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1. Dockground resource for protein recognition studies

   https://doi.org/10.1002/pro.4481  

   Collins, Keeley W.; Copeland, Matthew M.; Kotthoff, Ian; Singh, Amar; Kundrotas, Petras J.; Vakser, Ilya A. (December 2022, Protein Science)

   Abstract Structural information of protein–protein interactions is essential for characterization of life processes at the molecular level. While a small fraction of known protein interactions has experimentally determined structures, computational modeling of protein complexes (protein docking) has to fill the gap. TheDockgroundresource (http://dockground.compbio.ku.edu) provides a collection of datasets for the development and testing of protein docking techniques. Currently,Dockgroundcontains datasets for the bound and the unbound (experimentally determined and simulated) protein structures, model–model complexes, docking decoys of experimentally determined and modeled proteins, and templates for comparative docking. TheDockgroundbound proteins dataset is a core set, from which otherDockgrounddatasets are generated. It is devised as a relational PostgreSQL database containing information on experimentally determined protein–protein complexes. This report on theDockgroundresource describes current status of the datasets, new automated update procedures and further development of the core datasets. We also present a newDockgroundinteractive web interface, which allows search by various parameters, such as release date, multimeric state, complex type, structure resolution, and so on, visualization of the search results with a number of customizable parameters, as well as downloadable datasets with predefined levels of sequence and structure redundancy. 

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2. Characterization of promoter elements of isoprene‐responsive genes and the ability of isoprene to bind START domain transcription factors

   https://doi.org/10.1002/pld3.483  

   Weraduwage, Sarathi M.; Sahu, Abira; Kulke, Martin; Vermaas, Josh V.; Sharkey, Thomas D. (January 2023, Plant Direct)

   Abstract Isoprene has recently been proposed to be a signaling molecule that can enhance tolerance of both biotic and abiotic stress. Not all plants make isoprene, but all plants tested to date respond to isoprene. We hypothesized that isoprene interacts with existing signaling pathways rather than requiring novel mechanisms for its effect on plants. We analyzed the cis‐regulatory elements (CREs) in promoters of isoprene‐responsive genes and the corresponding transcription factors binding these promoter elements to obtain clues about the transcription factors and other proteins involved in isoprene signaling. Promoter regions of isoprene‐responsive genes were characterized using the Arabidopsis cis‐regulatory element database. CREs bind ARR1, Dof, DPBF, bHLH112, GATA factors, GT‐1, MYB, and WRKY transcription factors, and light‐responsive elements were overrepresented in promoters of isoprene‐responsive genes; CBF‐, HSF‐, WUS‐binding motifs were underrepresented. Transcription factors corresponding to CREs overrepresented in promoters of isoprene‐responsive genes were mainly those important for stress responses: drought‐, salt/osmotic‐, oxidative‐, herbivory/wounding and pathogen‐stress. More than half of the isoprene‐responsive genes contained at least one binding site for TFs of the class IV (homeodomain leucine zipper) HD‐ZIP family, such as GL2, ATML1, PDF2, HDG11, ATHB17. While the HD‐zipper‐loop‐zipper (ZLZ) domain binds to the L1 box of the promoter region, a special domain called the steroidogenic acute regulatory protein‐related lipid transfer, or START domain, can bind ligands such as fatty acids (e.g., linolenic and linoleic acid). We tested whether isoprene might bind in such a START domain. Molecular simulations and modeling to test interactions between isoprene and a class IV HD‐ZIP family START‐domain‐containing protein were carried out. Without membrane penetration by the HDG11 START domain, isoprene within the lipid bilayer was inaccessible to this domain, preventing protein interactions with membrane bound isoprene. The cross‐talk between isoprene‐mediated signaling and other growth regulator and stress signaling pathways, in terms of common CREs and transcription factors could enhance the stability of the isoprene emission trait when it evolves in a plant but so far it has not been possible to say what how isoprene is sensed to initiate signaling responses. 

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3. ProTaxoVis—protein taxonomic visualisation of presence

   https://doi.org/10.1186/s12859-025-06146-9  

   Hsieh, Yin-Chen; Bockwoldt, Mathias; Heiland, Ines (December 2025, BMC Bioinformatics)

   Abstract Background:Protein presence information is an essential component of biological pathway identification. Presence of certain enzymes in an organism points towards the metabolic pathways that occur within it, whereas the absence of these enzymes indicates either the existence of alternative pathways or a lack of these pathways altogether. The same inference applies to regulatory pathways such as gene regulation and signal transduction. Protein presence information therefore forms the basis for biological pathway studies, and patterns in presence-absence across multiple organisms allow for comparative pathway analyses. Results:Here we present ProTaxoVis, a novel bioinformatic tool that extracts protein presence information from database queries and maps it to a taxonomic tree or heatmap. ProTaxoVis generates a large-scale overview of presence patterns in taxonomic clades of interest. This overview reveals protein distribution patterns, and this can be used to deduce pathway evolution or to probe other biological questions. ProTaxoVis combines and filters sequence query results to extract information on the distribution of proteins and translates this information into two types of visual outputs: taxonomic trees and heatmaps. The trees supplement their topology with scaled pie-chart representations per node of the presence of target proteins and combinations of these proteins, such that patterns in taxonomic groups can easily be identified. The heatmap visualisation shows presence and conservation of these proteins for a user-determined set of species, allowing for a more detailed view over a larger group of proteins as compared to the trees. ProTaxoVis also allows for visual quality checks of hits based on a coverage plot and a length histogram, which can be used to determine e-value and minimum protein length cutoffs. Tabular output of resulting data from the query, combined, and heatmap building step are saved and easily accessible for further analyses. Conclusions:We evaluate our tool with the phosphoribosyltransferases, a transferase enzyme family with notable distribution patterns amongst organisms of varying complexities and across Eukaryota, Bacteria, and Archaea. ProTaxoVis is open-source and available at:https://github.com/MolecularBioinformatics/ProTaxoVis. 

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4. RCSB Protein Data Bank: improved annotation, search and visualization of membrane protein structures archived in the PDB

   https://doi.org/10.1093/bioinformatics/btab813  

   Bittrich, Sebastian; Rose, Yana; Segura, Joan; Lowe, Robert; Westbrook, John D.; Duarte, Jose M.; Burley, Stephen K.; Valencia, ed., Alfonso (December 2021, Bioinformatics)

   Abstract MotivationMembrane proteins are encoded by approximately one fifth of human genes but account for more than half of all US FDA approved drug targets. Thanks to new technological advances, the number of membrane proteins archived in the PDB is growing rapidly. However, automatic identification of membrane proteins or inference of membrane location is not a trivial task. ResultsWe present recent improvements to the RCSB Protein Data Bank web portal (RCSB PDB, rcsb.org) that provide a wealth of new membrane protein annotations integrated from four external resources: OPM, PDBTM, MemProtMD and mpstruc. We have substantially enhanced the presentation of data on membrane proteins. The number of membrane proteins with annotations available on rcsb.org was increased by ∼80%. Users can search for these annotations, explore corresponding tree hierarchies, display membrane segments at the 1D amino acid sequence level, and visualize the predicted location of the membrane layer in 3D. Availability and implementationAnnotations, search, tree data and visualization are available at our rcsb.org web portal. Membrane visualization is supported by the open-source Mol* viewer (molstar.org and github.com/molstar/molstar). Supplementary informationSupplementary data are available at Bioinformatics online. 

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5. Temporal transcriptomic profiling elucidates sorghum defense mechanisms against sugarcane aphids

   https://doi.org/10.1186/s12864-023-09529-5  

   Puri, Heena; Grover, Sajjan; Pingault, Lise; Sattler, Scott E.; Louis, Joe (August 2023, BMC Genomics)

   Abstract BackgroundThe sugarcane aphid (SCA;Melanaphis sacchari) has emerged as a key pest on sorghum in the United States that feeds from the phloem tissue, drains nutrients, and inflicts physical damage to plants. Previously, it has been shown that SCA reproduction was low and high on sorghum SC265 and SC1345 plants, respectively, compared to RTx430, an elite sorghum male parental line (reference line). In this study, we focused on identifying the defense-related genes that confer resistance to SCA at early and late time points in sorghum plants with varied levels of SCA resistance. ResultsWe used RNA-sequencing approach to identify the global transcriptomic responses to aphid infestation on RTx430, SC265, and SC1345 plants at early time points 6, 24, and 48 h post infestation (hpi) and after extended period of SCA feeding for 7 days. Aphid feeding on the SCA-resistant line upregulated the expression of 3827 and 2076 genes at early and late time points, respectively, which was relatively higher compared to RTx430 and SC1345 plants. Co-expression network analysis revealed that aphid infestation modulates sorghum defenses by regulating genes corresponding to phenylpropanoid metabolic pathways, secondary metabolic process, oxidoreductase activity, phytohormones, sugar metabolism and cell wall-related genes. There were 187 genes that were highly expressed during the early time of aphid infestation in the SCA-resistant line, including genes encoding leucine-rich repeat (LRR) proteins, ethylene response factors, cell wall-related, pathogenesis-related proteins, and disease resistance-responsive dirigent-like proteins. At 7 days post infestation (dpi), 173 genes had elevated expression levels in the SCA-resistant line and were involved in sucrose metabolism, callose formation, phospholipid metabolism, and proteinase inhibitors. ConclusionsIn summary, our results indicate that the SCA-resistant line is better adapted to activate early defense signaling mechanisms in response to SCA infestation because of the rapid activation of the defense mechanisms by regulating genes involved in monolignol biosynthesis pathway, oxidoreductase activity, biosynthesis of phytohormones, and cell wall composition. This study offers further insights to better understand sorghum defenses against aphid herbivory. 

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