| 1. |
- Blobel, Jascha, et al.
(författare)
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Protein loop compaction and the origin of the effect of arginine and glutamic acid mixtures on solubility, stability and transient oligomerization of proteins
- 2011
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Ingår i: European Biophysics Journal. - : Springer Science and Business Media LLC. - 0175-7571 .- 1432-1017. ; 40:12, s. 1327-1338
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Tidskriftsartikel (refereegranskat)abstract
- Addition of a 50 mM mixture of l-arginine and l-glutamic acid (RE) is extensively used to improve protein solubility and stability, although the origin of the effect is not well understood. We present Small Angle X-ray Scattering (SAXS) and Nuclear Magnetic Resonance (NMR) results showing that RE induces protein compaction by collapsing flexible loops on the protein core. This is suggested to be a general mechanism preventing aggregation and improving resistance to proteases and to originate from the polyelectrolyte nature of RE. Molecular polyelectrolyte mixtures are expected to display long range correlation effects according to dressed interaction site theory. We hypothesize that perturbation of the RE solution by dissolved proteins is proportional to the volume occupied by the protein. As a consequence, loop collapse, minimizing the effective protein volume, is favored in the presence of RE.
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| 2. |
- Brath, Ulrika, et al.
(författare)
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Mapping the sevoflurane-binding site of calmodulin
- 2014
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Ingår i: Pharmacology Research & Perspectives. - : Wiley. - 2052-1707 .- 2052-1707. ; 2:1
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Tidskriftsartikel (refereegranskat)abstract
- General anesthetics, with sevoflurane (SF) being the first choice inhalational anesthetic agent, provide reversible, broad depressor effects on the nervous system yet have a narrow margin of safety. As characterization of low-affinity binding interactions of volatile substances is exceptionally challenging with the existing methods, none of the numerous cellular targets proposed as chief protagonists in anesthesia could yet be confirmed. The recognition that most critical functions modulated by volatile anesthetics are under the control of intracellular Ca2+ concentration, which in turn is primarily regulated by calmodulin (CaM), motivated us for characterization of the SF–CaM interaction. Solution NMR (Nuclear Magnetic Resonance) spectroscopy was used to identify SF-binding sites using chemical shift displacement, NOESY and heteronuclear Overhauser enhancement spectroscopy (HOESY) experiments. Binding affinities were measured using ITC (isothermal titration calorimetry). SF binds to both lobes of (Ca2+)4-CaM with low mmol/L affinity whereas no interaction was observed in the absence of Ca2+. SF does not affect the calcium binding of CaM. The structurally closely related SF and isoflurane are shown to bind to the same clefts. The SF-binding clefts overlap with the binding sites of physiologically relevant ion channels and bioactive small molecules, but the binding affinity suggests it could only interfere with very weak CaM targets.
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| 3. |
- Carlsson, Anna-Carin, 1976, et al.
(författare)
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Solvent Effects on Halogen Bond Symmetry
- 2013
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Ingår i: CrysteEngComm. - 1466-8033. ; 15:16, s. 3087-3092
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Tidskriftsartikel (refereegranskat)abstract
- The symmetric arrangement of the iodine and bromine centred 3-center–4-electron halogen bond is revealed to remain preferred in a polar, aprotic solvent environment. Acetonitrile is unable to compete with pyridine for halogen bonding; however, its polarity weakly modulates the energy of the interaction and influences IPE-NMR experiments.
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| 4. |
- Carlsson, Anna-Carin, 1976, et al.
(författare)
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Symmetric Halogen Bonding is Preferred in Solution
- 2012
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Ingår i: Journal of the American Chemical Society. - : American Chemical Society (ACS). - 0002-7863 .- 1520-5126. ; 134, s. 5706-5715
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Tidskriftsartikel (refereegranskat)abstract
- Halogen bonding is a recently rediscovered secondary interaction that shows potential to become a complementary molecular tool to hydrogen bonding in rational drug design and in material sciences. Whereas hydrogen bond symmetry has been the subject of systematic studies for decades, the understanding of the analogous three-center halogen bonds is yet in its infancy. The isotopic perturbation of equilibrium (IPE) technique with 13C NMR detection was applied to regioselectively deuterated pyridine complexes to investigate the symmetry of [N−I−N]+ and [N−Br−N]+ halogen bonding in solution. Preference for a symmetric arrangement was observed for both a freely adjustable and for a conformationally restricted [N−X−N]+ model system, as also confirmed by computation on the DFT level. A closely attached counterion is shown to be compatible with the preferred symmetric arrangement. The experimental observations and computational predictions reveal a high energetic gain upon formation of symmetric, three-center four-electron halogen bonding. Whereas hydrogen bonds are generally asymmetric in solution and symmetric in the crystalline state, the analogous bromine and iodine centered halogen bonds prefer symmetric arrangement in solution.
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| 5. |
- Danelius, Emma, et al.
(författare)
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Insight into β-Hairpin Stability: Interstrand Hydrogen Bonding
- 2013
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Ingår i: Synlett : Accounts and Rapid Communications in Synthetic Organic Chemistry. - : Georg Thieme Verlag KG. - 0936-5214 .- 1437-2096. ; 24:18, s. 2407-2410
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Tidskriftsartikel (refereegranskat)abstract
- For evaluation of the role of interstrand hydrogen bonding for β-hairpin stability, two cyclic peptides differing only in side chain hydroxy-to-methyl substitution were designed and synthesized on solid phase following the Fmoc-t-Bu-Trt protection strategy. Subsequent to cyclization in solution, combined computational and experimental ensemble analysis revealed higher conformational stability of the peptide capable of interstrand hydrogen bonding.
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| 6. |
- Weininger, Ulrich, et al.
(författare)
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Off-resonance rotating-frame relaxation dispersion experiment for 13C in aromatic side chains using L-optimized TROSY-selection
- 2014
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Ingår i: Journal of Biomolecular NMR. - : Kluwer Academic Publishers. - 0925-2738 .- 1573-5001. ; 59:1, s. 23-29
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Tidskriftsartikel (refereegranskat)abstract
- Protein dynamics on the microsecond-millisecond time scales often play a critical role in biological function. NMR relaxation dispersion experiments are powerful approaches for investigating biologically relevant dynamics with site-specific resolution, as shown by a growing number of publications on enzyme catalysis, protein folding, ligand binding, and allostery. To date, the majority of studies has probed the backbone amides or side-chain methyl groups, while experiments targeting other sites have been used more sparingly. Aromatic side chains are useful probes of protein dynamics, because they are over-represented in protein binding interfaces, have important catalytic roles in enzymes, and form a sizable part of the protein interior. Here we present an off-resonance R1ρ experiment for measuring microsecond to millisecond conformational exchange of aromatic side chains in selectively 13C labeled proteins by means of longitudinal- and transverse-relaxation optimization. Using selective excitation and inversion of the narrow component of the 13C doublet, the experiment achieves significant sensitivity enhancement in terms of both signal intensity and the fractional contribution from exchange to transverse relaxation; additional signal enhancement is achieved by optimizing the longitudinal relaxation recovery of the covalently attached 1H spins. We validated the L-TROSY-selected R1ρ experiment by measuring exchange parameters for Y23 in bovine pancreatic trypsin inhibitor at a temperature of 328 K, where the ring flip is in the fast exchange regime with a mean waiting time between flips of 320 μs. The determined chemical shift difference matches perfectly with that measured from the NMR spectrum at lower temperatures, where separate peaks are observed for the two sites. We further show that potentially complicating effects of strong scalar coupling between protons (Weininger et al. in J Phys Chem B 117: 9241-9247, 2013b) can be accounted for using a simple expression, and provide recommendations for data acquisition when the studied system exhibits this behavior. The present method extends the repertoire of relaxation methods tailored for aromatic side chains by enabling studies of faster processes and improved control over artifacts due to strong coupling. © 2014 The Author(s).
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