Structural Analysis of a Helical Peptide Unfolding Pathway

The analysis of the folding mechanism in peptides adopting well‐defined secondary structure is fundamental to understand protein folding. Herein, we describe the thermal unfolding of a 15‐mer vascular endothelial growth factor mimicking α‐helical peptide (QK_L10A) through the combination of spectroscopic and computational analyses. In particular, on the basis of the temperature dependencies of QK_L10A H_α chemical shifts we show that the first phase of the thermal helix unfolding, ending at around 320 K, involves mainly the terminal regions. A second phase of the transition, ending at around 333 K, comprises the central helical region of the peptide. The determination of high‐resolution QK_L10A conformational preferences in water at 313 K allowed us to identify, at atomic resolution, one intermediate of the folding–unfolding pathway. Molecular dynamics simulations corroborate experimental observations detecting a stable central helical turn, which represents the most probable site for the helix nucleation in the folding direction. The data presented herein allows us to draw a folding–unfolding picture for the small peptide QK_L10A compatible with the nucleation–propagation model. This study, besides contributing to the basic field of peptide helix folding, is useful to gain an insight into the design of stable helical peptides, which could find applications as molecular scaffolds to target protein–protein interactions.     

Characterization of the volatile organic compounds of Italian 'Fossa' cheese by solid-phase microextraction gas chromatography/mass spectrometry

Fossa cheese is an Italian hard cheese, ripened for up to 3 months in underground pits dug into tuffaceous rock. During this period, the cheese develops a unique flavour and intense and somewhat piquant aroma. Solid-phase microextraction gas chromatography/mass spectrometry (SPME-GC/MS) was utilized to characterize the volatile organic compounds (VOCs) of Fossa cheese. A total of 75 VOCs were separated and identified; in particular, the major class of compounds found in the cheeses ripened in the pits were the esters of fatty acids. Discriminant analysis of volatile profiles allowed us to distinguish between cheeses in different stages of seasoning (60-day-old cheese and cheese ripened an additional 90 days in and out of the pits).     

Percolation transition in Yang-Mills matter at a finite number of colors

We examine baryonic matter at a quark chemical potential of the order of the confinement scale μ(q)～Λ(QCD). In this regime, quarks are supposed to be confined but baryons are close to the "tightly packed limit" where they nearly overlap in configuration space. We show that this system will exhibit a percolation phase transition when varied in the number of colors N(c): at high N(c), large distance correlations at the quark level are possible even if the quarks are essentially confined. At low N(c), this does not happen. We discuss the relevance of this for dense nuclear matter, and argue that our results suggest a new "phase transition," varying N(c) at constant μ(q).     

Refined methods for the identifiability of tensors

We prove that the general tensor of size \(2^n\) and rank \(k\) has a unique decomposition as the sum of decomposable tensors if \(k\le 0.9997\frac{2^n}{n+1}\) (the constant 1 being the optimal value). Similarly, the general tensor of size \(3^n\) and rank \(k\) has a unique decomposition as the sum of decomposable tensors if \(k\le 0.998\frac{3^n}{2n+1}\) (the constant 1 being the optimal value). Some results of this flavor are obtained for tensors of any size, but the explicit bounds obtained are weaker.     

On unitals in PG(2,q^2) stabilized by a homology group

The linear collineation group of a classical unital of $\mathrm{PG}(2,q^2)$ contains a group of homologies of order $q+1$ . In this paper we prove that if $\mathcal{U }$ is a unital of PG $(2,q^2)$ stabilized by a homology group of order $q+1$ and $q$ is a prime number, then $\mathcal{U }$ is classical.     

Approximate dynamic programming for stochastic N-stage optimization with application to optimal consumption under uncertainty

Stochastic optimization problems with an objective function that is additive over a finite number of stages are addressed. Although Dynamic Programming allows one to formally solve such problems, closed-form solutions can be derived only in particular cases. The search for suboptimal solutions via two approaches is addressed: approximation of the value functions and approximation of the optimal decision policies. The approximations take on the form of linear combinations of basis functions containing adjustable parameters to be optimized together with the coefficients of the combinations. Two kinds of basis functions are considered: Gaussians with varying centers and widths and sigmoids with varying weights and biases. The accuracies of such suboptimal solutions are investigated via estimates of the error propagation through the stages. Upper bounds are derived on the differences between the optimal value of the objective functional and its suboptimal values corresponding to the use at each stage of approximate value functions and approximate policies. Conditions under which the number of basis functions required for a desired approximation accuracy does not grow “too fast” with respect to the dimensions of the state and random vectors are provided. As an example of application, a multidimensional problem of optimal consumption under uncertainty is investigated, where consumers aim at maximizing a social utility function. Numerical simulations are provided, emphasizing computational pros and cons of the two approaches (i.e., value-function approximation and optimal-policy approximation) using the above-mentioned two kinds of basis functions. To investigate the dependencies of the performances on dimensionality, the numerical analysis is performed for various numbers of consumers. In the simulations, discretization techniques exploiting low-discrepancy sequences are used. Both theoretical and numerical results give insights into the possibility of coping with the curse of dimensionality in stochastic optimization problems whose decision strategies depend on large numbers of variables.     

A novel enantiopure tricyclic β-lactam via stereoselective intramolecular nitrilimine cycloaddition

Starting from the Staudinger [2+2] cycloaddition between the 1-azadiene 1 and acetoxyacetylketene, generated in situ from acetoxyacetyl chloride, we developed a seven-step synthesis of the novel azeto[3′,4′:2,3]pyrano[4,5-c]pyrazole skeleton 9 in both racemic and enantiopure forms. Silver carbonate treatment of the functionalised hydrazonoyl chloride 7 promoted in situ generation of the corresponding nitrilimine 8, which underwent a clean, stereoselective cycloaddition to the target tricyclic β-lactam 9. The key step of the synthetic pathway leading to enantiopure 9 was the production of the enantiopure azetidinone (3R,4S)-3 by enzymatic resolution with Amano Lypase PS of the racemic precursor (3S1,4R1)-2.     

Preparative Isoelectric Focusing

Electrophoretic mobility has been used for years as a basis for separation and characterization of proteins. The resolving power of conventional electrophoresis is limited, and the characterization by mobility is not unique because of the dependence of the protein mobilities on the pH and ionic strength of the buffers.     

The First Synthesis of a Ribo-Hexos-5-Ulose: the L-Enantiomer

ABSTRACT

The title compound, previously unreported in either enantioform, and its 2,6-di-O-benzyl derivative have been synthesized through a stereocontrolled epimerization at C-2 of 6-O-protected methyl 3,4-O-isopropylidene-5-C-methoxy-β-D-galactopyranosides. The epimerization, performed through a high yielding sequence of oxidation-reduction owing to the cooperative role of the equatorial C-1 aglycon and the steric hindrance of the isopropylidene group, turned out to be completely diastereoselective. Whereas the unprotected L-ribo-hexos-5-ulose exists, as proved by NMR in D₂O, in five main tautomeric forms in a ratio of about 4:2:2:1:1, only two anomeric 1,4-furanosic forms are present at equilibrium in its 2,6-di-O-benzyl derivative, in ratios ranging from 10:1 to 7:3, depending on the prevalence of D₂O or CD₃CN in the solvent mixture.