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Dataset results
7 results for “SNARE protein”
The QR code of SNARE proteins
<p>The raw data belong to a study in which we studied the geometric pattern of SNARE complexes. These proteins form stable four-helix bundles from four different helices. Some of the hydrophobic coiled-coil layers are asymmetric. We found that there is a matching pattern in the core of the complex that dictates the position of the four fundamental SNARE types in the bundle. The raw data include biochemical analyses, molecular dynamics simulations and other calculations. In addition, the data for the respective figures are included in the package. </p>
Prototypic SNARE proteins - extra datasets
<p>The dataset contains files of phylogenetic trees (.tree files) and accompanying alignments (.fasta). In addition, scanned images of Coomassie-stained gels and raw size exclusion chromatography data (.txt) are available. A description can be found in the ReadMe files.</p>
FIGURE 3 in A study of the SNARE protein syntaxin 16 and its role in the intracellular trafficking of glucose transporter GLUT4 in 3T3-L1 adipocytes
FIGURE 3. Scanning electron micrographic images of dorsal sides of (a) male and (b) female Aetacarus elanoides sp.n. Scales = 100 µm.
FIGURE 2 in A study of the SNARE protein syntaxin 16 and its role in the intracellular trafficking of glucose transporter GLUT4 in 3T3-L1 adipocytes
FIGURE 2. Aetacarus elanoides sp. n., female. a – dorsal view, b – genital area; gl = gland opening, gp = genital papilla, ia = cupule.
Sequences used for building HMMER profiles to search for SNAREs proteins
<p>This file contains the four sequence datasets that were used to build HMMER search profiles in order to find all SNAREs protein present in the predicted proteome of Oopsacas minuta: a human SNARE profile, a Qa-SNAREs profile, a Qb-SNAREs profile, a Qc-SNAREs profile.</p>
FIGURE 4 in A study of the SNARE protein syntaxin 16 and its role in the intracellular trafficking of glucose transporter GLUT4 in 3T3-L1 adipocytes
FIGURE 4. Scanning electron micrographic images of anatomy of Aetacarus elanoides sp. n.: a – male genital apparatus lateral view, b – male genital apparatus apical view (scales = 5 µm); c – male dorsal surface of tarsus IV with arrow indicating seta assumed to be seta d (scale = 20 µm); d – female posterior dorsum (scale = 50 µm).
Fast, streamlined fluorescence nanoscopy resolves rearrangements of SNARE and cargo proteins in platelets co-incubated with cancer cells.
<p><strong>This folder contains all raw data underlying the results presented in a manuscript, submitted to </strong><strong><em>Journal of Nanobiotechnology</em></strong><strong>, and entitled:</strong></p> <p> </p> <p><strong>Fast, streamlined fluorescence nanoscopy resolves rearrangements of SNARE and cargo proteins in platelets co-incubated with cancer cells.</strong></p> <p> </p> <p><strong>Authored by:</strong></p> <p>Jan Bergstrand<sup>a,+</sup>, Xinyan Miao<sup>a,+</sup>, Chinmaya Venugopal Srambickal<sup>a,+</sup>, Gert Auer<sup>b</sup>, Jerker Widengren<sup>a,*</sup></p> <p><sup>a</sup> Royal Institute of Technology (KTH), Department of Applied Physics, Experimental Biomolecular Physics, Albanova Univ Center, SE-106 91 Stockholm, Sweden</p> <p><sup>b</sup> Karolinska Institutet, Department of Oncology-Pathology, K7, Z1:00, Karolinska University Hospital, 171 76 Stockholm, Sweden</p> <p><sup>* </sup>To whom correspondence should be addressed. E-mail: <a href="mailto:jwideng@kth.se">jwideng@kth.se</a>, Phone: +46-8-7907813</p> <p><sup>+ </sup>These authors contributed equally</p> <p> </p> <p><strong>The data files are grouped into the different </strong><strong>figures where they are presented</strong><strong>.</strong></p> <p> </p> <p><strong>ABSTRACT</strong></p> <p>Background:</p> <p>Increasing evidence suggests that platelets play a central role in cancer progression, with altered storage and selective release from platelets of specific tumor-promoting proteins as a major mechanism. Fluorescence-based super-resolution microscopy (SRM) can resolve nanoscale spatial distribution patterns of such proteins, and how they are altered in platelets upon different activations. Analysing such alterations by SRM thus represents a promising, minimally invasive strategy for platelet-based diagnosis and monitoring of cancer progression. However, broader applicability beyond specialized research labs will require objective, more automated imaging procedures. Moreover, for statistically significant analyses many SRM platelet images are needed, of several different platelet proteins. Such proteins, showing alterations in their distributions upon cancer progression additionally need to be identified.</p> <p>Results:</p> <p>A fast, streamlined and objective procedure for SRM platelet image acquisition, analysis and classification was developed to overcome these limitations. By stimulated emission depletion SRM we imaged nanoscale patterns of six different platelet proteins; four different SNAREs (soluble N-ethylmaleimide factor attachment protein receptors) mediating protein secretion by membrane fusion of storage granules, and two angiogenesis regulating proteins, representing cargo proteins within these granules coupled to tumor progression. By an streamlined procedure, we recorded about 100 SRM images of platelets, for each of these six proteins, and for five different categories of platelets; incubated with cancer cells (MCF-7, MDA-MB-231, EFO-21), non-cancer cells (MCF-10A), or no cells at all. From these images, structural similarity and protein cluster parameters were determined, and probability functions of these parameters were generated for the different platelet categories. By comparing these probability functions between the categories, we could identify nanoscale alterations in the protein distributions, allowing us to classify the platelets into their correct categories, if they were co-incubated with cancer cells, non-cancer cells, or no cells at all.</p> <p>Conclusions:</p> <p>The fast, streamlined and objective acquisition and analysis procedure established in this work confirms the role of SNAREs and angiogenesis-regulating proteins in platelet-mediated cancer progression, provides additional fundamental knowledge on the interplay between tumor cells and platelets, and represent an important step towards using tumor-platelet interactions and redistribution of nanoscale protein patterns in platelets as a basis for cancer diagnostics.</p> <p> </p> <p><strong>Key Words:</strong></p> <p>STED, super-resolution microscopy, platelet, cancer, tumorigenesis, SNARE protein, dictionary learning</p>
ScienceDex guides
Understand access before you commit
These curated guides explain access requirements, typical timelines, costs, and reuse considerations for widely used research datasets.
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OpenNeuro
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