Modeling atomistic biomolecular dynamics from HS-AFM imaging

A collaboration team of researchers from the Nano Life Science Institute (WPI-NanoLSI), Kanazawa University, the Institute of Transformative Bio-Molecules (WPI-ITbM), Graduate School of Science at Nagoya University, and the RIKEN Center for Computational Science (R-CCS) reports in ACS Nano an integrative modeling workflow to understand with atomistic precision biomolecular dynamics from high-speed atomic force microscopy experiments.

High-speed atomic force microscopy (HS-AFM) is the only experimental technique to directly watch proteins in dynamic action. However, as a surface scanning technique with limited spatial resolution, HS-AFM will inevitably provide insufficient information for detailed atomistic understanding of biomolecular function. Despite previous efforts in computational modeling attempting to overcome such limitations, successful applications to retrieve atomistic-level information from measurements are yet practically absent.

A research team led by Holger Flechsig (WPI-NanoLSI, Kanazawa University) and Florence Tama (WPI-ITbM, Graduate School of Science at Nagoya University, and R-CCS) now presents a computational framework and its software implementation allowing to infer 3D atomistic models of dynamic protein conformations from AFM topography imaging. The scientists use a new computationally efficient flexible fitting method developed by Tama’s group, which models conformational dynamics of known static protein structure to identify atomistic models that best fit experimental AFM images. In their work, they first implement this method into the well-established BioAFMviewer software platform maintained by Flechsig’s group to provide a direct workflow for applications to measured AFM imaging data.

The presented analysis of HS-AFM data for different proteins obtained by experimental collaborators evidence that flexible fitting can infer atomistic models including large-amplitude motions to significantly improve understanding of functional conformational dynamics from resolution-limited measurements. Computational efficiency of flexible fitting within the BioAFMviewer even allows applications to large protein assemblies, as the authors show for the example of a 4 megadalton actin filament consisting of about 280,000 atoms.  A remarkable achievement is the demonstration of an atomistic molecular movie of protein dynamics, involving functional conformational transitions, reconstructed from HS-AFM topographic movie data.

The unique software implementation of computationally efficient flexible fitting, integrating available structural data and molecular modeling with experiments, opens the opportunity for a broad range of applications to fully exploit the explanatory power of HS-AFM by large-scale analysis of single molecule imaging data toward better understanding biological processes at the nanoscale.

This work is a collaborative effort of scientists from two WPI centers in Japan, the Nano Life Science Institute (WPI-NanoLSI) at Kanazawa University, and the Institute of Transformative Bio-Molecules (WPI-ITbM) at Nagoya University. Combining the expertise of protein dynamics modeling and computational science with Nanometrology experiments, leading contributions which further advance the interdisciplinary field of nanoscale biology are achieved.

Background

Flexible Fitting
Flexible fitting is a computational method which models conformational motions of a static protein structure to dynamically steer it into conformations that best represent experimental data. The normal mode flexible fitting AFM (NMFF-AFM) method, recently developed by Tama’s group (J. Phys. Chem. B, 2024), employs computational efficient iterative normal mode analysis to model large-amplitude conformational changes which allows to identify dynamic atomistic models that best represent measured AFM topographic images.

BioAFMviewer software
The BioAFMviewer project was initiated by Holger Flechsig in 2020, with Romain Amyot as the programming scientist, to provide a unique software platform integrating the enormous amount of available high-resolution biomolecular structure and modelling data for the analysis of resolution-limited AFM measurements. An integrated molecular viewer for biomolecular visualization, corresponding simulation AFM, and several analysis toolboxes provide a user-friendly interactive software interface for the convenient analysis of experimental AFM data. The performance of the integrated NMFF-AFM flexible fitting method is significantly enhanced by parallelized computations executed on graphic cards. The BioAFMviewer software is available for free download from the project website www.bioafmviewer.com.

Funding
This work was supported by the Ministry of Education, Culture, Sports, Science and Technology (MEXT), Japan, through the World Premier International Research Center Initiative (WPI)  (R.A., N.K., H.K., and H.F.), Grant-in-Aid for Scientific Research KAKENHI Nos 25K01631 (H.K.) and 24H02260 (O.M., F.T.) from the Japan Society for the Promotion of Science (JSPS), the Transdisciplinary Research Promotion Grant (R.A., N.K., N.K., and H.F.) from WPI-NanoLSI, and in part by MEXT as “Program for Promoting Researches on the Supercomputer Fugaku” (Development and application of large-scale simulation-based inferences for biomolecules JPMXP1020230119) (O.M., F.T.).

Contact
Project Planning and Outreach, NanoLSI Administration Office
Nano Life Science Institute, Kanazawa University
Email: nanolsi-office@adm.kanazawa-u.ac.jp
Kakuma-machi, Kanazawa 920-1192, Japan

About Nano Life Science Institute (WPI-NanoLSI), Kanazawa University
Understanding nanoscale mechanisms of life phenomena by exploring “uncharted nano-realms”.

Cells are the basic units of almost all life forms. We are developing nanoprobe technologies that allow direct imaging, analysis, and manipulation of the behavior and dynamics of important macromolecules in living organisms, such as proteins and nucleic acids, at the surface and interior of cells. We aim at acquiring a fundamental understanding of the various life phenomena at the nanoscale.
https://nanolsi.kanazawa-u.ac.jp/en/

About Institute of Transformative Bio-Molecules (WPI-ITbM), Nagoya University
The goal of ITbM is to develop transformative biomolecules, innovative functional molecules that can significantly change the fields of biological science and technology. Research at ITbM is conducted in a "Mix Lab" format, where international young researchers from various disciplines collaborate closely in the same laboratory, fostering interdisciplinary interactions. Through these endeavors, ITbM will create "transformative bio-molecules" that will dramatically change the way of research in chemistry, biology and other related fields to solve urgent problems, such as environmental issues, food production and medical technology that have a significant impact on the society.
https://www.itbm.nagoya-u.ac.jp/en/

About the World Premier International Research Center Initiative (WPI)
The WPI program was launched in 2007 by Japan's Ministry of Education, Culture, Sports, Science and Technology (MEXT) to foster globally visible research centers boasting the highest standards and outstanding research environments. Numbering more than a dozen and operating at institutions throughout the country, these centers are given a high degree of autonomy, allowing them to engage in innovative modes of management and research. The program is administered by the Japan Society for the Promotion of Science (JSPS).

See the latest research news from the centers at the WPI News Portal:
https://www.eurekalert.org/newsportal/WPI
Main WPI program site: www.jsps.go.jp/english/e-toplevel

About Kanazawa University
As the leading comprehensive university on the Sea of Japan coast, Kanazawa University has contributed greatly to higher education and academic research in Japan since it was founded in 1949. The University has three colleges and 17 schools offering courses in subjects that include medicine, computer engineering, and humanities.

The University is located on the coast of the Sea of Japan in Kanazawa, a city rich in history and culture. The city of Kanazawa has a highly respected intellectual profile since the time of the fiefdom (1598-1867). Kanazawa University is divided into two main campuses: Kakuma and Takaramachi for its approximately 10,200 students, including 600 from overseas.
http://www.kanazawa-u.ac.jp/en/