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| Author(s): |
Guilherme Menegon Arantes
Total Authors: 1
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| Document type: | Doctoral Thesis |
| Press: | São Paulo. , gráficos, ilustrações, tabelas. |
| Institution: | Universidade de São Paulo (USP). Conjunto das Químicas (IQ e FCF) (CQ/DBDCQ) |
| Defense date: | 2004-08-13 |
| Examining board members: |
Hernan Chaimovich Guralnik;
Sylvio Roberto Accioly Canuto;
Rogério Custódio;
Sandro Roberto Marana;
Mauro Carlos Costa Ribeiro
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| Advisor: | Hernan Chaimovich Guralnik; Michel Loos |
| Field of knowledge: | Biological Sciences - Biochemistry |
| Indexed in: | Banco de Dados Bibliográficos da USP-DEDALUS; Biblioteca Digital de Teses e Dissertações - USP |
| Location: | Universidade de São Paulo. Biblioteca do Conjunto das Químicas; CQ T/574.1925; A662s |
| Abstract | |
Protein tyrosine phosphatases (PTPs) catalyse the hydrolysis of phosphotyrosine from other proteins and, hence, regulate important biochemical processes. Two members from this family are the dual specificity phosphatases VHR and CDC25B. The first step of the catalysed reaction is the nucleophilic attack from the side chain of a cystein towards the substrate, with a possible H+ transfer from a general acid to the leaving group, forming a PTP thiophosphorylated intermediate and dephosphorylating the substrate. There are still some doubts about this step, involving the protonation states of the substrate and the nzymatic nucleophile, the inactivity of certain mutants and the identification of the general acid in CDC25s. We tried to solve this questions by computer simulations of the reactions catalysed by VHR and by CDC25B. Initially, reaction pathways of phosphate esters thiolysis and alcoholysis in the gas-phase were determined by ab initio electronic structure calculations and analysed as benchmarks for the intrinsic reactivity of phosphate esters and as models of the enzymatic activity. A hybrid potential of quantum mechanics and molecular mechanics was fully tested and calibrated, employing these reaction pathways and other ab initio data. The calibration allowed that semiquantitative conclusions could be obtained from the enzymatic simulations. Potentials of mean force were determined with the hybrid potential for the dephosphorylation of different substrates catalysed by the wild-type PTPs and their mutants. The results show that the catalysed reaction mechanism follows a concerted addition and elimination, with a dissociative transition state with metaphosphate-like. The calculated barriers are very close to the experimental activation energies. The enzymatic substrate is a deprotonated dianion and the nucleophile is ionised. The reactions of the protonated substrate or nucleophile have barriers, at least, 15 kcal/mol higher than the experimental results. The active site cystein to serine VHR mutant is inactive because the serine is protonated. The CDC25s do not employ a general acid for catalysis, differently from the other PTPs. Proposals that the general acid is the substrate or one of the glutamic acids present in the active site are not energetically accessible. (AU) | |