Using thioamides to site-specifically interrogate the dynamics of hydrogen bond formation in β-sheet folding

Thioamides are sterically almost identical to their oxoamide counterparts, but they are weaker hydrogen bond acceptors. Therefore, thioamide amino acids are excellent candidates for perturbing the energetics of backbone-backbone H-bonds in proteins and hence should be useful in elucidating protein folding mechanisms in a site-specific manner. Herein, we validate this approach by applying it to probe the dynamic role of interstrand H-bond formation in the folding kinetics of a well-studied β-hairpin, tryptophan zipper. Our results show that reducing the strength of the peptide's backbone-backbone H-bonds, except the one directly next to the β-turn, does not change the folding rate, suggesting that most native interstrand H-bonds in β-hairpins are formed only after the folding transition state.     

Determination of the equilibrium melting point of the β-form of polypropylene

The melting behavior of the -form of isotactic polypropylene (-iPP) was investigated as a function of crystallization time and temperature. Calcium suberate, a selective -nucleating agent was used to produce samples that consist entirely of -form i-PP. The experimental melting points were recorded at different crystallization times and were extrapolated to the start of the crystallization process in order to eliminate the effect of lamellar thickening. Using the non-linear Hoffman—Weeks approach to correlate these extrapolated experimental melting temperatures with the corresponding crystallization temperatures, an equilibrium melting point of 209°C was obtained for -iPP. The equilibrium melting point estimated through the non-linear Hoffman—Weeks analysis is about 30°C higher than that (T _m ⁰=177°C) obtained on the basis of the linear extrapolation. These results are consistent with earlier claims that a linear extrapolation of T _m–T _c data leads to an underestimation of the equilibrium melting point. The results obtained for -iPP exemplify the importance of accounting for both the isothermal lamellar thickening effects and the non-linearity in the T _m–T _c correlation, when the determination of an equilibrium melting point is carried out using a procedure based on the predictions of the Lauritzen—Hoffman secondary nucleation theory.This revised version was published online in November 2005 with corrections to the Cover Date.     

Synthesis of 4-vinyl substituted β-lactams of the oxamazin family

4-Vinyl-substituted oxamazins 15,16, and 3 have been prepared. Key steps of the synthesis are: the preparation of protected α-amino-β-hydroxyacid 6 through ester enolate condensation of ethyl glycinate STABASE adduct 8 with CH-protected propiolaldehyde 9, the coupling of this acid with an appropriate protected hydroxylamine, the cyclization of resulting hydroxamate, and finally the acylation of the amino-group in 3 with ATMO side chain.     

Hairpin folding behavior of mixed α/β-peptides in aqueous solution

The invention of new strategies for the design of protein-mimetic oligomers that manifest the folding encoded in natural amino acid sequences is a significant challenge. In contrast to the α-helix, mimicry of protein β-sheets is less understood. We report here the aqueous folding behavior of a prototype α-peptide hairpin model sequence varied at cross-strand positions by incorporation of 16 different β-amino acid monomers. Our results provide a folding propensity scale for β-residues in a protein β-sheet context as well as high-resolution structures of several mixed-backbone α/β-peptide hairpins in water.     

Regiochemistry of the ring expansion of unsymmetrically substituted ketones involving β-hydroxyalkylselenides

β-hydroxyalkylselenides derived from unsymmetrically substituted ketones have been rearranged to substituted ketones in the presence of soft electrophiles such as silver tetrafluoraborate or dichlorocarbenes. Although the migration of the more substituted carbon often prevails, subtle variations have been observed depending upon the structure of the starting material and the experimental conditions used.     

Crowding alters the folding kinetics of a β-hairpin by modulating the stability of intermediates

Crowded environments inside cells exert significant effects on protein structure, stability, and function, but their effects on (pre)folding dynamics and kinetics, especially at molecular levels, remain ill-understood. Here, we examine the latter for, as an initial candidate, a small de novo β-hairpin using extensive all-atom molecular dynamics simulations for crowder volume fractions φ up to 40%. We find that crowding does not introduce new folding intermediates or misfolded structures, although, as expected, it promotes compact structures and reduces the accessible conformational space. Furthermore, while hydrophobic-collapse-mediated folding is slightly enhanced, the turn-directed zipper mechanism (dominant in crowder-free situations) increases many-fold, becoming even more dominant. Interestingly, φ influences the stability of the folding intermediates (FI(1) and FI(2)) in an apparently counterintuitive manner, which can be understood only by considering specific intrachain interactions and intermediate (and hierarchical) structural transitions. For φ values <20%, native-turn formation is enhanced, and FI(1), characterized by a hairpin structure but slightly mismatched hydrophobic contacts, increases in frequency, thus enhancing eventual folding. However, higher φ values impede native-turn formation, and FI(2), which lacks native turns, re-emerges and increasingly acts as a kinetic trap. The change in the stability of these intermediates with φ strongly correlates with the hierarchical folding stages and their kinetics. The results show that crowding assists intermediate structural changes more by impeding backward transitions than by promoting forward transitions and that a delicate competition between reduction in configuration space and introduction of kinetic traps along the folding route is key to understanding folding kinetics under crowded conditions.     

Synthesis of β-keto esters in-flow and rapid access to substituted pyrimidines

We have developed an in-flow process for the synthesis of β-keto esters via the BF(3)·OEt(2)-catalyzed formal C-H insertion of ethyl diazoacetate into aldehydes. The β-keto esters were then condensed with a range of amidines to give a variety of 2,6-substituted pyrimidin-4-ols.     

A new access to β-methyl substituted secondary alcohols. Application to the synthesis of 4-methylheptan-3-ol

All four stereoisomers of 4-methylheptan-3-ol were synthesized by a five-step route starting from 4-thianones. Key steps in the synthesis include: (a) reduction of 3-propyl-4-thianone to yield an easily separable isomeric mixture of cis- and trans-3-propyl-4-thianols; and (b) a highly efficient resolution of the particular cis/trans-isomers through a chromatographic separation of their respective esters with (S)-chlorofluoroacetic acid. Subsequent hydrolysis and desulfurization gave the required compounds in 18% overall yield. All the stereoisomers are obtained with purities better than 90%.     

Using artificial neural networks to predict the rheological behavior of non-Newtonian graphene–ethylene glycol nanofluid

Journal of Thermal Analysis and Calorimetry - The ability of the artificial neural network (ANN) to predict the viscosity of graphene nanosheet/ethylene glycol ( $$\mu_{{\text{Gr/EG}}}$$ ) was...     

Using particle tracking to probe the local dynamics of barley β-glucan solutions upon gelation

The sol-gel transition of aqueous barley β-glucan solutions which undergo gelation with ageing has been studied by conventional bulk rheology, phase contrast microscopy and particle tracking microrheology. Characterisation of the primary structure of the β-glucan isolate was carried out by enzymic methods and HPLC. The Brownian diffusion of fluorescent microspheres (0.75 μm diameter, carboxylate-coated particles) was used to probe the spatial mechanical properties of the gelling systems at the scale of microns; the potential use of passive particle tracking to study biopolymer gelling systems that present spatial heterogeneities is thus explored. For the β-glucan gels cured at 25°C both microrheology and bulk rheology revealed that with increasing the polysaccharide concentration the gelation time decreased, while the gelation rate and gel strength of the barley β-glucan gels increased. The particle tracking method had higher sensitivity and could map molecular ordering and structural heterogeneities in the evolving polysaccharide network at a micro-level. That is, different size pores were generated upon ageing with regions of depleted or less amount of β-glucan molecules. Furthermore, this method could detect changes in the fine structure of the system before such events can be registered by bulk rheological measurements; i.e. microheterogeneity and aggregation of β-glucan chains were revealed by particle tracking at earlier temporal stages of the experiment.     

Gold(I)-catalyzed cycloisomerization of β-alkynylpropiolactones to substituted α-pyrones

Substituted α-pyrones were straightforwardly synthesized in good to excellent yields by a new gold(I)-catalyzed rearrangement of β-alkynylpropiolactones.     

A systematic study of the solid state and solution phase conformational preferences of β-peptides derived from C(3)-alkyl substituted transpentacin derivatives

The solid state and solution phase conformational preferences of a homologous series of β-peptides derived from a range of 2-amino-3-alkylcyclopentanecarboxylic acid residues have been investigated using a variety of spectroscopic and crystallographic techniques. These studies indicate that C(3)-alkyl substitution trans to the amino group on the cyclopentane backbone is tolerated by the established 12-helix secondary structural preference of the parent pentamer and hexamer derived from 2-aminocyclopentanecarboxylic acid (transpentacin) residues in both the solid state and solution phase. Evidence for the alternative turn type conformation identified for the C(3)-unsubstituted tetramer was not observed in the C(3)-alkyl substituted derivatives, consistent with the alkyl substituent anti to the amino functionality destabilising this motif. These results suggest that oligomers based around the transpentacin scaffold may be amenable to further elaboration at C(3) anti to the amino group with retention of the secondary structure.     

Using reversed phase high performance liquid chromatography to study the complexation of anthocyanins with β-cyclodextrin

It is shown by means of reversed phase high performance liquid chromatography (RP HPLC) with mobile phases containing additions of β-cyclodextrin that 5-glucosides of cyanidin and pelargonidin form stronger inclusion complexes than 3-glucosides; this is explained by the steric interference of the glucoside radical.     

Application of the Rayleigh—Schrödinger perturbation theory to the hydrogen atom

The Rayleigh-Schrödinger variational perturbation theory and the hyperspherical perturbation treatment of the ground state of a hydrogen-like atom are generalized to an arbitrary excited state. In both cases it is rigorously shown that the exact wavefunction is recovered by direct summation of the perturbation expansion through infinite order.     

A systematic study of the solid state and solution phase conformational preferences of β-peptides derived from transpentacin

The solid state and solution phase conformational preferences of a homologous series of β-peptides derived from (S,S)-2-aminocyclopentanecarboxylic acid (transpentacin) have been investigated using a variety of spectroscopic and crystallographic techniques. These studies indicate that the hexamer and pentamer persist as a 12-helix in both the solid state and solution phase. Although the conformational traits of a 12-helix are exhibited by oligomers with as few as three residues in the solid state, in solution the trimer exists as an equilibrium of many alternative conformers whilst the tetramer has been shown to predominantly exist in either a 12-helix or a turn-type conformation.     

Room temperature syntheses of entirely diverse substituted β-fluorofurans

Synthesis of highly substituted 3-fluorofurans is reported. The sequence began with preparation of tert-butyldimethylsilyl alk-1-en-3-yn-1-yl ethers from 1,4-disubstituted alk-3-yn-1-ones. Subsequent fluorination of alkenynyl silyl ethers with Selectfluor gave 2-fluoroalk-3-yn-1-ones in almost quantitative yield. Subsequent 5-endo-dig cyclizations using chlorotriphenylphosphine gold(I)/silver trifluoromethanesulfonate (5/5 mol%), N-bromo- or N-iodosuccinimide and gold(I) chloride/zinc bromide (5/20 mol%), all at room temperature, provided a facile method for the generation of substituted 3-fluoro-, 3-bromo-4-fluoro-, and 3-fluoro-4-iodofurans in good yields. Also, 2,2-difluoroalk-3-yn-1-ones were prepared by fluorination of alk-3-yn-1-ones under organocatalytic conditions. The structures of (Z)-tert-butyldimethylsilyl but-1-en-3-yn-1-yl ether, 3-bromo-4-fluorofuran, and 3-fluoro-4-(phenylethynyl)furan were confirmed by X-ray crystallography.     

Positional screening and NMR structure determination of side-chain-to-side-chain cyclized β3-peptides

Many β-peptides fold in a 14-helical secondary structure in organic solvents, but similar 14-helix formation in water requires additional stabilizing elements. Especially the 14-helix stabilization of short β-peptides in aqueous solution is critical, due to the limited freedom for incorporating stabilizing elements. Here we show how a single lactam bridge, connecting two β-amino acid side-chains, can lead to high 14-helix character in short β(3)-peptides in water. A comparative study, using CD and NMR spectroscopy and structure calculations, revealed the strong 14-helix inducing power of a side-chain-to-side-chain cyclization and its optimal position on the β(3)-peptide scaffold with respect to pH and ionic strength effects. The lactam bridge is ideally incorporated in the N-terminal region of the β(3)-peptide, where it limits the conformational flexibility of the peptide backbone. The lactam bridge induces a 14-helical conformation in methanol and water to a similar extent. Based on the presented first high resolution NMR 3D structure of a lactam bridged β(3)-peptide, the fold shows a large degree of high order, both in the backbone and in the side-chains, leading to a highly compact and stable folded structure.     

Further studies on the application of vinylogous amides and β-halovinylaldehydes to the regiospecific synthesis of unsymmetrical,polyfunctionalized 2,3,4- and 1,2,3,4- substituted pyrroles

Highly functionalized pyrroles with appropriate regiochemical functionality represent an important class of marine natural products and potential drug candidates. We describe herein a detailed study of the reaction of α-aminoacid esters with vinylogous amides and also β-halovinylaldehydes for the regiospecific synthesis of 2,3,4-trisubstituted and 1,2,3,4-tetrasubstituted pyrroles. Since the vinylogous amides and β-halovinylaldehydes are readily available precursors, rapid access to a wide variety of unsymmetrically substituted pyrroles is accomplished via this methodology.     

Application of the β-cyclodextrin supramolecules as a green accelerator hosts in one-step preparation of highly functionalised rhodanine scaffolds

β-Cyclodextrin (β-CD) supramolecule was found to be a convenient, green and economical tool in one-pot synthesis of rhodanine scaffolds as a highly efficient mediating agent in aqueous media in which the reaction accelerated to complete in 15 min and room temperature. In this work, amines reacted with equimolar ratio of CS₂ (not excess ratio of CS₂) and then with activated acetylenes in the presence of β-CD in aqueous media.     

Using TEMPO oxidation to tailor deacetylation of carboxyl β-chitin nanofibers from squid pen

Cellulose - 2,2,6,6-tetramethylpiperidine-1-oxyl-radical (TEMPO) oxidation is a classical method to obtain carboxyl chitin nanomaterials, but when the traditional TEMPO/NaBr/NaClO (TBN) oxidation...