Database of articles cited by EMDB/PDB/SASBDB data

Keywords
Structure methods	All X-ray diffraction NMR electron microscopy small angle scattering neutron diffraction fiber diffraction powder diffraction infrared spectroscopy EPR fluorescence transfer theoretical model Hybrid
Author
Journal
IF	>30 >20 >10 >5 all

Title	Annealing synchronizes the 70 ribosome into a minimum-energy conformation.
Journal, issue, pages	Proc Natl Acad Sci U S A, Vol. 119, Issue 8, Year 2022
Publish date	Feb 22, 2022
Authors	Xiaofeng Chu / Xin Su / Mingdong Liu / Li Li / Tianhao Li / Yicheng Qin / Guoliang Lu / Lei Qi / Yunhui Liu / Jinzhong Lin / Qing-Tao Shen /
PubMed Abstract	Researchers commonly anneal metals, alloys, and semiconductors to repair defects and improve microstructures via recrystallization. Theoretical studies indicate that simulated annealing on biological ...Researchers commonly anneal metals, alloys, and semiconductors to repair defects and improve microstructures via recrystallization. Theoretical studies indicate that simulated annealing on biological macromolecules helps predict the final structures with minimum free energy. Experimental validation of this homogenizing effect and further exploration of its applications are fascinating scientific questions that remain elusive. Here, we chose the apo-state 70 ribosome from as a model, wherein the 30 subunit undergoes a thermally driven intersubunit rotation and exhibits substantial structural flexibility as well as distinct free energy. We experimentally demonstrate that annealing at a fast cooling rate enhances the 70 ribosome homogeneity and improves local resolution on the 30 subunit. After annealing, the 70 ribosome is in a nonrotated state with respect to corresponding intermediate structures in unannealed or heated ribosomes. Manifold-based analysis further indicates that the annealed 70 ribosome takes a narrow conformational distribution and exhibits a minimum-energy state in the free-energy landscape. Our experimental results offer a facile yet robust approach to enhance protein stability, which is ideal for high-resolution cryogenic electron microscopy. Beyond structure determination, annealing shows great potential for synchronizing proteins on a single-molecule level and can be extended to study protein folding and explore conformational and energy landscapes.
External links	Proc Natl Acad Sci U S A / PubMed:35177473 / PubMed Central
Methods	EM (single particle)
Resolution	2.41 - 3.73 Å
Structure data	EMDB-31266: Annealing synchronizes 70S ribosome into minimum-energy conformation Method: EM (single particle) / Resolution: 2.61 Å EMDB-31267: Annealing synchronizes 70S ribosome into minimum-energy conformation Method: EM (single particle) / Resolution: 2.69 Å EMDB-31268: Annealing synchronizes 70S ribosome into minimum-energy conformation Method: EM (single particle) / Resolution: 2.42 Å EMDB-31269: Annealing synchronizes 70S ribosome into minimum-energy conformation Method: EM (single particle) / Resolution: 2.6 Å EMDB-31270: Annealing synchronizes 70S ribosome into minimum-energy conformation Method: EM (single particle) / Resolution: 2.41 Å EMDB-31271: Annealing synchronizes 70S ribosome into minimum-energy conformation Method: EM (single particle) / Resolution: 2.51 Å EMDB-31272: Annealing synchronizes 70S ribosome into minimum-energy conformation Method: EM (single particle) / Resolution: 2.6 Å EMDB-31273: Annealing synchronizes 70S ribosome into minimum-energy conformation Method: EM (single particle) / Resolution: 2.62 Å EMDB-31274: Annealing synchronizes 70S ribosome into minimum-energy conformation Method: EM (single particle) / Resolution: 2.51 Å EMDB-31275: Annealing synchronizes 70S ribosome into minimum-energy conformation Method: EM (single particle) / Resolution: 2.41 Å EMDB-31277: Annealing synchronizes 70S ribosome into minimum-energy conformation Method: EM (single particle) / Resolution: 2.88 Å EMDB-31278: Annealing synchronizes 70S ribosome into minimum-energy conformation Method: EM (single particle) / Resolution: 2.92 Å EMDB-31279: Annealing synchronizes 70S ribosome into minimum-energy conformation Method: EM (single particle) / Resolution: 2.59 Å EMDB-31280: Annealing synchronizes 70S ribosome into minimum-energy conformation Method: EM (single particle) / Resolution: 3.3 Å EMDB-31281: Annealing synchronizes 70S ribosome into minimum-energy conformation Method: EM (single particle) / Resolution: 3.73 Å EMDB-31282: Annealing synchronizes 70S ribosome into minimum-energy conformation Method: EM (single particle) / Resolution: 2.73 Å
Source	Escherichia coli (E. coli)