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.
Prachee Avasthi, Cameron Dale MacQuarrie, and Atanas Radkov
PA
BB
Published: Mar 29, 2023
Treating P. tricornutum cells with serine endopeptidases or certain cytoskeletal inhibitors induces the formation of cell wall-free protoplasts and suggests a novel role for actin and myosin in preventing protoplast formation.
Prachee Avasthi, Brae M. Bigge, Feridun Mert Celebi, Keith Cheveralls, Jase Gehring, Erin McGeever, Gilad Mishne, Atanas Radkov, and 1 more
PA
BB
KC
RD
+14
Published: Sep 29, 2023
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.
Prachee Avasthi, Feridun Mert Celebi, and Elizabeth A. McDaniel
PA
BB
+3
Published: Oct 06, 2023
Only some bacteria accumulate substantial amounts of polyphosphate (polyP). We thought that despite sequence divergence, polyP synthesis enzymes in these bacteria might have similar structures. We found this is sometimes true but doesn’t fully explain the phenomenon.
Prachee Avasthi, Ben Braverman, Tara Essock-Burns, Galo Garcia III, Cameron Dale MacQuarrie, David Q. Matus, David G. Mets, and Ryan York
PA
BB
TE
+7
Published: Jun 23, 2023
We’re crossing C. reinhardtii and C. smithii algae for high-throughput genotype-phenotype mapping. In preparation, we’re comparing the parents to uncover unique species-specific phenotypes.
Prachee Avasthi, Brae M. Bigge, Dennis A. Sun, and Ryan York
PA
BB
TR
DS
+1
Published: Feb 14, 2024
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.
Prachee Avasthi, Brae M. Bigge, Ilya Kolb, David G. Mets, Manon Morin, Austin H. Patton, and Ryan York
PA
AB
BB
IK
DM
+5
Published: Mar 06, 2024
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.