Conformational preferences of an amyloidogenic peptide: IR spectroscopy of Ac-VQIVYK-NHMe

The (306)VQIVYK(311) sequence in the tau peptide is essential for the formation of intracellular amyloid fibrils related to Alzheimer's disease, where it forms interdigitating cross-beta-structures. The inherent conformational preferences of the capped hexapeptide Ac-VQIVYK-NHMe were characterized in the gas phase. IR/UV double-resonance spectroscopy of the peptide isolated in a cold molecular beam was used to probe the conformation of the neutral peptide. The influence of protonation at the lysine side chain was investigated at 298 K by characterizing the protonated peptide ion, Ac-VQIVYK(H(+))-NHMe, with IRMPD spectroscopy in the fingerprint and amide I/II band region in an FTICR mass spectrometer. The conformations for both neutral and protonated peptides were predicted by an extensive conformational search procedure followed by cluster analysis and then DFT calculations. Comparison of the experimental and computed IR spectra, with consideration of the relative energies, was used to assign the dominant conformations observed. The neutral peptide adopts a beta-hairpin-like conformation with two loosely extended peptide chains, demonstrating the preference of the sequence for extended beta-strand-like structures. In the protonated peptide, the lysine NH3(+) disrupts this extended conformation by binding to the backbone and induces a transition to a random-coil-like structure.     

Conformational diastereoisomerism in a chiral pretzelane

The introduction of a stereogenic center by a stereospecific synthesis into an optically active, donor-acceptor pretzelane, that exhibits helicity as well as fixed chirality, leads to a marked preference for one conformational diastereoisomer over the other in both acetone and dimethylsulfoxide that can be understood from computational models.     

Conformational study of chiral heterocyclic enamino ketones

An assumption regarding the existence of a homoconjugation effect involving enaminoketo and phenyl groups as a result of the drawing together in space of their orbitals was made on the basis of circular dichroism (CD) data and an examination of the preferred conformations of two-ring enamino ketones with -phenylethyl and -benzylethyl substituents. A study of enamino ketones with a chiral alkyl substituent attached to the nitrogen atom made it possible to confirm this assumption.Communication XLIX from the series Stereochemical Studies. See [1] for communication XLVIII.Translated from Khimiya Geterotsiklicheskikh Soedinenii, No. 9, pp. 1230–1233, September, 1978.     

Conformational study of chiral cisoid enamino ketones

A study of a number of chiral cisoid cyclic enamino ketones by the circular dichroism method showed that they contain an inner disymmetric chromophore. The presence of homoconjugation of the phenyl and enamino ketone chromophores as a result of the drawing together of their orbitals in space was also established.Communication XXXVI from the series Stereochemical Studies; see [1] for communication XXXVTranslated from Khimiya Geterotsiklicheskikh Soedinenii, No. 4, pp. 511–515, April, 1976.     

Conformational flexibility in open chain molecules: chiral and achiral alkanes

Conformational partition functions of chiral and achiral alkanes have been computed by using a continuum approach (instead of rotational isomeric state approximations). The accessible conformational space per bond depends upon the structure of the compound and is only in the range of 5–13% of the maximum accessible range. In order to partly overcome the intrinsic ambiguity of the term “conformational flexibility”, the distinction between number flexibility (a measure of the number of accessible energy minima) and space flexibility (a measure of the total allotted space) is proposed. Further, the conformational versatility of each bond of a molecule is evaluated in terms of the a priori probability density function of that bond, and it is shown that the use of this function permits a comparison of the relative conformational flexibilities of the individual bonds, which is particularly useful for molecules having more than two rotation angles (where the conventional energy maps cannot be used). Optical rotations are calculated for a series of chiral alkanes by combining the continuum approach for conformational analysis and a recent optical activity calculation scheme. Contributions of single bonds to the molar optical rotation are evaluated and discussed. The influence of temperature upon conformational and chiral properties is evaluated.     

Conformational equilibria in diols: the rotational spectrum of chiral 1,3-butandiol

The rotational spectra of five conformers of 1,3-butandiol have been measured by pulsed jet Fourier transform microwave spectroscopy. All of them are stabilized by an internal hydrogen bond and all of them have a GG' or a G'G arrangement of the two hydroxyl oxygens, which means that both oxygen atoms are on the same side with respect to the C1C2C3 plane. Apart from the spectroscopic constants, the relative abundances in the supersonic expansion are provided.     

Conformational heterogeneity of surface-grafted amyloidogenic fragments of alpha-synuclein dimers detected by atomic force microscopy

A force-spectroscopy-based approach is used to characterize separation between amyloidogenic peptide fragments of alpha-synuclein. Interactions between individual molecules are studied using a scanning-force-microscopy-based technique. Alpha-synuclein fragments are attached to the solid surfaces via flexible long poly-(ethylene glycol) linkers removing aggregation state uncertainty of solution-based approaches and spurious surface effects. Tethering one fragment to the scanning probe tip and another fragment to the second surface ensures that interactions between tethered molecules are studied. Control experiments with only one tethered peptide indicate peptide-peptide interactions as the source of observed interaction forces in the double-tether experiment. The temperature dependence of rupture forces from 17.5 degrees C to 40 degrees C reveals similar molecular parameters indicating that no significant conformational changes occur in the associated molecules over this temperature range. Rate-dependent measurements indicate conformational heterogeneity of joined peptide molecules.     

Some properties of a Frank-type chiral amplification

In the Frank-type models for chiral amplification it is customary to assume that the concentration of the achiral reactant, from which the chiral species are formed in an autocatalytic process, is time-independent. We show that this assumption is neither acceptable nor necessary.     

Conformational analysis of chiral helical perfluoroalkyl chains by VCD

Vibrational circular dichroism (VCD) technique successfully revealed the absolute configuration of the biased helix of perfluoroalkyl chains in solution with the aid of theoretical calculations, which was supported by an X-ray crystallographic study.     

Conformational ordering of apolar, chiral m-phenylene ethynylene oligomers

A series of m-phenylene ethynylene oligomers containing nonpolar, (S)-3,7-dimethyl-1-octanoxy side chains have been synthesized and studied. In apolar alkane solvents, oligomers of sufficient length (n > 10) were found to adopt a helical conformation with a large twist sense bias. In contrast, in chloroform the oligomers adopt a random coil conformation. Surprisingly, the strong twist sense bias was determined to be highly time dependent and is partially attributed to intermolecular aggregation.     

Conformational polymorphism in a chiral spiro-cis-ansa-bridged cyclo­triphosphazene derivative

The reaction of spermidine with 2,2,4,4-tetra­chloro-6,6-di­phenyl­cyclo­triphosphazene produces a mixture of products of which one of the fractions is a spiro-cis-ansa deriv­ative, namely 12-chloro-14,14-di­phenyl-2,6,11,13,15,16-hexa­aza-1,12-di­phosphatri­cyclo­[10.3.1.0^1,6]­hexadeca-12,14-diene, C₁₉H₂₆Cl­N₆P₃. Recrystallization of this fraction from different solvents results in the formation of two different crystalline forms. The rod morphology formed in di­chloro­methane–n-hexane (1:1) produces a triclinic structure with three mol­ecules in the asymmetric unit. These three mol­ecules adopt different conformations as a result of two NH groups flipping in an ansa-bridged ring system. The plate morphology crystals, grown in di­chloro­methane–n-hexane–ethyl acetate (1:1:1), produce a C-centred monoclinic structure that adopts a conformation that is essentially the same as one of the forms in the triclinic structure.     

Capillary electrophoresis analysis of different variants of the amyloidogenic protein β2‐microglobulin as a simple tool for misfolding and stability studies

Free solution capillary electrophoresis with UV detection is here used to retrieve information on the conformational changes of wild‐type β₂‐microglobulin and a series of naturally and artificially created variants known to have different stability and amyloidogenic potential. Under nondenaturing conditions, the resolution of at least two folding conformers at equilibrium is obtained and a third species is detected for the less stable isoforms. Partial denaturation by using chaotropic agents such as acetonitrile or trifluoroethanol reveals that the separated peaks are at equilibrium, as the presence of less structured species is either enhanced or induced at the expenses of the native form. Reproducible CE data allow to obtain an interesting semiquantitative correlation between the peak areas observed and the protein stability. Thermal unfolding over the range 25–42°C is induced inside the capillary for the two pathogenic proteins (wtβ₂‐microglobulin and D76N variant): the large differences observed upon small temperature variation draw attention on the robustness of analytical methods when dealing with proteins prone to misfolding and aggregation.     

Conformational analysis of the covalent pirkle chiral stationary phases.

The multidimensional potential energy surface for a model Pirkle chiral stationary phase is computed with MM2. Five minimum energy conformations are located, the minimum energy reaction pathway between the three lowest energy forms is described and the ability of these chiral phases to act as templates is discussed.     

Conformational chirality and chiral crystallization of N-sulfonylpyrimidine derivatives

New N-sulfonylpyrimidine derivatives 1-(p-toluenesulfonyl)uracil (1), 1-(p-toluenesulfonyl)thymine (2), 5-bromo-1-(p-toluenesulfonyl)uracil (3), 1-(methanesulfonyl)uracil (4), 1-(1-naphthylsulfonyl)uracil (5), and 1-(1-naphthylsulfonyl)thymine (6) were prepared by the condensation reaction of silylated pyrimidine derivatives with selected sulfonyl chlorides in acetonitrile. Some members of the series showed unexpected crystal properties as a consequence of their conformational chirality in the solid state. Compounds 1 and 5 exhibited chiral crystallization, which was, in the case of 1, accompanied by the formation of racemically twinned crystals regardless of the solvent used, while 5 gave a conglomerate of enantiomorphous crystals. For 2, 3, and 6, substituents at the C-5 position of the pyrimidine ring prevented chiral crystallization by influencing the crystal packing. Analysis of the crystal structures of 1, 4, and 5, reveals the influence of the arylsulfonyl group on the occurrence or absence of chiral crystallization.     

A lattice protein with an amyloidogenic latent state: stability and folding kinetics

We have designed a model lattice protein that has two stable folded states, the lower free energy native state and a latent state of somewhat higher energy. The two states have a sizable part of their structures in common (two "alpha-helices") and differ in the content of "alpha-helices" and "beta-strands" in the rest of their structures; i.e. for the native state, this part is alpha-helical, and for the latent state it is composed of beta-strands. Thus, the lattice protein free energy surface mimics that of amyloidogenic proteins that form well organized fibrils under appropriate conditions. A Go-like potential was used and the folding process was simulated with a Monte Carlo method. To gain insight into the equilibrium free energy surface and the folding kinetics, we have combined standard approaches (reduced free energy surfaces, contact maps, time-dependent populations of the characteristic states, and folding time distributions) with a new approach. The latter is based on a principal coordinate analysis of the entire set of contacts, which makes possible the introduction of unbiased reaction coordinates and the construction of a kinetic network for the folding process. The system is found to have four characteristic basins, namely a semicompact globule, an on-pathway intermediate (the bifurcation basin), and the native and latent states. The bifurcation basin is shallow and consists of the structure common to the native and latent states, with the rest disorganized. On the basis of the simulation results, a simple kinetic model describing the transitions between the characteristic states was developed, and the rate constants for the essential transitions were estimated. During the folding process the system dwells in the bifurcation basin for a relatively short time before it proceeds to the native or latent state. We suggest that such a bifurcation may occur generally for proteins in which native and latent states have a sizable part of their structures in common. Moreover, there is the possibility of introducing changes in the system (e.g., mutations), which guide the system toward the native or misfolded state.     

Radiopolymerization of β(-)pinene: A case of chiral amplification

β(-)Pinene was treated with γ radiation at three dose levels: 150, 300 and 600 kGy. The expected effect of radiation at these high doses was the partial racemization of the substrate as already observed in the case of other terpene monomers. Unexpectedly β(-)pinene underwent a radiopolymerization reaction into a solid resin and into a dimer. The structure of the products was studied by FT–IR spectroscopy also in comparison to a reference β(-)pinene resin prepared by cationic polymerization. A highly ordered structure was found in the case of the radiopolymer in comparison to the resin from cationic polymerization. Polarimetric measurements have shown astonishing enhancement in the optical activity of the radiopolymer and radiodimer in comparison to the starting optical activity of the β(-)pinene monomer. The results have been discussed in terms of amplification of chirality caused by γ radiation and the implications of this fact on the mechanism of chiral amplification on prebiotic molecules.     

Conformational control of flexible molecules: design and synthesis of novel chiral 1,5-diaza-cis-decalins

Control of the conformational equilibria of 1,5-diaza-cis-decalins, a new class of chiral diamine ligands, has been investigated. Chiral 2,6- and 3,7-substituted derivatives of 1,5-diaza-cis-decalins were designed to stabilize the conformational form needed to chelate a lithium. These derivatives were synthesized in optically pure form starting from 1,5-diaza-cis-decalin. Due to the rigid and conformationally well-defined nature of these compounds, the potential of these compounds as chiral diamine ligands was investigated. Asymmetric lithiation-substitution reactions of N-Boc-pyrrolidine and N,N-diisopropyl-o-ethylbenzamide were performed using these ligands and up to 60% ee was obtained. For the latter substrate, results spanning a range from 32% ee (R) to 60% ee (S) were obtained (Delta ee = 92%) with 1,5-diaza-cis-decalin ligands differing only in the location of two methyl substituents. Unlike many other diamines that have been employed in asymmetric lithiation-substitution reactions, the limited conformational flexibility of the 1,5-diaza-cis-decalins is analogous to (-)-sparteine such that these results may permit the construction of structure-activity relationships.     

Metadynamics simulation of prion protein: beta-structure stability and the early stages of misfolding

In the present study we have used molecular dynamics simulations to study the stability of the antiparallel beta-sheet in cellular mouse prion protein (PrP(C)) and in the D178N mutant. In particular, using the recently developed non-Markovian metadynamics method, we have evaluated the free energy as a function of a reaction coordinate related to the beta-sheet disruption/growth. We found that the antiparallel beta-sheet is significantly weaker in the pathogenic D178N mutant than in the wild-type PrP(C). The destabilization of PrP(C) beta-structure in the D178N mutant is correlated to the weakening of the hydrogen bonding network involving the mutated residue, Arg164 and Tyr128 side chains. This in turn indicates that such a network apparently provides a safety mechanism for the unzipping of the antiparallel beta-sheet in the PrP(C). We conclude that the antiparallel beta-sheet is likely to undergo disruption rather than growth under pathogenic conditions, in agreement with recent models of the misfolded monomer that assume a parallel beta-helix.