Concurrent display of both α- and β-turns in a model peptide

This article describes a model peptide that concurrently displays both α- and β-turns, as demonstrated by structural investigations using single crystal X-ray crystallography and solution-state NMR studies. The motif reported herein has the potential for the design of novel conformationally ordered synthetic oligomers with structural architectures distinct from those classically observed.     

X-ray diffraction and DOSY NMR characterization of self-assembled supramolecular metallocyclic species in solution

Wide-angle X-ray scattering and diffusion NMR techniques have been used to obtain structural information on three self-assembled metallacyclic supramolecular complexes in solution: a rectangle, a triangle, and a three-diminsional cage. The low-angle region of the measured diffraction patterns and hydrodynamic radii calculations, determined from DOSY NMR experiments, suggest that the supramolecular assemblies retain their shape when dissolved in nitromethane. The experimental structure functions for the large-angle region have been analyzed, and the intramolecular contributions of the platinum-platinum interactions are discussed. These scattering measurements provide evidence that the supramolecular assemblies are not as rigid in solution as they are in the single crystal. Finally, by analysis of the radial distribution functions of the solutions, direct structural information (e.g., platinum-platinum intramolecular distances and coordination number) about the supramolecular assemblies has been obtained.     

Pre-organization-mediated macrocylization: efficient synthesis and structural investigations of BINOL-m-phenylenediamine-derived macrocycles

This letter describes a serendipitous discovery of an efficient synthetic route to BINOL-m-phenylenediamine-derived macrocycles. These macrocycles are quickly accessible in an one-pot procedure by the direct condensation of (R) and (S) BINOL bis-acids with suitably substituted m-phenylenediamine analogs. Structural investigations by single crystal X-ray crystallography and solution-state NMR studies provided convincing evidence of their intramolecular hydrogen bonding arrangement and rigid structural architecture. The striking feature of these macrocycles is their ready accessibility in optically pure form coupled with their ease of synthesis.     

Solid-state thiotropolone: an extremely rapid intramolecular proton transfer

Through variable-temperature solution-state NMR and molten- and solid-state CP/MAS (13)C NMR spectra, thiotropolone is found to exist as two rapidly equilibrated tautomeric structures, thione and enethiol, even in the solid state far below the melting point. The crystal structure shows an almost perpendicular packing, suggesting that the intramolecular hydrogen bond is dominant.     

Synthese sowie Kristall- und Molekülstruktur von Tetrafluoro[2-(pyrrolidinio)ethyl]silicat

Synthesis and Crystal and Molecular Structure of Tetrafluoro[2-(pyrrolidinio)ethyl]silicate The zwitterionic tetrafluoro[2-(pyrrolidinio)ethyl]silicate ( 4 ) was synthesized by reaction of trimethoxy(2-pyrrolidinoethyl)silane ( 5 ) with hydrogen fluoride in ethanol/hydrofluoric acid at 0°C. The crystal and molecular structure of 4 was studied at ?100°C by single-crystal X-ray diffraction. In addition, 4 was characterized by solution-state NMR studies (CD₃CN: ¹H, ¹³C).     

Contrast-Matched Small-Angle X-ray Scattering from a Heavy-Atom-Labeled Protein in Structure Determination: Application to a Lead-Substituted Calmodulin-Peptide Complex

The information content in 1-D solution X-ray scattering profiles is generally restricted to low-resolution shape and size information that, on its own, cannot lead to unique 3-D structures of biological macromolecules comparable to all-atom models derived from X-ray crystallography or NMR spectroscopy. Here we show that contrast-matched X-ray scattering data collected on a protein incorporating specific heavy-atom labels in 65% aqueous sucrose buffer can dramatically enhance the power of conventional small- and wide-angle X-ray scattering (SAXS/WAXS) measurements. Under contrast-matching conditions the protein is effectively invisible and the main contribution to the X-ray scattering intensity arises from the heavy atoms, allowing direct extraction of pairwise distances between them. In combination with conventional aqueous SAXS/WAXS data, supplemented by NMR-derived residual dipolar couplings (RDCs) measured in a weakly aligning medium, we show that it is possible to position protein domains relative to one another within a precision of 1 ?. We demonstrate this approach with respect to the determination of domain positions in a complex between calmodulin, in which the four Ca(2+) ions have been substituted by Pb(2+), and a target peptide. The uniqueness of the resulting solution is established by an exhaustive search over all models compatible with the experimental data, and could not have been achieved using aqueous SAXS and RDC data alone. Moreover, we show that the correct structural solution can be recovered using only contrast-matched SAXS and aqueous SAXS/WAXS data.     

Salalen aluminium complexes and their exploitation for the ring opening polymerisation of rac-lactide

In this paper we report the first use of Al(III) salalen complexes for the ring opening polymerisation of rac-lactide. Polylactides with narrow polydispersities (PDIs range from 1.04-1.65) and moderate degrees of stereoselectivity were formed. Eight salalen Al(III) complexes have been prepared and fully characterised by solution-state NMR spectroscopy and, where appropriate, single crystal X-ray diffraction. With ligand 3H(2) either a monomeric or dimeric Al(III) species was formed, the dimeric species was favoured at low concentrations. The complexes were tested for the ring opening polymerisation of rac-lactide in toluene at 80 or 100 °C. Interestingly, various tacticities of polymer were formed, which were dependent upon the nature of the group bound to the amine nitrogen centre.     

Supramolecular porphyrinic prisms: coordinative assembly and solution phase X-ray structural characterization

Supramolecular porphyrin prisms have been obtained via coordinative self-assembly and characterized by 1H NMR, PFG NMR, electronic absorption spectroscopy and synchrotron-based measurements of solution phase X-ray scattering and diffraction.     

Revealing the effect of oligo(ethylene glycol) side chains on n-doping process in FBDPPV-based polymers

The low doping efficiency of n-doped systems limits the development of n-type organic conducting materials. Oligo(ethylene glycol) (OEG) as the flexible chain in conjugated small molecules and polymers may improve doping efficiency. However, OEG side chains also bring unexpected low mobility and poor film morphology. Herein, we propose the stronger solution-state aggregation plays a dominated role in charge transport and morphology of OEG-substituted polymer. The solution-state aggregation also affects doping process. Therefore, we develop a series of polymers based on 3,7-bis((E)-7-fluoro-1-(2-octyldodecyl)-2-oxoindolin-3-ylidene)-3,7-dihydrobenzo[1,2-b:4,5-b']difuran-2,6-dione (FBDPPV) with different ratios of OEG side chain to investigate the effect of side chain on solution-state aggregation and n-doping process. After n-doped by hexahydro-1H,3a1H,4H,7H-3a,6a,9a-triazaphenalene (TAM), FBDPPV with 50% OEG affords the highest doping efficiency and conductivity, while FBDPPV with 100% OEG shows lower conductivity. Combination of ultraviolet–visible–near infrared absorption spectra, grazing-incidence wide-angle X-ray scattering and atomic force microscopy, we reveal that serious aggregated extent in solution of OEG-substituted polymer result in phase separation and rough morphology, which are the origins of poor conductivity. Our work provides a new perspective on the effect of the OEG side chain on the doped polymer systems, suggesting suitable solution-state aggregation is crucial to high doping efficiency and high conductivity.     

Refinement of multidomain protein structures by combination of solution small-angle X-ray scattering and NMR data

Determination of the 3D structures of multidomain proteins by solution NMR methods presents a number of unique challenges related to their larger molecular size and the usual scarcity of constraints at the interdomain interface, often resulting in a decrease in structural accuracy. In this respect, experimental information from small-angle scattering of X-ray radiation in solution (SAXS) presents a suitable complement to the NMR data, as it provides an independent constraint on the overall molecular shape. A computational procedure is described that allows incorporation of such SAXS data into the mainstream high-resolution macromolecular structure refinement. The method is illustrated for a two-domain 177-amino-acid protein, gammaS crystallin, using an experimental SAXS data set fitted at resolutions from approximately 200 A to approximately 30 A. Inclusion of these data during structure refinement decreases the backbone coordinate root-mean-square difference between the derived model and the high-resolution crystal structure of a 54% homologous gammaB crystallin from 1.96 +/- 0.07 A to 1.31 +/- 0.04 A. Combining SAXS data with NMR restraints can be accomplished at a moderate computational expense and is expected to become useful for multidomain proteins, multimeric assemblies, and tight macromolecular complexes.     

Carbon-13 chemical shift anisotropy in DNA bases from field dependence of solution NMR relaxation rates

Knowledge of (13)C chemical shift anisotropy (CSA) in nucleotide bases is important for the interpretation of solution-state NMR relaxation data in terms of local dynamic properties of DNA and RNA. Accurate knowledge of the CSA becomes particularly important at high magnetic fields, prerequisite for adequate spectral resolution in larger oligonucleotides. Measurement of (13)C relaxation rates of protonated carbons in the bases of the so-called Dickerson dodecamer, d(CGCGAATTCGCG)(2), at 500 and 800 MHz (1)H frequency, together with the previously characterized structure and diffusion tensor yields CSA values for C5 in C, C6 in C and T, C8 in A and G, and C2 in A that are closest to values previously reported on the basis of solid-state FIREMAT NMR measurements, and mostly larger than values obtained by in vacuo DFT calculations. Owing to the noncollinearity of dipolar and CSA interactions, interpretation of the NMR relaxation rates is particularly sensitive to anisotropy of rotational diffusion, and use of isotropic diffusion models can result in considerable errors.     

Enforcing periodic secondary structures in hybrid peptides: a novel hybrid foldamer containing periodic gamma-turn motifs

This note describes the design, synthesis, and conformational studies of a novel hybrid foldamer that adopts a definite compact, three-dimensional structure determined by a combined effect of the special conformational properties of the foldamer constituents. The striking feature of this de novo designed foldamer is its ability to display periodic gamma-turn conformations stabilized by intramolecular hydrogen bonds. Conformational investigations by single-crystal X-ray studies, solution-state NMR, and ab initio MO theory at the HF/6-31G* level strongly support the prevalence of gamma-turn motifs in both the di- and tetrapeptide foldamers, which are presumably stabilized by bifurcated hydrogen bonds in the solid and solution states. The strategy disclosed herein for the construction of hybrid foldamers with periodic gamma-turn motifs has the potential to significantly augment the conformational space available for foldamer design with diverse backbone structures and conformations.     

Simulated unfolded-state ensemble and the experimental NMR structures of villin headpiece yield similar wide-angle solution X-ray scattering profiles

With the advent of powerful synchrotron sources, solution X-ray scattering is being increasingly used to get basic information about the structure of polypeptides. The solution scattering technique essentially provides one-dimensional data, which are then interpreted in terms of a three-dimensional structure through model building. Here we calculate wide-angle solution scattering patterns for an ensemble of simulated unfolded structures of villin headpiece, which differ from the native structure by rmsd = 8.8 +/- 1.0 A and have only negligible amounts of native secondary structure. We show that the wide-angle solution scattering pattern of such an ensemble shares significant similarity with the one based on the experimental NMR structures of the molecule. Our results suggest that solution scattering in the wide-angle limit, by itself, provides very little information about the secondary structure content of a polypeptide or its side-chain packing.     

Solid-state NMR spectroscopy applied to a chimeric potassium channel in lipid bilayers

We show that solid-state NMR can be used to investigate the structure and dynamics of a chimeric potassium channel, KcsA-Kv1.3, in lipid bilayers. Sequential resonance assignments were obtained using a combination of (15)N- (13)C and (13)C- (13)C correlation experiments conducted on fully labeled and reverse-labeled as well as C-terminally truncated samples. Comparison of our results with those from X-ray crystallography and solution-state NMR in micelles on the closely related KcsA K (+) channel provides insight into the mechanism of ion channel selectivity and underlines the important role of the lipid environment for membrane protein structure and function.     

A self-assembled framework that interpenetrates in crystal but does not interpenetrate in solution

A porous supramolecular framework has been for the first time revealed to undergo interpenetration in crystal and noninterpenetration in solution. A new supramolecular organic framework Bu-SOF has been constructed from the co-assembly of a tetracationic tetrahedral monomer and cucurbit[8]uril(CB[8]) in water through the encapsulation of two anti-parallel n-butyl chains by CB[8]. X-ray diffraction analysis reveals that Bu-SOF forms 3-fold interpenetrated networks in crystals grown by evaporation of its solution in water.1 H NMR, dynamic light scattering and isothermal titration calorimetric experiments confirm that Bu-SOF is also formed in water. Solid samples, prepared by lyophilizing the aqueous solution of Bu-SOF, can adsorb nanoscaled organic dyes, supporting the porosity of the framework and thus non-interpenetration in solution. The avoidance of interpenetration of Bu-SOF in solution has been attributed to the filling of water inside the porous framework as well as the electrostatic repulsion of the appended bipyridinium units of the tetrahedral building block.     

A solid-state NMR method for solution of zeolite crystal structures

Since zeolites are notoriously difficult to prepare as large single crystals, structure determination usually relies on powder X-ray diffraction (XRD). However, structure solution (i.e., deriving an initial structural model) directly from powder XRD data is often very difficult due to the diffraction phase problem and the high degree of overlap between the individual reflections, particularly for materials with the structural complexity of most zeolites. Here, we report a method for structure determination of zeolite crystal structures that combines powder XRD and nuclear magnetic resonance (NMR) spectroscopy in which the crucial step of structure solution is achieved using solid-state (29)Si double-quantum dipolar recoupling NMR, which probes the distance-dependent dipolar interactions between naturally abundant (29)Si nuclei in the zeolite framework. For two purely siliceous zeolite blind test samples, we demonstrate that the NMR data can be combined with the unit cell parameters and space group to solve structural models that refine successfully against the powder XRD data.     

Crystal structure of lead(II) acetylacetonate and the structure of the acetylacetone solvated lead(II) ion in solution studied by large-angle X-ray scattering

The crystal structure of bis(acetylacetonato)lead(II) and the structure of the acetylacetone solvated lead(II) ion in solution have been determined by single-crystal X-ray diffraction and large-angle X-ray scattering (LAXS), respectively. The acetylacetone is deprotonated and acts as a bidentate anionic ligand (acac-) in the solid Pb(acac)2 compound. The lead(II) ion binds four oxygen atoms strongly in a nearly flat pyramidal configuration with Pb-O bond lengths in the range 2.32-2.37 A, and additionally three oxygens from neighboring complexes at 3.01-3.26 A. Acetylacetone acts as a solvent (Hacac) at dissolution of lead(II) trifluoromethanesulfonate forming a pentasolvate with a mean Pb-O bond distance of 2.724(5) A. The 6s2 lone electron pair on the lead(II) ion becomes stereochemically active in the crystalline acetylacetonate complex, while it is inactive in the solvate in solution. The solution was also analysed using IR and 1H NMR spectroscopy.     

Solution and solid-state models of peptide CH...O hydrogen bonds

Fumaramide derivatives were analyzed in solution by (1)H NMR spectroscopy and in the solid state by X-ray crystallography in order to characterize the formation of CH...O interactions under each condition and to thereby serve as models for these interactions in peptide and protein structure. Solutions of fumaramides at 10 mM in CDCl(3) were titrated with DMSO-d(6), resulting in chemical shifts that moved downfield for the CH groups thought to participate in CH...O=S(CD(3))(2) hydrogen bonds concurrent with NH...O=S(CD(3))(2) hydrogen bonding. In this model, nonparticipating CH groups under the same conditions showed no significant change in chemical shifts between 0.0 and 1.0 M DMSO-d(6) and then moved upfield at higher DMSO-d(6) concentrations. At concentrations above 1.0 M DMSO-d(6), the directed CH...O=S(CD(3))(2) hydrogen bonds provide protection from random DMSO-d(6) contact and prevent the chemical shifts for participating CH groups from moving upfield beyond the original value observed in CDCl(3). X-ray crystal structures identified CH...O=C hydrogen bonds alongside intermolecular NH...O=C hydrogen bonding, a result that supports the solution (1)H NMR spectroscopy results. The solution and solid-state data therefore both provide evidence for the presence of CH...O hydrogen bonds formed concurrent with NH...O hydrogen bonding in these structures. The CH...O=C hydrogen bonds in the X-ray crystal structures are similar to those described for antiparallel beta-sheet structure observed in protein X-ray crystal structures.     

Narcissistic aggregation of steroid compounds in diluted solution elucidated by CSI-MS, PFG NMR and X-ray analysis

Large-scale aggregated chain structures of progesterone, estrone, cortisone, hydrocortisone and cholic acid were observed in diluted solution by means of cold-spray ionization mass spectrometry (CSI-MS) and pulsed field gradient (PFG) NMR. The crystal structures were determined by X-ray crystallography, and the relationship between the crystal and solution structures is discussed. It is suggested that the intermolecular hydrogen bondings observed in the crystal might be partly retained in diluted solution.     

Comparing pharmacophore models derived from crystallography and NMR ensembles

NMR and X-ray crystallography are the two most widely used methods for determining protein structures. Our previous study examining NMR versus X-Ray sources of protein conformations showed improved performance with NMR structures when used in our Multiple Protein Structures (MPS) method for receptor-based pharmacophores (Damm, Carlson, J Am Chem Soc 129:8225–8235, 2007). However, that work was based on a single test case, HIV-1 protease, because of the rich data available for that system. New data for more systems are available now, which calls for further examination of the effect of different sources of protein conformations. The MPS technique was applied to Growth factor receptor bound protein 2 (Grb2), Src SH2 homology domain (Src-SH2), FK506-binding protein 1A (FKBP12), and Peroxisome proliferator-activated receptor-γ (PPAR-γ). Pharmacophore models from both crystal and NMR ensembles were able to discriminate between high-affinity, low-affinity, and decoy molecules. As we found in our original study, NMR models showed optimal performance when all elements were used. The crystal models had more pharmacophore elements compared to their NMR counterparts. The crystal-based models exhibited optimum performance only when pharmacophore elements were dropped. This supports our assertion that the higher flexibility in NMR ensembles helps focus the models on the most essential interactions with the protein. Our studies suggest that the “extra” pharmacophore elements seen at the periphery in X-ray models arise as a result of decreased protein flexibility and make very little contribution to model performance.