Hiroaki Kominami

Immunoactive two-dimensional self-assembly of monoclonal antibodies in aqueous solution revealed by atomic force microscopy

The conformational flexibility of antibodies in solution directly affects their immune function. Namely, the flexible hinge regions of immunoglobulin G (IgG) antibodies are essential in epitope-specific antigen recognition and biological effector function. The antibody structure, which is strongly related to its functions, has been partially revealed by electron microscopy and X-ray crystallography, but only under non-physiological conditions. Here we observed monoclonal IgG antibodies in aqueous solution by high-resolution frequency modulation atomic force microscopy (FM-AFM). We found that monoclonal antibodies self-assemble into hexamers, which form two-dimensional crystals in aqueous solution. Furthermore, by directly observing antibody-antigen interactions using FM-AFM, we revealed that IgG molecules in the crystal retain immunoactivity. As the self-assembled monolayer crystal of antibodies retains immunoactivity at a neutral pH and is functionally stable at a wide range of pH and temperature, the antibody crystal is applicable to new biotechnological platforms for biosensors or bioassays.

Atomic-resolution three-dimensional hydration structures on a heterogeneously charged surface

Local hydration structures at the solid–liquid interface around boundary edges on heterostructures are key to an atomic-level understanding of various physical, chemical and biological processes. Recently, we succeeded in visualising atomic-scale three-dimensional hydration structures by using ultra-low noise frequency-modulation atomic force microscopy. However, the time-consuming three-dimensional-map measurements on uneven heterogeneous surfaces have not been achieved due to experimental difficulties, to the best of our knowledge. Here, we report the local hydration structures formed on a heterogeneously charged phyllosilicate surface using a recently established fast and nondestructive acquisition protocol. We discover intermediate regions formed at step edges of the charged surface. By combining with molecular dynamics simulations, we reveal that the distinct structural hydrations are hard to observe in these regions, unlike the charged surface regions, possibly due to the depletion of ions at the edges. Our methodology and findings could be crucial for the exploration of further functionalities.Local hydration structures at solid-liquid interfaces are important in catalytic, electrochemical, and biological processes. Here, the authors demonstrate atomic-scale 3D hydration structures around the boundary on a heterogeneous mineral surface using atomic force microscopy experiments and molecular dynamics simulations.

Flexible DNA Path in the MCM Double Hexamer Loaded on DNA

The formation of the pre-replicative complex (pre-RC) during the G1 phase, which is also called the licensing of DNA replication, is the initial and essential step of faithful DNA replication during the subsequent S phase. It is widely accepted that in the pre-RC, double-stranded DNA passes through the holes of two ring-shaped minichromosome maintenance (MCM) 2-7 hexamers; however, the spatial organization of the DNA and proteins involved in pre-RC formation is unclear. Here we reconstituted the pre-RC from purified DNA and proteins and visualized the complex using atomic force microscopy (AFM). AFM revealed that the MCM double hexamers formed elliptical particles on DNA. Analysis of the angle of binding of DNA to the MCM double hexamer suggests that the DNA does not completely pass through both holes of the MCM hexamers, possibly because the DNA exited from the gap between Mcm2 and Mcm5. A DNA loop fastened by the MCM double hexamer was detected in pre-RC samples reconstituted from purified proteins as well as those purified from yeast cells, suggesting a higher-order architecture of the loaded MCM hexamers and DNA strands.

Immunoactivity of self-assembled antibodies investigated by atomic force microscopy

Immunoglobulin G (IgG), an antibody, plays a significant role in the immune system, and the functions of IgG molecules have been studied in many research fields such as medicine and engineering. Recently, we found the self-assembly of monoclonal mouse IgG molecules on a mica substrate using atomic force microscopy (AFM); the IgG molecules self-assemble into hexamers and the hexamers form a two-dimensional (2D) crystal. The self-assembly of the IgG molecules is of great interest in terms of the enhancement of the immunoactivity of the antibodies. In this study, we investigated the self-assembly of various IgG molecules on a mica substrate to discuss if the hexamerization of the IgG molecules is a general phenomenon. We also investigated the antigen binding site in the IgG antibody hexamers, and estimated the association rate constant of the self-assembled IgG molecules based on the AFM measurements. The estimated value was lower than that reported in a previous study probably because of the limited mobility of the antigen-binding fragments on the substrate.

Author Correction: Atomic-resolution three-dimensional hydration structures on a heterogeneously charged surface

The original version of the Supplementary Information associated with this Article contained an error in Supplementary Figure 9e,f in which the y-axes were incorrectly labelled from ‘−40’ to ‘40’, rather than the correct ‘-400’ to ‘400’. The HTML has been updated to include a corrected version of the Supplementary Information.