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opencc-by-4.0Apr 2019View details →

X-ray diffraction images for Adenylate kinase from M. thermolithotrophicus.

Anomalous data collected at ESRF (Grenoble, France) using beamline ID23-1. The crystal was in the presence of the crystallophore Tb-Xo4.   Related Publication: Engilberge et al. (2019) Data collection:   Detector: PILATUS 6M.    OSCILLATION_RANGE= 0.1000   X-RAY_WAVELENGTH=  1.64862   DETECTOR_DISTANCE= 183.94

opencc-by-4.0Aug 2024View details →

Identification of Mitoxantrone as a Potent Inhibitor of Transcriptional Cyclin-Dependent Kinase 7 via Structure-based Virtual Screening

Data associated with the manuscript - Identification of Mitoxantrone as a Potent Inhibitor of Transcriptional Cyclin-Dependent Kinase 7 via Structure-based Virtual Screening

opencc-by-4.0Aug 2024View details →

All tandem kinase proteins from 104 plant genomes

Open the record for dataset details and reuse information.

opencc-by-4.0Apr 2024View details →

Predicted protein-protein interactions of the human tyrosine kinase Lck by AF2Complex

Structural models and Supplementary data described in the publication: Predicting protein interactions of the kinase Lck critical to T cell modulation Structure (Cell Press), 2024 Reference Authors: Mu Gao and Jeffrey Skolnick screening_results -- Virtual PPI screening results of the protein kinase Lck (SH3-SH2 domains as the bait). predicted structural models.zip -- Compressed structural models described in the publication. af2c_input_features -- Input features used to predict protein complex models with AF2Complex.

opencc-by-4.0Sep 2024View details →

Regulation of minimal spindle midzone organization by mitotic kinases

This depository contains the raw data for mass-spectrometry that were used in the research article Regulation of minimal spindle midzone organization by mitotic kinases by W.M.Lim et al. Nat. Comm. 2024. These data (single set) are used in this work shown in Fig 1C and supplementary figure 1C.

opengpl-3.0-or-laterSep 2024View details →

Code for Regulation of minimal spindle midzone organization by mitotic kinases

This depository contains the simulation files used in the research article 'Regulation of minimal spindle midzone organization by mitotic kinases'.

opencc-by-4.0Aug 2021View details →

X-ray diffraction images of juvenile hormone diol kinase from the silk worm Bombyx mori

X-ray diffraction images of juvenile hormone diol kinase (JHDK) from the silk worm Bombyx mori

opencc-zeroSep 2021View details →

Influence of YES1 kinase and tyrosine phosphorylation on the activity of OCT1

Organic cation transporter 1 (OCT1) is a transporter that regulates the hepatic uptake and subsequent elimination of diverse cationic compounds. Although OCT1 has been involved in drug-drug interactions and causes pharmacokinetic variability of many prescription drugs, details of the molecular mechanisms that regulate the activity of OCT1 remain incompletely understood. Based on an unbiased phospho-proteomics screen, we identified OCT1 as a tyrosine-phosphorylated transporter, and functional validation studies using genetic and pharmacological approaches revealed that OCT1 is highly sensitive to small molecules that target the protein kinase YES1, such as dasatinib. In addition, we found that dasatinib can inhibit hepatic OCT1 function in mice as evidenced from its ability to modulate levels of isobutyryl L-carnitine, a hepatic OCT1 biomarker identified from a targeted metabolomics analysis. These findings provide novel insight into the post-translational regulation of OCT1 and suggest that caution is warranted with polypharmacy regimes involving the combined use of OCT1 substrates and kinase inhibitors that target YES1.

opencc-zeroFeb 2022View details →

Data from: SNF1-related protein kinase 1: the many-faced signaling hub regulating developmental plasticity in plants

The Snf1-Related Protein Kinase 1 (SnRK1) is the plant homolog of the heterotrimeric AMP-activated Protein Kinase/ Sucrose Non-Fermenting 1 (AMPK/Snf1), which works as a major regulator of growth under nutrient-limiting conditions in eukaryotes. Along with its conserved role as a master regulator of sugar starvation responses, SnRK1 is involved in controlling the developmental plasticity and resilience under diverse environmental conditions in plants. In this review, through mining and analyzing the interactome and phosphoproteome data of SnRK1, we are highlighting its role in fundamental cellular processes such as gene regulation, protein synthesis, primary metabolism, protein trafficking, nutrient homeostasis, autophagy, etc. Along with the well-characterized molecular interaction in SnRK1 signaling, our analysis highlights several unchartered regions of SnRK1 signaling in plants such as its possible communication with chromatin remodelers, histone modifiers, inositol phosphate signaling, etc. We also discuss potential reciprocal interactions of SnRK1 signaling with other signaling pathways and cellular processes, which could be involved in maintaining flexibility and homeostasis under different environmental conditions. Overall, this review provides a comprehensive overview of the SnRK1 signaling network in plants and suggests many novel directions for future research.

opencc-by-4.0Sep 2022View details →

"The prolactin receptor scaffolds Janus kinase 2 via co-structure formation with phosphoinositide-4,5-bisphosphate" -- MD Trajectories

MD trajectories and related files for the simulations related to the work: "The prolactin receptor scaffolds Janus kinase 2 via co-structure formation with phosphoinositide-4,5-bisphosphate" by Araya-Secchi R., Bugge K. and Seiffert et al.  This dataset contains: 1) Trajectories of CG-MD simulations of PRLR-LID1 in lipid bilayers with POPC on the upper leaflet and two compositions on the lower leaflet: POPC:POPS:PIP2 80:10:10 and 90:5:5. These simulations were performed using the open beta version of the Martini 3 (3.b3.2) force field modified to increase the strength of Protein-water interactions by 10% (m3pws10). 2) Trajectory of the all-atom simulation of the JAK2-FERM-SH2 + PRLR-LID1 complex in solution. 3) Trajectories of CG-MD simulations of the JAK2-FERM-SH2 + PRLR-LID1 complex near a POPC:POPS (70:30) bilayer (8 initial conformations) performed using the Martini2 forcefield. 4) Trajectories of CG-MD simulations of the JAK2-FERM-SH2 + PRLR-LID1 complex near a POPC:POPS:PIP2 (80:10:10) bilayer (16 initial conformations) performed using the Martini2 forcefield.

opencc-by-4.0Feb 2023View details →

ActTemp+sMSA dataset of "Biasing AlphaFold2 to predict GPCRs and Kinases with user-defined functional or structural properties"

PDB models generated with the protocol described in "Biasing AlphaFold2 to predict GPCRs and Kinases with user-defined functional or structural properties"

opencc-by-4.0May 2022View details →

Salt-inducible kinase 3 protects tumor cells from cytotoxic T-cell attack by promoting TNF-induced NF-κB activation

WHAT IS ALREADY KNOWN ON THIS TOPIC <ul> <li> Tumor-intrinsic resistance to T cell (TC)-released cytokines, such as tumor necrosis factor (TNF)-α, has recently emerged as a major mechanism of tumor immune evasion. Yet, a deeper characterization of the genes that are responsible for this effect is needed. </li> </ul> WHAT THIS STUDY ADDS <ul> <li> Salt-inducible kinase 3 (SIK3) is a novel regulator of tumor-intrinsic resistance to cytotoxic TC attack. </li> <li> SIK3 confers tumor cell protection from TC-released TNF by sustaining the expression of pro-survival and anti-apoptotic genes under the control of nuclear factor kappa B (NF-κB). </li> <li> A TNF/SIK3/NF-κB-mediated gene signature correlated with significantly reduced patient survival in pancreatic cancer. </li> </ul> HOW THIS STUDY MIGHT AFFECT RESEARCH, PRACTICE AND/OR POLICY <ul> <li> Pharmacological inhibition of SIK3 might be an effective strategy to sensitize cancer cells to TC-based immunotherapies by rewiring tumor cell responses to TC-secreted TNF. </li> </ul>

opencc-zeroMar 2023View details →

An unusual tandem kinase fusion protein confers leaf rust resistance in wheat

The introgression of chromosome segments from wild relatives is an established strategy to enrich crop germplasm with novel disease-resistance genes. Here, we use mutagenesis and transcriptome sequencing to clone the leaf rust resistance gene Lr9, which was introduced into bread wheat from the wild grass species Aegilops umbellulata. We establish that Lr9 encodes an unusual tandem kinase fusion protein. Long-read sequencing of a wheat Lr9 introgression line and the putative Ae. umbellulata Lr9 donor enabled us to assemble the ~28.4-Mb Lr9 translocation and to identify the translocation breakpoint. We likewise cloned Lr58, which was reportedly introgressed from Ae. triuncialis, but has an identical coding sequence compared to Lr9. Cytogenetic and haplotype analyses corroborate that the two genes originate from the same translocation event. Our work sheds light on the emerging role of kinase fusion proteins in wheat disease resistance, expanding the repertoire of disease-resistance genes for breeding.

opencc-zeroApr 2023View details →

Asymmetric evolution of protein domains in the leucine-rich repeat receptor-like kinase (LRR-RLK) family of plant developmental coordinators

The coding sequences of developmental genes are expected to be conserved over deep time, with cis-regulatory change driving the modulation of gene function. In contrast, proteins with roles in defense are expected to evolve rapidly, in molecular arms races with pathogens. However, some gene families include both developmental and defense genes. In these families, do the tempo and mode of evolution differ between developmental and defense genes, despite shared ancestry and structure? The leucine-rich repeat receptor-like kinase (LRR-RLKs) protein family includes many members with roles in plant development and defense, thus providing an ideal system for answering this question. LRR-RLKs are receptors that traverse plasma membranes. LRR domains bind extracellular ligands, RLK domains initiate intracellular signaling cascades in response to ligand binding. In LRR-RLKs with roles in defense, LRR domains evolve faster than RLK domains. To determine whether this asymmetry extends to developmental LRR-RLKs, we assessed evolutionary rates and tested for selection acting on eleven clades of LRR-RLK proteins, using deeply sampled protein trees. To assess functional evolution, we performed heterologous complementation assays using Arabidopsis thaliana (arabidopsis) LRR-RLK mutants. We found that the LRR domains of developmental LRR-RLK proteins evolved faster than their cognate RLK domains. LRR-RLKs with roles in development and defense had strikingly similar patterns of molecular evolution. Heterologous transformation experiments revealed that the evolution of developmental LRR-RLKs likely involves multiple mechanisms, including changes to cis-regulation, coding sequence evolution, and escape from adaptive conflict. Our results indicate similar evolutionary pressures acting on developmental and defense signaling proteins, despite divergent organismal functions. In addition, deep understanding of the molecular evolution of developmental receptors can help guide targeted genome engineering in agriculture.

opencc-by-4.0Jun 2023View details →

hERG Kv11.1 and Janus Kinase 2 interplay in retinoblastoma cell migration

Docking poses, Molecular Dynamics simulation starting structures and MD trajectories

Fig. 7 in Deciphering the roles of leucine-rich repeat receptor-like protein kinases (LRR-RLKs) in response to Fusarium wilt in the Vernicia fordii (Tung tree)

Fig. 7. The expression patterns of two gene pairs (i.e. Vf01G2125 and Vf03G1740, and Vf06G2687 and Vf10G1659) were generated by tandem duplication events. Numbers on the x-axis indicate the following: seeds at 10, 15, 20, 25, and 30 weeks after flowering (WAF; 10_WAF, 15_WAF, 20_WAF, 25_WAF, and 30_WAF), male flowers at 30, 20, 10, and 1 days before flowering (X1-X4), female flowers at 30, 20, 10, and 1 days before flowering (C1–C4), young leaves, roots, stems, and hermaphrodite (CX).

Fig. 5 in Deciphering the roles of leucine-rich repeat receptor-like protein kinases (LRR-RLKs) in response to Fusarium wilt in the Vernicia fordii (Tung tree)

Fig. 5. Expression of VfLRR-RLK gene family members. The heat map depicts expression profiles of VfLRR-RLKs in V. fordii (left) and V. montana (right) in response to Fusarium wilt at four infection stages: 0, uninfected stage; 1, 2 days after Fusarium wilt infection (dpi); 2, 8 dpi; 3, 13 dpi. F0–F3 indicated the expression of VfLRRRLKs in V. fordii during the infection stage (0, 1, 2, 3) by the pathogen Fusarium wilt; M0-M3 indicated the expression of VfLRR-RLKs in V. montana during the infection stage (0, 1, 2, 3) by the pathogen Fusarium wilt. The innermost circle represents 0, followed by 1, 2, and the outermost circle represents 3.

Fig. 4 in Deciphering the roles of leucine-rich repeat receptor-like protein kinases (LRR-RLKs) in response to Fusarium wilt in the Vernicia fordii (Tung tree)

Fig. 4. The similar expression patterns between duplicated VfLRR-RLK gene pairs during vegetative and reproductive development. Numbers on the x-axis indicate the following: seeds at 10, 15, 20, 25, and 30 weeks after flowering (WAF; 10_WAF, 15_WAF, 20_WAF, 25_WAF, and 30_WAF), male flowers at 30, 20, 10, and 1 days before flowering (X1-X4), female flowers at 30, 20, 10, and 1 days before flowering (C1–C4), young leaves, roots, stems, and hermaphrodite (CX).

Fig. 6 in Deciphering the roles of leucine-rich repeat receptor-like protein kinases (LRR-RLKs) in response to Fusarium wilt in the Vernicia fordii (Tung tree)

Fig. 6. The qRT-PCR experiments of four VfLRR-RLKs in response to Fusarium wilt. Black represents these VfLRR-RLKs in response to Fusarium wilt in V. fordii. Grey represents these VfLRR-RLKs in response to Fusarium wilt in V. montana. The numbers in the x-axis indicate the two stages of infection, as follows: 1, uninfected stage; 2, late stage of infection.

Fig. 3 in Deciphering the roles of leucine-rich repeat receptor-like protein kinases (LRR-RLKs) in response to Fusarium wilt in the Vernicia fordii (Tung tree)

Fig. 3. Collinearity relationships of LRR-RLKs in V. fordii and the other four Euphorbiaceae genomes. The chromosomes of different Euphorbiaceae species were depicted as blocks of different colors. Gene pairs with a syntenic relationship between different Euphorbiaceae species were connected by different colored lines. (For interpretation of the references to color in this figure legend, the reader is referred to the Web version of this article.)