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      Studying the Structure and Dynamics of Biomolecules by Using Soluble Paramagnetic Probes

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          Abstract

          Characterisation of the structure and dynamics of large biomolecules and biomolecular complexes by NMR spectroscopy is hampered by increasing overlap and severe broadening of NMR signals. As a consequence, the number of available NMR spectroscopy data is often sparse and new approaches to provide complementary NMR spectroscopy data are needed. Paramagnetic relaxation enhancements (PREs) obtained from inert and soluble paramagnetic probes (solvent PREs) provide detailed quantitative information about the solvent accessibility of NMR-active nuclei. Solvent PREs can be easily measured without modification of the biomolecule; are sensitive to molecular structure and dynamics; and are therefore becoming increasingly powerful for the study of biomolecules, such as proteins, nucleic acids, ligands and their complexes in solution. In this Minireview, we give an overview of the available solvent PRE probes and discuss their applications for structural and dynamic characterisation of biomolecules and biomolecular complexes.

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          Very fast two-dimensional NMR spectroscopy for real-time investigation of dynamic events in proteins on the time scale of seconds.

          We demonstrate for different protein samples that 2D 1H-15N correlation NMR spectra can be recorded in a few seconds of acquisition time using a new band-selective optimized flip-angle short-transient heteronuclear multiple quantum coherence experiment. This has enabled us to measure fast hydrogen-deuterium exchange rate constants along the backbone of a small globular protein fragment by real-time 2D NMR.
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            Structural basis for dimethylarginine recognition by the Tudor domains of human SMN and SPF30 proteins.

            Arginine dimethylation plays critical roles in the assembly of ribonucleoprotein complexes in pre-mRNA splicing and piRNA pathways. We report solution structures of SMN and SPF30 Tudor domains bound to symmetric and asymmetric dimethylated arginine (DMA) that is inherent in the RNP complexes. An aromatic cage in the Tudor domain mediates dimethylarginine recognition by electrostatic stabilization through cation-π interactions. Distinct from extended Tudor domains, dimethylarginine binding by the SMN and SPF30 Tudor domains is independent of proximal residues in the ligand. Yet, enhanced micromolar affinities are obtained by external cooperativity when multiple methylation marks are presented in arginine- and glycine-rich peptide ligands. A hydrogen bond network in the SMN Tudor domain, including Glu134 and a tyrosine hydroxyl of the aromatic cage, enhances cation-π interactions and is impaired by a mutation causing an E134K substitution associated with spinal muscular atrophy. Our structural analysis enables the design of an optimized binding pocket and the prediction of DMA binding properties of Tudor domains.
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              Identification of protein surfaces by NMR measurements with a pramagnetic Gd(III) chelate.

              Gd-diethylenetriamine pentaacetic acid-bismethylamide, Gd(DTPA-BMA), is shown to be a reagent suitable for the identification of protein surfaces. Compared to the conventionally used spin-label TEMPOL, Gd(DTPA-BMA) is a stronger relaxation agent, requiring lesser concentrations to achieve the same paramagnetic relaxation enhancement of solvent-exposed protein protons. It is also less hydrophobic and therefore less prone to specific binding to proteins. Relaxation enhancements predicted by a second-sphere interaction model correlated with experimental data recorded with ubiquitin, while the correlation with corresponding data recorded with TEMPOL was poor.
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                Author and article information

                Journal
                Chemphyschem
                Chemphyschem
                cphc
                Chemphyschem
                WILEY-VCH Verlag (Weinheim )
                1439-4235
                1439-7641
                16 September 2013
                08 July 2013
                : 14
                : 13
                : 3082-3094
                Affiliations
                [[a] ]Chair of Biomolecular NMR, Department Chemie Technische Universität München 85747 Garching (Germany) E-mail: t.madl@ 123456tum.de
                [[b] ]Institute of Structural Biology, Helmholtz Zentrum München 85764 Neuherberg (Germany)
                [[c] ]Institute of Chemistry, Karl-Franzens Universität Graz 8010 Graz (Austria)
                Article
                10.1002/cphc.201300219
                4171756
                23836693
                f93ca370-444b-4197-a200-c31534ee77fc
                © 2013 The Authors. Published by Wiley-VCH Verlag GmbH&Co. KGaA.

                This is an open access article under the terms of the Creative Commons Attribution Non-Commercial NoDerivs License, which permits use and distribution in any medium, provided the original work is properly cited, the use is non-commercial and no modifications or adaptations are made.

                History
                : 01 March 2013
                Categories
                Minireviews

                Physical chemistry
                magnetic properties,nmr spectroscopy,proteins,solvent effects,structural biology

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