Simulation atomic force microscopy to predict correlated conformational dynamics in proteins from topographic imaging

Atomic force microscopy (AFM) of proteins can detect only changes within the scanned molecular surface, missing all motions in other regions and thus information about functionally relevant conformational couplings. We show that simulation AFM can overcome this drawback by reconstruction of 3D molecular structures from topographic AFM images. A proof of principle demonstration is provided for an in-silico AFM experiment visualizing the conformational dynamics of a membrane transporter. The application shows that the alternating access mechanism underlying its operation can be retrieved from only AFM imaging of one membrane side. Simulation AFM is implemented in the freely available BioAFMviewer software platform, providing the convenient applicability to better understand experimental AFM observations.

Computational Evolution of Beta-2-Microglobulin Binding Peptides for Nanopatterned Surface Sensors

The bottom-up design of smart nanodevices largely depends on the accuracy by which each of the inherent nanometric components can be functionally designed with predictive methods. Here, we present a rationally designed, self-assembled nanochip capable of capturing a target protein by means of pre-selected binding sites. The sensing elements comprise computationally evolved peptides, designed to target an arbitrarily selected binding site on the surface of beta-2-Microglobulin (β2m), a globular protein that lacks well-defined pockets. The nanopatterned surface was generated by an atomic force microscopy (AFM)-based, tip force-driven nanolithography technique termed nanografting to construct laterally confined self-assembled nanopatches of single stranded (ss)DNA. These were subsequently associated with an ssDNA–peptide conjugate by means of DNA-directed immobilization, therefore allowing control of the peptide’s spatial orientation. We characterized the sensitivity of such peptide-containing systems against β2m in solution by means of AFM-based differential topographic imaging and surface plasmon resonance (SPR) spectroscopy. Our results show that the confined peptides are capable of specifically capturing β2m from the surface–liquid interface with micromolar affinity, hence providing a viable proof-of-concept for our approach to peptide design.

Utilization of Topographic Imagery using Watershed Transformation in Watersheds Prone to Natural Disasters

Indonesia is an archipelago that has abundant natural resources, however, problems arise in the process of utilizing natural resources, namely the emergence of natural disasters that have the potential to cause serious damage in several areas. The threat of floods and landslides in watersheds has become the main focus to be addressed as early as possible with the best solutions and planning. The use of topographic imaging in the field of remote sensing is one solution that is very useful in developing better natural disaster management systems. With the support of the use of the watershed transformation method, this study aims to obtain geographical situation data, both from the flow dimensions and slope conditions that affect the watershed discharge capacity. Thus, the risk of natural disasters can be minimized both from the level of material and non-material damage as early as possible.