title: In silico investigation of conformational motions in superfamily 2 helicase proteins.
abstract: Helicases are motor proteins that play a central role in the metabolism of DNA and RNA in biological cells. Using the energy of ATP molecules, they are able to translocate along the nucleic acids and unwind their duplex structure. They have been extensively characterized in the past and grouped into superfamilies based on structural similarities and sequential motifs. However, their functional aspects and the mechanism of their operation are not yet well understood. Here, we consider three helicases from the major superfamily 2--Hef, Hel308 and XPD--and study their conformational dynamics by using coarse-grained relaxational elastic network models. Specifically, their responses to mechanical perturbations are analyzed. This enables us to identify robust and ordered conformational motions which may underlie the functional activity of these proteins. As we show, such motions are well-organized and have large amplitudes. Their possible roles in the processing of nucleic substrate are discussed.
authors.affiliation: Department of Physical Chemistry, Fritz Haber Institute of the Max Planck Society, Berlin, Germany. flechsig@fhi-berlin.mpg.de
authors.forename: Holger
authors.initials: H
authors.lastname: Flechsig
authors.forename: Denny
authors.initials: D
authors.lastname: Popp
authors.forename: Alexander S
authors.initials: AS
authors.lastname: Mikhailov
mesh_terms: D048868:Adaptor Proteins, Signal Transducing / Q000737:chemistry* / Q000378:metabolism; D004247:DNA / Q000378:metabolism; D004265:DNA Helicases / Q000737:chemistry* / Q000378:metabolism; D006801:Humans; D008958:Models, Molecular; D009038:Motion; D010750:Phosphoproteins / Q000737:chemistry* / Q000378:metabolism; D011487:Protein Conformation; D051759:Xeroderma Pigmentosum Group D Protein / Q000737:chemistry* / Q000378:metabolism
chemical_list: D048868:Adaptor Proteins, Signal Transducing; C099942:NEDD9 protein, human; D010750:Phosphoproteins; D004247:DNA; D004265:DNA Helicases; D051759:Xeroderma Pigmentosum Group D Protein; C497292:ERCC2 protein, human; C451406:HELQ protein, human