Estimating conformational landscapes from Cryo-EM particles by
3D Zernike polynomials

J 2023

Estimating conformational landscapes from Cryo-EM particles by 3D Zernike polynomials

HERREROS, David, Roy R. LEDERMAN, James M. KRIEGER, Amaya JIMÉNEZ-MORENO, Marta MARTÍNEZ et. al.

Základní údaje

Originální název

Estimating conformational landscapes from Cryo-EM particles by 3D Zernike polynomials

Autoři

HERREROS, David, Roy R. LEDERMAN, James M. KRIEGER, Amaya JIMÉNEZ-MORENO, Marta MARTÍNEZ, David MYŠKA (203 Česká republika, domácí), David STŘELÁK (203 Česká republika, domácí), Jiří FILIPOVIČ (203 Česká republika, garant, domácí), Carlos O. S. SORZANO a José M. CARAZO

Vydání

Nature Communications, 2023, 2041-1723

Další údaje

Jazyk

angličtina

Typ výsledku

Článek v odborném periodiku

Obor

10201 Computer sciences, information science, bioinformatics

Stát vydavatele

Velká Británie a Severní Irsko

Utajení

není předmětem státního či obchodního tajemství

Odkazy

URL

Impakt faktor

Impact factor: 16.600 v roce 2022

Kód RIV

RIV/00216224:14610/23:00130195

Organizační jednotka

Ústav výpočetní techniky

DOI

http://dx.doi.org/10.1038/s41467-023-35791-y

UT WoS

000991281000008

Klíčová slova anglicky

3D reconstruction and image processing; single-particle cryo-EM; spherical harmonics; Zernike polynomials; conformations

Štítky

J-D1, rivok

Příznaky

Mezinárodní význam, Recenzováno

Změněno: 20. 3. 2024 14:38, Mgr. Alena Mokrá

Anotace

V originále

The new developments in Cryo-EM Single Particle Analysis are helping us to understand how the macromolecular structure and function meet to drive biological processes. By capturing many states at the particle level, it is possible to address how macromolecules explore different conformations, information that is classically extracted through 3D classification. However, the limitations of classical approaches prevent us from fully understanding the complete conformational landscape due to the reduced number of discrete states accurately reconstructed. To characterize the whole structural spectrum of a macromolecule, we propose an extension of our Zernike3D approach, able to extract per-image continuous flexibility information directly from a particle dataset. Also, our method can be seamlessly applied to images, maps or atomic models, opening integrative possibilities. Furthermore, we introduce the ZART reconstruction algorithm, which considers the Zernike3D deformation fields to revert particle conformational changes during the reconstruction process, thus minimizing the blurring induced by molecular motions.

Návaznosti

LM2018140, projekt VaV

Název: e-Infrastruktura CZ (Akronym: e-INFRA CZ)

Investor: Ministerstvo školství, mládeže a tělovýchovy ČR, e-Infrastruktura CZ

Citovat

HERREROS, David, Roy R. LEDERMAN, James M. KRIEGER, Amaya JIMÉNEZ-MORENO, Marta MARTÍNEZ, David MYŠKA, David STŘELÁK, Jiří FILIPOVIČ, Carlos O. S. SORZANO a José M. CARAZO. Estimating conformational landscapes from Cryo-EM particles by 3D Zernike polynomials. Nature Communications. 2023, roč. 14, č. 1, s. 1-10. ISSN 2041-1723. Dostupné z: https://dx.doi.org/10.1038/s41467-023-35791-y.

@article{2247618,
   author = {Herreros, David and Lederman, Roy R. and Krieger, James M. and JiménezandMoreno, Amaya and Martínez, Marta and Myška, David and Střelák, David and Filipovič, Jiří and Sorzano, Carlos O. S. and Carazo, José M.},
   article_number = {1},
   doi = {http://dx.doi.org/10.1038/s41467-023-35791-y},
   keywords = {3D reconstruction and image processing; single-particle cryo-EM; spherical harmonics; Zernike polynomials; conformations},
   language = {eng},
   issn = {2041-1723},
   journal = {Nature Communications},
   title = {Estimating conformational landscapes from Cryo-EM particles by 3D Zernike polynomials},
   url = {https://www.nature.com/articles/s41467-023-35791-y},
   volume = {14},
   year = {2023}
}

TY  - JOUR
ID  - 2247618
AU  - Herreros, David - Lederman, Roy R. - Krieger, James M. - Jiménez-Moreno, Amaya - Martínez, Marta - Myška, David - Střelák, David - Filipovič, Jiří - Sorzano, Carlos O. S. - Carazo, José M.
PY  - 2023
TI  - Estimating conformational landscapes from Cryo-EM particles by 3D Zernike polynomials
JF  - Nature Communications
VL  - 14
IS  - 1
SP  - 1-10
EP  - 1-10
SN  - 20411723
KW  - 3D reconstruction and image processing
KW  - single-particle cryo-EM
KW  - spherical harmonics
KW  - Zernike polynomials
KW  - conformations
UR  - https://www.nature.com/articles/s41467-023-35791-y
N2  - The new developments in Cryo-EM Single Particle Analysis are helping us to understand how the macromolecular structure and function meet to drive biological processes. By capturing many states at the particle level, it is possible to address how macromolecules explore different conformations, information that is classically extracted through 3D classification. However, the limitations of classical approaches prevent us from fully understanding the complete conformational landscape due to the reduced number of discrete states accurately reconstructed. To characterize the whole structural spectrum of a macromolecule, we propose an extension of our Zernike3D approach, able to extract per-image continuous flexibility information directly from a particle dataset. Also, our method can be seamlessly applied to images, maps or atomic models, opening integrative possibilities. Furthermore, we introduce the ZART reconstruction algorithm, which considers the Zernike3D deformation fields to revert particle conformational changes during the reconstruction process, thus minimizing the blurring induced by molecular motions.
ER  -

HERREROS, David, Roy R. LEDERMAN, James M. KRIEGER, Amaya JIMÉNEZ-MORENO, Marta MARTÍNEZ, David MYŠKA, David STŘELÁK, Jiří FILIPOVIČ, Carlos O. S. SORZANO a José M. CARAZO. Estimating conformational landscapes from Cryo-EM particles by 3D Zernike polynomials. \textit{Nature Communications}. 2023, roč.~14, č.~1, s.~1-10. ISSN~2041-1723. Dostupné z: https://dx.doi.org/10.1038/s41467-023-35791-y.

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