Functional conformational changes of endo-1,4-xylanase II from Trichoderma reesei: a molecular dynamics study.
Recent crystallographic studies have revealed a range of structural changes in the three-dimensional structure of endo-1,4-xylanase (XYNII) from Trichoderma reesei. The observed conformational changes can be described as snapshots of an open-close movement of the active site of XYNII. These structures were further analyzed in this study. In addition, a total of four 1 ns molecular dynamics (MD) simulations were performed representing different states of the enzyme. A comparison of the global and local changes found in the X-ray structures and the MD runs suggested that the simulations reproduced a similar kind of active site opening and closing as predicted by the crystal structures. The open-close movement was characterized by the use of distance difference matrixes and the Hinge-find program (Wriggers and Schulten, Proteins 29:1-14, 1997) to be a 'hinge-bending' motion involving two large rigidly-moving regions and an extended hinge. This conformational feature is probably inherent to this molecular architecture and probably plays a role in the function of XYNII.
Muilu
J
J
Department of Chemistry, University of Joensuu, Finland.
Törrönen
A
A
Peräkylä
M
M
Rouvinen
J
J
D001665:Binding Sites; D002384:Catalysis; D003198:Computer Simulation; D018360:Crystallography, X-Ray; D043364:Endo-1,4-beta Xylanases; D005656:Fungal Proteins / Q000737:chemistry*; D008958:Models, Molecular; D011487:Protein Conformation; D012984:Software; D014242:Trichoderma / Q000201:enzymology*; D014995:Xylosidases / Q000737:chemistry*
D005656:Fungal Proteins; D014995:Xylosidases; D043364:Endo-1,4-beta Xylanases