Re-examining the spectra of macromolecules. Current practice of spectral quasi B-factor flattening

Publication date: Available online 3 January 2020Source: Journal of Structural BiologyAuthor(s): J.L. Vilas, J. Vargas, M. Martinez, E. Ramirez-Aportela, R. Melero, A. Jimenez-Moreno, E. Garduño, P. Conesa, R. Marabini, D. Maluenda, J.M. Carazo, C.O.S. SorzanoAbstractThe analysis of structure factors in 3D cryo-EM Coulomb potential maps and their “enhancement” at the end of the reconstruction process is a well-established practice, normally referred to as sharpening. The aim is to increase contrast and, in this way, to help tracing the atomic model. The most common way to accomplish this enhancement is by means of the so-called B-factor correction, which applies a global filter to boost high frequencies with some dampening considerations related to noise amplification. The results are maps with a better visual aspect and a quasiflat spectrum at medium and high frequencies. This practice is so widespread that most map depositions in the Electron Microscopy Data Base (EMDB) only contain sharpened maps. Here, the use in cryoEM of global B-factor corrections is theoretically and experimentally analyzed. Results clearly illustrate that protein spectra present a falloff. Thus, spectral quasi-flattening may produce protein spectra with distortions when compared with experimental ones, this fact, combined with the practice of reporting only sharpened maps, generates a sub-optimal situation in terms of data preservation, reuse and reproducibility. Now that the field is more advan...

Source: Journal of Structural Biology - January 5, 2020 Category: Biology Source Type: research