing protein-structure models from electron-density maps produced via X-ray crystallography. ACMI uses a Markov Random Field to model the three-dimensional (3D) location of each non-hydrogen atom in a protein. Calculating the best structure in this model is intractable, so ACMI uses approximate inference methods to estimate the optimal structure. …