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Publications of the Week

Mapping Functional Regions of Essential Bacterial Proteins with Dominant-Negative Protein Fragments

By July 7, 2022No Comments

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This week we profile a recent publication in PNAS from Dr. Andrew Savinov (pictured, left) and the laboratory of Dr. Stanley Fields (right) at UW.

Can you provide a brief overview of your lab’s current research focus?

The major focus of our laboratory has been the development and implementation of new technologies, most of them centered on protein analysis. For the last few years, we have been working on adaptations of deep mutational scanning, a method that uses high throughput DNA sequence reads to assess the functions of protein variants. Projects include approaches to extend deep mutational scanning into living organisms and to covalently link proteins to nucleic acid barcodes to allow biochemical assays of protein variants.

What is the significance of the findings in this publication?

Peptide fragments can inhibit the interactions of the full-length proteins from which the fragments derive. We employed a high throughput assay to measure how the growth of E. coli is affected by fragments that derive from each of ten essential E. coli proteins. We used the resulting data to decipher general principles for how this type of inhibition occurs.

What are the next steps for this research?

Additional work based on this research may go in multiple directions. In one, fragments of proteins orthologous to the E. coli ones and derived from other bacteria, particularly human pathogens, can be tested to determine whether similar fragments inhibit the growth of these other bacteria. In another, it may be feasible to develop methods for the identification of inhibitory fragments on a proteome-wide basis. In a third, assays for inhibiting the growth of bacteria can be carried out under multiple conditions, such as in the presence of drugs.

If you’d like us to mention your funding sources, please list them.

NRSA fellowship and grants from the NIH.

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