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276 results for “protein domains”
Figure 3 in Solution structure of the first RRM domain of human spliceosomal protein SF3b49
Figure 3. – Diagrams of the first gill arch of the right side of Lutjanus madras. A: UPVMI 1084; B: MUFS 46214 (226.0 mm SL, Beruwala, Sri Lanka). Arrowhead and arrows indicate soft flesh-like mass and rudimentary gill rakers, respectively.
Production and purification of receptor-binding domain (RBD) of the Spike protein from a transiently transfected mammalian cell
<p> </p> <p>Production and purification of recombinant receptor-binding domain (RBD) of the Spike protein from a transiently transfected EXPI293 mammalian cell .</p>
X-ray structure ensemble refinement of the second bromodomain of Pleckstrin homology domain interacting protein (PHIP) (space group P21212)
<p>X-ray structure ensemble refinement of the second bromodomain of Pleckstrin homology domain interacting protein (PHIP) (space group P21212). Raw diffraction images are available on Zenodo: 10.5281/zenodo.4086066. A single conformer model was deposited in the Protein Data Bank under accession code <a href="https://www.ebi.ac.uk/pdbe/entry/pdb/7AV8">7AV8</a>. Refinement was carried out with <a href="https://www.phenix-online.org/documentation/reference/ensemble_refinement.html">phenix.ensemble_refinement</a> and the repository contains all input and output files:</p> <p>Input:</p> <ul> <li>mx8421v63_xPHIPAx1521_free.mtz</li> <li>refine9.pdb</li> </ul> <p>Output:</p> <ul> <li>PHIPA-P21212_ensemble_refinement_ensemble.geo</li> <li>PHIPA-P21212_ensemble_refinement_ensemble.pdb</li> <li>PHIPA-P21212_ensemble_refinement_ensemble.mtz</li> <li>PHIPA-P21212_ensemble_refinement_ensemble.log</li> </ul>
Simulated complex structures of the h-FBP21 tandem WW domain with proline-rich ligand extracted from SmB/B' core-splicing protein
<p>The tandem WW domain of the human formin-binding protein 21 (h-FBP21 tWW) consists of two WW domains separated by a flexible linker. It can bind target sequences in two different orientations and the flexibility of the linker additionally allows the two WW domains to adopt various relative orientations to each other. As consequence, the elucidation of possible complex structures for the h-FBP21 tWW is very challenging.</p> <p>Here, we present two complex structures for the h-FBP21 tWW and a proline-rich sequence from its natural binding partner, the core-splicing protein SmB/B’. Showing parallel (‘6’) and antiparallel (’14’) binding orientation, the two structures also differ in the relative positioning of the WW domains.</p> <p>For further instructions regarding the files, please refer to ‘README’.</p>
Movies of Interactions of the parts of the MeCP2 protein (MBD and NTD domains) in solution and interacting with a surface
<p>Four movies illustrating the interactions of the methyl-CpG binding domain (MBD; 486 amino acids) and N-terminal (NTD; residues 1-77 of the full length MeCp2) domains of the Methyl CpG binding protein 2 (MeCP2; residues 78-162 of the full length MeCp2) with a solid surface. The MBD domain is the only region of the MeCP2 protein.</p> <p>These movies are supplementary material to the manuscript (submitted)<br> <br> <strong>Structure and Dynamics of the Rett Syndrome Protein, MeCP2 </strong><br> Noriyuki Kodera, Anna A. Kalashnikova, Mary E. Porter-Goff, Catherine A. Musselman, Cecilia<br> Chávez-García, Mikko Karttunen, Borries Demeler, Tatiana G. Kutateladze, Toshio Ando,<br> and Jeffrey C. Hansen</p> <p> </p> <ul> <li>MBD in water was simulated for 3 microseconds. All the rest of the systems were simulated for 1 microsecond. The movies show the last 20 nanoseconds of the full length simulations. The movies come in pairs with the same system in solution and when a surface is present (as listed below)</li> <li>Files: <ul> <li> <p>MBD+NTD2_last20ns.mpg: MBD and NTD domains in solution (reference simulation).</p> </li> <li> <p>MBD+NTD_last20ns.mpg: MBD and NTD domains in the presence of a surface.</p> </li> <li> <p>MBD+halfNTD2_last20ns.mpg: MBD domain and half of the NTD domain in solution (reference simulation).</p> </li> <li> <p>MBD+halfNTD2_last20ns.mpg: MBD domain and half of the NTD domain in the presence of a surface.</p> </li> </ul> </li> </ul>
Crystal structure of the tandem kinase & triphosphate tunnel metalloenzyme domain module of the TTM1 protein from Arabidoposis thaliana in complex with inorganic phosphate and citric acid - 3lambda SeMAD dataset
<p>bzip2ed tar archive containing the diffraction images (Pilatus 2M-F detector, SLS beamline PXIII, collected on 19.12.2016) for 3 wavelength Se MAD experiment (infl, inflection point, peak, peak, rem, high energy remote) and the associated data processing files (xds_inf, xds_peak, xds_rem) </p>
Crystal structure of the tandem kinase & triphosphate tunnel metalloenzyme domain module of the TTM1 protein from Arabidoposis thaliana in complex with an adenosine nucleotide analog.
<p>bzip2ed tar archive containing the diffraction images (Pilatus 2M-F detector, SLS beamline PXIII, collected on 19.12.2016) and the associated data processing files (xds) </p>
Crystal structure of the tandem kinase & triphosphate tunnel metalloenzyme domain module of the TTM1 protein from Arabidoposis thaliana in complex with inorganic phosphate and citric acid - native dataset
<p>bzip2ed tar archive containing the diffraction images (Pilatus 2M-F detector, SLS beamline PXIII, collected on 19.12.2016) and the associated data processing files (xds) </p>
Amino acid sequences of RWP-RK domain containing proteins used for the construction of phylogenetic tree shown in Fig. 1
<p><span>The RWP-RK protein family is a group</span><span> of transcription factors containing </span><span>the RWP-RK DNA-binding domain. The RWP-RK DNA-binding domain is an ancient motif that emerged before the establishment of the Viridiplantae (green plants), which consist of green algae and land plants. This domain is mostly absent in other kingdoms but widely distributed in Viridiplantae. In green algae, a liverwort, and several angiosperms, RWP-RK proteins play essential roles in nitrogen responses and sexual reproduction-associated processes, which</span><span> </span><span>are seemingly unrelated phenomena but possible interdependent processes</span><span> </span><span>in autotrophs. Consistent with</span><span> related but diversified roles of the RWP-RK proteins in these organisms, the RWP-RK protein family appears to have expanded intensively, but independently, in the algal and land plant lineages. Therefore, bryophyte RWP-RK proteins occupy a unique position in the evolutionary process of establishing the RWP-RK protein family. In this review, we summarize current knowledge about the RWP-RK protein family in the Viridiplantae, and discuss the significance of bryophyte RWP-RK proteins in clarifying the relationship between diversification in the RWP-RK protein family and </span><span>procurement</span><span> of sophisticated mechanisms for adaptation to the terrestrial environment.</span></p>
Critical Domains for NACC2-NTRK2 Fusion Protein Activation
<p><strong>Critical Domains for NACC2-NTRK2 Fusion Protein Activation</strong>. <strong>Authors:</strong> Wei Yang, April N. Meyer, Zian Jiang, Xuan Jiang, and Daniel J. Donoghue. This dataset contains annotated raw images of immunoblots to accompany article, as well as files showing quantitation presented in various figures. <strong>Abstract: </strong>Neurotrophic receptor tyrosine kinases (NTRKs) belong to the receptor tyrosine kinase (RTK) family. NTRKs are responsible for the activation of multiple downstream signaling pathways that regulate cell growth, proliferation, differentiation, and apoptosis. NTRK-associated mutations often result in oncogenesis and lead to aberrant activation of downstream signaling pathways including MAPK, JAK/STAT, and PLCγ. This study characterizes the NACC2-NTRK2 oncogenic fusion protein that leads to pilocytic astrocytoma and pediatric glioblastoma. This fusion joins the BTB domain (Broad-complex, Tramtrack, and Bric-a-brac) domain of NACC2 (Nucleus Accumbens-associated protein 2) with the transmembrane helix and tyrosine kinase domain of NTRK2. We focus on identifying critical domains for the biological activity of the fusion protein. Mutations were introduced in the charged pocket of the BTB domain or in the monomer core, based on a structural comparison of the NACC2 BTB domain with that of PLZF, another BTB-containing protein. Mutations were also introduced into the NTRK2-derived portion to allow comparison of two different breakpoints that have been clinically reported. We show that activation of the NTRK2 kinase domain relies on multimerization of the BTB domain in NACC2-NTRK2. Mutations which disrupt BTB-mediated multimerization significantly reduce kinase activity and downstream signaling. The ability of these mutations to abrogate biological activity suggests that BTB domain inhibition could be a potential treatment for NACC2-NTRK2-induced cancers. Removal of the transmembrane helix leads to enhanced stability of the fusion protein and increased activity of the NACC2-NTRK2 fusion, suggesting a mechanism for the oncogenicity of a distinct NACC2-NTRK2 isoform observed in pediatric glioblastoma.</p>
Code and data for: Evolutionary assembly of the plant terrestrialization toolkit from protein domains
<p><strong>Evolutionary assembly of the plant terrestrialization toolkit from protein domains</strong></p> <ul> <li>We want to trace the evolutionary predisposition the green lineage had at the time of terrestrialization.</li> <li>Terrestrialization is a complete change in environment from water, and these acted like new and/or intensified stress factors on the green lineage.</li> <li>Thus, in order to trace the evolutionary predisposition which led to successful overcoming of challenges of a new environment, we carefully annotate, dissect and analyse the stress proteome of the extant Green lineage.</li> </ul> <p><strong>Key Concepts</strong></p> <ul> <li>Already existing Concept: <ul> <li>Orthology</li> </ul> </li> <li>New/Redefined Concept <ul> <li>Embryophytic Domain: Protein domain which has an Embryophytic ancestor, that is, present in at least one Bryophyte species and at least one Tracheophyte species</li> <li>Latent Genetic Potential (LGP): Key (functional) Embryophytic protein domains having Last Common Ancestor (LCA) prior to the LCA of protein with corresponding function</li> </ul> </li> </ul> <p><strong>Data: (Figure 1 A)</strong></p> <ul> <li>We take 6 species from Cholorophyte algae lineage, 7 from Streptophyte algae lineage, 5 from Bryophyte lineage and 14 from Tracheophyte lineage. 5 species from Cyanobacteria were taken as an outgroup lineage.</li> </ul> <p><strong>Stress-annotation (Figure 1B)</strong></p> <ul> <li>First 57,796 orthogroups were obtained from 37 proteome. This is computed by using OrthoFinder2.</li> <li>Next we need to annotate stress-related proteins across our dataset. Following are existing ways of annotation: <ul> <li>Extensive experiments have been done on <em>A.thaliana</em> and <em>P.patens</em> in the green lineage. Thus, we stress-annotated 37 proteomes using TAIR10 and PEATmoss respectively. From this method, we stress-annotated 4,902 orthogroups</li> <li>Eggnogmapper is a known tool with an extensive database used for gene ontology purposes. We stress-annotated 17,349 orthogroups.</li> </ul> </li> <li>In order to avoid experimental bias and tool-based randomness we overlap the two methods to have our final stress-annotation. We finally filtered 2,475 stress-annotated orthogroups from 57,796 orthogroups.</li> </ul> <p><strong>Overview of Stress-annotation (Figure 1C, 1D)</strong></p> <ul> <li>To have an overview of stress-annotation, overlaps of stress-annotated protein domains, proteins and orthogroups across our dataset lineages and various response to stresses are shown.</li> </ul> <p><strong>Distribution of Stress-annotation (Figure 2)</strong></p> <ul> <li>Using the overlap annotation approach explained earlier, the stress-annotated orthogroups and corresponding protein domains are in Figure 2A. A standard pattern is observed in both, that is, the unique number of stress orthogroups and protein domains increase from Cyanobacteria to Tracheophytes. The number of proteins and average number of protein domains also increases similarly.</li> <li>Top 10 bursts of protein domains from one lineage to the next is shown in Figure 2B.</li> </ul> <p><strong>Changes in stress-annotation with respect to Protein Domains (Figure 3)</strong></p> <ul> <li>Figure 3 is a 4-dimensional plot with the following parameters: Species(37), Protein Domains (100), Number of Orthgogroups with Protein Domain (size of circle), Number of Proteins with Protein Domain (Color of circle). The plot is sorted from top to bottom based on the number of orthogroups, and the top 100 protein domains are chosen for the plot.</li> <li>This plot is used to express an overview of the most significant occurances of sub- and neo-functionalizations. Here, each orthogroup is considered to be a protein family. 2 protein families can have an overlapping number of functions. That is why there are more than 1 orthogroup which have the same protein domain.</li> </ul> <p><strong>Assembling LGP from protein domains (Figure 4) - refer to Key Concepts to understand LGP</strong></p> <ul> <li>In Figure 1A, we show 2 categories (x/y) of orthogroups at each node (a,b,c,d,e,f). The number <strong>y</strong> for example at node <strong>b</strong> indicates the number of orthogroups (4) in Tracheophyta+Bryophyta+Zygnemaotphyceae that have LGP (or key Embryophytic protein domains) in Charophyceae. The number <strong>x</strong> at node <strong>b</strong> indicates the number of orthogroups (131) in Tracheophyta+Bryophyta+Zygnemaotphyceae that have LGP in all the rest of the lineages (Charophyceae+Klebsormidiophyceae+Chlorokybophyceae+Mesostigmatophyceae+Chlorophytes) in the figure.</li> <li>Since we are concerned about the LGP for Land Plants (Embryophytes), we look at node <strong>a</strong>. Next, we functionally annotate 96 orthogroups. 50 annotations that occur the most number of times is shown in Figure 4B.</li> <li>In Figure 4C, we can see in which species the key Embryophytic Domains are present whose proteins and protein families are only seen in Embryophytes.</li> </ul> <p>Thus, from the final figure we can trace the LGP present at the time of terrestrialization in the LCA of Land Plants.</p> <p><strong>Database files:</strong> These are intermediate files used in code for different figures. Following is the link to access them:<a href="https://data.mendeley.com/datasets/mnrn7j7hrw/draft?a=b981b40f-01a8-48ff-9d6a-151f6223810c" rel="nofollow">https://data.mendeley.com/datasets/mnrn7j7hrw/draft?a=b981b40f-01a8-48ff-9d6a-151f6223810c</a> [OR]<a href="https://owncloud.gwdg.de/index.php/s/dH3Y4MAHSfbmhrA" rel="nofollow">https://owncloud.gwdg.de/index.php/s/dH3Y4MAHSfbmhrA</a></p>
SASDM55 – GTP-binding domain of Candida albicans Ras-like protein 1
Open the record for dataset details and reuse information.
Evolutionary assembly of the plant terrestrialization toolkit from protein domains
<p>Land plants (embryophytes) came about in a momentous evolutionary singularity: plant terrestrialization. This event marks not only the conquest of land by plants but also the massive radiation of embryophytes into a diverse array of novel forms and functions. The unique suite of traits present in the earliest land plants is thought to have been ushered in by a burst genomic novelty. Here, we asked the question of how these bursts were possible. For this, we used phylostratigraphy to explore the (i) initial emergence and (ii) reshuffling of domains to give rise to hallmark environmental response genes of land plants. We pinpoint that a quarter of the embryophytic stress physiology is specific to the lineage, yet a significant portion of this novelty arises not de novo but from re-shuffling and recombining of pre-existing domains. Our data suggest that novel combinations of old genomic substrates shaped the plant terrestrialization toolkit, including hallmark processes in signaling, biotic interactions, and specialized metabolism.</p>
Data file with manuscript titled 'A Structurally Validated Sequence Alignment of 497 Human Protein Kinase Domains'
<p>The files used in different analysis reported in the manuscript titled - 'A Structurally-Validated Multiple Sequence Alignment of 497 Human Protein Kinase Domains' are shared at two locations. Following is a brief description of these files.</p> <p>Location - https://github.com/DunbrackLab/Kinases<br> 1. HMM profile files - HMM files for each of the nine groups computed separately labeled as Groupname.hmm, like AGC.hmm<br> 2. HMM profile file - HMM file computed from the full alignment including all the sequences - Human-PK.hmm<br> 3. Score files - HMM scores of each kinase sequence against all the groupwise HMMs both for iteration1 (HMM-iter1-scores-tables.txt) and iteration2 (HMM-iter1-scores-tables.txt)<br> 4. Jalview session file - Kinase alignment with sequences colored by secondary structure information from PDB file if the structure is known; or predicted secondary structure if the experimental structure is not known. The file could be opened in Jalview - kinases-PDB-SSPred.jvp</p> <p>Location - https://zenodo.org/record/3445533<br> 1. The file contains list of residue pairs aligned in pairwise structural alignments of 272 human protein kinases which were used as a benchmark in the study. The alignments were created by FATCAT and optimized by SE program.</p>
Figure 1 in Solution structure of the first RRM domain of human spliceosomal protein SF3b49
Figure 1. – Sampling locality of the present specimen of Lutjanus madras.
Codes and source data files for: Proximity labeling identifies LOTUS domain proteins that promote the formation of perinuclear germ granules in C. elegans
<p>The germ line produces gametes that transmit genetic and epigenetic information to the next generation. Maintenance of germ cells and development of gametes require germ granules—well-conserved membraneless and RNA-rich organelles. The composition of germ granules is elusive owing to their dynamic nature and their exclusive expression in the germ line. Using <i>C. elegans</i> germ granule, called P granule, as a model system, we employed a proximity-based labeling method in combination with mass spectrometry to comprehensively define its protein components. This set of experiments identified over 200 proteins, many of which contain intrinsically disordered regions. An RNAi-based screen identified factors that are essential for P granule assembly, notably EGGD-1 and EGGD-2, two putative LOTUS-domain proteins. Loss of <i>eggd-1</i> and <i>eggd-2</i> results in separation of P granules from the nuclear envelope, germline atrophy and reduced fertility. We show that intrinsically disordered regions of EGGD-1 are required to anchor EGGD-1 to the nuclear periphery while its LOTUS domains are required to promote perinuclear localization of P granules. Together, our work expands the repertoire of P granule constituents and provides new insights into the role of LOTUS-domain proteins in germ granule organization.</p>
PLAT Domain Protein 1 (PLAT1/PLAFP) Binds to the Arabidopsis thaliana Plasma Membrane and Inserts a Lipid
<p>Harvest yields depend on the plant's ability to fix carbon and deal with changing environmental conditions. Especially during seasonal and diurnal cycles, the plant must constantly adjust its metabolism according to available resources or external stressors. The metabolic changes that a plant undergoes in response to stress are well understood, but the long-distance signaling mechanisms that facilitate communication throughout the plant are less studied. The phloem is considered the predominant conduit for the bidirectional transport of these signals through metabolites, nucleic acids, proteins, and lipids. Lipid trafficking through the phloem in particular attracted our attention due to its reliance on soluble lipid-binding proteins (LBP) that generate and solubilize otherwise membrane-associated lipids. The Phloem Lipid-Associated Family Protein (PLAFP) from <em>Arabidopsis thaliana </em>is generated in response to abiotic stress as is its lipid-ligand phosphatidic acid (PA). PLAFP is proposed to transport PA through the phloem in response to drought stress. To understand the interactions between PLAFP and PA, almost 100 independent systems comprised of the protein and one PA, or a plasma membrane containing varying amounts of PA, were simulated. In the simulations, PLAFP does bind to the plasma membrane independent of the PA concentration, and it adopts a binding pose, where W41 and R82 penetrate the membrane surface and anchor PLAFP. This triggers a separation of the two loop regions containing W41 and R82. Subsequently, PA does insert into PLAFP's beta-sandwich and multiple amino acids besides W41 and R82 are identified that drive the insertion. Fine-tuning the protein-membrane and protein-PA interface by mutating a selection of these amino acids could allow modulating the signaling sensitivity to the climate the plant is supposed to grow in.</p>
Data for: A unique C-terminal domain contributes to the molecular function of restorer-of-fertility proteins in plant mitochondria
<p><em><span>Restorer-of-fertility</span></em><span><em> </em>(<em>Rf</em>) genes have practical applications in hybrid seed production as a means to control self-pollination. They encode pentatricopeptide repeat (PPR) proteins that are targeted to mitochondria where they specifically bind to transcripts that induce cytoplasmic male sterility and repress their expression. </span></p> <p>We have identified a unique domain, RfCTD (Restorer-of-fertility C-terminal domain), which discriminates <em>Restorer-of-fertility-like</em> (RFL) proteins from hundreds of PPR proteins encoded in plant genomes. Using the sequence of this domain from hundreds of plant species, we have constructed a sequence profile that can quickly and accurately identify RfCTD sequences in plant genomes or transcriptomes. </p> <p>This data set contains PPR genes identified in 213 plant genomes (as summarised in accompanying table). </p>
Data from: Dissection of the role of a SH3 domain in the evolution of binding preference of paralogous proteins
<p><span>Protein-protein interactions drive many cellular processes. Some protein interactions are directed by Src homology 3 (SH3) domains that bind proline-rich motifs on other proteins. The evolution of the binding specificity of SH3 domains is not completely understood, particularly following gene duplication. Paralogous genes accumulate mutations that can modify protein functions and, for SH3 domains, their binding preferences. Here, we examined how the binding of the SH3 domains of two paralogous yeast type I myosins, Myo3 and Myo5, evolved following duplication. We found that the paralogs have subtly different SH3-dependent interaction profiles. However, by swapping SH3 domains between the paralogs and characterizing the SH3 domains freed from their protein context, we find that few of the differences in interactions, if any, depend on the SH3 domains themselves. We used ancestral sequence reconstruction to resurrect the pre-duplication SH3 domains and examined, moving back in time, how the binding preference changed. Although the closest ancestor of the two domains had a very similar binding preference as the extant ones, older ancestral domains displayed a gradual loss of interaction with the modern interaction partners when inserted in the extant paralogs. Molecular docking and experimental characterization of the free ancestral domains showed that their affinity with the proline motifs is likely not the cause for this loss of binding. Taken together, our results suggest that the SH3 and its host protein could create intramolecular or allosteric interactions essential for the SH3-dependent PPIs, making domains not functionally equivalent even when they have the same binding specificity. </span></p>
Phase II Trial to Correlate Radiographic Response Induced By Gefitinib With Mutations in the Protein-Tyrosine Kinase Domain of the EGF Receptor Gene
ClinicalTrials.gov study NCT00588445. IPD Sharing: Not stated. Countries: 1. Publications: 2.
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