A deeper mechanistic understanding of the saccharification of cellulosic biomass could enhance the efficiency of biofuels development. We report here the real-time visualization of crystalline cellulose degradation by individual cellulase enzymes through use of an advanced version of high-speed atomic force microscopy. Trichoderma reesei cellobiohydrolase I (TrCel7A) molecules were observed to slide unidirectionally along the crystalline cellulose surface but at one point exhibited collective halting analogous to a traffic jam. Changing the crystalline polymorphic form of cellulose by means of an ammonia treatment increased the apparent number of accessible lanes on the crystalline surface and consequently the number of moving cellulase molecules. Treatment of this bulky crystalline cellulose simultaneously or separately with T. reesei cellobiohydrolase II (TrCel6A) resulted in a remarkable increase in the proportion of mobile enzyme molecules on the surface. Cellulose was completely degraded by the synergistic action between the two enzymes.

The atomic force microscope (AFM) has a unique capability of allowing the high-resolution imaging of biological samples on substratum surfaces in physiological solutions. Recent technological progress of AFM in biological research has resulted in remarkable improvements in both the imaging rate and the tip force acting on the sample. These improvements have enabled the direct visualization of dynamic structural changes and dynamic interactions occurring in individual biological macromolecules, which is currently not possible with other techniques. Therefore, high-speed AFM is expected to have a revolutionary impact on biological sciences. In addition, the recently achieved atomic resolution in liquids will further expand the usefulness of AFM in biological research. In this article, we first describe the various capabilities required of AFM in biological sciences, which is followed by a detailed description of various devices and techniques developed for high-speed AFM and atomic-resolution in-liquid AFM. We then describe various imaging studies performed using our cutting-edge microscopes and their current capabilities as well as their limitations, and conclude by discussing the future prospects of AFM as an imaging tool in biological research.

One-sentence summary:Intrinsic cooperativity engenders cyclical propagation of conformational states in the stator ring of an ATP-driven rotary motor. 2 ABSTRACTF 1 is an ATP-driven motor in which three torque-generating β subunits in the α 3 β 3 stator ring sequentially undergo conformational changes upon ATP hydrolysis to rotate the central shaft γ unidirectionally. Although extensive experimental and theoretical work has been done, the structural basis of cooperative torque generation to realize the unidirectional rotation remains elusive. We use high-speed atomic force microscopy to show that the rotor-less F 1 still "rotates"; in the isolated α 3 β 3 stator ring, the three β subunits cyclically propagate conformational states in the counterclockwise direction, similar to the rotary shaft rotation in F 1 . The structural basis of unidirectionality is programmed in the stator ring. These findings have implications for cooperative interplay between subunits in other hexameric ATPases.3 F 1 -ATPase, a water-soluble portion of ATP synthase (1), is a rotary motor protein. The α 3 β 3 γ subcomplex (referred to here as F 1 ) suffices as the motor, in which the rotor γ subunit rotates in the stator α 3 β 3 ring upon ATP hydrolysis (2). The concept of the "rotary catalysis" of F 1 was proposed based on biochemical studies (3). It was strongly supported by the first crystal structure (4) and directly proven by observations of rotating single molecules (5). In F 1 , the catalytic sites are located at the α-β interfaces, mainly on the β subunits. In the crystal structure (4), three catalytic sites are in different nucleotide-bound states; one binds to an ATP analog (α TP -β TP in Fig. 1E), another binds to ADP (α DP -β DP ), and the third is unbound (α E -β E ). Both β TP and β DP assume the closed conformation, swinging the C-terminal domain toward γ, whereas β E assumes the open conformation, swinging the domain away from γ. As these two general conformational states appear to push or be pushed by γ, respectively, it was proposed that interactions with γ control the conformational and catalytic states of individual βs to sequentially generate torque (6). In fact, some biochemical studies are thought to suggest that the α 3 β 3 ring alone does not possess intrinsic cooperativity and γ mediates the interplay among βs (7-9). This view was reinforced by studies showing that backward mechanical rotation of γ with external force reverses the chemical reaction toward ATP synthesis (10, 11), whereas forced forward rotation results in accelerated ATP binding (12). 4Recently, however, this contention has been challenged by the finding that even when most interaction sites between β and γ are abolished, F 1 retains catalytic power to rotate γ unidirectionally (13, 14). A few biochemical studies also suggest the intrinsic cooperativity of the α 3 β 3 ring (15, 16). However, as conventional single-molecule optical microscopy requires attachment of a probe onto the rotary shaft for visualization (5), it does not allow direct examin...

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Remarkably, the bR-bR interaction in the transiently formed assembly elicits both positive and negative cooperative effects on the decay kinetics as the initial bR recovers. By the bipolar nature of the cooperativity, however, the turnover rate of the phtocycle is maintained constant on average, irrespective of the light intensity.Thus, the direct and high-resolution visualization of dynamically acting molecules is a powerful new approach to gaining insight into elaborate bimolecular processes. 2 The biological function of proteins is closely associated with their ability to undergo structural changes. In many cases, these structural changes are triggered by external stimuli including pH, temperature, ligand binding, mechanical stress, and light.Although their direct real-space and real-time visualization is a straightforward approach to understanding the dynamic molecular processes, the lack of suitable techniques has precluded it. Atomic force microscopy (AFM) is a versatile technique to image proteins in liquids at sub-molecular resolution, but its poor temporal resolution has meant an availability of only static or slow time-lapse images of proteins [1][2][3][4][5] . In the last decade, various efforts have been carried out to increase the scan speed of AFM 6-9 .As a result, single protein molecules exhibiting Brownian motion are captured on video at a highest temporal resolution of ~30 ms 10 . However, dynamic visualization of physiologically relevant conformational changes in proteins has been difficult because tip-sample interaction tends to interfere with the physiological functions. To solve this problem, a new method has recently been developed which allows fast and precise control of the tip-sample distance with a minimum load to the sample 7 . This report presents the first ever exemplification of dynamic imaging of a functioning biological sample.Bacteriorhodopsin (bR) is a well-known example of the association between stimulus-triggered structural dynamics and biological function 11,12 , and its direct visualization has long been a goal. bR contains seven transmembrane α-helices (named A-G) enclosing the chromophore retinal 13,14 . In the photocycle, a series of spectral intermediates, designated J, K, L, M, N, and O, occur in that order 12 . The light-induced conformational changes in bR have been investigated by various methods 15-25 , leading to a consensus that the proton channel at the cytoplasmic surface is opened by the tilting of helix F away from the protein center 21,23,24 . Sass et al. reported helix F displacement of ~0.1 nm in the late M state, based on X-ray diffraction of the three-dimensional crystal of wild type (WT) 21 . However, a larger structural change in bR was reported in 3 the electron crystallography study of the D96G, F171C, F219L triple mutant of bR: displacement of helix F by ~0.35 nm away from the center of the protein 23 . The electron crystallography study of the F219L mutant further reported that helices E and F tilt away from the center of the protein, which is ...

High-speed atomic force microscopy (HS-AFM) allows direct visualization of dynamic structural changes and processes of functioning biological molecules in physiological solutions, at subsecond to sub-100-ms temporal and submolecular spatial resolution. Unlike fluorescence microscopy, wherein the subset of molecular events that you see is dependent on the site where the probe is placed, dynamic molecular events unselectively appear in detail in an AFM movie, facilitating our understanding of how biological molecules function. Here we present protocols for HS-AFM imaging of proteins in action, including preparation of cantilever tips, step-by-step procedures for HS-AFM imaging, and recycling of cantilevers and sample stages, together with precautions and troubleshooting advice for successful imaging. The protocols are adaptable in general for imaging many proteins and protein-nucleic acid complexes, and examples are described for looking at walking myosin, ATP-hydrolyzing rotorless F(1)-ATPase and cellulose-hydrolyzing cellulase. The entire protocol takes 10-15 h, depending mainly on the substrate surface to be used.

Directly observing individual protein molecules in action at high spatiotemporal resolution has long been a holy grail for biological science. This is because we long have had to infer how proteins function from the static snapshots of their structures and dynamic behavior of optical makers attached to the molecules. This limitation has recently been removed to a large extent by the materialization of high-speed atomic force microscopy (HS-AFM). HS-AFM allows us to directly visualize the structure dynamics and dynamic processes of biological molecules in physiological solutions, at subsecond to sub-100-ms temporal resolution, without disturbing their function. In fact, dynamically acting molecules such as myosin V walking on an actin filament and bacteriorhodopsin in response to light are successfully visualized. In this review, we first describe theoretical considerations for the highest possible imaging rate of this new microscope, and then highlight recent imaging studies. Finally, the current limitation and future challenges to explore are described.

The CRISPR-associated endonuclease Cas9 binds to a guide RNA and cleaves double-stranded DNA with a sequence complementary to the RNA guide. The Cas9–RNA system has been harnessed for numerous applications, such as genome editing. Here we use high-speed atomic force microscopy (HS-AFM) to visualize the real-space and real-time dynamics of CRISPR-Cas9 in action. HS-AFM movies indicate that, whereas apo-Cas9 adopts unexpected flexible conformations, Cas9–RNA forms a stable bilobed structure and interrogates target sites on the DNA by three-dimensional diffusion. These movies also provide real-time visualization of the Cas9-mediated DNA cleavage process. Notably, the Cas9 HNH nuclease domain fluctuates upon DNA binding, and subsequently adopts an active conformation, where the HNH active site is docked at the cleavage site in the target DNA. Collectively, our HS-AFM data extend our understanding of the action mechanism of CRISPR-Cas9.