Synthesis and conformational analysis by 1H NMR and restrained molecular dynamics simulations of the cyclic decapeptide [Ser-Tyr-Ser-Met-Glu-His-Phe-Arg-Trp-Gly]

Summary The design of enzyme mimics with therapeutic and industrial applications has interested both experimental and computational chemists for several decades. Recent advances in the computational methodology of restrained molecular dynamics, used in conjunction with data obtained from two-dimensional ¹H NMR spectroscopy, make it a promising method to study peptide and protein structure and function. Several issues, however, need to be addressed in order to assess the validity of this method for its explanatory and predictive value. Among the issues addressed in this study are: the accuracy and generizability of the GROMOS peptide molecular mechanics force field; the effect of inclusion of solvent on the simulations; and the effect of different types of restraining algorithms on the computational results. The decapeptide Ser-Tyr-Ser-Met-Glu-His-Phe-Arg-Trp-Gly, which corresponds to the sequence of ACTH_1–10, has been synthesized, cyclized, and studied by two-dimensional ¹H NMR spectroscopy. Restrained molecular dynamics (RMD) and time-averaged restrained molecular dynamics (TARMD) simulations were carried out on four different distance-geometry starting structures in order to determine and contrast the behavior of cyclic ACTH_1–10 in vacuum and in solution. For the RMD simulations, the structures did not fit the NOE data well, even at high values of the restraining potential. The TARMD simulation method, however, was able to give structures that fit the NOE data at high values of the restraining potential. In both cases, inclusion of explicit solvent molecules in the simulation had little effect on the quality of the fit, although it was found to dampen the motion of the cyclic peptide. For both simulation techniques, the number and size of the NOE violations increased as the restraining potential approached zero. This is due, presumably, to inadequacies in the force field. Additional TARMD vacuum-phase simulations, run with a larger memory length or with a larger sampling size (16 additional distance-geometry structures), yielded no significantly different results. The computed data were then analyzed to help explain the sparse NOE data and poor chymotryptic activity of the cyclic peptide. Cyclic ACTH_1–10, which contains the functional moieties of the catalytic triad of chymotrypsin, was evaluated as a potential mimic of chymotrypsin by measurement of the rate of hydrolysis of esters of L-and d-phenylalanine. The poor rate of hydrolysis is attributed to the flexibility of the decapeptide, the motion of the side chains, which result in the absence of long-range NOEs, the small size of the macrocycle relative to that of the substrate, and the inappropriate orientation of the Gly, His, and Ser residues. The results demonstrate the utility of this method in computer-aided molecular design of cyclic peptides and suggest structural modifications for future work based on a larger and more rigid peptide framework.     

2-(Glucosylthio)ethyl Groups as Potential Biolabile Phosphate- Protecting Groups of Mononucleotides

The in vitro anti-HIV effects and the stability studies of mononucleoside phosphotriester derivatives 1 – 3 of 3′-azido-3′-deoxythymidine (AZT) containing 2-(glucosylthio)ethyl moieties as potential biolabile phosphate-protecting groups are reported. The results of the anti-HIV evaluation demonstrate that the described compounds act via the release of the free nucleoside analogue and cannot be considered as mononucleotide prodrugs (pronucleotides). These data can be related to the lack of substrate affinity of these derivatives towards target-enzymes as corroborated by decomposition studies in various media and experiments with a purified β-D glucosidase.     

The search for a new model structure of β-Factor XIIa

We present the search for a new model of -factor XIIa, a blood coagulation enzyme, with an unknown experimental 3D-structure. We decided to build not one but three different models using different homologous proteins as well as different techniques and different modellers. Additional studies, including extensive molecular dynamics simulations on the solvated state, allowed us to draw several conclusions concerning homology modelling, in general, and -factor XIIa, in particular.     

β‐CdC2O4

Crystals of an­hydrous cadmium oxalate, β‐[Cd(C₂O₄)], have been synthesized hydro­thermally and the crystal structure solved using single‐crystal X‐ray diffraction data. The Cd and oxalate ions lie about independent inversion centres. The structure consists of a three‐dimensional framework built from sheets of cadmium octahedra linked together by oxalate groups.     

Evaluation of Vanadium(IV) as a Non-radioactive Surrogate for Technetium(IV) by Comparison of Stability Constants for Polyamino Polycarboxylate Ligand Complexation

The stability constants for the Tc(IV) and V(IV) complexation with the polyamino polycarboxylate ligands IDA, NTA, HEDTA and DTPA were determined using liquid–liquid extraction techniques. These stability constants were then used to evaluate the validity of using V(IV) as a chemical analogue for Tc(IV). Results suggest that Tc(IV), as TcOOH⁺, will form β _1?11 complexes with the selected ligands, while V(IV), as VO²⁺, will form β ₁₀₁ complexes. The values for these determined stability constants are (in log₁₀ unit) 10.9 ± 0.1, 11.4 ± 0.1, 14.9 ± 0.1, and 20.1 ± 0.1 for Tc(IV) in 0.5 mol·L^?1 NaCl at 25 °C, for IDA, NTA, HEDTA and DTPA, respectively, they are 9.3 ± 0.1, 11.6 ± 0.2, 15.8 ± 0.1, and 20.8 ± 0.1 for V(IV) in 0.5 mol·L^?1 NaCl at 25 °C, for the same suite of ligands. The incorporation of a hydroxide into the metal ligand complexes formed by Tc(IV) is proposed as the largest factor differentiating the apparent stability constants of Tc(IV) and V(IV). This work shows that V(IV) is a poor analog for Tc(IV); however, despite the differences in complexation mechanism between V(IV) and Tc(IV), V(IV) still appears to have some use for predicting Tc(IV) complexation behavior.     

A new method for estimating derivatives based on a distribution approach

In many applications, the estimation of derivatives has to be done from noisy measured signal. In this paper, an original method based on a distribution approach is presented. Its interest is to report the derivatives on infinitely differentiable functions. Thus, the estimation of the derivatives is done only from the signal. Besides, this method gives some explicit formulae leading to fast calculus. For all these reasons, it is an efficient method in the case of noisy signals as it will be confirmed in several examples.     

Snapshot gradient-recalled echo-planar images of rat brains at long echo time at 9.4 T

With improved B 0 homogeneity along with satisfactory gradient performance at high magnetic fields, snapshot gradient-recalled echo-planar imaging (GRE-EPI) would perform at long echo times (TEs) on the order of T2*, which intrinsically allows obtaining strongly T2*-weighted images with embedded substantial anatomical details in ultrashort time. The aim of this study was to investigate the feasibility and quality of long TE snapshot GRE-EPI images of rat brain at 9.4 T. When compensating for B 0 inhomogeneities, especially second-order shim terms, a 200 x 200 microm2 in-plane resolution image was reproducibly obtained at long TE (>25 ms). The resulting coronal images at 30 ms had diminished geometric distortions and, thus, embedded substantial anatomical details. Concurrently with the very consistent stability, such GRE-EPI images should permit to resolve functional data not only with high specificity but also with substantial anatomical details, therefore allowing coregistration of the acquired functional data on the same image data set.     

New figuring model based on surface slope profile for grazing‐incidence reflective optics

Surface slope profile is widely used in the metrology of grazing‐incidence reflective optics instead of surface height profile. Nevertheless, the theoretical and experimental model currently used in deterministic optical figuring processes is based on surface height, not on surface slope. This means that the raw slope profile data from metrology need to be converted to height profile to perform the current height‐based figuring processes. The inevitable measurement noise in the raw slope data will introduce significant cumulative error in the resultant height profiles. As a consequence, this conversion will degrade the determinism of the figuring processes, and will have an impact on the ultimate surface figuring results. To overcome this problem, an innovative figuring model is proposed, which directly uses the raw slope profile data instead of the usual height data as input for the deterministic process. In this paper, first the influence of the measurement noise on the resultant height profile is analyzed, and then a new model is presented; finally a demonstration experiment is carried out using a one‐dimensional ion beam figuring process to demonstrate the validity of our approach.     

Femtosecond laser Fourier transform absorption spectroscopy

A femtosecond mode-locked laser is used for what is believed to be the first time as a broadband infrared source for high-resolution Fourier transform absorption spectroscopy. A demonstration is made with a Cr(4+):YAG laser. The entire nu(1)+nu(3) vibration-rotation band region of acetylene, observed after passing through a single-pass 80-cm-long cell, is simultaneously recorded between 1480 and 1600 nm, in 7.9 s with a signal-to-noise ratio equal to 1000. Two hot bands of the most abundant acetylene isotopologue and the nu(1)+nu(3) band of the (13)C(12)CH(2) are also present. Replacement of the usual conventional tungsten lamp by the bright laser source reduces by about a factor of 150 the recording time needed to get similar results. The noise equivalent absorption coefficient at 1 s averaging is equal to 7x10(-7) cm(-1)Hz(-1/2) per spectral element.