https://3demmethods.i2pc.es/index.php?action=history&feed=atom&title=2012Zhang_IPET 2026-05-24T20:12:31Z Revision history for this page on the wiki MediaWiki 1.44.2 https://3demmethods.i2pc.es/index.php?title=2012Zhang_IPET&diff=4834&oldid=prev 2024-11-12T08:52:12Z

<p></p> <table style="background-color: #fff; color: #202122;" data-mw="interface"> <col class="diff-marker" /> <col class="diff-content" /> <col class="diff-marker" /> <col class="diff-content" /> <tr class="diff-title" lang="en"> <td colspan="2" style="background-color: #fff; color: #202122; text-align: center;">← Older revision</td> <td colspan="2" style="background-color: #fff; color: #202122; text-align: center;">Revision as of 08:52, 12 November 2024</td> </tr><tr><td colspan="2" class="diff-lineno" id="mw-diff-left-l24">Line 24:</td> <td colspan="2" class="diff-lineno">Line 24:</td></tr> <tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9493104/</div></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9493104/</div></td></tr> <tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>https://www.nature.com/articles/s41565-023-01321-6</div></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>https://www.nature.com/articles/s41565-023-01321-6</div></td></tr> <tr><td class="diff-marker" data-marker="−"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div><del style="font-weight: bold; text-decoration: none;"></del></div></td><td colspan="2" class="diff-side-added"></td></tr> <tr><td class="diff-marker" data-marker="−"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div><del style="font-weight: bold; text-decoration: none;">== Related software ==</del></div></td><td colspan="2" class="diff-side-added"></td></tr> <tr><td class="diff-marker" data-marker="−"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div><del style="font-weight: bold; text-decoration: none;"></del></div></td><td colspan="2" class="diff-side-added"></td></tr> <tr><td class="diff-marker" data-marker="−"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div><del style="font-weight: bold; text-decoration: none;">== Related methods ==</del></div></td><td colspan="2" class="diff-side-added"></td></tr> <tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><br></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><br></td></tr> <tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>== Comments ==</div></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>== Comments ==</div></td></tr> </table>

Garygangren https://3demmethods.i2pc.es/index.php?title=2012Zhang_IPET&diff=4833&oldid=prev 2024-11-12T08:51:36Z

<p>Created page with &quot;== Citation == Zhang L, Ren G (2012) IPET and FETR: Experimental Approach for Studying Molecular Structure Dynamics by Cryo-Electron Tomography of a Single-Molecule Structure. PLoS ONE 7(1): e30249 == Abstract == The dynamic personalities and structural heterogeneity of proteins are essential for proper functioning. Structural determination of dynamic/heterogeneous proteins is limited by conventional approaches of X-ray and electron microscopy (EM) of single-particle re...&quot;</p> <p><b>New page</b></p><div>== Citation ==<br /> Zhang L, Ren G (2012) IPET and FETR: Experimental Approach for Studying Molecular Structure Dynamics by Cryo-Electron Tomography of a Single-Molecule Structure. PLoS ONE 7(1): e30249<br /> <br /> == Abstract ==<br /> The dynamic personalities and structural heterogeneity of proteins are essential for proper functioning. Structural determination of dynamic/heterogeneous proteins is limited by conventional approaches of X-ray and electron microscopy (EM) of single-particle reconstruction that require an average from thousands to millions different molecules. Cryo-electron tomography (cryoET) is an approach to determine three-dimensional (3D) reconstruction of a single and unique biological object such as bacteria and cells, by imaging the object from a series of tilting angles. However, cconventional reconstruction methods use large-size whole-micrographs that are limited by reconstruction resolution (lower than 20 Å), especially for small and low-symmetric molecule (400 kDa). In this study, we demonstrated the adverse effects from image distortion and the measuring tilt-errors (including tilt-axis and tilt-angle errors) both play a major role in limiting the reconstruction resolution. Therefore, we developed a &quot;focused electron tomography reconstruction&quot; (FETR) algorithm to improve the resolution by decreasing the reconstructing image size so that it contains only a single-instance protein. FETR can tolerate certain levels of image-distortion and measuring tilt-errors, and can also precisely determine the translational parameters via an iterative refinement process that contains a series of automatically generated dynamic filters and masks. To describe this method, a set of simulated cryoET images was employed; to validate this approach, the real experimental images from negative-staining and cryoET were used. Since this approach can obtain the structure of a single-instance molecule/particle, we named it individual-particle electron tomography (IPET) as a new robust strategy/approach that does not require a pre-given initial model, class averaging of multiple molecules or an extended ordered lattice, but can tolerate small tilt-errors for high-resolution single &quot;snapshot&quot; molecule structure determination. Thus, FETR/IPET provides a completely new opportunity for a single-molecule structure determination, and could be used to study the dynamic character and equilibrium fluctuation of macromolecules.<br /> <br /> == Keywords ==<br /> Protein dynamics; protein structure; equilibrium fluctuation; single-molecule structure; focused electron tomography reconstruction; FETR; individual-particle electron tomography; IPET; electron microscopy; EM; electron tomography; ET; cryo-electron tomography; CryoET.<br /> <br /> == Related publications ==<br /> https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0030249<br /> https://www.nature.com/articles/s41598-020-66793-1<br /> https://www.nature.com/articles/s41598-019-44978-7<br /> https://pubmed.ncbi.nlm.nih.gov/30557627/<br /> https://pubmed.ncbi.nlm.nih.gov/30420636/<br /> https://www.nature.com/articles/s41467-018-03018-0<br /> https://pubmed.ncbi.nlm.nih.gov/27621318/<br /> https://pubmed.ncbi.nlm.nih.gov/27538822/<br /> https://www.nature.com/articles/srep29231<br /> https://www.nature.com/articles/srep09803<br /> https://www.nature.com/articles/srep01089<br /> https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6409128/<br /> https://www.nature.com/articles/s41467-021-23966-4<br /> https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9493104/<br /> https://www.nature.com/articles/s41565-023-01321-6<br /> <br /> == Related software ==<br /> <br /> == Related methods ==<br /> <br /> == Comments ==</div>

Garygangren