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Research Overview
Our research focuses on characterizing the structural and functional dynamics of biomolecules (proteins, nucleic acids, biological membranes) in action, including their conformational changes, diffusion, self-assembly, intermolecular interactions, etc. We develop and apply novel high-speed atomic force microscopy (HS-AFM) techniques and other structural and functional characterization tools (e.g. confocal laser scanning microscopy, electron microscopy, electrophysiology) to visualize biomolecules' structural and functional dynamics in physiological-relevant conditions at high spatial and temporal resolution. Our current research builds upon our expertise in HS-AFM imaging & force spectroscopy, single-molecule biophysics, structural biology, image processing and data analysis, machine learning, kinetic modeling, and instrumental development.
High-Speed Atomic Force Microscopy
High-Speed Atomic Force Microscopy (HS-AFM) is a cutting-edge imaging technique that allows scientists to visualize biological molecules and dynamic processes at nanometer spatial resolution and millisecond temporal resolution. Unlike conventional AFM, which is often too slow to capture rapid biological motions, HS-AFM uniquely captures dynamic biological processes in real time and under near-physiological conditions, enabling the observation of dynamic events such as transient molecular interactions, conformational changes, and complex biological assemblies.
HS-AFM has revolutionized single-molecule biophysics and structural biology by providing unprecedented insight into:
Protein dynamics in physiological conditions
Membrane proteins and their interactions with lipids
Protein-Nucleic Acid Interactions
Biomolecular assemblies and structural changes under force
By integrating HS-AFM with complementary techniques like cryo-EM, fluorescence microscopy, and molecular dynamics simulations, we aim to build a comprehensive understanding of dynamic molecular processes, opening doors to new discoveries in biology and medicine.
HS-AFM operates by scanning a sharp nanoscale probe across a sample surface, detecting changes in height and producing high-resolution topographical images.
How HS-AFM Compares to Other Structural and Functional Characterization Tools
High-Speed Atomic Force Microscopy (HS-AFM) occupies a unique niche in structural and functional characterization, complementing other high-resolution techniques like cryo-electron microscopy (cryo-EM), X-ray crystallography, and fluorescence microscopy. While cryo-EM and X-ray crystallography excel at providing atomic-level static structures, HS-AFM uniquely captures dynamic molecular processes in real time and under near-physiological conditions. Unlike fluorescence microscopy, which often relies on labels or dyes, HS-AFM provides label-free imaging, preserving the native state of biomolecules.
Moreover, HS-AFM stands out for its ability to probe mechanical properties and molecular interactions at the single-molecule level, offering insights into force-induced conformational changes and protein-lipid dynamics. Its compatibility with aqueous environments allows for direct observation of biomolecular assemblies, bridging the gap between static structural data and dynamic functional studies. By integrating HS-AFM with computational modeling and complementary techniques, our research group leverages the strengths of these tools to uncover the intricate mechanisms driving molecular function and assembly.
Protein Dynamics in Physiological Conditions
Our group applies HS-AFM to explore the dynamic behavior of proteins in their native-like environments. By capturing real-time conformational changes and transient states, we aim to uncover the molecular mechanisms governing essential protein functions, such as folding, ligand binding, and enzymatic activity. Our research focuses on understanding how proteins respond to physiological stimuli and interact with other biomolecules in complex environments. Through advanced HS-AFM imaging techniques and methodological innovations, we bridge structural and functional studies, providing new insights into protein dynamics and their roles in cellular processes.
Membrane-reconsituted OmpF trimers viewed from extracellular side.
Membrane Proteins and Their Interactions with Lipids
Membrane proteins (transmembrane and membrane-binding proteins ) play an essential role in maintaining the homeostasis of cells by functioning as transporters for signal transaction and energy conversion, among other functions. Therefore, knowledge of the atomic resolution structures of membrane proteins is extremely crucial to understanding their functions.
Our research utilizes High-Speed Atomic Force Microscopy (HS-AFM) to investigate the structure and dynamics of membrane proteins and their interactions with surrounding lipid bilayers. Using HS-AFM, we directly visualize real-time conformational changes, lipid-protein interactions, and membrane remodeling events at nanometer resolution. Our research aims to uncover how the lipid bilayer influences protein function and how proteins, in turn, modulate membrane properties, providing key insights into their roles in cellular physiology and disease mechanisms.
Membrane-reconsituted OmpF trimers viewed from extracellular side.
Protein-Nucleic Acid Interactions
Our research leverages High-Speed Atomic Force Microscopy (HS-AFM) to study the dynamic interactions between proteins and nucleic acids, including DNA and RNA. Protein-nucleic acid complexes are central to essential cellular processes such as replication, transcription, and repair. Using HS-AFM, we visualize these processes in real time, capturing transient conformational states and tracking the movement of proteins along nucleic acid strands. This allows us to investigate mechanisms such as DNA unwinding by helicases, polymerase activity, and nucleosome remodeling at nanometer resolution. By combining HS-AFM with complementary techniques, we aim to reveal how proteins recognize, bind, and modify nucleic acids, shedding light on the molecular basis of gene regulation and genome stability.
DNA topological dynamics
Instrument & Software Development
Compared to electron and fluorescence microscopy widely used in biology, HS-AFM is still a young biophysical and bioanalytical technique. To improve the performance of our HS-AFMs, we develop various signal processors and controllers. In addition to instrument development, we also develop novel algorithms and artificial intelligence methods to characterize the structural dynamics of our targeted biomolecules.
Our current research interests include new Feedback Control Systems, Image Processing and Data Analysis, Molecular Recognition, and Kinetic & Biophysical Modeling.
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