Time Window Expansion for HDX Analysis of an Intrinsically Disordered Protein

Application of typical HDX methods to examine intrinsically disordered proteins (IDP), proteins that are natively unstructured and highly dynamic at physiological pH, is limited because of the rapid exchange of unprotected amide hydrogens with solvent. The exchange rates of these fast exchanging amides are usually faster than the shortest time scale (10 s) employed in typical automated HDX-MS experiments. Considering the functional importance of IDPs and their association with many diseases, it is valuable to develop methods that allow the study of solution dynamics of these proteins as well as the ability to probe the interaction of IDPs with their wide range of binding partners. Here, we report the application of time window expansion to the millisecond range by altering the on-exchange pH of the HDX experiment to study a well-characterized IDP; the activation domain of the nuclear receptor coactivator, peroxisome proliferator-activated receptor gamma coactivator-1 alpha (PGC-1α). This method enabled mapping the regions of PGC-1α that are stabilized upon binding the ligand binding domain (LBD) of the nuclear receptor peroxisome proliferator-activated receptor gamma (PPARγ). We further demonstrate the method’s applicability to other binding partners of the IDP PGC-1α and pave the way for characterizing many other biologically important ID proteins.

Ethylene spacer-linked bis-acetamidopyridine for dicarboxylic acid recognition and polymeric new wave-like anti-perpendicular arrangement of a host–guest in the solid state

In this paper, 1,2-bis(2-acetamido-6-pyridyl)ethane, receptor 1, having an ethylene spacer is reported to recognise dicarboxylic acids. The binding study in the solution phase is carried out using ¹H NMR (1:1) and UV–vis experiments and in the solid phase by single-crystal X-ray analysis. In ¹H NMR, the downfield shifts of specific amide protons of receptor 1 in 1:1 complexes of receptor and guest diacids, and in the UV–vis experiment, the appearance of an isosbestic point as well as significant binding constants are observed, which thus unambiguously support the complexation of receptor 1 with dicarboxylic acids in solution. Receptor 2, simple 2-acetamido-6-methylpyridine, has lower binding constants than receptor 1 due to cooperative binding of two pyridine amide groups with two acid groups of diacids. In the solid phase, the ditopic receptor 1 shows a grid-like polymeric hydrogen-bonded network that changes to a polymeric wave-like 1:1 anti-perpendicular network instead of the syn–syn polymeric 1:1 (Goswami, S.; Dey, S.; Fun, H.-K.; Anjum, S.; Rahman, A.-U. Tetrahedron Lett. 2005 (a) Goswami, S., Ghosh, K. and Dasgupta, S. 2000. J. Org. Chem., 65: 1907–1914. (b) Goswami, S.; Ghosh, K.; Mukherjee, R. Tetrahedron2001, 57, 4987–4993. (c) Goswami, S.; Ghosh, K.; Halder, M. Tetrahedron Lett.1999, 40, 1735–1738. (d) Goswami, S.; Dey, S.; Fun, H.-K.; Anjum, S.; Rahman, A.-U. Tetrahedron Lett.2005, 46, 7187–7191. (e) Goswami, S.; Jana, S.; Dey, S.; Razak, I.A.; Fun, H.-K. Supramol. Chem.2006, 18, 571–574. (f) Goswami, S.; Jana, S.; Fun, H.-K. Cryst. Eng. Comm.2008, 10, 507–517. (g) Goswami, S.; Jana, S.; Dey, S.; Sen, D.; Fun, H.-K.; Chantrapromma, S. Tetrahedron2008,64, 6426–6433. (h) Goswami, S.; Dey, S.; Jana, S. Tetrahedron2008, 64, 6358–6363 [Google Scholar], 46, 7187–7191), anti–anti polymeric 1:1 (Goswami, S.; Jana, S.; Dey, S.; Razak, I.A.; Fun, H.-K. Supramol. Chem. 2006 (a) Goswami, S., Ghosh, K. and Dasgupta, S. 2000. J. Org. Chem., 65: 1907–1914. (b) Goswami, S.; Ghosh, K.; Mukherjee, R. Tetrahedron2001, 57, 4987–4993. (c) Goswami, S.; Ghosh, K.; Halder, M. Tetrahedron Lett.1999, 40, 1735–1738. (d) Goswami, S.; Dey, S.; Fun, H.-K.; Anjum, S.; Rahman, A.-U. Tetrahedron Lett.2005, 46, 7187–7191. (e) Goswami, S.; Jana, S.; Dey, S.; Razak, I.A.; Fun, H.-K. Supramol. Chem.2006, 18, 571–574. (f) Goswami, S.; Jana, S.; Fun, H.-K. Cryst. Eng. Comm.2008, 10, 507–517. (g) Goswami, S.; Jana, S.; Dey, S.; Sen, D.; Fun, H.-K.; Chantrapromma, S. Tetrahedron2008,64, 6426–6433. (h) Goswami, S.; Dey, S.; Jana, S. Tetrahedron2008, 64, 6358–6363 [Google Scholar], 18, 571–574; Goswami, S.; Jana, S.; Fun, H.-K. Cryst. Eng. Comm. 2008, 10, 507–517; Goswami, S.; Jana, S.; Dey, S.; Sen, D.; Fun, H.-K.; Chantrapromma, S. Tetrahedron 2008, 64, 6426–6433), syn–syn 2:2 (Karle, I.L.; Ranganathan, D.; Haridas, V. J. Am. Chem. Soc. 1997 (a) Garcia-Tellado, F., Goswami, S., Chang, S.K., Geib, S.J. and Hamilton, A.D. 1990. J. Am. Chem. Soc., 112: 7393–7394. (b) Geib, S.J.; Vicent, C.; Fan, E.; Hamilton, A.D. Angew. Chem. Int. Ed. Engl.1993, 32, 119–121. (c) Garcia-Tellado, F.; Geib, S.J.; Goswami, S.; Hamilton, A.D. J. Am. Chem. Soc.1991, 113, 9265–9269. (d) Karle, I.L.; Ranganathan, D.; Haridas, V. J. Am. Chem. Soc.1997, 119, 2777–2783. (e) Moore, G.; Papamicaël, C.; Levacher, V.; Bourguignon, J.; Dupas, G. Tetrahedron2004, 60, 4197–4204. (f) Korendovych, I.V.; Cho, M.; Makhlynets, O.V.; Butler, P.L.; Staples, R.J.; Rybak-Akimova, E.V. J. Org. Chem.2008, 73, 4771–4782. (g) Ghosh, K.; Masanta, G.; Fröhlich, R.; Petsalakis, I.D.; Theodorakopoulos, G. J. Phys. Chem. B2009, 113, 7800–7809 [Google Scholar], 119, 2777–2783) or top–bottom-bound 1:1 (Garcia-Tellado, F.; Goswami, S.; Chang, S.K.; Geib, S.J.; Hamilton, A.D. J. Am. Chem. Soc. 1990 (a) Goswami, S., Ghosh, K. and Dasgupta, S. 2000. J. Org. Chem., 65: 1907–1914. (b) Goswami, S.; Ghosh, K.; Mukherjee, R. Tetrahedron2001, 57, 4987–4993. (c) Goswami, S.; Ghosh, K.; Halder, M. Tetrahedron Lett.1999, 40, 1735–1738. (d) Goswami, S.; Dey, S.; Fun, H.-K.; Anjum, S.; Rahman, A.-U. Tetrahedron Lett.2005, 46, 7187–7191. (e) Goswami, S.; Jana, S.; Dey, S.; Razak, I.A.; Fun, H.-K. Supramol. Chem.2006, 18, 571–574. (f) Goswami, S.; Jana, S.; Fun, H.-K. Cryst. Eng. Comm.2008, 10, 507–517. (g) Goswami, S.; Jana, S.; Dey, S.; Sen, D.; Fun, H.-K.; Chantrapromma, S. Tetrahedron2008,64, 6426–6433. (h) Goswami, S.; Dey, S.; Jana, S. Tetrahedron2008, 64, 6358–6363 [Google Scholar], 112, 7393–7394) co-crystals.

     

Recognition of anions and monocarboxylic acids by a fluorescent guanidine-based receptor

A guanidine-based fluorescent receptor has been synthesised to study its binding behaviour towards anions (F^? , Cl^? , Br^? , I^?  and AcO^? ). The two donor N–H bonds of the receptor do not point in the same direction; rather, one N–H bond is intramolecularly hydrogen-bonded with the carbonyl oxygen atom. The nature of the donor–acceptor (DA) arrangement induces moderate binding properties. The binding behaviour towards monocarboxylic acids (benzoic acid and phenylacetic acid) is also compared. The binding behaviour of receptor 1 towards the F^?  anion is higher among the anions studied, whereas in the case of monocarboxylic acid, the binding constant with phenylacetic acid is higher than benzoic acid.     

Supramolecular heterogeneity in β-turn forming synthetic tripeptides nucleated by isomers of fluorinated phenylalanine and aib as corner residues

The influences of fluorines in chemistry have emerged as a breakthrough in various arenas of bio-organic and medicinal chemistry. But its incorporation in β-turn design and its implications for supramolecular chemistry remains in a rudimentary stage. Inspired by the diversity displayed by the isomers of mono-fluorinated phenylalanine in biological sciences, here our effort is to modulate the solid state conformational analysis of three terminally protected synthetic tripeptides Boc-(Y)-F-Phe-Aib-Xaa-OMe, where (Y is (2)-F-Phe, Xaa; Leu in peptide I, (3)-F-Phe, Xaa; Leu in peptide II and (4)-F-Phe, Xaa; Ile in peptide III). Interestingly, all the three peptides display a conformational preference for β-turns, stabilized by 4→1 intramolecular hydrogen bonding. Our investigation further demonstrates that mere interchange of positions of fluorines in mono-fluorinated phenylalanine in peptides I–III introduces significant diversity in supramolecular chemistry. X-ray crystallography sheds some light at atomic resolution. Furthermore, this supramolecular heterogeneous behavior is evident from the morphologies obtained from the materials of all the three peptides grown from acetone to petroleum ether solution, studied by field emission scanning electron microscopy. Thus, these monofluorinated peptides I–III may serve as prominent candidates in understanding the structure and function of misfolded disease causing peptides like prion and Alzheimer's amyloid.     

Similarities and differences in the structures of 5‐bromo‐6‐hydroxy‐7,8‐dimethylchroman‐2‐one and 6‐hydroxy‐7,8‐dimethyl‐5‐nitrochroman‐2‐one

The title compounds, C₁₁H₁₁BrO₃, (I), and C₁₁H₁₁NO₅, (II), respectively, are derivatives of 6‐hydroxy‐5,7,8‐trimethylchroman‐2‐one substituted at the 5‐position by a Br atom in (I) and by a nitro group in (II). The pyranone rings in both molecules adopt half‐chair conformations, and intramolecular O—H...Br [in (I)] and O—H...O_nitro [in (II)] hydrogen bonds affect the dispositions of the hydroxy groups. Classical intermolecular O—H...O hydrogen bonds are found in both molecules but play quite dissimilar roles in the crystal structures. In (I), O—H...O hydrogen bonds form zigzag C(9) chains of molecules along the a axis. Because of the tetragonal symmetry, similar chains also form along b. In (II), however, similar contacts involving an O atom of the nitro group form inversion dimers and generate R₂²(12) rings. These also result in a close intermolecular O...O contact of 2.686 (4) Å. For (I), four additional C—H...O hydrogen bonds combine with π–π stacking interactions between the benzene rings to build an extensive three‐dimensional network with molecules stacked along the c axis. The packing in (II) is much simpler and centres on the inversion dimers formed through O—H...O contacts. These dimers are stacked through additional C—H...O hydrogen bonds, and further weak C—H...O interactions generate a three‐dimensional network of dimer stacks.     

Dually Activated Organo- and Nano-cocatalyzed Synthesis of Coumarin Derivatives

A wide range of substituted coumarin derivatives were synthesized by refluxing in acetonitrile, ethyl acetoacetate, and ethyl benzoyl acetate with a wide range of structurally diverse phenol derivatives within a short reaction time with a catalytic combination of pyridine dicarboxylic acid as organocatalyst and nanocrystalline ZnO.     

Regioselective Synthesis and Photophysical and Electrochemical Studies of 20‐Substituted Cyanine Dye–Purpurinimide Conjugates: Incorporation of NiII into the Conjugate Enhances its Tumor‐Uptake and Fluorescence‐Imaging Ability

We report herein a simple and efficient approach to the synthesis of a variety of meso‐substituted purpurinimides. The reaction of meso ‐ substituted purpurinimide with N‐bromosuccinimide regioselectively introduced a bromo functionality at the 20‐position, which on further reaction with a variety of boronic acids under Suzuki reaction conditions yielded the corresponding meso‐substituted analogues. Interestingly, the free base and the metalated analogues showed remarkable differences in photosensitizing efficacy (PDT) and tumor‐imaging ability. For example, the free‐base conjugate showed significant in vitro PDT efficacy, but limited tumor avidity in mice bearing tumors, whereas the corresponding Ni^II derivative did not produce any cell kill, but showed excellent tumor‐imaging ability at a dose of 0.3 μmol kg^?1 at 24, 48, and 72 h post‐injection. The limited PDT efficacy of the Ni^II analogue could be due to its inability to produce singlet oxygen, a key cytotoxic agent required for cell kill in PDT. Based on electrochemical and spectroelectrochemical data in DMSO, the first one‐electron oxidation (0.52 V vs. SCE) and the first one‐electron reduction (?0.57–0.67 V vs. SCE) of both the free base and the corresponding Ni^II conjugates are centered on the cyanine dye, whereas the second one‐electron reduction (?0.81 V vs. SCE) of the two conjugates is assigned to the purpurinimide part of the molecule. Reduction of the cyanine dye unit is facile and occurs prior to reduction of the purpurinimide group, which suggests that the cyanine dye unit as an oxidant could be the driving force for quenching of the excited triplet state of the molecules. An interaction between the cyanine dye and the purpurinimide group is clearly observed in the free‐base conjugate, which compares with a negligible interaction between the two functional groups in the Ni^II conjugate. As a result, the larger HOMO–LUMO gap of the free‐base conjugate and the corresponding smaller quenching constant is a reason to decrease the intramolecular quenching process and increase the production of singlet oxygen to some degree.     

Existence and examples of quantum isometry groups for a class of compact metric spaces

We formulate a definition of isometric action of a compact quantum group (CQG) on a compact metric space, generalizing Banica's definition for finite metric spaces. For metric spaces (X,d)$(X,d)$ which can be isometrically embedded in some Euclidean space, we prove the existence of a universal object in the category of the compact quantum groups acting isometrically on (X,d)$(X,d)$. In fact, our existence theorem applies to a larger class, namely for any compact metric space (X,d)$(X,d)$ which admits a one-to-one continuous map f:X→Rⁿ$f:X\to {\mathbb{R}}^n$ for some n   such that _d0(f(x),f(y))=?(d(x,y))$d_0(f(x),f(y))=?(d(x,y))$ (where _d0$d_0$ is the Euclidean metric) for some homeomorphism ?   of R⁺${\mathbb{R}}^{+}$.     

FRET based selective and ratiometric ‘naked-eye’ detection of CN in aqueous solution on fluorescein–Zn–naphthalene ensemble platform

We have developed a FRET-based ratiometric fluorescent probe for the detection of CN⁻ using a fluorescein–Zn–naphthalene ensemble (NFH·Zn²⁺). The sensing mechanism was ascribed by displacement approach. The chemosensor exhibits high selectivity and sensibility for CN⁻. The speculation was supported by fluorescence emission spectra, UV–vis spectrum, ¹H NMR titration experiments, and mass spectra. The interconversion of probe NFH and NFH·Zn²⁺ via the complexation/decomplexation by the modulation of Zn²⁺/CN⁻ mimics INHIBIT gate. In addition, it also shows an excellent performance in ‘dip stick’ method.