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- Luzhkov, Victor B., et al.
(författare)
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Computational study of the binding affinity and selectivity of the bacterial ammonium transporter AmtB
- 2006
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Ingår i: Biochemistry. - : American Chemical Society (ACS). - 0006-2960 .- 1520-4995. ; 45:36, s. 10807-10814
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Tidskriftsartikel (refereegranskat)abstract
- We report results from microscopic molecular dynamics and free energy perturbation simulations of substrate binding and selectivity for the Escherichia coli high-affinity ammonium transporter AmtB. The simulation system consists of the protein embedded in a model membrane/water surrounding. The calculated absolute binding free energies for the external NH4+ ions are between -5.8 and -7.3 kcal/mol and are in close agreement with experimental data. The apparent pK(a) of the bound NH4+ increases by more than 4 units, indicating a preference for binding ammonium ion and not neutral ammonia. The external binding site is also selective for NH4+ toward monovalent metal cations by 2.4-4.4 kcal/mol. The externally bound NH4+ shows strong electrostatic interactions with the proximal buried Asp160, stabilized in the anionic form, whereas the interactions with the aromatic rings of Phe107 and Trp148, lining the binding cavity, are less pronounced. Simulated mutation of the highly conserved Asp160 to Asn reduces the pK(a) of the bound ammonium ion by similar to 7 units and causes loss of its binding. The calculations further predict that the substrate affinity of E. coli AmtB depends on the ionization state of external histidines. The computed free energies of hypothetical intermediate states related to transfer of NH3, NH4+, or H2O from the external binding site to the first position inside the internal channel pore favor permeation of the neutral species through the channel interior. However, the predicted change in the apparent pK(a) of NH4+ upon translocation from the external site, Am1, to the first internal site, Am2, indicates that ammonium ion becomes deprotonated only when it enters the channel interior.
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- Gutiérrez-de-Terán, Hugo, et al.
(författare)
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Computational analysis of plasmepsin IV bound to an allophenylnorstatine inhibitor
- 2006
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Ingår i: FEBS Letters. - : Wiley. - 0014-5793 .- 1873-3468. ; 580:25, s. 5910-5916
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Tidskriftsartikel (refereegranskat)abstract
- The plasmepsin proteases from the malaria parasite Plasmodium falciparum are attracting attention as putative drug targets. A recently published crystal structure of Plasmodium malariae plasmepsin IV bound to an allophenylnorstatine inhibitor [Clemente, J.C. et al. (2006) Acta Crystallogr. D 62, 246252] provides the first structural insights regarding interactions of this family of inhibitors with plasmepsins. The compounds in this class are potent inhibitors of HIV-1 protease, but also show nM binding affinities towards plasmepsin IV. Here, we utilize automated docking, molecular dynamics and binding free energy calculations with the linear interaction energy LIE method to investigate the binding of allophenylnorstatine inhibitors to plasmepsin IV from two different species. The calculations yield excellent agreement with experimental binding data and provide new information regarding protonation states of active site residues as well as conformational properties of the inhibitor complexes.
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- Gutiérrez-de-Terán, Hugo, et al.
(författare)
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Inhibitor binding to the Plasmepsin IV aspartic protease from Plasmodium falciparum
- 2006
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Ingår i: Biochemistry. - : American Chemical Society (ACS). - 0006-2960 .- 1520-4995. ; 45:35, s. 10529-10541
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Tidskriftsartikel (refereegranskat)abstract
- Plasmepsin IV (Plm IV) is one of the aspartic proteases present in the food vacuole of the malaria parasite Plasmodium falciparum involved in host hemoglobin degradation by the parasite. Using a series of previously synthesized plasmepsin inhibitors [Ersmark, K., et al. (2005) J. Med. Chem. 48, 6090-106], we report here experimental data and theoretical analysis of their inhibitory activity toward Plm IV. All compounds share a 1,2-dihydroxyethylene unit as the transition state mimic. They possess symmetric P1 and P1' side chains and either a diacylhydrazine, a five-membered oxadiazole ring, or a retroamide at the P2 and P2' positions. Experimental binding affinities are compared to those predicted by the linear interaction energy (LIE) method and an empirical scoring function, using both a crystal structure and a homology model for the enzyme. Molecular dynamics (MD) simulations of the modeled complexes allow a rational interpretation of the structural determinants for inhibitor binding. A ligand bearing a P2 and P2' symmetric oxadiazole which is devoid of amide bonds is identified both experimentally and theoretically as the most potent inhibitor of Plm IV. For the P2 and P2' asymmetric compounds, the results are consistent with earlier predictions regarding the mode of binding of this class of inhibitors to Plm II. Theoretical estimation of selectivity for some compounds is also reported. Significant features of the Plm IV binding pocket are discussed in comparison to related enzymes, and the results obtained here should be helpful for further optimization of inhibitors.
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