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  1. Free, publicly-accessible full text available March 1, 2023
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  9. Musier-Forsyth, Karin (Ed.)
    RNA-binding proteins play crucial roles in various cellular functions, and contain abundant disordered protein regions. The disordered regions in RNA-binding proteins are rich in repetitive sequences, such as poly-K/R, poly-N/Q, poly-A, and poly-G residues. Our bioinformatic analysis identified a largely neglected repetitive sequence family we define as electronegative clusters (ENCs) that contain acidic residues and/or phosphorylation sites. The abundance and length of ENCs exceed other known repetitive sequences. Despite their abundance, the functions of ENCs in RNA-binding proteins are still elusive. To investigate the impacts of ENCs on protein stability, RNA-binding affinity, and specificity, we selected one RNA-binding protein, themore »ribosomal biogenesis factor 15 (Nop15) as a model. We found that the Nop15 ENC increases protein stability and inhibits nonspecific RNA binding, but minimally interferes with specific RNA binding. To investigate the effect of ENCs on sequence specificity of RNA binding, we grafted an ENC to another RNA-binding protein, Ser/Arg-rich splicing factor 3 (SRSF3). Using RNA Bind-n-Seq, we found that the engineered ENC inhibits disparate RNA motifs differently, instead of weakening all RNA motifs to the same extent. The motif site directly involved in electrostatic interaction is more susceptible to the ENC inhibition. These results suggest that one of functions of ENCs is to regulate RNA binding via electrostatic interaction. This is consistent with our finding that ENCs are also overrepresented in DNA-binding proteins, while underrepresented in halophiles, in which nonspecific nucleic acid binding is inhibited by high concentrations of salts.« less
    Free, publicly-accessible full text available July 9, 2022
  10. Existing network planning models for electric vehicle (EV) services usually treat the battery swap and the on-board supercharging as two independent processes. This study makes an early attempt to design an EV charging network where battery swap and supercharging are jointly coordinated. The swap and supercharge processes are characterized by Erlang B and Erlang C priority queues, respectively. A strategic location-allocation model is formulated to optimize the station sites, battery stock level, and the number of superchargers at chosen sites. Three design criteria, namely, battery state-of-charge, maximum service time, and power grid constraint, are simultaneously taken into account. Meta-heuristics algorithmsmore »incorporating Tabu search are developed to tackle the proposed non-linear mixed integer optimization model. Computational results on randomly generated instances show that the priority battery service scheme outperforms the pure battery swap station in terms of spare battery investment cost and charging flexibility. The case study on a real-world traffic network comprised of 0.714 million households further shows the efficacy and advantage of the dual battery charging process for ensuring state-of-charge, service time commitment, and network-wide grid stability.« less