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

Abstract

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.

Simulation atomic force microscopy for atomic reconstruction of biomolecular structures from resolution-limited experimental images

“…Simulation AFM can be conducted for entire molecular movies, e.g., obtained from modeling simulations [ 16 ]. This opens the opportunity to employ data of functional conformational dynamics for fitting to experimental AFM images [ 22 ].…”

“…We have previously shown that new structural models with atomistic resolution can be retrieved for higher oligomeric arrangements of the Annexin V protein seen under HS-AFM [ 20 ]. Simulation AFM was recently applied in a demonstration study of a membrane transporter protein, showing that based on topographic imaging of only one membrane side, the functionally coupled conformational state at the remote opposite site can be predicted [ 22 ].…”

“…The explanatory power of simulation AFM to predict correlated conformational dynamics in proteins from topopgraphic AFM imaging [ 22 ] will play a major role in the future to complement AFM experiments.…”

“…The simulated scanning method computationally emulates scanning of the molecular structure to produce pseudo AFM images. It has been employed in several studies to interpret experimental AFM images of proteins [ 8 , 17 – 22 ], and in molecular simulations of flexible fitting biomolecular structures to experimental images [ 23 ] or to deduce information on the AFM tip shape [ 24 ].…”