Electron crystallography of organic and biological molecules--techniques and comparison to X-ray crystallographic results

Atomic-Scale Corrugations in Crystalline Polypeptoid Nanosheets Revealed by Three-Dimensional Cryogenic Electron Microscopy

Amphiphilic molecules that can crystallize often form molecularly thin nanosheets in aqueous solutions. The possibility of atomic-scale corrugations in these structures has not yet been recognized. We have studied the self-assembly of amphiphilic polypeptoids, a family of bio-inspired polymers that can self-assemble into various crystalline nanostructures. Atomic-scale structure of the crystals in these systems has been inferred using both X-ray diffraction and electron microscopy. Here we use cryogenic electron microscopy to determine the in-plane and out-of-plane structures of a crystalline nanosheet. Data were collected as a function of tilt angle and analyzed using a hybrid single-particle crystallographic approach. The analysis reveals that adjacent rows of peptoid chains, which are separated by 4.5 Å in the plane of the nanosheet, are offset by 6 Å in the direction perpendicular to the plane of the nanosheet. These atomic-scale corrugations lead to a doubling of the unit cell dimension from 4.5 to 9 Å. Our work provides an alternative interpretation for the observed Å X-ray diffraction peak often reported in polypeptoid crystals.

Negative staining permits 4.0 A resolution with low-dose electron diffraction of catalase crystals

Low-dose electron diffraction of thin single crystals of catalase that are negatively stained with the light-atom compound, dipotassium glucose-1,6-diphosphate, reveals Bragg reflections extending to 4.0A (= 0.40 nm). Under the same conditions, negative staining with the traditional heavy-metal salt, ammonium molybdate, also gives diffraction spots extending to 4.0 A. These results establish that negative staining of protein crystals preserves periodic structural information into the high-resolution range, unlike the widely accepted current belief that this methodology can give a resolution limited to only 20-25 A.

Light atom derivatives of structure-preserving sugars are unconventional negative stains

Although glucose and certain other sugars are known to greatly reduce distortion and denaturation of proteins during drying, use of this monosaccharide as an experimental negative stain does not permit imaging of lattice periodicities in test specimens of thin catalase crystals. However, the potassium and sodium salts of several forms of monophosphorylated glucose (200 mM), diphosphorylated glucose, monosulfated glucose, maltose-1-phosphate, and trehalose-6-phosphate, all dry into a glassy layer and scatter transmitted electrons sufficiently to show the 86 A major periods in catalase crystals. Glucose-6-phosphate provides sufficient image contrast at concentrations from 2 mM (=0.067%) to 500 mM (= 16.8%). Underfocusing increases visualization of the periodic lattice, indicating a large contribution of phase contrast to these images. Upon exposure to the electron beam, thicker regions of derivatized saccharides or pure glucose develop bubbling; this redistribution of dried stain largely can be precluded by imaging with low-dose exposures. Power spectra of images of catalase crystals contained within 200 mM disodium glucose-6-phosphate show that periodic information can be recorded to 21 A; some individual features of dipotassium glucose-6-phosphate distribution within the protein lattice have a measured width of around 5 A. The experimental results demonstrate that structure-preserving mono- and di-saccharides also serve successfully as negative stains after they are coupled to light atom scatterers.

Direct structure determination by electron crystallography: protein data sets

Applications of the Sayre equation to the electron crystallographic analysis of protein structures are demonstrated. Starting with a lower-resolution basis phase set obtained from the Fourier-transform of an electron micrograph, it is possible, for example, to extend directly to the higher resolution of the electron diffraction pattern. Examples of such analyses include bacteriorhodopsin, halorhodopsin and the Omp F porin from the outer membrane of Escherichia coli. If a multisolution approach is taken, it may also be possible to carry out ab initio phase determinations, as demonstrated with low-resolution diffraction amplitudes from a negatively-stained membrane protein crystal.