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(The FASEB Journal. 1999;13:S195-S200.)
© 1999 FASEB

Imaging biological matter across dimensions: from cells to molecules and atoms

DANIEL STOFFLER, MICHEL O. STEINMETZ1 and UELI AEBI2

Biozentrum, M.E. Müller Institute for Structural Biology, University of Basel, CH-4056 Basel, Switzerland

2Correspondence: Biozentrum, M. E. Müller Institute for Structural Biology, Klingelbergstrasse 70, CH-4056 Basel, Switzerland. E-mail: aebi{at}ubaclu.unibas.ch


   INTRODUCTION
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INTRODUCTION
LIGHT MICROSCOPY: FROM OPTICAL...
TOWARD ATOMIC INTERPRETATION OF...
WATCHING MACROMOLECULAR MACHINES...
OUTLOOK
REFERENCES
 
IN ADDITION TO X-ray diffraction and NMR spectroscopy, microscopes (i.e., light, electron, and scanning probe microscopes) definitely have become an integrated part of modern structure research. The primary advantages of microscopes are threefold: 1) they directly produce images rather than diffraction patterns or spectras; 2) they enable us to explore biological structure at all levels from the macroscopic to the atomic scale; and 3) they allow biological matter to be imaged in its functional environment. Hence microscopes are complementary to–and not competing with–diffraction methods and spectroscopies.


   LIGHT MICROSCOPY: FROM OPTICAL SECTIONING TO TRACKING SINGLE PARTICLE EVENTS
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INTRODUCTION
LIGHT MICROSCOPY: FROM OPTICAL...
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At the light microscopic (LM) level, fluorescence microscopy (FM) allows us to locate the relative distribution of distinct cellular components (e.g., the different cytoskeletal filament systems) relative to each other within their in vivo environment. The confocal laser scanning microscope (CLSM) makes it possible to look inside cells and tissues in a noninvasive manner by optical sectioning, thereby dissecting the 3-dimensional cell architecture at the level of the cytoskeleton and the various organelles. By using video-enhanced light microscopy (VELM), cell structures with dimensions that are typically 10x below the diffraction-limited resolution of light can be visualized; hence molecular motors can directly be watched at work, and, in combination with optical tweezers, their mechano-chemical performance can be quantified. For example, using a feedback-enhanced double-laser trap system has allowed Finer et al. (1) to directly quantify the force and displacement that results from the interaction of a single myosin motor molecule with a single suspended fluorescent actin filament. By doing so, discrete stepwise movements averaging 11 nm were depicted under conditions of low load, and single-force transients averaging 3–4 pN were measured under isometric conditions. Most exciting, Noji et al. (2) watched single F1-ATPase molecules acting as a rotary motor. To achieve this remarkable result, these investigators attached a fluorescent actin filament to the rotor (i.e., the {gamma}-subunit) of the motor as a marker, thereby enabling them to videotape the rotary motion for >100 revolutions in a row in the presence of ATP.


   TOWARD ATOMIC INTERPRETATION OF ELECTRON MICROSCOPIC DATA
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INTRODUCTION
LIGHT MICROSCOPY: FROM OPTICAL...
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The widest range of dimensions is covered by electron microscopes (EMs). These microscopes are capable of imaging tissues and cells, their organelles, and cytoskeleton and supramolecular assemblies, as well as individual biomolecules, their 3-dimensional molecular architecture, and, ultimately, single atoms (3) . Transmission EM (TEM) in combination with 3-dimensional image reconstruction is now routinely used to determine the overall size and shape of protein molecules and their supramolecular organization and dynamic behavior at the 1–3 nm resolution level (4 5 6) . As an example, in the case of actin filaments, a major constituent of muscle and the cytoskeleton of nonmuscle cells, we have been able to interpret particular structural features at atomic detail (4 , 7 8) . Moreover, we have prepared an undecagold-tagged phalloidin derivative (Au11-PHD) to determine this mushroom toxin’s binding site and orientation within the F-actin filament by scanning transmission electron microscopy (STEM) and 3-dimensional helical reconstruction (9) . Remarkably, when stoichiometrically bound to F-actin, the Au11-PHD moiety of the derivative could be directly visualized by STEM along the two half-staggered long-pitch helical strands of single filaments (Fig. 1C, D ), hence serving as a structural hallmark. The identified phalloidin binding site within F-actin agreed well with the site proposed by the atomic model of Lorenz et al. (10) . However, atomic modeling of the Au11-PHD derivative within the refined and averaged filament reconstruction (Fig. 1E ) yielded an orientation of the toxin within its binding site that was distinct from that obtained by Lorenz et al. (10) . In order for the Au11-tag, which is linked to the phalloidin moiety by an ~17-Å spacer, not to collide with an adjacent intersubunit contact, the phalloidin molecule had to be rotated ~180° around an axis parallel to the filament axis relative to the orientation proposed by Lorenz et al. (10) (Fig. 1F ). Moreover, we critically evaluated two distinct atomic models of the F-actin filament [e.g., the Holmes-Lorenz model (10) versus to the Schutt-Lindberg model (11) ] by combining the structural data obtained by various biochemical constraints (9) . Whereas the Holmes-Lorenz model of the F-actin filament produced a close match with our EM-based Au11-PHD location and orientation with the F-actin 3-dimensional reconstruction and crosslinking data from Vandekerckhove et al. (12) , both our EM and the crosslinking data yielded a rather poor fit with the Schutt-Lindberg model of F-actin.



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Figure 1. Upper panel: Structural analysis of native, PHD- stabilized and Au11-PHD stabilized rabbit muscle F-actin filaments and orientation of PHD within its F-actin binding site (9 , 36) . A) STEM dark-field (ADF) micrograph of a negatively stained (i.e., with 0.75% uranyl formate, pH 4.25) PHD stabilized F-actin filament stretch. B) As in panel A, but freeze-dried and unstained. C) Unstained and freeze-dried Au11-PHD stabilized F-actin filament stretch. D) As in panel C, but contrast adjusted so as to display the highest intensities only, which correspond to single Au11-clusters (diameter ~1 nm) spaced every ~5.5 nm along the two long-pitch helical strands that are staggered by 2.75 nm relative to one another (see yellow lines). E) An averaged and refined 3-dimensional helical reconstruction computed from negatively stained Au11-PHD stabilized F-actin filament stretches (see panel A) has been surface-rendered to include 100% of its nominal molecular mass. The location of the Au11-clusters has been determined from a difference map (i.e., Au11-PHD stabilized F-actin filament reconstruction minus PHD-stabilized F-actin filament reconstruction) and visualized by 1 nm diameter gold spheres. F) Alignment and overlay of an atomic PHD-stabilized F-actin trimer (yellow ribbon; data from Lorenz et al. (10) with the Au11-PHD: F-actin 3-dimensional reconstruction displayed in panel E. The PHD molecule was rotated by ~180° roughly parallel to the filament axis and then replaced by our Au11-PHD derivative (violet CPK with a golden sphere). Bar, 25 nm (AD). Lower panel: Visualization of native (i.e., completely unfixed, never dehydrated/rehydrated, and without any detergent treatment) NPCs by AFM kept alive in near-physiological buffer medium (15) . Corresponding AFM images revealed a distinct morphology for the cytoplasmic (G) and the nuclear face (H) of Xenopus oocyte NEs. The upper right inset in panel G depicts a high-magnification view of the cytoplasmic face so that the eightfold rotational symmetry of individual NPCs is resolved. The lower right inset in panel G depicts a pair of NPCs, one with a plug and one unplugged. H) On the nuclear face, note the remnants of the nuclear lamina depicted in areas devoid of NPCs (27) . The right inset reveals a high-magnification view of the nuclear face. Both the cytoplasmic fibrils (G) and the nuclear basket structures (H) were apparently too flexible to be resolved at higher detail. Superimposed onto these two micrographs are schematic representations of a consensus model of the ~125-MDa vertebrate NPC (13 , 35) . In this model, the ~55-MDa central framework (in pink), made of eight multi-domain spokes embracing a central pore, is sandwiched between a 32-MDa cytoplasmic ring (in blue) and a 21-MDa nuclear ring (in red). From the cytoplasmic ring, eight short kinky fibrils emanate, while the nuclear ring is topped with a basket assembled from eight thin filaments joining distally into a ring. The blue arrowheads indicate the AFM scanning tip relative to the NPC periphery. I) Determination of possible structural changes of the central channel region and possible induction of plugging or unplugging occurring in response to adding calcium to completely unfixed NEs kept in near-physiological buffer by time-lapse AFM. For this purpose, the same specimen area, adsorbed with its nuclear face, was imaged without calcium (upper micrograph) and after addition of 100 µM calcium (lower micrograph). As documented, no plugging or unplugging of individual NPCs was induced by addition of calcium. Two corresponding pairs of NPCs, one unplugged and one plugged, have been marked by blue arrowheads. For a more quantitative comparison, the same 211 unplugged NPCs have been aligned and averaged, and their average radial height profiles computed. In addition, 18 corresponding plugged NPCs have been selected, averaged and their average radial height profiles computed. K) Visualization of the reversible calcium-mediated opening (i.e., +100 µM Ca2+) and closing (i.e., -Ca2+) of the nuclear baskets (i.e., via dilatation of the distal rings, which may act as an iris-like aperture) by time-lapse AFM. The same specimen area has been imaged in the two distinct conformational states with three corresponding NPCs marked by blue arrowheads. For a more quantitative comparison of the closed and open state, 30 corresponding NPCs have been aligned and averaged, and their average radial height profiles computed. Bars, 100 nm.

Nuclear pore complexes (NPCs) are large (~125 MDa) supramolecular assemblies embedded in the double-membraned nuclear envelope (NE) of interphase cells, representing the major gateways mediating nucleocytoplasmic transport (13 14) . To evaluate more systematically the 3-dimensional molecular architecture of native NPCs, energy-filtering transmission electron microscopy (EFTEM) of unfixed and unstained Xenopus oocyte NEs embedded in thick (i.e., ~250 nm) amorphous ice is now pursued and combined with tomographic imaging and reconstruction (15) . This approach, in combination with specific labeling of distinct NPC constitutents, will eventually extend the resolution of this massive organelle to ~2.5 nm so that novel structural features may be located 3-dimensionally andidentified molecularly. This information, in turn, will be a prerequisite for a molecular understanding of NPC function (see below).


   WATCHING MACROMOLECULAR MACHINES IN ACTION BY ATOMIC FORCE MICROSCOPY
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INTRODUCTION
LIGHT MICROSCOPY: FROM OPTICAL...
TOWARD ATOMIC INTERPRETATION OF...
WATCHING MACROMOLECULAR MACHINES...
OUTLOOK
REFERENCES
 
Recently, spectacular advances have been achieved with the atomic force microscope (AFM), the first imaging device allowing direct correlation between structural and functional states of biomolecules in their physiological environment (16 17 18 19 20 21) . To directly watch transport of cargo through individual NPCs, time-lapse AFM of completely unfixed NE preparations kept in near-physiological buffer environment has been performed.

To reproducibly visualize native NPCs under physiological conditions (i.e., without detergent treatment, chemical fixation, or dehydration/rehydration during preparation steps), novel preparation techniques had to be explored (15 , 22) . Typical AFM specimen supports such as mica or glass could not be used for native NEs because these failed to adsorb with stability on these supports. Instead, the best image quality was achieved when carbon-coated EM grids were used. In agreement with earlier EM data of chemically fixed NEs (23 24 25) , AFM images of native NEs revealed a distinct morphology for the cytoplasmic and nuclear face of their NPCs. As the highly flexible cytoplasmic fibrils and the filamentous architecture of the fragile nuclear baskets could not be resolved by AFM, the cytoplasmic face of the NPC exhibited donut-like rings protruding ~35 nm from the NE surface (Fig. 1G ), whereas its nuclear face exhibited ~70-nm high dome-like structures (Fig. 1H ) that were extremely susceptible to mechanical damage by the scanning tip. These height measurements are comparable to values determined by EM of thin sectioned/embedded NEs (26) . In areas devoid of NPCs, remnants of the nuclear lamina (27) could readily be depicted (Fig. 1H ). High-magnification views revealed indications of the eightfold rotational symmetry of individual NPCs (Fig. 1G , upper right inset). Under near-physiological preparation conditions, only a small fraction (i.e., <=10%) of the NPCs harbored a plug within the central pore (Fig. 1G ).

Intrigued by studies of Clapham and co-workers (28) that showed that manipulating the calcium stores residing in the lumen of the NE caused reversible plugging or unplugging of the NPCs, we performed time-lapse AFM experiments to monitor the cytoplasmic channel topography in response to adding or removing micromolar amounts of calcium to the buffer medium surrounding fully native NEs (15) . We started by scanning well-preserved NPC patches kept in low-salt buffer (LSB) completely free of calcium (Fig. 1I , top micrograph). Subsequently, micromolar amounts of calcium were added to the buffer medium. After equilibration of the new buffer condition, the same specimen area was rescanned (Fig. 1i , lower micrograph) so that the same NPCs could be compared with those of the scan before calcium addition. Under these conditions, only ~10% of all NPCs harbored a central cytoplasmic plug before addition of calcium. No plugging or unplugging of corresponding native NPCs was induced by adding calcium; those NPCs that were plugged before addition of calcium remained plugged on addition and vice versa. For a more quantitative comparison, the same 211 unplugged NPCs (Fig. 1I , donut-shaped particle) and 18 plugged NPCs (Fig. 1I , donut-shaped particle with clearly visible plug) before and after addition of calcium were aligned and averaged, and their average radial height profiles were computed. Consistent with earlier observations of negatively stained NEs imaged by EM (23) , the cytoplasmic face of the NPC did not appear to undergo any significant change in response to calcium.

Next, we addressed the question of whether calcium could induce structural changes of the NPC topography (15) , given that Jarnik and Aebi (23) documented that the nuclear baskets of NPCs are dynamic structures in the sense that they disassemble on complete removal of divalent cations and reform on their addition. For this purpose, the same specimen areas of completely unfixed NEs kept in LSB medium were imaged by contact mode before and after adding or removing calcium. By this scenario, topographic changes of the same individual NPCs could be induced (Fig. 1K ) by adding micromolar amounts of calcium to the buffer medium so that previously closed baskets opened up at their tops. Conversely, it could be demonstrated that NEs kept in near-physiological buffer containing micromolar amounts of calcium harbored NPCs with open baskets that could be closed to >90% by adding a calcium chelator (i.e., EGTA; data not shown). To demonstrate the specificity of the calcium-mediated opening and closing of the nuclear baskets, the same type of specimens were imaged in response to adding or removing magnesium instead of calcium. Accordingly, magnesium did not affect the basket structure (data now shown). To analyze the calcium-induced structural changes of the nuclear baskets more quantitatively, the same set of NPCs was translationally aligned and averaged in the two distinct morphological states. Average radial height profiles revealed openings appearing at the distal end of the baskets with diameters of 20–30 nm after addition of calcium (Fig. 1K ). This structural change may be interpreted in terms of the distal ring of the basket acting as an iris-like aperture, as suggested by Panté and Aebi (14) , which might act as a docking or even a gating site for cargo transported in and out of the nucleus. Moreover, the overall height of the baskets protruding out of the NEs did not significantly change; it was 70 nm with or without calcium or magnesium.


   OUTLOOK
TOP
INTRODUCTION
LIGHT MICROSCOPY: FROM OPTICAL...
TOWARD ATOMIC INTERPRETATION OF...
WATCHING MACROMOLECULAR MACHINES...
OUTLOOK
REFERENCES
 
Novel optical techniques have been developed recently that allow mechanical and ligand-binding events of single myosin molecules to be monitored simultaneously (29) . Also, the axial rotation of single actin filaments sliding over myosin molecules immobilized on a glass surface could directly be visualized through fluorescence polarization imaging of individual fluorophores sparsely bound to the filaments (30) . These examples effectively document that LM, in addition to videotaping single particle events, can now also be used to directly evaluate mechanical properties, chemical states, and conformational changes of single macromolecular machines.

A milestone in high-resolution EM has been the elucidation of atomic models of membrane and cytoskeletal proteins by electron crystallography (31 32 33) . Currently, EM at a resolution sufficient to depict atomic detail (<=3.5 Å) requires a 2-dimensional crystalline protein array analogous to the 3-dimensional crystal required for X-ray crystallography. However, the potential exists to bypass this limitation and collect the data from randomly oriented single particles embedded in an amorphous ice film, thus rendering any macromolecular assembly with a well-defined structure accessible to high-resolution structural analysis.

As outlined above, time-lapse AFM of native NPCs recorded in near-physiological buffer environment has opened the possibility to directly and reproducibly track functionally significant structural changes such as the opening and closing of the nuclear baskets (i.e., the distal rings) at the level of individual NPCs (15) . Therefore, the NPC may become a role model for directly correlating structural data with functional states and dynamic features of living matter by time-lapse AFM at the level of individual macromolecular machines. Another hallmark in single-molecule AFM has been the tracking of the reversible unfolding of titin immunoglobulin domains by repeated stretching of individual titin molecules (34) . The potential for such experiments to provide a more rational understanding of single-molecule mechanics is evident, and the emergence of novel findings along these lines is only limited by our imagination.


   ACKNOWLEDGMENTS
 
This work was supported by the M. E. Müller Foundation of Switzerland, the Swiss National Science Foundation Priority Program NFP 36 (‘Nano-Sciences’), and a grant from the Chemical Industry Foundation of Basel to D.S.


   FOOTNOTES
 
1 Present address: Novartis Pharma Research, CH-4002 Basel, Switzerland.


   REFERENCES
TOP
INTRODUCTION
LIGHT MICROSCOPY: FROM OPTICAL...
TOWARD ATOMIC INTERPRETATION OF...
WATCHING MACROMOLECULAR MACHINES...
OUTLOOK
REFERENCES
 

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