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      The influence of pH and divalent/monovalent cations on the internal electron transfer (IET), enzymatic activity, and structure of fructose dehydrogenase

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          Abstract

          We report on the influence of pH and monovalent/divalent cations on the catalytic current response, internal electron transfer (IET), and structure of fructose dehydrogenase (FDH) by using amperometry, spectrophotometry, and circular dichroism (CD). Amperometric measurements were performed on graphite electrodes, onto which FDH was adsorbed and the effect on the response current to fructose was investigated when varying the pH and the concentrations of divalent/monovalent cations in the contacting buffer. In the presence of 10 mM CaCl 2, a current increase of up to ≈ 240% was observed, probably due to an intra-complexation reaction between Ca 2+ and the aspartate/glutamate residues found at the interface between the dehydrogenase domain and the cytochrome domain of FDH. Contrary to CaCl 2, addition of MgCl 2 did not show any particular influence, whereas addition of monovalent cations (Na + or K +) led to a slight linear increase in the maximum response current. To complement the amperometric investigations, spectrophotometric assays were carried out under homogeneous conditions in the presence of a 1-electron non-proton-acceptor, cytochrome c, or a 2-electron-proton acceptor, 2,6-dichloroindophenol (DCIP), respectively. In the case of cytochrome c, it was possible to observe a remarkable increase in the absorbance up to 200% when 10 mM CaCl 2 was added. However, by further increasing the concentration of CaCl 2 up to 50 mM and 100 mM, a decrease in the absorbance with a slight inhibition effect was observed for the highest CaCl 2 concentration. Addition of MgCl 2 or of the monovalent cations shows, surprisingly, no effect on the electron transfer to the electron acceptor. Contrary to the case of cytochrome c, with DCIP none of the cations tested seem to affect the rate of catalysis. In order to correlate the results obtained by amperometric and spectrophotometric measurements, CD experiments have been performed showing a great structural change of FDH when increasing the concentration CaCl 2 up to 50 mM, at which the enzyme molecules start to agglomerate, hindering the substrate access to the active site probably due to a chelation reaction occurring at the enzyme surface with the glutamate/aspartate residues.

          Graphical Abstract

          Fructose dehydrogenase (FDH) consists of three subunits, but only two are involved in the electron transfer process: (I) 2e /2H + fructose oxidation, (II) internal electron transfer (IET), (III) direct electron transfer (DET) through 2 heme c; FDH activity either in solution or when immobilized onto an electrode surface is enhanced about 2.5-fold by adding 10 mM CaCl 2 to the buffer solution, whereas MgCl 2 had an “inhibition” effect. Moreover, the additions of KCl or NaCl led to a slight current increase

          Electronic supplementary material

          The online version of this article (10.1007/s00216-018-0991-0) contains supplementary material, which is available to authorized users.

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          Computed circular dichroism spectra for the evaluation of protein conformation.

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            FireDock: fast interaction refinement in molecular docking.

            Here, we present FireDock, an efficient method for the refinement and rescoring of rigid-body docking solutions. The refinement process consists of two main steps: (1) rearrangement of the interface side-chains and (2) adjustment of the relative orientation of the molecules. Our method accounts for the observation that most interface residues that are important in recognition and binding do not change their conformation significantly upon complexation. Allowing full side-chain flexibility, a common procedure in refinement methods, often causes excessive conformational changes. These changes may distort preformed structural signatures, which have been shown to be important for binding recognition. Here, we restrict side-chain movements, and thus manage to reduce the false-positive rate noticeably. In the later stages of our procedure (orientation adjustments and scoring), we smooth the atomic radii. This allows for the minor backbone and side-chain movements and increases the sensitivity of our algorithm. FireDock succeeds in ranking a near-native structure within the top 15 predictions for 83% of the 30 enzyme-inhibitor test cases, and for 78% of the 18 semiunbound antibody-antigen complexes. Our refinement procedure significantly improves the ranking of the rigid-body PatchDock algorithm for these cases. The FireDock program is fully automated. In particular, to our knowledge, FireDock's prediction results are comparable to current state-of-the-art refinement methods while its running time is significantly lower. The method is available at http://bioinfo3d.cs.tau.ac.il/FireDock/. 2007 Wiley-Liss, Inc.
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              Enzymes as working or inspirational electrocatalysts for fuel cells and electrolysis.

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                Author and article information

                Contributors
                Lo.Gorton@biochemistry.lu.se
                Riccarda.Antiochia@uniroma1.it
                Journal
                Anal Bioanal Chem
                Anal Bioanal Chem
                Analytical and Bioanalytical Chemistry
                Springer Berlin Heidelberg (Berlin/Heidelberg )
                1618-2642
                1618-2650
                22 March 2018
                22 March 2018
                2018
                : 410
                : 14
                : 3253-3264
                Affiliations
                [1 ]GRID grid.7841.a, Department of Chemistry and Drug Technologies, , Sapienza University of Rome, ; Piazzale Aldo Moro 5, 00185 Rome, Italy
                [2 ]ISNI 0000 0001 0930 2361, GRID grid.4514.4, Department of Analytical Chemistry/Biochemistry, , Lund University, ; P.O. Box 124, 221 00 Lund, Sweden
                [3 ]ISNI 0000 0004 0372 2033, GRID grid.258799.8, Division of Applied Life Sciences, Graduate School of Agriculture, , Kyoto University, ; Sakyo, Kyoto, 606-8502 Japan
                Author notes

                Published in the topical collection Euroanalysis XIX with guest editors Charlotta Turner and Jonas Bergquist.

                Article
                991
                10.1007/s00216-018-0991-0
                5937911
                29564502
                9c65887b-b904-4a83-a7d4-32bddff283cb
                © The Author(s) 2018

                Open Access This article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made.

                History
                : 15 November 2017
                : 17 January 2018
                : 27 February 2018
                Funding
                Funded by: FundRef http://dx.doi.org/10.13039/501100004359, Vetenskapsrådet;
                Award ID: 2014-5908
                Funded by: FundRef http://dx.doi.org/10.13039/100011264, FP7 People: Marie-Curie Actions;
                Award ID: FP7-PEOPLE-2013-ITN-607793
                Categories
                Paper in Forefront
                Custom metadata
                © Springer-Verlag GmbH Germany, part of Springer Nature 2018

                Analytical chemistry
                fructose dehydrogenase (fdh),calcium chloride,direct electron transfer (det),enzyme activity,enzyme structure

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