Ginell, G. M. | bioRxiv Science

bioRxiv2022

SHEPHARD: a modular and extensible software architecture for analyzing and annotating large protein datasets

The emergence of high-throughput experiments and high-resolution computational predictions has led to an explosion in the quality and volume of protein sequence annotations at proteomic scales. Unfortunately, integrating and analyzing complex sequence annotations remains logistically challenging. Here we present SHEPHARD, a software package that makes large-scale integrative protein bioinformatics trivial. SHEPHARD is provided as a stand-alone package and with a pre-compiled set of human annotations in a Google Colab notebook.

bioinformatics↗

bioRxiv2022

The formation of a fuzzy complex in the negative arm regulates the robustness of the circadian clock.

The circadian clock times cellular processes to the day/night cycle via a Transcription-Translation negative Feedback Loop (TTFL). However, a mechanistic understanding of the negative arm in both the timing of the TTFL and its control of output is lacking. We posited that the formation of negative-arm protein complexes was fundamental to clock regulation stemming from the negative arm. Using a modified peptide microarray approach termed Linear motif discovery using rational design (LOCATE), we characterized the interaction of the disordered negative-arm clock protein FREQUENCY to its partner protein FREQUENCY-Interacting RNA helicase. LOCATE identified a specific Short Linear Motif (SLiM) and interaction "hotspot" as well as positively charged "islands" that mediate electrostatic interactions, suggesting a model where negative arm proteins form a "fuzzy" complex essential for clock timing and robustness. Further analysis revealed that the positively charged islands were an evolutionarily conserved feature in higher eukaryotes and contributed to proper clock function.

molecular biology↗