Two-dimensional crystals of Escherichia coli maltoporin and their interaction with the maltose-binding protein

Negative Staining and Image Classification - Powerful Tools in Modern Electron Microscopy

Vitrification is the state-of-the-art specimen preparation technique for molecular electron microscopy (EM) and therefore negative staining may appear to be an outdated approach. In this paper we illustrate the specific advantages of negative staining, ensuring that this technique will remain an important tool for the study of biological macromolecules. Due to the higher image contrast, much smaller molecules can be visualized by negative staining. Also, while molecules prepared by vitrification usually adopt random orientations in the amorphous ice layer, negative staining tends to induce preferred orientations of the molecules on the carbon support film. Combining negative staining with image classification techniques makes it possible to work with very heterogeneous molecule populations, which are difficult or even impossible to analyze using vitrified specimens.

General model for lipid-mediated two-dimensional array formation of membrane proteins: application to bacteriorhodopsin

Based on experimental evidence for 2D array formation of bacteriorhodopsin, we propose a general model for lipid-mediated 2D array formation of membrane proteins in lipid bilayers. The model includes two different lipid species, "annular" lipids and "neutral" lipids, and one protein species. The central assumption of the model is that the annular lipids interact more strongly with the protein than with the neutral lipids. Monte Carlo simulations performed on this model show that 2D arrays of proteins only form when there are annular lipids present. In addition, no arrays form if all of the lipids present are annular lipids. The geometry of the observed arrays is for the most part hexagonal. However, for a certain range of low annular lipid/protein ratios, arrays form that have geometries other than hexagonal. Using the assumption that the hydrocarbon chains of the annular lipids are restricted in motion when close to a protein, we expand the model to include a ground state and an excited state of the annular lipids. The main result from the extended model is that within a certain temperature range, increasing the temperature will lead to larger and more regular protein arrays.

2D crystallization of membrane proteins: rationales and examples

The difficulty in crystallizing channel proteins in three dimensions limits the use of X-ray crystallography in solving their structures. In contrast, the amphiphilic character of integral membrane proteins promotes their integration into artificial lipid bilayers. Protein-protein interactions may lead to ordering of the proteins within the lipid bilayer into two-dimensional crystals that are amenable to structural studies by electron crystallography and atomic force microscopy. While reconstitution of membrane proteins with lipids is readily achieved, the mechanisms for crystal formation during or after reconstitution are not well understood. The nature of the detergent and lipid as well as pH and counter-ions is known to influence the crystal type and quality. Protein-protein interactions may also promote crystal stacking and aggregation of the sheet-like crystals, posing problems in data collection. Although highly promising, the number of well-studied examples is still too small to draw conclusions that would be applicable to any membrane protein of interest. Here we discuss parameters influencing the outcome of two-dimensional crystallization trials using prominent examples of channel protein crystals and highlight areas where further improvements to crystallization protocols can be made.

Structure of maltoporin from Salmonella typhimurium ligated with a nitrophenyl-maltotrioside

The maltodextrin-specific (malto-)porin from Salmonella typhimurium has been crystallized. Its three-dimensional structure was determined at 2.4 A resolution (1 A = 0.1 nm). A comparison with the structure of the homologous porin from Escherichia coli as well as with the sequences of other related porins showed that there are regions of appreciable sequence and structure variability, despite close overall similarity. The maltoporin structure was analyzed with a bound nitrophenyl-maltotrioside as well as without ligand. Maltotrioside binding had a negligible effect on the polypeptide structure. It binds at the pore eyelet assuming a conformation close to the natural amylose helix.

The Campylobacter jejuni porin trimers pack into different lattice types when reconstituted in the presence of lipid

Purified major outer membrane protein of Campylobacter jejuni exhibited different classes of molecules by SDS/PAGE and immunoblotting. A high-molecular-mass product (120-140 kDa) was observed under mild conditions of solubilization, a folded monomeric form of 35 kDa was seen when treated at high SDS concentrations and finally, a single band around 45 kDa occurred when the sample was heated to 96 degrees C [Bolla, J. M., Loret, E., Zalewski. M. & Pages, J. M. (1995) J. Bacteriol. 177, 4266-4271]. The high-molecular-mass product was reconstituted into two-dimensional crystals in the presence of phospholipids and Mg2+. The C. jejuni porin required different conditions for successful reconstitution into two-dimensional crystals than the Escherichia coli porin OmpF. Electron microscopy and digital image processing of negatively stained specimens revealed a rectangular lattice with a unit cells size of a = 8.9 nm, b = 14.9 nm, an oblique lattice with a = 8.9 nm, b = 30.1 nm, gamma = 98 degrees, and a trigonal lattice with a = b = 9.6 nm. Projection maps were calculated to a resolution of 2 nm, and exhibited a trimeric protein with three stain-filled indentations.

Bacterial porins: structure and function

Within the class of integral membrane proteins, the bacterial porins display a remarkable resistance to denaturants and proteases. This stability is probably crucial for the formation of highly ordered, three-dimensional crystals. Structural analysis of these crystals has been possible in atomic detail. This analysis has revealed interesting features, such as the aromatic girdles, and has helped to explain several observations, including the porins' ability to discriminate between polar and non-polar solutes. Recent research has thus improved our understanding of the porins in a qualitative fashion.

S-layer protein from Thermus thermophilus HB8 assembles into porin-like structures

The cells of the extreme thermophile Thermus thermophilus are surrounded by a regular layer (S-layer) built up by a protein with an apparent molecular mass of 100 kDa (P100). From purified membrane fractions, three different class of two-dimensional crystals can be obtained by following alternative extractive procedures. One of these crystals, with p6 symmetry, clearly represents the native S-layer detected by freeze etching on whole cells, while the other two, showing p2 and p3 symmetries respectively, closely resemble aggregates of bacterial porins. We demonstrate here by limited proteolysis and Western blotting the surprising fact that the protein component of the three crystals is the P100 protein. Our biochemical data also show how this protein forms Ca(2+)-stabilized trimers in each crystal, which support the structural analysis that points to p3 units as the common structural block in all of them, and again resembles the situation found in bacterial porins.

2D crystallization: from art to science

The techniques as well as the principles of the 2D crystallization of membrane and water-soluble proteins for electron crystallography are reviewed. First, the biophysics of the interactions between proteins, lipids and detergents is surveyed. Second, crystallization of membrane proteins in situ and by reconstitution methods is discussed, and the various factors involved are addressed. Third, we elaborate on the 2D crystallization of water-soluble proteins, both in solution and at interfaces, such as lipid monolayers, mica, carbon film or mercury surfaces. Finally, techniques and instrumentations that are required for 2D crystallization are described.

Has negative staining still a place in biomacromolecular electron microscopy?

Transmission electron microscopy of proteins has provided molecular- and in a few cases near-atomic-resolution structural information. In this review, we critically evaluate the potential and the limitations in obtaining molecular resolution, particularly with negatively stained specimens, and put these into perspective with cryomicroscopy of unstained frozen-hydrated and sugar-embedded preparations.