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| Author(s): |
Gustavo Avelar Molina
Total Authors: 1
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| Document type: | Master's Dissertation |
| Press: | Ribeirão Preto. |
| Institution: | Universidade de São Paulo (USP). Faculdade de Filosofia, Ciências e Letras de Ribeirão Preto (PCARP/BC) |
| Defense date: | 2016-02-29 |
| Examining board members: |
Richard John Ward;
Francisco Eduardo Gontijo Guimarães;
Arthur Henrique Cavalcante de Oliveira
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| Advisor: | Richard John Ward |
| Abstract | |
The structural dynamics underlying the function of GH11 xylanases is still unclear. New insights into the catalytic dynamics of these enzymes are crucial for engineering novel improved enzymes benefiting biotechnological and green chemistry industries. The objective of this work was to obtain new information concerning the catalytic dynamics of a GH11 xylanase, by using a combination of advanced molecular biophysics techniques, both at the bulk level and at the single molecule level (sm). Mutant GH11 xylanases from Bacillus subtilis ssp. subtilis 168 (XynA) were designed with single point cysteine mutations for labeling the residues D119 and R122 on the thumb domain, N54 on the fingers domain, and N151 on the alpha helix, followed by their construction and production by molecular biology methods. These mutants were labeled at their respective thiol groups by the polarity sensitive fluorescent probe Acrylodan, by the electron spin probe MTSSL, and by the photostable fluorescent probe AttoOxa11. The wild-type xylanase was labeled at its N-terminus by the photostable fluorescent probe Alexa Fluor® 488 5-SDP Ester. Bulk fluorescence spectrophotometry and electron paramagnetic resonance assays were used to investigate how the thumb domain dynamics of the GH11 xylanase, temperature and substrate binding were correlated. These results demonstrated that a temperature controlled, open, dynamical and flexible thumb domain state is more likely to effectively bind the substrate in a productive way, which is in complete agreement with previous studies from molecular dynamics simulations, crystallography, thermal denaturation, and function analysis by the rational design of thumb mutants for GH11 xylanases. Based on this evidence and previous studies, we proposed a hypothesis for the xylanase catalytic dynamics, focusing on the role of the thumb domain. In order to determine the xylanase affinity constant for its substrate and the relaxation times and rate constants of the thumb domain movements, fluorescence correlation spectroscopy measurements were performed. Both simple and combined measurements with photoinduced electron transfer were performed, using the xylanases labeled with photostable fluorescent probes, in the presence and absence of substrate. The results have shown longer diffusion times for the xylanases in the presence of substrate, as an effect of the enzyme affinity for it. However, it was not verified any decay curve as an effect of the dynamic suppression of the probe via PET. The same conjugates were successfully applied to fluorescence-lifetime imaging microscopy, aiming to systematically analyze the affinity for xylanase of substrates in the form of insoluble particles and films, and for water insoluble fractions from sugarcane bagasse delignification processes. In addition, the composition, structure and topology of these materials was examined. It was possible to verify the presence of xylan in most fractions of this treated bagasse, although in variable quantities (AU) | |
| FAPESP's process: | 14/06319-1 - Catalytic dynamics study of the endo-1,4-beta-xylanase from Bacillus subtilis by fluorescence correlation spectroscopy |
| Grantee: | Gustavo Avelar Molina |
| Support Opportunities: | Scholarships in Brazil - Master |