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| Author(s): |
Davi Serradella Vieira
Total Authors: 1
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| Document type: | Doctoral Thesis |
| Press: | Ribeirão Preto. |
| Institution: | Universidade de São Paulo (USP). Faculdade de Filosofia, Ciências e Letras de Ribeirão Preto (PCARP/BC) |
| Defense date: | 2007-10-03 |
| Examining board members: |
Leo Degreve;
Antonio Carlos Borin;
Richard Charles Garratt;
Dimitrios Samios;
Richard John Ward
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| Advisor: | Leo Degreve |
| Abstract | |
The enzymes xylanases (EC 3.2.1.8) are produced by several microorganisms and used to hydrolyze the -1,4 bonds of the xylan main chain, the most abundant hemicellulose in nature. The great biotechnological potential of the xylanases is due to its application in the pulp-bleaching processes when the xylan is hydrolyzed under high temperature condition to optimize the lignin removal. This procedure presents the advantage to reduce the amount of chlorine chemicals used in the pulp-bleaching process. The required properties of a biotechnologically useful xylanase include thermostability and high affinity for xylan. The mesophilic, XBC, (from Bacillus circulans) and thermophilic, XTL, (from Thermomyces lanuginosus) xylanases were studied by molecular dynamics simulations. The primary structures of these enzymes are almost completely different while the tertiary structures are identical. The objective of the study is to get some insight on the factors that are responsible for the xylanase thermostability. The systems were modeled by the GROMOS96-(43A1) force field and the molecular dynamic simulations were performed by the GROMACS 3.2 package in the temperature range from 25 to 80ºC. The results obtained with both xylanases were compared. The existence of two kinds of regions was identified in XBC and XTL: the first one conserved and highly stable is formed by the so-called palm and fingers domains. The second region exhibits large movements: this is the thumb domain. A kind of open-close motion was identified that maybe can facilitate the access of the xylane to the active center. The inter/intramolecular hydrogen bonds and salt bridges allow to explain at great length the thermostability differences between the two enzymes. It was possible to identify 14 charged residues present in the XTL with no similar in the XBC: such residues must be considered outstanding mutation sites in XBC. In the presence of the substrate, the characteristics of each domain/region are not modified but the stability of the thumb domain is increased. No difference in the affinity for the substrate was detected between the xylanases and it can be suggested that the activation energies are similar. Two water molecules were found in the active site supporting the hydrolysis mechanisms proposed in the literature. (AU) | |
| FAPESP's process: | 03/01457-2 - Structure, thermostability and activity of xylanases: a molecular dynamics study |
| Grantee: | Davi Serradella Vieira |
| Support Opportunities: | Scholarships in Brazil - Doctorate |