Rigid-body fitting to atomic force microscopy images for inferring probe shape and biomolecular structure

Atomic force microscopy (AFM) can visualize functional biomolecules near the physiological condition, but the observed data are limited to the surface height of specimens. Since the AFM images highly depend on the probe tip shape, for successful inference of molecular structures from the measurement, the knowledge of the probe shape is required, but is often missing. Here, we developed a method of the rigid-body fitting to AFM images, which simultaneously finds the shape of the probe tip and the placement of the molecular structure via an exhaustive search. First, we examined four similarity scores via twin-experiments for four test proteins, finding that the cosine similarity score generally worked best, whereas the pixel-RMSD and the correlation coefficient were also useful. We then applied the method to two experimental high-speed-AFM images inferring the probe shape and the molecular placement. The results suggest that the appropriate similarity score can differ between target systems. For an actin filament image, the cosine similarity apparently worked best. For an image of the flagellar protein FlhAC, we found the correlation coefficient gave better results. This difference may partly be attributed to the flexibility in the target molecule, ignored in the rigid-body fitting. The inferred tip shape and placement results can be further refined by other methods, such as the flexible fitting molecular dynamics simulations. The developed software is publicly available.

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High-speed atomic force microscopy directly visualizes conformational dynamics of the HIV Vif protein in complex with three host proteins

Journal of Biological Chemistry ◽

10.1074/jbc.ra120.014442 ◽

2020 ◽

Vol 295 (34) ◽

pp. 11995-12001

Author(s):

Yangang Pan ◽

Luda S. Shlyakhtenko ◽

Yuri L. Lyubchenko

Keyword(s):

Atomic Force Microscopy ◽

Conformational Changes ◽

High Speed ◽

Conformational Dynamics ◽

Time Lapse ◽

Hiv Treatment ◽

Force Microscopy ◽

X Ray Crystallography ◽

Atomic Force ◽

Dynamics Simulations

Vif (viral infectivity factor) is a protein that is essential for the replication of the HIV-1 virus. The key function of Vif is to disrupt the antiviral activity of host APOBEC3 (apolipoprotein B mRNA-editing enzyme catalytic subunit 3) proteins, which mutate viral nucleic acids. Inside the cell, Vif binds to the host cell proteins Elongin-C, Elongin-B, and core-binding factor subunit β, forming a four-protein complex called VCBC. The structure of VCBC–Cullin5 has recently been solved by X-ray crystallography, and, using molecular dynamics simulations, the dynamics of VCBC have been characterized. Here, we applied time-lapse high-speed atomic force microscopy to visualize the conformational changes of the VCBC complex. We determined the three most favorable conformations of this complex, which we identified as the triangle, dumbbell, and globular structures. Moreover, we characterized the dynamics of each of these structures. Our data revealed the very dynamic behavior of all of them, with the triangle and dumbbell structures being the most dynamic. These findings provide insight into the structure and dynamics of the VCBC complex and may support efforts to improve HIV treatment, because Vif is essential for virus survival in the cell.

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High-speed atomic force microscopy reveals structural dynamics of amyloid β1–42 aggregates

Proceedings of the National Academy of Sciences ◽

10.1073/pnas.1524807113 ◽

2016 ◽

Vol 113 (21) ◽

pp. 5835-5840 ◽

Cited By ~ 91

Author(s):

Takahiro Watanabe-Nakayama ◽

Kenjiro Ono ◽

Masahiro Itami ◽

Ryoichi Takahashi ◽

David B. Teplow ◽

...

Keyword(s):

Atomic Force Microscopy ◽

High Speed ◽

Amyloid Β ◽

Structural Features ◽

Molecular Structures ◽

Amyloid Β Protein ◽

Force Microscopy ◽

Amyloidogenic Proteins ◽

Atomic Force ◽

Growth Modes

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.

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Rigid-body fitting to atomic force microscopy images for inferring probe shape and biomolecular structure

10.1101/2021.02.21.432132 ◽

2021 ◽

Author(s):

Toru Niina ◽

Yasuhiro Matsunaga ◽

Shoji Takada

Keyword(s):

Atomic Force Microscopy ◽

Rigid Body ◽

Real Time ◽

High Speed ◽

Surface Shape ◽

Time Dynamics ◽

Force Microscopy ◽

Small Proteins ◽

Atomic Force ◽

Functional Dynamics

AbstractHigh-speed (HS) atomic force microscopy (AFM) can visualize real-time dynamics of functional biomolecules near the physiological condition, but the observed data are limited to the surface height of specimens. Since the HS-AFM images highly depend on the probe tip shape, for successful inference of molecular structures from the measurement, the knowledge of the probe shape is required, but is often missing. Here, we developed a method of the rigid-body fitting to HS-AFM images, which simultaneously finds the shape of the probe tip and the placement of the molecular structure via an exhaustive search. We examined four similarity scores via twin-experiments for four test proteins: Of the four scores, the cosine similarity generally worked best, whereas the pixel-RMSD was also useful especially for the placement of small proteins. We then applied the method to two experimental HS-AFM images inferring the probe shape and the molecular placement. The inferred tip shape and placement results can be further refined by other methods, such as the flexible fitting molecular dynamics simulations. The developed software is publicly available.Author SummaryObservation of functional dynamics of individual biomolecules is important to understand molecular mechanisms of cellular phenomena. High-speed (HS) atomic force microscopy (AFM) is a powerful tool that enables us to visualize the real-time dynamics of working biomolecules under near-physiological conditions. However, the information available by the HS-AFM images is limited to the two-dimensional surface shape detected via the force to the probe. While the surface information is affected by the shape of the probe tip, the probe shape itself cannot be directly measured before each HS-AFM measurement. To overcome this problem, we have developed a computational method to simultaneously infer the probe tip shape and the molecular placement from an HS-AFM image. We show that our method successfully estimates the effective HS-AFM tip shape and visualizes a structure with a more accurate placement. The estimation of a molecular placement with the correct probe tip shape enables us to obtain more insights into functional dynamics of the molecule from HS-AFM images.

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Flexible Fitting of Biomolecular Structures to Atomic Force Microscopy Images via Biased Molecular Simulations

10.1101/793901 ◽

2019 ◽

Cited By ~ 1

Author(s):

Toru Niina ◽

Sotaro Fuchigami ◽

Shoji Takada

Keyword(s):

Atomic Force Microscopy ◽

Rigid Body ◽

Protein Structures ◽

Three Dimensional ◽

Molecular Structures ◽

Surface Shape ◽

Dimensional Structure ◽

Force Microscopy ◽

Atomic Force ◽

Afm Image

AbstractAtomic force microscopy (AFM) is a prominent imaging technology that observes large-scale structural dynamics of biomolecules near the physiological condition, but the AFM data are limited to the surface shape of specimens. Rigid-body fitting methods were developed to obtain molecular structures that fit to an AFM image, without accounting for conformational changes. Here we developed a method to fit flexibly a three-dimensional biomolecular structure into an AFM image. First, we describe a method to produce a pseudo-AFM image from a given three-dimensional structure in a differentiable form. Then, using a correlation function between the experimental AFM image and the computational pseudo-AFM image, we developed a flexible fitting molecular dynamics (MD) simulation method, by which we obtain protein structures that well fit to the given AFM image. We first test it with a twin-experiment; for a synthetic AFM image produced from a protein structure different from its native conformation, the flexible fitting MD simulations sampled those that fit well the AFM image. Then, parameter dependence in the protocol is discussed. Finally, we applied the method to a real experimental AFM image for a flagellar protein FlhA, demonstrating its applicability. We also test the rigid-body fitting of a fixed structure to the AFM image. Our method will be a general tool for structure modeling based on AFM images and is publicly available through CafeMol software.

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