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In silico investigation of conformational motions in superfamily 2 helicase proteins.

Flechsig H, Popp D, Mikhailov AS - PLoS ONE (2011)

Bottom Line: Specifically, their responses to mechanical perturbations are analyzed.As we show, such motions are well-organized and have large amplitudes.Their possible roles in the processing of nucleic substrate are discussed.

View Article: PubMed Central - PubMed

Affiliation: Department of Physical Chemistry, Fritz Haber Institute of the Max Planck Society, Berlin, Germany. flechsig@fhi-berlin.mpg.de

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.

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Helicase function on DNA.(A) Structure of Hel308 helicase with partially unwound DNA bound to it (2P6R) in the front and side views. The DNA strands are shown as green; the direction of translocation along the unwound single strand is  to . The coloring of the domains is the same as in the other figures, but the top part of domain 3, referred to as the arch subdomain, is colored in purple here. (B) Schematic drawing of XPD helicase with the single DNA translocation strand positioned according to Ref. [32]. In this protein, the direction of translocation is  to . (C) Possible orientation of the branched duplex DNA in Hef helicase as proposed in Ref. [30] (schematic drawing). In all panels, arrows indicate possible domain motions.
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pone-0021809-g008: Helicase function on DNA.(A) Structure of Hel308 helicase with partially unwound DNA bound to it (2P6R) in the front and side views. The DNA strands are shown as green; the direction of translocation along the unwound single strand is to . The coloring of the domains is the same as in the other figures, but the top part of domain 3, referred to as the arch subdomain, is colored in purple here. (B) Schematic drawing of XPD helicase with the single DNA translocation strand positioned according to Ref. [32]. In this protein, the direction of translocation is to . (C) Possible orientation of the branched duplex DNA in Hef helicase as proposed in Ref. [30] (schematic drawing). In all panels, arrows indicate possible domain motions.

Mentions: The structure of this protein complexed with DNA is still not available. Nonetheless, conserved motifs crucial for DNA binding have been identified in the two motor domains [30]. Analysis of the electrostatic surface potential and mutational studies of the protein have revealed that the third domain can recognize and bind specific (e.g. fork-structured) DNA. According to the model in Ref. [30], the two motor domains can bind double- or single-stranded DNA (see Fig. 8). Our study shows that in Hef helicase a mobile motor domain is able to perform large-amplitude hinge motions with respect to the other motor domain and the third domain, which are rigidly connected. This observation is in accordance with what has been previously proposed based on the crystallographic studies of this protein [30]. The hinge motion brings together or spatially separates, respectively, the residues of the conserved motifs which are located on the two motor domains. These motifs are involved in binding and hydrolysis of ATP and thus it is likely that such conformational motions are functional and essential for the motor operation. Our investigations suggest, that, in Hef helicase, DNA is actively transported by the two motor domains and is further processed by the third domain. This behavior closely resembles that of the HCV helicase, where large relative motions of the motor domains are enabling hydrolysis of ATP and drive progressive translocation along the nucleic acid [29]. Remarkably, both in Hef and HCV helicase, the motions of the motor domain can be induced by the forces applied only in the ATP binding region.


In silico investigation of conformational motions in superfamily 2 helicase proteins.

Flechsig H, Popp D, Mikhailov AS - PLoS ONE (2011)

Helicase function on DNA.(A) Structure of Hel308 helicase with partially unwound DNA bound to it (2P6R) in the front and side views. The DNA strands are shown as green; the direction of translocation along the unwound single strand is  to . The coloring of the domains is the same as in the other figures, but the top part of domain 3, referred to as the arch subdomain, is colored in purple here. (B) Schematic drawing of XPD helicase with the single DNA translocation strand positioned according to Ref. [32]. In this protein, the direction of translocation is  to . (C) Possible orientation of the branched duplex DNA in Hef helicase as proposed in Ref. [30] (schematic drawing). In all panels, arrows indicate possible domain motions.
© Copyright Policy
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC3139591&req=5

pone-0021809-g008: Helicase function on DNA.(A) Structure of Hel308 helicase with partially unwound DNA bound to it (2P6R) in the front and side views. The DNA strands are shown as green; the direction of translocation along the unwound single strand is to . The coloring of the domains is the same as in the other figures, but the top part of domain 3, referred to as the arch subdomain, is colored in purple here. (B) Schematic drawing of XPD helicase with the single DNA translocation strand positioned according to Ref. [32]. In this protein, the direction of translocation is to . (C) Possible orientation of the branched duplex DNA in Hef helicase as proposed in Ref. [30] (schematic drawing). In all panels, arrows indicate possible domain motions.
Mentions: The structure of this protein complexed with DNA is still not available. Nonetheless, conserved motifs crucial for DNA binding have been identified in the two motor domains [30]. Analysis of the electrostatic surface potential and mutational studies of the protein have revealed that the third domain can recognize and bind specific (e.g. fork-structured) DNA. According to the model in Ref. [30], the two motor domains can bind double- or single-stranded DNA (see Fig. 8). Our study shows that in Hef helicase a mobile motor domain is able to perform large-amplitude hinge motions with respect to the other motor domain and the third domain, which are rigidly connected. This observation is in accordance with what has been previously proposed based on the crystallographic studies of this protein [30]. The hinge motion brings together or spatially separates, respectively, the residues of the conserved motifs which are located on the two motor domains. These motifs are involved in binding and hydrolysis of ATP and thus it is likely that such conformational motions are functional and essential for the motor operation. Our investigations suggest, that, in Hef helicase, DNA is actively transported by the two motor domains and is further processed by the third domain. This behavior closely resembles that of the HCV helicase, where large relative motions of the motor domains are enabling hydrolysis of ATP and drive progressive translocation along the nucleic acid [29]. Remarkably, both in Hef and HCV helicase, the motions of the motor domain can be induced by the forces applied only in the ATP binding region.

Bottom Line: Specifically, their responses to mechanical perturbations are analyzed.As we show, such motions are well-organized and have large amplitudes.Their possible roles in the processing of nucleic substrate are discussed.

View Article: PubMed Central - PubMed

Affiliation: Department of Physical Chemistry, Fritz Haber Institute of the Max Planck Society, Berlin, Germany. flechsig@fhi-berlin.mpg.de

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.

Show MeSH