Protein dynamics by the combination of high-speed AFM and computational modeling

Analysis of protein-protein and protein-membrane interactions by isotope-edited infrared spectroscopy

The objective of this work is to highlight the power of isotope-edited Fourier transform infrared (FTIR) spectroscopy in resolving important problems encountered in biochemistry, biophysics, and biomedical research, focusing on protein-protein and protein membrane interactions that play key roles in practically all life processes. An overview of the effects of isotope substitutions in (bio)molecules on spectral frequencies and intensities is given. Data are presented demonstrating how isotope-labeled proteins and/or lipids can be used to elucidate enzymatic mechanisms, the mode of membrane binding of peripheral proteins, regulation of membrane protein function, protein aggregation, and local and global structural changes in proteins during functional transitions. The use of polarized attenuated total reflection FTIR spectroscopy to identify the spatial orientation and the secondary structure of a membrane-bound interfacial enzyme and the mode of lipid hydrolysis is described. Methods of production of site-directed, segmental, and domain-specific labeling of proteins by the synthetic, semisynthetic, and recombinant strategies, including advanced protein engineering technologies such as nonsense suppression and frameshift quadruplet codons are overviewed.

High-Speed Atomic Force Microscopy for Filming Protein Molecules in Dynamic Action

Structural biology is currently undergoing a transformation into dynamic structural biology, which reveals the dynamic structure of proteins during their functional activity to better elucidate how they function. Among the various approaches in dynamic structural biology, high-speed atomic force microscopy (HS-AFM) is unique in the ability to film individual molecules in dynamic action, although only topographical information is acquirable. This review provides a guide to the use of HS-AFM for biomolecular imaging and showcases several examples, as well as providing information on up-to-date progress in HS-AFM technology. Finally, we discuss the future prospects of HS-AFM in the context of dynamic structural biology in the upcoming era.

Atomic force microscopy 3D structural reconstruction of individual particles in the study of amyloid protein assemblies

Recent developments in atomic force microscopy (AFM) image analysis have made three-dimensional (3D) structural reconstruction of individual particles observed on 2D AFM height images a reality. Here, we review the emerging contact point reconstruction AFM (CPR-AFM) methodology and its application in 3D reconstruction of individual helical amyloid filaments in the context of the challenges presented by the structural analysis of highly polymorphous and heterogeneous amyloid protein structures. How individual particle-level structural analysis can contribute to resolving the amyloid polymorph structure-function relationships, the environmental triggers leading to protein misfolding and aggregation into amyloid species, the influences by the conditions or minor fluctuations in the initial monomeric protein structure on the speed of amyloid fibril formation, and the extent of the different types of amyloid species that can be formed, are discussed. Future perspectives in the capabilities of AFM-based 3D structural reconstruction methodology exploiting synergies with other recent AFM technology advances are also discussed to highlight the potential of AFM as an emergent general, accessible and multimodal structural biology tool for the analysis of individual biomolecules.

Employing Atomic Force Microscopy (AFM) for Microscale Investigation of Interfaces and Interactions in Membrane Fouling Processes: New Perspectives and Prospects

Membrane fouling presents a significant challenge in the treatment of wastewater. Several detection methods have been used to interpret membrane fouling processes. Compared with other analysis and detection methods, atomic force microscopy (AFM) is widely used because of its advantages in liquid-phase in situ 3D imaging, ability to measure interactive forces, and mild testing conditions. Although AFM has been widely used in the study of membrane fouling, the current literature has not fully explored its potential. This review aims to uncover and provide a new perspective on the application of AFM technology in future studies on membrane fouling. Initially, a rigorous review was conducted on the morphology, roughness, and interaction forces of AFM in situ characterization of membranes and foulants. Then, the application of AFM in the process of changing membrane fouling factors was reviewed based on its in situ measurement capability, and it was found that changes in ionic conditions, pH, voltage, and even time can cause changes in membrane fouling morphology and forces. Existing membrane fouling models are then discussed, and the role of AFM in predicting and testing these models is presented. Finally, the potential of the improved AFM techniques to be applied in the field of membrane fouling has been underestimated. In this paper, we have fully elucidated the potentials of the improved AFM techniques to be applied in the process of membrane fouling, and we have presented the current challenges and the directions for the future development in an attempt to provide new insights into this field.

Technical advances in high-speed atomic force microscopy

It has been 30 years since the outset of developing high-speed atomic force microscopy (HS-AFM), and 15 years have passed since its establishment in 2008. This advanced microscopy is capable of directly visualizing individual biological macromolecules in dynamic action and has been widely used to answer important questions that are inaccessible by other approaches. The number of publications on the bioapplications of HS-AFM has rapidly increased in recent years and has already exceeded 350. Although less visible than these biological studies, efforts have been made for further technical developments aimed at enhancing the fundamental performance of HS-AFM, such as imaging speed, low sample disturbance, and scan size, as well as expanding its functionalities, such as correlative microscopy, temperature control, buffer exchange, and sample manipulations. These techniques can expand the range of HS-AFM applications. After summarizing the key technologies underlying HS-AFM, this article focuses on recent technical advances and discusses next-generation HS-AFM.