Abstract
We provide a stand-alone software, the BioAFMviewer, which transforms biomolecular structures into the graphical representation corresponding to the outcome of atomic force microscopy (AFM) experiments. The AFM graphics is obtained by performing simulated scanning over the molecular structure encoded in the corresponding PDB file. A versatile molecular viewer integrates the visualization of PDB structures and control over their orientation, while synchronized simulated scanning with variable spatial resolution and tip-shape geometry produces the corresponding AFM graphics. We demonstrate the applicability of the BioAFMviewer by comparing simulated AFM graphics to high-speed AFM observations of proteins. The software can furthermore process molecular movies of conformational motions, e.g. those obtained from servers which model functional transitions within a protein, and produce the corresponding simulated AFM movie. The BioAFMviewer software provides the platform to employ the plethora of structural and dynamical data of proteins in order to help in the interpretation of biomolecular AFM experiments.
Highlights
Seeing is believing paraphrases the holy grail of molecular biophysics—the imaging of molecular processes which establish Life at the nanoscale
We provide a stand-alone software, the BioAFMviewer, which transforms biomolecular structures into the graphical representation corresponding to the outcome of atomic force microscopy (AFM) experiments
The BioAFMviewer computationally emulates the scanning of any biomolecular structure to produce graphical images that mimic the outcome of Atomic force microscopy (AFM) experiments
Summary
Seeing is believing paraphrases the holy grail of molecular biophysics—the imaging of molecular processes which establish Life at the nanoscale. At the single protein level, this task is challenging, due to the tininess of structures and the rapid timescales of functional conformational motions. Atomic force microscopy (AFM) experiments can provide high-resolution images of biological structures and probe functional properties at the single-molecule level, e.g. With the development of the high-speed atomic force microscopy (hs-AFM) technique, the breakthrough of visualizing functionally relevant motions became possible. Hs-AFM allows to observe conformational dynamics in proteins under physiological conditions by rapidly scanning over the protein surface and imaging its shape [6,7,8,9,10]. Hs-AFM is a leading method to observe dynamical processes in proteins and its success has been evidenced in a plethora of studies [11,12,13,14]
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