Aggregation of amyloidogenic proteins into insoluble amyloid fibrils is implicated in various neurodegenerative diseases. This process involves protein assembly into oligomeric intermediates and fibrils with highly polymorphic molecular structures. These structural differences may be responsible for different disease presentations. For this reason, elucidation of the structural features and assembly kinetics of amyloidogenic proteins has been an area of intense study. We report here the results of high-speed atomic force microscopy (HS-AFM) studies of fibril formation and elongation by the 42-residue form of the amyloid β-protein (Aβ1–42), a key pathogenetic agent of Alzheimer's disease. Our data demonstrate two different growth modes of Aβ1–42, one producing straight fibrils and the other producing spiral fibrils. Each mode depends on initial fibril nucleus structure, but switching from one growth mode to another was occasionally observed, suggesting that fibril end structure fluctuated between the two growth modes. This switching phenomenon was affected by buffer salt composition. Our findings indicate that polymorphism in fibril structure can occur after fibril nucleation and is affected by relatively modest changes in environmental conditions.

F 1 -ATPase is a nanosized biological energy transducer working as part of F o F 1 -ATP synthase. Its rotary machinery transduces energy between chemical free energy and mechanical work and plays a central role in the cellular energy transduction by synthesizing most ATP in virtually all organisms. However, information about its energetics is limited compared to that of the reaction scheme. Actually, fundamental questions such as how efficiently F 1 -ATPase transduces free energy remain unanswered. Here, we demonstrated reversible rotations of isolated F 1 -ATPase in discrete 120°s teps by precisely controlling both the external torque and the chemical potential of ATP hydrolysis as a model system of F o F 1 -ATP synthase. We found that the maximum work performed by F 1 -ATPase per 120°step is nearly equal to the thermodynamical maximum work that can be extracted from a single ATP hydrolysis under a broad range of conditions. Our results suggested a 100% free-energy transduction efficiency and a tight mechanochemical coupling of F 1 -ATPase.electrorotation | molecular motor | nonequilibrium physics A TP synthase F o F 1 plays a central role in the cellular energy transduction by synthesizing most ATP in virtually all organisms, including bacteria, chloroplasts, and mitochondria (1, 2). This enzyme consists of two motors: F o -motor, which is embedded in the membrane, and F 1 -motor (F 1 -ATPase), which protrudes from the membrane (Fig. 1A). F 1 -motor is a reversible motor/generator. As part of F o F 1 -ATP synthase, it acts as a generator. Proton flux through the F o -motor along the transmembrane electrochemical potential drives rotation of the F o -motor's c-ring. Because the rotor subunit (γ-shaft) of F 1 -motor is coupled with the c-ring (3-5), c-ring rotation forces γ-shaft to rotate. Under these conditions, F 1 -motor synthesizes ATP from ADP and phosphate (P i ) (6-8). On the other hand, when isolated, F 1 -motor works as a motor, hydrolyzing ATP to ADP and P i and rotating the γ-shaft counter to the direction it takes during ATP-synthetic rotations (9-12) (Fig. 1B). An ATP hydrolysis makes a 120°rotation of the γ-shaft.Despite the critical role played by F 1 -motor as a mechanochemical energy transducer, information about its energetics remains limited compared to that of the reaction scheme (13-15). In fact, fundamental questions remain unanswered; these questions include how efficiently F 1 -motor can convert energy between the chemical free energy change of an ATP hydrolysis (Δμ) and mechanical work. Previous studies (12, 16) suggested that F 1 -motor works at a high efficiency in the sense that the work against viscous drag during a rotational step in the absence of external torque is nearly equal to Δμ. However, this efficiency should be distinguished from the free-energy transduction efficiency because the work against viscous drag finally dissipates as heat to the surrounding environment and cannot be fully utilized further (17). To evaluate the efficiency of the mechanochemical free-energy trans...

Molecular motors drive mechanical motions utilizing the free energy liberated from chemical reactions such as ATP hydrolysis. Although it is essential to know the efficiency of this free energy transduction, it has been a challenge due to the system's microscopic scale. Here, we evaluate the single-molecule energetics of a rotary molecular motor, F1-ATPase, by applying a recently derived nonequilibrium equality together with an electrorotation method. We show that the sum of the heat flow through the probe's rotational degree of freedom and the work against an external load is almost equal to the free energy change per a single ATP hydrolysis under various conditions. This implies that F1-ATPase works at an efficiency of nearly 100% in a thermally fluctuating environment.

Amyloid β‐protein (Aβ) molecules tend to aggregate and subsequently form low MW (LMW) oligomers, high MW (HMW) aggregates such as protofibrils, and ultimately fibrils. These Aβ species can generally form amyloid plaques implicated in the neurodegeneration of Alzheimer disease (AD), but therapies designed to reduce plaque load have not demonstrated clinical efficacy. Recent evidence implicates amyloid oligomers in AD neuropathology, but the precise mechanisms are uncertain. We examined the mechanisms of neuronal dysfunction from HMW‐Aβ1‐42 exposure by measuring membrane integrity, reactive oxygen species (ROS) generation, membrane lipid peroxidation, membrane fluidity, intracellular calcium regulation, passive membrane electrophysiological properties, and long‐term potentiation (LTP). HMW‐Aβ1‐42 disturbed membrane integrity by inducing ROS generation and lipid peroxidation, resulting in decreased membrane fluidity, intracellular calcium dysregulation, depolarization, and impaired LTP. The damaging effects of HMW‐Aβ1‐42 were significantly greater than those of LMW‐Aβ1‐42 Therapeutic reduction of HMW‐Aβ1‐42 may prevent AD progression by ameliorating direct neuronal membrane damage.—Yasumoto, T., Takamura, Y., Tsuji, M., Watanabe‐Nakayama, T., Imamura, K., Inoue, H., Nakamura, S., Inoue, T., Kimura, A., Yano, S., Nishijo, H., Kiuchi, Y., Teplow, D. B., Ono, K. High molecular weight amyloid β1‐42 oligomers induce neurotoxicity via plasma membrane damage. FASEB J. 33, 9220–9234 (2019). http://www.fasebj.org

Molecular motors drive mechanical motions utilizing the free energy liberated from chemical reactions such as ATP hydrolysis. Although it is essential to know the efficiency of this free energy transduction, it has been a challenge due to the system's microscopic scale. Here, we evaluate the single-molecule energetics of a rotary molecular motor, F1-ATPase, by applying a recently derived nonequilibrium equality together with an electrorotation method. We show that the sum of the heat flow through the probe's rotational degree of freedom and the work against external load is almost equal to the free energy change per a single ATP hydrolysis under various conditions. This implies that F1-ATPase works at an efficiency of nearly 100% in a thermally fluctuating environment.PACS numbers: 05.70.Ln,05.40.Jc,87.16.Nn F 1 -ATPase, a water soluble part of F o F 1 -ATP syntheses, is a rotary molecular motor [1][2][3][4]. The central γ shaft rotates unidirectionally within a cylinder consisting of three α and three β subunits while hydrolyzing ATP to ADP and phosphate ( Fig. 1a). A single ATP hydrolysis triggers a 120 • rotation [4,5]. By fixing an F 1 motor to a glass surface and attaching a probe filament or particle to the γ shaft, we can observe its ATP-driven rotations using conventional optical microscopes at a single molecule level [3,4,6]. In cells, combined with the membrane embedded proton driven motor F o , they couple ATP synthesis/hydrolysis and proton flow. Thus, F 1 -ATPase plays a central role in biological energy transduction. Therefore, it is crucial to reveal its energetics, especially the efficiency, to understand the principle of its operation [7]. Although F 1 -ATPase is known to be highly efficient[4], well-controlled precise evaluation has not been achieved. In this study, we evaluated the energetics of the F 1 -ATPase by measuring thermodynamic quantities of its probe particle using a new nonequilibrium equality [8-10] together with an electrorotatoin method developed for torque manipulation of microscopic objects [11][12][13].In single molecule experiments, what we can access is only the probe attached to molecular motors since motor proteins are quite small with a dimension of around 10 nm. Accordingly, a methodology to extract energetic information of motors from the probe motion is required. Although the probe is much larger than the motor protein, it is still sufficiently small that thermal fluctuations have a dominant effect on its behavior. The probe exchanges energy with an environment through thermal fluctuations as heat [14,15]. Consider a microscopic object moving in a viscous fluid with a frictional coefficient Γ and a velocity v(t). It feels a force of −Γv(t) + ξ(t) from the fluid, where ξ(t) is the thermal fluctuating force. Then, the heat flow per unit time from the system to the heat bath is naturally defined as J ≡ [Γv(t) − ξ(t)] v(t) , ADP+Pi ATP 0 2 3 5 1 4 0 2 1 Time (s) Rotations FIG. 1: (Color online) a, Schematic of F1-ATPase molecule. The central γ shaft rotates unidirectionall...

To probe the structure of the quinol oxidation site in loop VI/VII of the Escherichia coli cytochrome bd, we substituted three conserved residues (Gln249, Lys252, and Glu257) in the N-terminal region and three glutamates (Glu278, Glu279, and Glu280) in the first internal repeat. We found that substitutions of Glu257 by Ala or Gln, and Glu279 and Glu280 by Gln, severely reduced the oxidase activity and the expression level of cytochrome bd. In contrast, Lys252 mutations reduced only the oxidase activity. Blue shifts in the 440 and 630 nm peaks of the reduced Lys252 mutants and in the 561 nm peak of the reduced Glu257 mutants indicate the proximity of Lys252 to the heme b(595)-d binuclear center and Glu257 to heme b(558), respectively. Perturbations of reduced heme b(558) upon binding of aurachin D support structural changes in the quinol-binding site of the mutants. Substitutions of Lys252 and Glu257 caused large changes in kinetic parameters for the ubiquinol-1 oxidation. These results indicate that Lys252 and Glu257 in the N-terminal region of the Q-loop are involved in the quinol oxidation by bd-type terminal oxidase.

Nuclear pore complexes (NPCs) are the sole turnstile implanted in the nuclear envelope (NE), acting as a central nanoregulator of transport between the cytosol and the nucleus. NPCs consist of ∼30 proteins, termed nucleoporins. About one-third of nucleoporins harbor natively unstructured, intrinsically disordered phenylalanine-glycine strings (FG-Nups), which engage in transport selectivity. Because the barriers insert deeply in the NPC, they are nearly inaccessible. Several in vitro barrier models have been proposed; however, the dynamic FG-Nups protein molecules themselves are imperceptible in vivo. We show here that high-speed atomic force microscopy (HS-AFM) can be used to directly visualize nanotopographical changes of the nuclear pore inner channel in colorectal cancer (CRC) cells. Furthermore, using MLN8237/alisertib, an apoptotic and autophagic inducer currently being tested in relapsed cancer clinical trials, we unveiled the functional loss of nucleoporins, particularly the deformation of the FG-Nups barrier, in dying cancer cells. We propose that the loss of this nanoscopic resilience is an irreversible dying code in cells. These findings not only illuminate the potential application of HS-AFM as an intracellular nanoendoscopy but also might aid in the design of future nuclear targeted nanodrug delivery tailored to the individual patient.

Abstract. Recent advancement of dynamic-mode atomic force microscopy (AFM) for liquid-environment applications enabled atomic-scale studies on various interfacial phenomena. However, instabilities and poor reproducibility of the measurements often prevent systematic studies. To solve this problem, we have investigated the effect of various tip treatment methods for atomic-scale imaging and force measurements in liquid. The tested methods include Si coating, Ar plasma, Ar sputtering and UV/O 3 cleaning. We found that all the methods provide significant improvements in both the imaging and force measurements in spite of the tip transfer through the air. Among the methods, we found that the Si coating provides the best stability and reproducibility in the measurements. To understand the origin of the fouling resistance of the cleaned tip surface and the difference between the cleaning methods, we have investigated the tip surface properties by x-ray photoelectron spectroscopy and contact angle measurements. The results show that the contaminations adsorbed on the tip during the tip transfer through the air should desorb from the surface when it is immersed in aqueous solution due to the enhanced hydrophilicity by the tip treatments. The tip surface prepared by the Si coating is oxidized when it is immersed in aqueous solution. This creates local spots where stable hydration structures are formed. For the other methods, there is no active mechanism to create such local hydration sites. Thus, the hydration structure formed under the tip apex is not necessarily stable. These results reveal the desirable tip properties for atomic-scale AFM measurements in liquid, which should serve as a guideline for further improvements of the tip treatment methods.