Molecular orientation of bacteriorhodopsin within the purple membrane of Halobacterium halobium

Perspective: Biochemical and Physical Constraints Associated With Preparing Thin Specimens for Single-Particle Cryo-EM

While many aspects of single-particle electron cryo-microscopy (cryo-EM) of biological macromolecules have reached a sophisticated level of development, this is not yet the case when it comes to preparing thin samples on specimen grids. As a result, there currently is considerable interest in achieving better control of both the sample thickness and the amount of area that is useful, but this is only one aspect in which improvement is needed. This Perspective addresses the further need to prevent the macromolecular particles from making contact with the air-water interface, something that can result in preferential orientation and even structural disruption of macromolecular particles. This unwanted contact can occur either as the result of free diffusion of particles during the interval between application, thinning and vitrification of the remaining buffer, or-when particles have been immobilized-by the film of buffer becoming too thin prior to vitrification. An opportunity now exists to apply theoretical and practical insights from the fields of thin-film physical chemistry and interfacial science, in an effort to bring cryo-EM sample preparation to a level of sophistication that is comparable to that of current data collection and analysis.

Highlighting membrane protein structure and function: A celebration of the Protein Data Bank

Biological membranes define the boundaries of cells and compartmentalize the chemical and physical processes required for life. Many biological processes are carried out by proteins embedded in or associated with such membranes. Determination of membrane protein (MP) structures at atomic or near-atomic resolution plays a vital role in elucidating their structural and functional impact in biology. This endeavor has determined 1198 unique MP structures as of early 2021. The value of these structures is expanded greatly by deposition of their three-dimensional (3D) coordinates into the Protein Data Bank (PDB) after the first atomic MP structure was elucidated in 1985. Since then, free access to MP structures facilitates broader and deeper understanding of MPs, which provides crucial new insights into their biological functions. Here we highlight the structural and functional biology of representative MPs and landmarks in the evolution of new technologies, with insights into key developments influenced by the PDB in magnifying their impact.

Factors that Influence the Formation and Stability of Thin, Cryo-EM Specimens

Poor consistency of the ice thickness from one area of a cryo-electron microscope (cryo-EM) specimen grid to another, from one grid to the next, and from one type of specimen to another, motivates a reconsideration of how to best prepare suitably thin specimens. Here we first review the three related topics of wetting, thinning, and stability against dewetting of aqueous films spread over a hydrophilic substrate. We then suggest that the importance of there being a surfactant monolayer at the air-water interface of thin, cryo-EM specimens has been largely underappreciated. In fact, a surfactant layer (of uncontrolled composition and surface pressure) can hardly be avoided during standard cryo-EM specimen preparation. We thus suggest that better control over the composition and properties of the surfactant layer may result in more reliable production of cryo-EM specimens with the desired thickness.

Nanosized optoelectronic devices based on photoactivated proteins

Molecular nanoelectronics is attracting much attention, because of the possibility to add functionalities to silicon-based electronics by means of intrinsically nanoscale biological or organic materials. The contact point between active molecules and electrodes must present, besides nanoscale size, a very low resistance. To realize Metal-Molecule-Metal junctions it is, thus, mandatory to be able to control the formation of useful nanometric contacts. The distance between the electrodes has to be of the same size of the molecule being put in between. Nanogaps technology is a perfect fit to fulfill this requirement. In this work, nanogaps between gold electrodes have been used to develop optoelectronic devices based on photoactive proteins. Reaction Centers (RC) and Bacteriorhodopsin (BR) have been inserted in nanogaps by drop casting. Electrical characterizations of the obtained structures were performed. It has been demonstrated that these nanodevices working principle is based on charge separation and photovoltage response. The former is induced by the application of a proper voltage on the RC, while the latter comes from the activation of BR by light of appropriate wavelengths.

Electron and atomic force microscopy of membrane proteins

Electron crystallography is becoming a powerful tool for the resolution of membrane protein structures. The past year has seen the production of a bacteriorhodopsin model at 3.5 A and the structure of aquaporin 1 approaching atomic resolution. Determination of surface topographies of 2D crystals using the atomic force microscope is similarly advancing to a level that reveals submolecular details. As the latter is operated in solution, membrane proteins can be observed at work.

Imaging purple membranes in aqueous solutions at sub-nanometer resolution by atomic force microscopy

Purple membranes adsorbed to mica were imaged in buffer solution using the atomic force microscope. The hexagonal diffraction patterns of topographs from the cytoplasmic and the extracellular surface showed a resolution of 0.7 and 1.2 nm, respectively. On the cytoplasmic surface, individual bacteriorhodopsin molecules consistently exhibited a distinct substructure. Depending on the pH value of the buffer solution, the height of the purple membranes decreased from 5.6 nm (pH 10.5) to 5.1 nm (pH 4). The results are discussed with respect to the structure determined by cryo-electron microscopy.

Interfacial energies and surface-tension forces involved in the preparation of thin, flat crystals of biological macromolecules for high-resolution electron microscopy

It is generally agreed that surface-tension forces and the direct interaction between the specimen and either the air-water interface or the water-substrate interface can influence significantly the preparation of biological materials for electron microscopy. Even so, there is relatively little systematic information available that would make it possible to control surface-tension forces and interfacial energies in a quantitative fashion. The main objective in undertaking the present work has been to understand somewhat better the factors that influence the degree of specimen flatness of large, monolayer crystals of biological macromolecules. However, the data obtained in our work should be useful in understanding the preparation of specimens of biological macromolecules in general. Data collection by electron diffraction and electron microscopy at high resolution and high tilt angles requires thin crystals of biological macromolecules that are flat to at least 1 degree, and perhaps less than 0.2 degrees, over areas as large as 1 micron2 or more. In addition to determining empirically by electron diffraction experiments whether sufficiently flat specimens can be prepared on various types of modified or unmodified carbon support films, we have begun to use other techniques to characterize both the surfaces involved and the interaction of our specimen with these surfaces. In the specific case of large, monolayer crystals of bacteriorhodopsin prepared as glucose-embedded specimens on hydrophobic carbon films, it was concluded that the initial interfacial interaction involves adsorption of the specimen to the air-water interface rather than adsorption of the specimen to the substrate. Surface-tension forces at the air-water interface and an apparently repulsive interaction between the specimen and the hydrophobic carbon seem to be major factors influencing the specimen flatness in this case. In the more general case it seems likely that interfacial interactions with either the substrate or the air-water interface can be variously manipulated in the search to find desirable conditions of specimen preparation.

Monolayer freeze-fracture and scanning tunneling microscopy

This article reviews research on planar monolayer methods, application of the methods to analyses of transmembrane signaling, and the combination of these methods with scanning tunneling microscopy (STM). Past research has involved the development of monolayer freeze-fracture methods. These include monolayer freeze-fracture autoradiography (MONOFARG), an electron microscopic cytochemical method to analyze in-plane distributions of radioisotopes, and double-labeled membrane splitting (DBLAMS) and single-membrane monolayer splitting (SMMS), methods to analyze transmembrane distributions of native and radiolabeled proteins and lipids. Present research has focussed on using these methods to investigate mechanisms of transmembrane signaling mediated by protein kinase C (PKC), including the transbilayer distribution of the tumor promoter TPA, a lipophilic activator of PKC, and the transbilayer distribution of peripheral membrane proteins phosphorylated by PKC. Future work will involve the combination of planar sample preparation with STM. The principles and applications of biological STM are briefly reviewed and a low-resolution STM image of a planar purple-membrane monolayer is included. The combination of planar methods and STM can provide the chemical information lacking in STM images enabling microscopists to investigate biochemical phenomena at nanometer resolution.

Cryo-electron microscopy of vitrified specimens

Cryo-electron microscopy of vitrified specimens was just emerging as a practical method when Richard Henderson proposed that we should teach an EMBO course on the new technique. The request seemed to come too early because at that moment the method looked more like a laboratory game than a useful tool. However, during the months which ellapsed before the start of the course, several of the major difficulties associated with electron microscopy of vitrified specimens found surprisingly elegant solutions or simply became non-existent. The course could therefore take place under favourable circumstances in the summer of 1983. It was repeated the following years and cryo-electron microscopy spread rapidly. Since that time, water, which was once the arch enemy of all electronmicroscopists, became what it always was in nature – an integral part of biological matter and a beautiful substance.

Projected structure of the pore-forming OmpC protein from Escherichia coli outer membrane

A single-projection structure analysis of a bacterial outer membrane protein, OmpC, has been carried out by electron microscopy of frozen hydrated specimens. Two distinct crystal polymorphs have been observed in the frozen-hydrated samples, and projection structures of both forms have been obtained to a resolution of 13.5 A. Preliminary examination of negatively stained samples revealed the expected, trimeric appearance of pores in the OmpC specimens. Electron microscopy of unstained, frozen-hydrated OmpC reveals the trimeric pore structure with equal clarity. In addition, the overall molecular envelope of the protein is readily discerned, and a major lipid-containing domain can also be seen. Because of the small coherent patch size, mosaic disorder, and unpredictable polymorphism of the presently available specimens, three-dimensional reconstruction of frozen-hydrated OmpC has not been carried out.

Cryo-electron microscopy of viruses

Thin vitrified layers of unfixed, unstained and unsupported virus suspensions can be prepared for observation by cryo-electron microscopy in easily controlled conditions. The viral particles appear free from the kind of damage caused by dehydration, freezing or adsorption to a support that is encountered in preparing biological samples for conventional electron microscopy. Cryo-electron microscopy of vitrified specimens offers possibilities for high resolution observations that compare favourably with any other electron microscopical method.

Electron crystallographic studies of DNA

The conformation of DNA in thin, platelet crystals is being studied by electron microscopy and diffraction, and by other techniques including circular dichroism spectroscopy. Specimens are prepared in the frozen-hydrated state for the electron microscope. Electron diffraction patterns from the crystals extend to 3.5 A, and lattice images with resolution to 6.5 A have been obtained. Electron diffraction patterns from fibers in the same preparations show a stacking distance between base pairs which is larger than in most DNA conformations. The data so far available can be interpreted to indicate that the DNA in the crystals is in a conformation which has not previously been reported and which is in the B family, unwound to have 12 base pairs per turn. Model calculations have been performed which support this interpretation and which show that a three-dimensional reconstruction, with even very limited data, could confirm the helix parameters.

Specimen preparative methods for electron crystallography of soluble proteins

Technical factors which influence the choice of specimen preparation method for electron crystallographic study of thin crystals of soluble proteins are discussed. Ice embedding appears to be the most desirable choice of preparation method. However, in terms of the yield of major structural information, we conclude that negative stain remains a useful method for low resolution and glucose embedding for high resolution.

Monolayer freeze-fracture autoradiography: origins and directions

Monolayer freeze-fracture autoradiography (MONOFARG) is a product of two earlier methods: freeze-fracture autoradiography (FARG) and cell monolayer freeze-fracture. MONOFARG incorporates many of the basic principles and cytochemical goals of FARG while exploiting the technical advantages of monolayer freeze-fracturing. The latter method offers the opportunity to process freeze-dried 'half' membranes at room temperature. Although the feasibility of MONOFARG has been shown for qualitative analyses of split membranes, it's quantitative feasibility for transmembrane and in-plane analyses has just begun to be documented. An example of one aspect of that documentation is included in this report. The distribution of 125I-FITC-Concanavalin-A in the plane of split plasma membranes, human erythrocyte extracellular fracture faces, was examined and found to be homogeneous. The relevance of this finding to recently described double labelled membrane splitting experiments is discussed. The future of MONOFARG appears promising, especially in the application of the technique to biologically significant questions.

Linking regions between helices in bacteriorhodopsin revealed

Three-dimensional electron-microscopic structural analysis requires the combination of many different tilted views of the same specimen. The relative difficulty of tilting the sample to high angles >60 degrees without introducing severe distortion due to different focal distances across the specimen entails that the observable range of electron diffraction data is often limited to this range of angles. Thus, it is generally not possible to observe the diffraction maxima that lie within the conical region of reciprocal space around the direction perpendicular to the electron microscope grid. The absence of data in this region leads to a predictable distortion in the object, and for +/-60 degrees tilting makes the resolution essentially twice as bad in the direction perpendicular to the grid as it is for the in-plane image. Constrained density map modification and refinement methods can significantly reduce these effects. A method has been developed, tested on model cases, and applied to the electron-microscopic structure determination of bacteriorhodopsin in order to visualize the location of linking regions between helices. Electron-microscopic structural analysis of bacteriorhodopsin (Henderson and Unwin. 1975 Nature [Lond.] 257:28-32.) showed that the molecule consists of seven rods of density each nearly spanning the lipid bilayer. Owing to the distortion introduced by the missing conical region of reciprocal space data, no density was visible for the polypeptide segments linking the alpha-helices. Density in the refined maps indicates the location of at least five of the extrahelical segments of the polypeptide. The total number of possible ways of interconnecting the helices is reduced from 7! (5,040) to the five most consistent possibilities without recourse to other considerations. In addition, the density for the helical regions is more uniform and cylindrical throughout their length, and the length of the helices increases from 35 to 45 A, close to the membrane thickness of 49 A obtained for membranes dried in vacuo. Only three of the five structures consistent with the location of observed linkers place the seventh helix, onto which the chromophore can be attached by reduction in the light, at a position consistent with the main peak for deuterated retinal in the structure, as derived from neutron diffraction analysis. Two of these models are also consistent with the possible location of some of the reduced chromophore on helix B, at lys 40/41 after reduction in the dark, as well as lys 216 on helix G.

Reproducibility of electron diffraction intensity data obtained from hydrated microcrystals of rat hemoglobin

Analysis of electron diffraction patterns from rat hemoglobin taken at 200 kV on a wet stage yields intensity data to a resolution of 2-3 A which are as reproducible as those from typical X-ray diffraction. Some crystals were so similar that the differences in measured intensities were insignificant (R = 0.056), but in other cases real differences between crystals were observed (R = 0.33). Dynamic scattering was insignificant under our diffraction conditions; however, exposures to electron doses as low as 10(-2) e/A2 produced detectable changes in measured intensities. Limits to the reproducibility of the data are set by radiation damage and errors in microdensitometry.

Single bacteriorhodopsin molecules revealed on both surfaces of freeze-dried and heavy metal-decorated purple membranes

The flat sheets of the purple membrane from Halobacterium halobium contain only a single protein (bacteriorhodopsin) arranged in a hexagonal lattice. After freeze-drying at -80 degrees C (a method that is superior to air-drying), shadowing with tantalum/tungsten, and image processing, structural details on both surfaces are portrayed in the range of 2 nm. One surface is rough and lattice lines are clearly visible, whereas the other is smooth and the hexagonal order seems to be absent. The optical diffraction patterns, however, indicate a hexagonal lattice for both surfaces. In addition, these diffraction patterns are characteristic and easily distinguished. The orientation of the two surfaces was identified by silver decoration: partial condensation of silver on purple membranes enabled the smooth surface to be identified as the plasmatic and the rough surface as the exoplasmic surface. After image processing, the exoplasmic surface shows a triplet structure which exactly fits the projected structure determined by Unwin and Henderson (1975. Nature(Lond.). 257:28-32) at molecular resolution, whereas, on the plasmatic surface, four image details per unit cell are visible. Three of them match the arrangement of bacteriorhodopsin, whereas the fourth must be located over a lipidic array. Summarizing these results, it is possible to show the part of each single bacteriorhodopsin protein that is present in the surfaces of the purple membrane. By "shadowing" the membranes perpendicularly, we prove that these components of the surfaces are mainly portrayed by a decoration effect of the tantalum/tungsten condensate.

Location of the chromophore in bacteriorhodopsin

We present a location for the retinylidene chromophore in dark-adapted bacteriorhodopsin based on the differences in neutron scattering between purple membrane preparations reconstituted with retinal and with deuterated retinal. The Fourier difference density map contains more peaks than expected, and additional arguments are introduced to exclude artificial peaks, caused by the reconstitution techniques or the limited resolution of the diffraction data. The membrane preparation used is necessarily dark-adapted and therefore contains 13-cis- and all-trans-retinal isomers in roughly equal amounts. However, we find only a single position for both isomers. Presumably, the difference in conformation caused by isomerization around the C13-C14 double bond is minimized by rotation around other bonds. The retinal is located between alpha-helical segments of the protein and its nearest neighbor (intratrimer) distance is 26 A; the next-nearest neighbor (intertrimer) distance is 38 A.

Path of the polypeptide in bacteriorhodopsin

An attempt has been made to fit the amino acid sequence of bacteriorhodopsin to the three-dimensional density map of the molecule. First, seven segments of the sequence were selected as being probable transmembrane alpha helices. Then each of the 5040 possible ways of fitting these seven segments into the seven regions of helical density in the map were evaluated based on the criteria of connectivity of the nonhelical link regions, charge neutralization, and total scattering density per helix. A single model that may be experimentally tested emerged as the most probable.

Prospects for extending the resolution limit of the electron microscope

The factors that limit the performance of present-day high-resolution electron microscopes include the source brightness, the temporal coherence of the illumination, and phase contrast 'artefacts' due to spherical aberration and defocus. Further advancement of the instrumental performance might be accomplished in different ways, including the use of high coherence conditions combined with image restoration; the use of higher accelerating voltages; the use of aberration correctors; or the use of conditions for incoherent image formation. Current efforts in each of these directions are reviewed, from which it is evident that the combined use of higher voltages and improved coherence is the direction that is presently leading to the greatest degree of progress.