Molecular dynamics simulation of SRP GTPases: Towards an understanding of the complex formation from equilibrium fluctuations
- Creators
- Yang, Mingjun
- Zhang, Xin
- Han, Keli
Abstract
Signal recognition particle (SRP) and its receptor (SR) play essential role in the SRP-dependent protein targeting pathway. They interact with one another to precisely regulate the targeting reaction. The mechanism of this interaction consists of at least two discrete conformational states: complex formation and GTPase activation. Although structural studies have provided valuable insights into the understanding of the SRP-SR interaction, it still remains unclear that how SRP and SR GTPases use their intrinsic conformational flexibilities to exert multiple allosteric regulations on this interaction process. Here, we use computational simulations to present the dynamic behavior of the SRP GTPases at an atomic level to gain further understanding of SRP-SR interaction. We show that: (i) equilibrium conformational fluctuations contain a cooperative inter- and intradomain structural rearrangements that are functionally relevant to complex formation, (ii) a series of residues in different domains are identified to correlate with each other during conformational rearrangements, and (iii) α3 and α4 helices at domain interface actively rearrange their relative conformation to function as a bridge between the N domain and the core region of the G domain. These results, in addition to structural studies, would harness our understanding of the molecular mechanism for SRP and SR interaction
Additional Information
© 2010 Wiley-Liss, Inc. Received 17 September 2009; Revised 25 February 2010; Accepted 2 March 2010. Published online 31 March 2010. The authors thank Michael J. Bradley (currently at the Molecular Biophysics and Biochemistry Department at Yale University) for his kindly help and useful suggestions to UPGMA clustering. They would also like to thank the anonymous reviewers for their helpful comments.Additional details
- Eprint ID
- 19111
- DOI
- 10.1002/prot.22734
- Resolver ID
- CaltechAUTHORS:20100719-135633269
- 2007CB815202
- NKBRSF
- 20721004
- National Natural Science Foundation of China (NSFC)
- 20833008
- National Natural Science Foundation of China (NSFC)
- Created
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2010-08-04Created from EPrint's datestamp field
- Updated
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2021-11-08Created from EPrint's last_modified field