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The mapping of flexible protein domains with the atomic force microscope is reviewed.
Examples discussed are the bacteriorhodopsin from Halobacterium salinarum, the head-tail-connector
from phage phi29, and the hexagonally packed intermediate layer from Deinococcus radiodurans
which all were recorded in physiological buffer solution. All three proteins undergo
reversible structural changes that are reflected in standard deviation maps calculated
from aligned topographs of individual protein complexes. Depending on the lateral
resolution (up to 0.8 nm) flexible surface regions can ultimately be correlated with
individual polypeptide loops. In addition, multivariate statistical classification
revealed the major conformations of the protein surface.