Two-dimensional infrared spectral signatures of 3(10)- and alpha-helical peptides

Two-dimensional infrared (2D IR) spectra of Calpha-alkylated model octapeptides Z-(Aib)8-OtBu, Z-(Aib)5-L-Leu-(Aib)2-OMe, and Z-[L-(alphaMeVal)]8-OtBu have been measured in the amide I region to acquire 2D spectral signatures characteristic of 3(10)- and alpha-helical conformations. Phase-adjusted 2D absorptive spectra recorded with parallel polarizations are dominated by intense diagonal peaks, whereas 2D rephasing spectra obtained at the double-crossed polarization configuration reveal cross-peak patterns that are essential for structure determination. In CDCl3, all three peptides are of the 3(10)-helix conformation and exhibit a doublet cross-peak pattern. In 1,1,1,3,3,3-hexafluoroisopropanol, Z-[L-(alphaMeVal)]8-OtBu undergoes slow acidolysis and 3(10)-to-alpha-helix transition. In the course of this conformational change, its 2D rephasing spectrum evolves from an elongated doublet, characteristic of a distorted 3(10)-helix, to a multiple-peak pattern, after becoming an alpha-helix. The linear IR and 2D absorptive spectra are much less informative in discerning the structural changes. The experimental spectra are compared to simulations based on a vibrational exciton Hamiltonian model. The through-bond and through-space vibrational couplings are modeled by ab initio coupling maps and transition dipole interactions. The local amide I frequency is evaluated by a new approach that takes into account the effects of hydrogen-bond geometry and sites. The static diagonal and off-diagonal disorders are introduced into the Hamiltonian through statistical models to account for conformational fluctuations and inhomogeneous broadening. The sensitivity of cross-peak patterns to different helical conformations and the chain length dependence of the spectral features for short 3(10)- and alpha-helices are discussed.     

Diffusion and residence time of hydrogen peroxide and water in crowded protein environments

Reactive oxygen species (ROS) have important functions in cell signaling and, when present at overly high levels, may cause oxidation of important biological molecules. Kinetic models to study diffusion of ROS inside of mitochondria often assume dynamics similar to that in solution. However, it is well-known that separation of proteins in the cytosol or inside of mitochondria, where ROS are most predominant, can be smaller than 1 nm. Diffusion of small molecules can be better regarded as a percolation process. In this article, we report results of diffusivity and residence of water and hydrogen peroxide in the proximity of proteins. In carrying out this study, we found some issues with the conventional way of computing residence times by means of survival time correlation functions. The main problem is that particles remaining on the surface of a protein for long times and for which one has very poor statistics contribute significantly to the short time behavior of the survival time correlation function. We mathematically describe this problem and propose methodology to overcome it.     

Oxidative degradations of the side chain of unsaturated ent-labdanes. Part I

A selective route for the degradation of the unsaturated side chain of ent-labdanes has been devised, giving two useful synthons: 2beta-acetoxy-14,15,17-trinor-ent-labdane-8,13- dione (5) and 2beta-acetoxy-14,15-dinor-ent-labd-8(17)-en-13-one (7), the use of which for the preparation of terpenylquinone derivatives shall be reported elsewhere.     

Peptide δ‐Turn: Literature Survey and Recent Progress

Among the various types of α‐peptide folding motifs, δ‐turn, which requires a central cis‐amide disposition, has been one of the least extensively investigated. In particular, this main‐chain reversal topology has been studied in‐depth neither in linear/cyclic peptides nor in proteins. This Minireview article assembles and critically analyzes relevant data from a literature survey on the δ‐turn conformation in those compounds. Unpublished results from recent conformational energy calculations and a preliminary solution‐state analysis on a small model peptide, currently ongoing in our laboratories, are also briefly outlined.     

Machine‐Assisted Organic Synthesis

In this Review we describe how the advent of machines is impacting on organic synthesis programs, with particular emphasis on the practical issues associated with the design of chemical reactors. In the rapidly changing, multivariant environment of the research laboratory, equipment needs to be modular to accommodate high and low temperatures and pressures, enzymes, multiphase systems, slurries, gases, and organometallic compounds. Additional technologies have been developed to facilitate more specialized reaction techniques such as electrochemical and photochemical methods. All of these areas create both opportunities and challenges during adoption as enabling technologies.     

Differences in Dynamics between Crosslinked and Non‐Crosslinked Hyaluronates Measured by using Fast Field‐Cycling Relaxometry

The dynamic properties of water molecules in gels containing linear and crosslinked hyaluronic acid polymers are investigated by using an integrated approach that includes relaxometry, solid‐state NMR spectroscopy, and scanning electron microscopy. A model‐free analysis of field‐dependent nuclear relaxation is applied to obtain information on mobility and the population of different pools of water molecules in the gels. Differences between linear and crosslinked hyaluronic acid polymers are observed, indicating that crosslinking increases both the fraction and the correlation time of water molecules with slow dynamics.     

A noninvasive complementary study of an Egyptian polychrome cartonnage pigments using SEM,EPMA, and Raman spectroscopy

Raman spectroscopy, optical microscopy, scanning electron microscopy (SEM), and electron probe microanalysis (EPMA) were used to study pigments on an Egyptian cartonnage from the Ptolemaic period (305–30 bc ). The surface morphology of each color region was examined using backscattering (BS) and secondary electron imaging. SEM X-ray energy dispersive spectrometry and EPMA wavelength dispersive spectroscopy provided semiquantitative chemical analysis of each pigment. Raman spectroscopy was used to identify the minerals associated with the pigments. This technique confirmed the presence of cinnabar (α-HgS) in the red part of the fragments. A mixture of orpiment (As₂S₃) and bonazziite (β-As₄S₄) and/or alacránite (As₈S₉) was detected in the yellow regions of the fragments. The orange pigment was confirmed to be a mixture of orpiment, uzonite (χ-As₄S₅), and pararealgar (As₄S₄). Egyptian blue (CaCuSi₄O₁₀) and Egyptian green ((Cu,Ca)SiO₃) pigments were detected from blue/green dark-colored regions of the fragments.     

Controllability,uniqueness and existence of the incremental response: A mathematical criterion for elastoplastic constitutive laws

In this paper the onset of instabilities in elastoplastic materials is theoretically studied and a conceptual basis for understanding the physical implications of a loss of uniqueness and/or existence of the incremental response is provided. For this purpose, the concept of test controllability is reinterpreted and mixed stress–strain loading programmes are accounted for. A set of scalar indices, the moduli of instability, related with the inception of an unstable response is introduced and their dependency on the loading programme is explicitly illustrated. The paper shows that the use of these newly defined scalar measures provides support for an alternative definition for mechanical stability, which is closely related with the mathematical notions of existence and uniqueness of the predicted incremental response. In the final section, some mathematical properties of the moduli of instability are discussed, suggesting a novel reinterpretation of other well established theories and providing additional tools for the future application of the proposed framework.     

Risk processes with shot noise Cox claim number process and reserve dependent premium rate

We consider a suitable scaling, called the slow Markov walk limit, for a risk process with shot noise Cox claim number process and reserve dependent premium rate. We provide large deviation estimates for the ruin probability. Furthermore, we find an asymptotically efficient law for the simulation of the ruin probability using importance sampling. Finally, we present asymptotic bounds for ruin probabilities in the Bayesian setting.     

The Role of the Cricothyroid Joint Anatomy in Cricothyroid Approximation Surgery

Objectives/Hypothesis

Cricothyroid approximation (CTA) surgery aims at raising the voice pitch in male-to-female transsexuals. However, 30% of the patients are not satisfied with the result. The purpose of our study was to examine the cricothyroid joint (CTJ) biomechanics and to analyze if (and how) the CTJ anatomy influences the movement of the cricoid and, consequently, the elongation of the vocal fold and the voice pitch after CTA.

Methods

Twenty-four cadaver larynges were examined with high-resolution computerized tomography and MIMICS three-dimensional imaging software (Materialise Interactive Medical Image Control System, Leuven, Belgium). After superimposing the two scans taken in “neutral” and in “CTA” positions, vector geometrical analysis was used to determine the effective rotation axis of the CTJ and to calculate the elongation of the vocal folds after CTA.

Results

Our results showed that the cricoid rotates around an axis, the position of which depends on the anatomical structure of the CTJ. Based on the location of this effective rotation axis, we could distinguish three groups. In group I (N = 13), the rotation axis was located in the lower third; in group II (N = 5), it was located in the middle third; and in group III (N = 6), it was located in the upper third of the cricoid. The elongations of the vocal fold were 12%, 8%, and 3%, in groups I, II, and III, respectively.

Conclusions

The anatomical structure of the CTJ influences directly (1) the position of the effective rotation axis and (2) the elongation of the vocal folds.