Model-dependent and model-independent visualization of hydrogen atoms in high-resolution cryoEM maps

In this study, two methods are described for visualizing the H atoms in cryoEM maps of macromolecules. The first involves comparing experimental charge-density (CD) maps with calculated CD maps computed using structural models from which hydrogens are excluded. After the hydrogen-free model has been refined into the experimental map, the vector-difference Fourier map one computes, i.e. the (Fobs, αobs) - (Fcalc, αcalc) residual CD map, will reveal the H atoms missing from the model. The second method is model-independent and is known as a shoulder-peak decomposition method. It relies on the difference in the one-dimensional CD profile of a non-H atom between the side of the atom that adjoins a H atom and the side that does not. Here, the utility of both methods is demonstrated using both cryoEM CD maps derived from experimental electrostatic potential (ESP) maps for mouse heavy-chain ferritin at 1.09 Å resolution and X-ray crystallographic electron-density (ED) maps reported for the human enzyme at 1.06 Å resolution. A comparison shows that hydrogen signals in cryoEM maps are about 5-10 times stronger than those of X-ray crystallographic ED maps. Both methods should be applicable to cryoEM maps with a wide range of resolutions. The model-independent method is important for nucleoprotein complexes such as the ribosome because it bypasses the necessity of modeling the contribution that unscreened atomic partial charges make to cryoEM maps, which are difficult to model properly.