Conformational space exploration of cryo-EM structures by variability refinement

Journal Article · 02 February 2023 · Biochimica et Biophysica Acta. Biomembranes

DOI: https://doi.org/10.1016/j.bbamem.2023.184133 · OSTI ID:2234148

Afonine, Pavel V. ^[1]; Gobet, Alexia ^[2]; Moissonnier, Loïck ^[2]; Martin, Juliette ^[2]; Poon, Billy K. ^[1]; Chaptal, Vincent ^[2]

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1. Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States)
2. Univ. of Lyon (France); Centre National de la Recherche Scientifique (CNRS) (France)

Cryo-EM observation of biological samples enables visualization of sample heterogeneity, in the form of discrete states that are separable, or continuous heterogeneity as a result of local protein motion before flash freezing. Variability analysis of this continuous heterogeneity describes the variance between a particle stack and a volume, and results in a map series describing the various steps undertaken by the sample in the particle stack. While this observation is absolutely stunning, it is very hard to pinpoint structural details to elements of the maps. Here, in order to bridge the gap between observation and explanation, we designed a tool that refines an ensemble of structures into all the maps from variability analysis. Using this bundle of structures, it is easy to spot variable parts of the structure, as well as the parts that are not moving. Comparison with molecular dynamics simulations highlights the fact that the movements follow the same directions, albeit with different amplitudes. Ligand can also be investigated using this method. Variability refinement is available in the Phenix software suite, accessible under the program name phenix.varref.

• Research Organization: Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States)
• Sponsoring Organization: USDOE Office of Science (SC)
• Grant/Contract Number: AC02-05CH11231
• OSTI ID: 2234148
• Journal Information: Biochimica et Biophysica Acta. Biomembranes, Journal Name: Biochimica et Biophysica Acta. Biomembranes Journal Issue: 4 Vol. 1865; ISSN 0005-2736
• Publisher: ElsevierCopyright Statement
• Country of Publication: United States
• Language: English