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Induced conformational changes upon Cd2+ binding at photosynthetic reaction centers.

ABSTRACT: Cd(2+) binding at the bacterial photosynthetic reaction center (bRC) from Rhodobacter sphaeroides is known to inhibit proton transfer (PT) from bulk solvent to the secondary quinone Q(B). To elucidate this mechanism, we calculated the pK(a) for residues along the water channels connecting Q(B) with the stromal side based on the crystal structures of WT-bRC and Cd(2+)-bound bRC. Upon Cd(2+) binding, we observed the release of two protons from His-H126/128 at the Cd(2+) binding site and significant pK(a) shifts for residues along the PT pathways. Remarkably, Asp-L213 near Q(B), which is proposed to play a significant role in PT, resulted in a decrease in pK(a) upon Cd(2+) binding. The direct electrostatic influence of the Cd(2+)-positive charge on these pK(a) shifts was small. Instead, conformational changes of amino acid side chains induced electrostatically by Cd(2+) binding were the main mechanism for these pK(a) shifts. The long-range electrostatic influence over approximately 12 A between Cd(2+) and Asp-L213 is likely to originate from a set of Cd(2+)-induced successive reorientations of side chains (Asp-H124, His-H126, His-H128, Asp-H170, Glu-H173, Asp-M17, and Asp-L210), which propagate along the PT pathways as a "domino" effect.

SUBMITTER: Ishikita H

PROVIDER: S-EPMC1283420 | biostudies-literature | 2005 Nov

REPOSITORIES: biostudies-literature

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Induced conformational changes upon Cd2+ binding at photosynthetic reaction centers.

Ishikita Hiroshi H Knapp Ernst-Walter EW

Proceedings of the National Academy of Sciences of the United States of America 20051027 45

Cd(2+) binding at the bacterial photosynthetic reaction center (bRC) from Rhodobacter sphaeroides is known to inhibit proton transfer (PT) from bulk solvent to the secondary quinone Q(B). To elucidate this mechanism, we calculated the pK(a) for residues along the water channels connecting Q(B) with the stromal side based on the crystal structures of WT-bRC and Cd(2+)-bound bRC. Upon Cd(2+) binding, we observed the release of two protons from His-H126/128 at the Cd(2+) binding site and significan ...[more]

PMID: 16254054

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Project description:Protein-protein interactions represent difficult but increasingly important targets for the design of therapeutic compounds able to interfere with biological processes. Recently, fragment-based strategies have been proposed as attractive approaches for the elaboration of protein-protein surface inhibitors from fragment-like molecules. One major challenge in targeting protein-protein interactions is related to the structural adaptation of the protein surface upon molecular recognition. Methods capable of identifying subtle conformational changes of proteins upon fragment binding are therefore required at the early steps of the drug design process. In this report we present a fast NMR method able to probe subtle conformational changes upon fragment binding. The approach relies on the comparison of experimental fragment-induced Chemical Shift Perturbation (CSP) of amine protons to CSP simulated for a set of docked fragment poses, considering the ring-current effect from fragment binding. We illustrate the method by the retrospective analysis of the complex between the anti-apoptotic Bcl-xL protein and the fragment 4'-fluoro-[1,1'-biphenyl]-4-carboxylic acid that was previously shown to bind one of the Bcl-xL hot spots. The CSP-based approach shows that the protein undergoes a subtle conformational rearrangement upon interaction, for residues located in helices [Formula: see text]2, [Formula: see text]3 and the very beginning of [Formula: see text]5. Our observations are corroborated by residual dipolar coupling measurements performed on the free and fragment-bound forms of the Bcl-xL protein. These NMR-based results are in total agreement with previous molecular dynamic calculations that evidenced a high flexibility of Bcl-xL around the binding site. Here we show that CSP of protein amine protons are useful and reliable structural probes. Therefore, we propose to use CSP simulation to assess protein conformational changes upon ligand binding in the fragment-based drug design approach.

Dataset Information

Induced conformational changes upon Cd2+ binding at photosynthetic reaction centers.

Publications

Induced conformational changes upon Cd2+ binding at photosynthetic reaction centers.

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