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PEDS Advance Access originally published online on April 8, 2005
Protein Engineering Design and Selection 2005 18(3):127-137; doi:10.1093/protein/gzi017
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© The Author 2005. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oupjournals.org

Conservation and specialization in PAS domain dynamics

A. Pandini and L. Bonati1

Dipartimento di Scienze dell'Ambiente e del Territorio, Università degli Studi di Milano-Bicocca, Piazza della Scienza 1, 20126 Milan, Italy

1 To whom correspondence should be addressed. E-mail: laura.bonati{at}unimib.it

The PAS (Per-ARNT-Sim) superfamily is presented as a well-suited study case to demonstrate how comparison of functional motions among distant homologous proteins with conserved fold characteristics may give insight into their functional specialization. Based on the importance of structural flexibility of the receptive structures in anticipating the signal-induced conformational changes of these sensory systems, the dynamics of these structures were analysed. Molecular dynamics was proved to be an effective method to obtain a reliable picture of the dynamics of the crystal structures of HERG, phy3, PYP and FixL, provided that an extensive conformational space sampling is performed. Other reliable sources of dynamic information were the ensembles of NMR structures of hPASK, HIF-2{alpha} and PYP. Essential dynamics analysis was successfully employed to extract the relevant information from the sampled conformational spaces. Comparison of motion patterns in the essential subspaces, based on the structural alignment, allowed identification of the specialized region in each domain. This appears to be evolved in the superfamily by following a specific trend, that also suggests the presence of a limited number of general solutions adopted by the PAS domains to sense external signals. These findings may give insight into unknown mechanisms of PAS domains and guide further experimental studies.

Keywords: essential motions/molecular dynamics/protein structures

Received August 3, 2004; revised February 12, 2005; accepted March 2, 2005.

Edited by David Thirumalai


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Home page
 Protein Eng Des SelHome page
A. Pandini, G. Mauri, A. Bordogna, and L. Bonati
Detecting similarities among distant homologous proteins by comparison of domain flexibilities
Protein Eng. Des. Sel., June 30, 2007; (2007) gzm021v2.
[Abstract] [Full Text] [PDF]


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