3D reconstruction from electron micrographs: its potential and practical limitations

Assembly of 2-D membrane protein crystals: dynamics, crystal order, and fidelity of structure analysis by electron microscopy

Membrane protein reconstitution into two-dimensional (2-D) ordered arrays is described. The assembly of 2-D crystals may be modeled as a two-step process: the membrane protein is first integrated in the lipid bilayer and then crystallized by removal of excess detergent or lipid and/or by precipitating agents. Lipid-detergent, protein-detergent, and lipid-protein interactions are critical during the first step, while lipid-protein and protein-protein interactions dominate events in the second step. The evidence supporting this model results from quasielastic light scattering analyses and electron microscopy of different lipid-detergent systems and reconstitution experiments with Escherichia coli porin OmpF, Phormidium laminosum photosystem I reaction centers, and integral membrane proteins of mammalian lens fiber cells.

A common channel-forming motif in evolutionarily distant porins

Four new crystal packings of Escherichia coli porins are presented (phosphoporin, maltoporin, and two crystal forms of matrix porin). These were determined by molecular replacement methods using a polyalanine trial model acquired from the refined coordinates of porin from Rhodobacter capsulatus. The successful molecular replacement shows that the dominant motif found in R. capsulatus porin (a 16-stranded antiparallel beta-barrel) also applies to the E. coli porins, despite the lack of significant amino acid sequence homology. A 30 degrees-40 degrees tilt of the beta-strands with respect to the membrane normal was derived from the intensity distributions in the X-ray diffraction patterns for each porin studied, stressing their similarity. In view of the evolutionary distance between enteric and photosynthetic bacteria, the antiparallel beta-barrel may have significance as a basic structural motif for the formation of bacterial membrane channel structures.

The three-dimensional structure of the Na,K-ATPase from electron microscopy

The structure of Na,K-ATPase has been studied by electron microscopy and image reconstruction. A three-dimensional structure of this enzyme has been obtained to an overall resolution of 2.5 nm using data from specimens of negatively stained dimer sheets tilted through a range of angles +/- 60 degrees. The reconstruction shows a complex mass distribution consisting of ribbons of paired molecules extending approximately 6.0 nm from the cytoplasmic side of the membrane. The molecular envelope consists of a massive "body" with "lobe" and "arm" structures projecting from it. The body has a columnar shape and is tilted with respect to the plane of the membrane. The region of interaction responsible for dimer formation is located between two bodies and is clearly visible in the reconstruction. It has been identified as a segment in the amino-terminal portion of the alpha subunit. The arms that interconnect the ribbons are located close to the membrane and are most probably formed by the beta subunits.

Porin channel triplets merge into single outlets in Escherichia coli outer membranes

Previous observations on the structural and functional properties of porin, the matrix protein of Escherichia coli, have indicated that the channel-forming trimers span the outer membranes of the bacterial cell, forming a molecular sieve. By using electron microscopy and image reconstruction, we demonstrate here that three channels on the outer surface of the cell merge into a single channel at the periplasmic face. Conductance measurements using conditions under which single activated triplets could be observed led us to conclude that the three individual consecutive closing steps reflect three channels within a single trimeric unit. Statistical analysis of conductance levels revealed that the first relaxation step is distinctly smaller than the two subsequent channel closings. This functional observation can be explained if the channels of porin trimers coalesce.

The structure of the stalk surface layer of a brine pond microorganism: correlation averaging applied to a double layered lattice structure

The surface layer of the stalk of a prosthecate halophilic microorganism is a periodic array (space group p3m1) comprised of electron dense trimers with a centre to centre spacing of 9.0 nm. The structure is reminiscent of E. coli porin. We have demonstrated that the method of correlation averaging can be effectively used to separate overlapping lattices, and that this results in a higher fidelity reconstruction, when compared to the established method of Fourier filtration. Two statistical methods are used to determine the resolution of the correlation average as a function of the number of 'windows' averaged. (i) The phase residual of spatial frequencies in Fourier space is computed between independently obtained subaverages, and (ii) a new method of Q factor analysis examines the cumulative vector sum in Fourier space as a function of the number of windows averaged. Both methods give a resolution of 1/2.1 nm-1.