Resolving the geometry of biomolecules imaged by cryo electron tomography.
In this paper, we describe two methods for computerized analysis of cryo electron tomography reconstructions of biomolecules. Both methods aim at quantifying the degree of structural flexibility of macromolecules and eventually resolving the inner dynamics through automatized protocols. The first method performs a Brownian dynamics evolution of a simplified molecular model into a fictitious force field generated by the tomograms. This procedure enables us to dock the simplified model into the experimental profiles. The second uses a fuzzy framework to delineate the subparts of the proteins and subsequently determine their interdomain relations. The two methods are discussed and their complementarities highlighted with reference to the case of the immunoglobulin antibody. Both artificial maps, constructed from immunoglobulin G entries in the Protein Data Bank and real tomograms are analyzed. Robustness issues and agreement with previously reported measurements are discussed.
Bongini
L
L
Dipartimento di Fisica, Università di Firenze, Florence, Italy.
Fanelli
D
D
Svensson
S
S
Gedda
M
M
Piazza
F
F
Skoglund
U
U
D000818:Animals; D000911:Antibodies, Monoclonal / Q000737:chemistry*; D020285:Cryoelectron Microscopy / Q000379:methods*; D007074:Immunoglobulin G / Q000737:chemistry*; D051379:Mice; D008958:Models, Molecular; D014054:Tomography / Q000379:methods*
D000911:Antibodies, Monoclonal; D007074:Immunoglobulin G