Xylanases ( EC 3.2.1.8 ) belong to the large group of glycosyl hydrolases that catalyze the degradation of xylan, the most abundant hemicellulose in nature. Xylanases have been used in industrial processes specially in pulp and paper industries where they reduce the amount of chlorine chemicals used in the pulp-bleaching processes. The mesophilic xylanase from Bacillus circulans, BCX, was studied by molecular dynamics simulation. The objective of the analysis is to investigate, as a function of temperature, the protein stability by monitoring the hydrogen bond network. The molecular dynamics calculations were performed in the isothermal-isobaric ensemble under physiological conditions at 298K, 308K, 318K, 328K and 338K. All molecular dynamics simulations run with the GROMACS 3.2 software package using the GROMOS-96(43a1) force field. The intramolecular hydrogen bonds (HB) were detected by the geometric criteria distance d_HB < 0.26nm, angle (A-H…O) a > 110º and occurrence fraction Fr>20%. The Ramachandran angles and root mean square deviation per residue indicate that the palm and finger domains are essentially rigid structures, and that enhanced flexibility necessary for catalysis lies in the segments that are in the immediate vicinity of glycine residues. The HB backbone-backbone (BB), backbone-side-chain (BS) and side-chain-side-chain (SS) were monitored in all temperatures an analyzed in each domain. In all domains it was detected that BS and SS-HB are less stable than BB-HB. The BB-HB are present during more than 50% of the time mainly in finger and palm domains. The stability of the finger domain is due to the interaction between the dipole calculated as -140kcal.mol^-1, approximately two times the stabilization in the palm domain. In the cleft region (common region between palm and fingers) where the active site is localized, the more stable HB are present. In the cleft, a complex HB network is maintained with Fr around 90% for most of HB in all temperatures. The minimum occurrence detected in this region was 72%. It is clear that the role of HB is to maintain the rigidity of finger and palm domains and consequently of the catalytic region that needs this rigidity in the molecular recognition process during the binding of the substrate. 
FAPESP and CNPq