PEDS Advance Access originally published online on October 30, 2007
Protein Engineering Design and Selection 2007 20(11):551-559; doi:10.1093/protein/gzm056
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Molecular dynamics studies on the thermostability of family 11 xylanases
1Department of Chemistry, University of Joensuu, PO Box 111, 80101 Joensuu, Finland 2 Institute of Medical Technology, University of Tampere, 33014 Tampere, Finland 3 Tampere University Hospital, Biokatu 6-8, 33520 Tampere, Finland 4 VTT Technical Research Centre of Finland, PO Box 1000, 02044 VTT, Finland 5Department of Pharmaceutical Chemistry, University of Kuopio, PO Box 1627, 70211 Kuopio, Finland
6To whom correspondence should be addressed. E-mail: juha.rouvinen{at}joensuu.fi
Twelve members of the family 11 xylanases, including both mesophilic and thermophilic proteins, were studied using molecular dynamics (MD). Simulations of xylanases were carried out in an explicit water environment at four different temperatures, 300, 400, 500 and 600 K. A difference in thermotolerance between mesophilic and thermophilic xylanases became clear: thermophilic xylanases endured heat in higher simulation temperatures better than mesophilic ones. The unfolding pathways seemed to be similar for all simulations regardless of the protein. The unfolding initiates at the N-terminal region or alternatively from the 
-helix region and proceeds to the ‘finger region’. Unfolding of these regions led to denaturated structures within the 4.5 ns simulation at 600 K. The results are in agreement with experimental mutant studies. The results show clearly that the stability of the protein is not evenly distributed over the whole structure. The MD analysis suggests regions in the protein structure which are more unstable and thus potential targets for mutation experiments to improve thermostability.
Keywords: denaturation/molecular dynamics/thermostability/unfolding pathway/xylanase family 11
Received December 15, 2006; revised September 20, 2007; accepted September 25, 2007.
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