title: Large conformational fluctuations of the multi-domain xylanase Z of Clostridium thermocellum.
abstract: The cellulosome is a multi-enzyme machinery which efficiently degrades plant cell-wall polysaccharides. The multiple domains of the cellulosome complexes are often tethered to one another by intrinsically disordered regions. The properties and functions of these disordered linkers are unknown to a large extent. In this work, we study the conformational variability of one component of the cellulosome - the multi-domain xylanase Z (XynZ) of Clostridium thermocellum. We use a coarse-grained protein model to efficiently simulate conformations of the enzyme. Our simulation results are in excellent agreement with data from small angle X-ray scattering experiments, which validates the simulation outcome. Both in the presence and absence of the cohesin domain, the XynZ enzyme appears to be flexible in the sense that it takes various compact and extended conformations. The physical interactions between the individual domains are rather weak and transient, and the XynZ enzyme is held together mainly by the flexible linkers connecting the domains. The end-to-end distance distributions for the flexible linkers can be rationalized by the excluded volume effect. Taken together, our results provide a detailed picture of the conformational ensemble of the XynZ enzyme in solution.
authors.affiliation: Institute of Physics, Polish Academy of Sciences, Aleja Lotników 32/46, 02-668 Warsaw, Poland. Electronic address: rozycki@ifpan.edu.pl.
authors.forename: Bartosz
authors.initials: B
authors.lastname: Różycki
authors.affiliation: Institute of Physics, Polish Academy of Sciences, Aleja Lotników 32/46, 02-668 Warsaw, Poland.
authors.forename: Marek
authors.initials: M
authors.lastname: Cieplak
authors.affiliation: Sorbonne Universités, UPMC, Université Paris 06, and Centre National de la Recherche Scientifique, UMR 8227, Integrative Biology of Marine Models, Station Biologique de Roscoff, CS 90074, F-29688 Roscoff cedex, Bretagne, France.
authors.forename: Mirjam
authors.initials: M
authors.lastname: Czjzek
mesh_terms: D048013:Acetivibrio thermocellus / Q000201:enzymology*; D043364:Endo-1,4-beta Xylanases / Q000737:chemistry*; D011487:Protein Conformation; D017434:Protein Structure, Tertiary
chemical_list: D043364:Endo-1,4-beta Xylanases
keywords: Cellulosome; Coarse-grained simulations; Conformational ensemble; Intrinsically disordered proteins; Multi-domain proteins; Small angle X-ray scattering