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Computational Prediction of Structure, Substrate Binding Mode, Mechanism, and Rate for a Malaria Protease with a Novel Type of Active Site
Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Biology, Department of Cell and Molecular Biology.
2004 In: Biochemistry, ISSN 0006-2960, Vol. 43, no 46, 14521-14528 p.Article in journal (Refereed) Published
Place, publisher, year, edition, pages
2004. Vol. 43, no 46, 14521-14528 p.
URN: urn:nbn:se:uu:diva-95443OAI: oai:DiVA.org:uu-95443DiVA: diva2:169646
Available from: 2007-02-07 Created: 2007-02-07Bibliographically approved
In thesis
1. Molecular Simulation of Enzyme Catalysis and Inhibition
Open this publication in new window or tab >>Molecular Simulation of Enzyme Catalysis and Inhibition
2007 (English)Doctoral thesis, comprehensive summary (Other academic)
Abstract [en]

The reaction mechanisms for the hemoglobin degrading enzymes in the Plasmodium falciparum malaria parasite, plasmepsin II (Plm II) and histo-aspartic protease (HAP), have been analyzed by molecular simulations. The reaction free energy profiles, calculated by the empirical valence bond (EVB) method in combination with molecular dynamics (MD) and free energy perturbation (FEP) simulations are in good agreement with experimental data. Additional computational methods, such as homology modelling and automated substrate docking, were necessary to generate a 3D model and a reactive substrate conformation before the reaction mechanism in HAP could be investigated. HAP is found to be an aspartic protease with a peptide cleaving mechanism similar to plasmepsin II. The major difference between these enzymes is that the negatively charged tetrahedral intermediate is stabilized by the charged histidine in HAP while in Plm II it is a neutral aspartic acid. Also the reaction mechanism for two other aspartic proteases, cathepsin D and HIV-1 protease, was simulated. These enzymes are relevant both for the inhibitor selectivity and for obtaining a general picture of catalysis in aspartic proteases.

Another project involves inhibitor design towards plasmepsins. In particular, Plm II directed inhibitors based on the dihydroxyethylene scaffold have been characterized computationally. Molecular dynamics (MD) simulations were used to propagate the investigated system through time and to generate ensembles used for the calculation of free energies. The ligand binding affinities were calculated with the linear interaction energy (LIE) method. The most potent inhibitor had a Ki value of 6 nM and showed 78 % parasite inhibition when tested on red blood cells infected by malaria parasite P. falciparum.

Citrate synthase is part of the citric acid cycle and is present in organisms that live in cold sea water as well as hot springs. The temperature adaptation of citrate synthase to cold and heat was investigated in terms of the difference in transition state stabilization between the psychrophilic, mesophilic and hyperthermophilic homologues. The EVB, FEP and MD methods were used to generate reaction free energy profiles. The investigated energetics points toward the electrostatic stabilization during the reaction as the major difference between the different citrate synthase homologues. The electrostatic stabilization of the transition state is most effective in the following order of the citrate synthase homologues: hyperthermophile, mesophile, psycrophile. This could be a general rule for temperature adaptation of enzyme catalysis.

Place, publisher, year, edition, pages
Uppsala: Acta Universitatis Upsaliensis, 2007. 56 p.
Digital Comprehensive Summaries of Uppsala Dissertations from the Faculty of Science and Technology, ISSN 1651-6214 ; 270
Theoretical chemistry, enzyme catalysis, enzyme inhibition, computer simulations, molecular dynamics, empirical valence bond method, structure-based inhibitor design, Teoretisk kemi
urn:nbn:se:uu:diva-7468 (URN)978-91-554-6794-6 (ISBN)
Public defence
2007-03-02, C8:305, BMC, Husargatan 3, Uppsala, 13:15 (English)
Available from: 2007-02-07 Created: 2007-02-07 Last updated: 2010-04-28Bibliographically approved

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