2012Zhang IPET FETR - Revision history

Garygangren: /* Links */

2023-08-24T18:40:16Z

Links

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	https://www.nature.com/articles/srep01089		https://www.nature.com/articles/srep01089

			https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6409128/

			https://www.nature.com/articles/s41467-021-23966-4

			https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9493104/

			https://www.nature.com/articles/s41565-023-01321-6

	== Related software ==		== Related software ==

Garygangren: /* Links */

2020-06-30T14:37:41Z

Links

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	== Links ==		== Links ==
	https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0030249		https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0030249

	https://www.nature.com/articles/s41598-020-66793-1		https://www.nature.com/articles/s41598-020-66793-1

	https://www.nature.com/articles/s41598-019-44978-7		https://www.nature.com/articles/s41598-019-44978-7

	https://pubmed.ncbi.nlm.nih.gov/30557627/		https://pubmed.ncbi.nlm.nih.gov/30557627/

	https://pubmed.ncbi.nlm.nih.gov/30420636/		https://pubmed.ncbi.nlm.nih.gov/30420636/

	https://www.nature.com/articles/s41467-018-03018-0		https://www.nature.com/articles/s41467-018-03018-0

	https://pubmed.ncbi.nlm.nih.gov/27621318/		https://pubmed.ncbi.nlm.nih.gov/27621318/

	https://pubmed.ncbi.nlm.nih.gov/27538822/		https://pubmed.ncbi.nlm.nih.gov/27538822/

	https://www.nature.com/articles/srep29231		https://www.nature.com/articles/srep29231

	https://www.nature.com/articles/srep09803		https://www.nature.com/articles/srep09803

	https://www.nature.com/articles/srep01089		https://www.nature.com/articles/srep01089

Garygangren: /* Links */

2020-06-29T20:53:02Z

Links

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 == Links ==
 https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0030249
 == Related software ==

Garygangren: /* Keywords */

2020-06-29T20:07:37Z

Keywords

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	== Keywords ==		== Keywords ==
			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.

	== Links ==		== Links ==

Garygangren at 20:05, 29 June 2020

2020-06-29T20:05:21Z

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	== Citation ==		== 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
	Zhang, ~~L. &~~ Ren, G. IPET and FETR: ~~experimental approach~~ for ~~studying molecular structure dynamics~~ by ~~cryo~~-~~electron tomography~~ of a ~~single~~-~~molecule structure~~. PLoS One, Molecular Foundry, Lawrence Berkeley National Laboratory, Berkeley, California, United States of America., Molecular Foundry, Lawrence Berkeley National Laboratory, Berkeley, California, United States of America., 2012, 7, e30249

	== Abstract ==		== 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 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 "focused electron tomography reconstruction" (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 "snapshot" 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.		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 "focused electron tomography reconstruction" (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 "snapshot" 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.

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	== Links ==		== Links ==
			https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0030249
	~~http~~://journals.plos.org/plosone/article?id=10.1371/journal.pone.0030249

	== Related software ==		== Related software ==

CoSS: Created page with "== Citation == Zhang, L. & Ren, G. IPET and FETR: experimental approach for studying molecular structure dynamics by cryo-electron tomography of a single-molecule structure...."

2016-10-21T14:00:28Z

Created page with "== Citation == Zhang, L. & Ren, G. IPET and FETR: experimental approach for studying molecular structure dynamics by cryo-electron tomography of a single-molecule structure...."

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== Citation ==

Zhang, L. & Ren, G. IPET and FETR: experimental approach for studying molecular structure dynamics by cryo-electron tomography of a single-molecule structure. PLoS One, Molecular Foundry, Lawrence Berkeley National Laboratory, Berkeley, California, United States of America., Molecular Foundry, Lawrence Berkeley National Laboratory, Berkeley, California, United States of America., 2012, 7, 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 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 "focused electron tomography reconstruction" (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 "snapshot" 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.

== Keywords ==

== Links ==

http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0030249

== Related software ==

== Related methods ==

== Comments ==