Designed helical peptides inhibit an intramembrane protease

gamma-Secretase cleaves the transmembrane domain of the amyloid precursor protein, a process implicated in the pathogenesis of Alzheimer's disease, and this enzyme is a founding member of an emerging class of intramembrane proteases. Modeling and mutagenesis suggest a helical conformation for the substrate transmembrane domain upon initial interaction with the protease. Moreover, biochemical evidence supports the presence of an initial docking site for substrate on gamma-secretase that is distinct from the active site, a property predicted to be generally true of intramembrane proteases. Here we show that short peptides designed to adopt a helical conformation in solution are inhibitors of gamma-secretase in both cells and enzyme preparations. Helical peptides with all d-amino acids are the most potent inhibitors and represent potential therapeutic leads. Subtle modifications that disrupt helicity also substantially reduce potency, suggesting that this conformation is critical for effective inhibition. Fluorescence lifetime imaging in intact cells demonstrates that helical peptides disrupt binding between substrate and protease, whereas an active site-directed inhibitor does not. These findings are consistent with helical peptides interacting with the initial substrate docking site of gamma-secretase, suggesting a general strategy for the development of potent and specific inhibitors of intramembrane proteases.     

Intermolecular coupling of the CO stretching vibrations in liquid acetone: an isotopic dilution study

The separation Δv between the isotropic and anisotropic component of the CO stretching Raman band was studied in mixtures of acetone-¹⁶O and acetone-¹⁸O. An explanation is proposed for the observed invariance of the aniso tropic frequency. The isotropic bandwidth and the concentration threshold for the appearance of Δv are discussed.     

Simulation of infrared spectra for beta-hairpin peptides stabilized by an Aib-Gly turn sequence: correlation between conformational fluctuation and vibrational coupling

Vibrational spectra of a 12-residue beta-hairpin peptide, RYVEVBGKKILQ (HBG), stabilized by an Aib-Gly turn sequence (B = Aib) were investigated theoretically using a combination of molecular dynamics (MD) and density functional theory (DFT) calculations. Selected conformations of HBG were extracted from a classical MD trajectory and used for spectral simulations. DFT calculations, based on the Cartesian coordinate spectral property transfer protocol, were carried out for peptide structures in which all residues are replaced with Ala, except for the Aib and Gly residues, but the backbone (phi, psi, omega) structure of the original configuration is retained. The simulations provide a basis for interpretation of the HBG amide I infrared spectra in terms of structural variables such as detailed secondary structure and thermal conformational fluctuation as well as vibrational coupling as indicated by spectra of 13C isotope-labeled variants. The characteristic amide I band shape of such small beta-hairpin peptides appears to arise from the structure of the short antiparallel beta-sheet strands. The role of structural parameter fluctuation in vibrational coupling is evaluated by comparison of DFT-derived amide coupling constants for selected configurations and from transition dipole coupling calculations of coupling parameters between (13)C isotopically labeled residues for a MD-derived ensemble of configurations. Calculated results were compared with the experimentally obtained spectra for several (13)C isotope-labeled peptides of this sequence.     

Intermolecular vibrational coupling in glycine

A study of isotopomers of α-glycine by Raman, inelastic neutron scattering and i.r. methods reveals intermolecular vibrational coupling on modes which, superficially, appear vibrationally insulated.     

Theoretical study on solvation effects in chemical reactions: A vibrational coupling model

A vibrational coupling model to treat the solvation effects in chemical reaction rate calculations is proposed and applied to the intramolecular hydrogen transfer reaction CH₃O· → ·CH₂OH in the condensed phase. The effect of solvation is taken into account in two ways: (1) the solvent effect on the activation energy of the reaction is simulated by including 39 surrounding water molecules, represented by fractional charges at the assumed atomic positions, in the potential energy surface calculation; and (2) the vibrational couplings between the 10 nearest solvent molecules and the molecules constituting the reaction system are explicitly included in a vibrational frequency calculation. RRKM theory with Miller's tunneling correction included is employed to calculate the rate constants. The effect of solvation causes a significant change in the chemical reaction rate, mainly through a lowering of the activation energy. The vibrational coupling causes a slight increase of the rate constant in the tunneling region by perturbing the vibrational frequencies of the reactant and transition states, which appear in the rate-constant expression, but has little effect at higher temperatures.     

Characterization of a three-component coupling reaction on proteins by isotopic labeling and nuclear magnetic resonance spectroscopy

A three-component Mannich-type electrophilic aromatic substitution reaction was previously developed to target the phenolic side chain of tyrosine residues on proteins. This reaction proceeds under mild conditions and provides a convenient alternative to lysine-targeting strategies. However, the use of reactive aldehydes, such as formaldehyde, warrants careful inspection of the reaction products to ensure that other modifications have not occurred. Through the use of isotopically enriched reagents, nuclear magnetic resonance (NMR)-based studies were used to obtain structural confirmation of the tyrosine-modification products. These experiments also revealed the formation of a reaction byproduct arising from the indole ring of tryptophan residues. Cysteine residues were shown to not participate in the reaction, except in the case of a reduced disulfide, which formed a dithioacetal. We anticipate that this analysis method will prove useful for the detailed study of a number of bioconjugation reactions.     

Water-anion vibrational coupling in some crystallohydrates

In treating the vibrational spectra of crystallohydrates, it is usually assumed that the water molecules vibrate independently (or nearly so) from the rest of the structural units and, consequently, the bands which shift on deuteration are automatically assigned to water modes (internal or external). In a number of hydrates of metal carboxylates, however, we were able to detect indications of water-anion vibrational coupling.     

Simulation of vibrational spectra of isotopic benzenes by an extended molecular mechanics method

Vibrational spectra of benzene and benzene-d₆ in the gas and liquid phase have been simulated by a molecular mechanics method including the calculation of equilibrium structures, thermodynamic quantities, normal frequencies and vibrational transition probabilities. The potential parameters have been estimated by referring to the observed frequencies of benzene, benzene-d₆ and 1,3,5-benzene-d₃ and also to results of ab initio calculations. Four and ten independent parameters are required, respectively, for elucidating the infrared absorption and Raman intensities of these compounds in the gas and liquid phase. The infrared absorption spectrum of benzene-d₁ is reproduced well by using the potential and the intensity parameters estimated for benzene and benzene-d₆. The change of relative band intensities on the phase change has been elucidated in terms of the change of various intensity parameters.     

IR study of cross-strand coupling in a beta-hairpin peptide using isotopic labels

Model beta-hairpin peptides can be used to develop understanding of fundamental elements of beta-sheet secondary structure formation and stability. We have studied two 13C-labeled variants of a beta-hairpin peptide modified from a design originally proposed by Gellman: Arg-Tyr-Val-Glu-Val-Aib-Gly-Lys-Lys-Ile-Leu-Gln. (In this peptide, the two italicized residues form a beta-turn, while 13C-labels are on the amide C=O of Val3, Lys8 in HBG-L and Val3, Ile10 in HBG-S.) Both these peptides are labeled on opposite strands of the hairpin, but differ in the labeling pattern. One (HBG-L) forms a large (14-atom) H-bonded ring of labeled C=Os, while the other (HBG-S) forms a small (10-atom) H-bonded ring. These impact the amide I infrared spectra, with HBG-L having a 13C frequency and intensity higher than that of HBG-S, in good agreement with our spectral simulations based on quantum mechanically derived force fields. The thermal behavior of both peptides yields a broad thermal transition and lacks an isosbestic point. The 13C band for HBG-L has the largest intensity change with temperature, distinct from the 12C change and the HBG-S 13C change.     

211At标记蛋白质或多肽的方法研究

α核素211At具有良好的辐射生物学性质,以对肿瘤细胞具有高亲和性的单克隆抗体或多肽类配体为载体则是实现211At肿瘤靶向治疗的最理想方式之一。本文介绍了211At标记蛋白质或多肽的方法的现状与进展,对存在的一些问题及今后的发展方向进行了讨论。     

Dioxirane mediated asymmetric epoxidations: stereochemical studies via isotopic labeling

A study, via isotopic labeling, of the stereoselective processes in a Shi-type epoxidation, has revealed that the chiral platform provided by the catalyst mediates the transfer of the pro-S "O" of the related dioxirane species to the alkene in a doubly stereoselective manner.     

Properties of polyvinylchloride in solution: an hydrodynamic and vibrational spectroscopy study

The polymer polyvinylchloride has been studied in binary solvent mixtures and as a function of temperature in solution. A discontinuity of the polymer chain dimensions has been observed, as measured by hydrodynamic methods. This phenomenon is further examined by infrared and Raman spectroscopy. © 1999 John Wiley & Sons, Inc. J Polym Sci B: Polym Phys 37: 1351–1356, 1999     

Redox regulation of helical structures in short peptides with an intramolecular ferrocenyl cross-linking agent

We redox-regulated alpha-helicity of short peptides intramolecularly cross-linked with a ferrocenyl linker between amino acid side chains. The helical content of the cross-linked peptide was estimated to be 56% in the neutral state of the ferrocene core at 25 degrees C. The addition of an oxidant to the solution of the cross-linked peptide enhanced the helicity up to 75%. The increased helical content returned to the same level as that in the previous ferrocene state by further addition of a reductant.     

Intramolecular vibrational coupling contribution to temperature dependence of vibrational mode frequencies

High-frequency vibrational modes in molecules in solution are sensitive to temperature and shift either to lower or higher frequencies with the temperature increase. These frequency shifts are often attributed to specific interactions of the molecule and to the solvent polarization effect. We found that a substantial and often dominant contribution to sensitivity of vibrational high-frequency modes to temperature originates from anharmonic interactions with other modes in the molecule. The temperature dependencies were measured for several modes in ortho-, meta-, and para-isomers of acetylbenzonitrile in solution and in a solid matrix and compared to the theoretical predictions originated from the intramolecular vibrational coupling (IVC) evaluated using anharmonic density functional theory calculations. It is found that the IVC contribution is essential for temperature dependencies of all high-frequency vibrational modes and is dominant for many modes. As such, the IVC contribution alone permits predicting the main trend in the temperature dependencies, especially for vibrational modes with smaller transition dipoles. In addition, an Onsager reaction field theory was used to describe the solvent contribution to the temperature dependencies.     

Vibronic coupling in naphthalene anion: vibronic coupling density analysis for totally symmetric vibrational modes

Vibronic coupling, or electron-phonon coupling, of naphthalene is calculated. A method of vibronic coupling density analysis, which has been proposed for the vibronic coupling of the Jahn-Teller active modes in a Jahn-Teller molecule, is extended for totally symmetric vibrational modes of a molecule including a non-Jahn-Teller molecule. Contrary to non-totally-symmetric modes, orbital relaxation upon a charge transfer plays a crucial role in the vibronic coupling calculation for the totally symmetric modes. The method is applied for the ground state of the naphthalene anion to compare with that of the benzene anion. The relationship between the vibronic coupling density and a nuclear Fukui function is also discussed.     

Ab initio modeling of amide I coupling in antiparallel beta-sheets and the effect of 13C isotopic labeling on infrared spectra

Isotopic substitution with 13C on the amide C=O has become an important means of determining localized structural information about peptide conformations with vibrational spectroscopy. Various approaches to the modeling of the interactions between labeled amide sites, specifically for antiparallel two-stranded, beta-forming peptides, were investigated, including different force fields [dipole-dipole interaction vs density functional theory (DFT) treatments], basis sets, and sizes of model peptides used for ab initio calculations, as well as employing models of solvation. For these beta-sheet systems the effect of the relative positions of the 13C isotopic labels in each strand on their infrared spectra was investigated. The results suggest that the interaction between labeled amide groups in different strands can be used as an indicator of local beta-structure formation, because coupling between close-lying C=O groups on opposing chains leads to the largest frequency shifts, yet some alternate placements can lead to intensity enhancements. The basic character of the coupling interaction between labeled modes on opposing strands is independent of changes in peptide length, water solvent environment, twisting of the sheet structure, and basis set used in the calculations, although the absolute frequencies and detailed coupling magnitudes change under each of these perturbations. In particular, two strands of three amides each contain the basic interactions needed to simulate larger sheets, with the only exception that the C=O groups forming H-bonded rings at the termini can yield different coupling values than central ones of the same structure. Spectral frequencies and intensities were modeled ab initio by DFT primarily at the BPW91/6-31G** level for pairs of three, four, and six amide strands. Comparison to predictions of a classical coupled oscillator model show qualitative but not quantitative agreement with these DFT results.     

Use of isotopic dilution to study the structure of crystalline complex compounds by vibrational spectroscopy

Institute of Chemistry and Chemical Technology, Siberian Branch, Academy of Sciences of the USSR. Krasnoyarsk State University. Translated from Zhurnal Strukturnoi Khimii, Vol. 29, No. 6, pp. 58–69, November–December, 1988.     

Short-time vibrational dynamics of acetylene versus its isotopic variants

The short-time intramolecular dynamics of highly vibrationally excited HCCD and DCCD, as determined by classical trajectories, have qualitative features distinct from HCCH and from one another. The possible differences are also considered from the point of view of the symmetries of the normal modes. The short-time evolution will be reflected in the coarse-grained frequency spectrum and could be detectable via stimulation emission pumping.     

Synthesis of conformationally constrained cyclic peptides using an intramolecular sonogashira coupling

[Reaction: see text]. Small peptides having a 3-bromobenzyl group at the C-termini and n-alkynoyl group at the N-termini undergo a smooth copper-free intramolecular Sonogashira coupling reaction to afford the corresponding cyclic peptides in moderate yields. Scope and limitations of this macrocyclization is demonstrated with di-, tri-, and tetrapeptides.