Brae M. Bigge

The process of deciding whether a candidate actin homolog represents a “true” actin is tricky. We propose clear and data-driven criteria to define actin that highlight the functional importance of this protein while accounting for phylogenetic diversity.

The ProteinCartography pipeline identifies proteins related to a query protein using sequence- and structure-based searches, compares all protein structures, and creates a navigable map that can be used to look at protein relationships and make hypotheses about function.

We've applied ProteinCartography, a tool for protein family exploration, to the well-studied actin family. We’re able to categorize actins and related proteins into distinguishable functional buckets, and we uncovered some surprising hypotheses that could prompt further study.

We outline a comparative approach to investigate protein function by correlating the presence or absence of a protein with species-level phenotypes. We applied this strategy to a novel actin isoform in fungi but didn’t find an association with any of the phenotypes we considered.

To test its utility in analyzing biological samples, we built an open-source Raman spectrometer and collected spectra from chilis, beer, and algae. We could stratify samples, classify replicates, and link spectra with quantitative traits of beer (ABV) and chilis (perceived heat).

We’re using the well-studied superfamily of small monomeric GTPases, the Ras GTPases, to evaluate our structure-based clustering tool, ProteinCartography. We’re seeking feedback on working with this protein family and determining which individual proteins to study.

We aim to validate ProteinCartography, a tool for structure-based protein clustering, by evaluating two foundational hypotheses: that proteins within a cluster have similar functions and proteins in different clusters have differing functions.

The human deoxycytidine kinase, a member of the nucleoside salvage pathway, has been studied extensively. We’ll use this family to assess our structure-based protein clustering tool, ProteinCartography. We’d love feedback on how we might work with this protein for validation.

Inspired by wasps co-opting viral capsids to deliver genes to the caterpillars they parasitize, we looked for capsid-like proteins in other species. We found capsid homologs in ticks and other parasites, suggesting this phenomenon could be wider spread than previously known.