On the transferability of folding and threading potentials and sequence-independent filters for protein folding simulations

Significant progress has recently been made in de novo protein structure prediction. The Rosetta method by Baker and colleagues, which is based on the idea of assembling putative models from a library of k-mer fragments derived from known three-dimensional protein structures, proved to be particularly successful. Critical components of the Rosetta approach are various sequence-dependent as well as sequence-independent measures that are used to rank alternative models and to enhance sampling of native-like conformations. In the present work we revisit several sequence-independent filters that have been used to enhance the discrimination of native and native-like structures from misfolded structures, such as the overall compactness of the structure and its contact order. We also propose a novel sequence-independent filter, based on the shape of the mean inter-residue radial distribution function. Using the Rosetta, Park–Levitt and CASP4 sets of decoys it is shown that sequence-independent filters are in fact more successful in distinguishing native structures in Rosetta and CASP4 tests than commonly used knowledge-based pairwise potentials. The latter are typically designed to distinguish native structures in a population of well-folded alternatives, and they fail to discriminate between native-like and non-physically packed misfolded structures from Rosetta simulations. Moreover, a rigorous attempt to optimize pairwise potentials for recognition of homologous structures in threading by using a linear programming approach leads to further deterioration of performance in terms of recognition of native structures from the Rosetta set. These findings shed light onto the success of tailored scoring functions used in the Rosetta protocol and provide support for explicit inclusion of both sequence dependent and sequence independent measures in the design of scoring functions. A Web server that enables ranking of decoy structures according to sequence independent filters considered here is available at http://sift.chmcc.org.     

An Efficient Microwave-Assisted Synthesis of Structurally Diverse Styrylquinolines

Summary. Aromatic aldehydes undergo condensation with quinaldines under microwave irradiation to afford structurally diverse styrylquinolines in high yields under solvent-free conditions. A comparison with the conventional method clearly indicates the advantages of the new protocol.     

Glycosylation of organic thio- and selenoacids of phosphorus : The reaction of organic monothio acids of phosphorus with glycosyl bromides. Thiono-thiolo rearrangement of glycosyl phosphorothioates

Ambident anions derived from phosphorus monothio acids have been glycosylated by 2,3,4,6-tetra-O-acetyl-α-D-glucopyranosyl-, 2,3,4,6-tetra-O-acetyl-α-D-galactopyranosyl- and 2,3,4-tri-acetyl-α-D-xylopyranosyl bromides, yielding β-S-glycosyl- and /gb-O-glycosylthioates. The S/O ratio of the glycosylated phosphorothioates depends markedly on the salt used. Ammonium salts favour the formation of S-derivatives, whereas silver salts give mainly O-derivatives. O-Glucosyl phosphorothioate undergoes thermal isomerisation to S-glucosyl phosphorothioate, with retention of configuration at the glycosylic centre. The implications of this stereochemical result are briefly discussed.     

ON THE ITERATED ω-RULE

Let Γ_n(φ) be a formula of L_PA (PA = Peano Arithmetic) meaning “there is a proof of φ from PA-axioms, in which ω-rule is iterated no more than n times”. We examine relations over pairs of natural numbers of the kind. (n, k) ≦_H (n', k') iff PA + RFN_n' (H_k') ? RFN_n (H_k). Where H denotes one of the hierarchies ∑ or Π and RFN_n(C) is the scheme of the reflection principle for Γ_n restricted to formulas from the class C(Γ_n(φ) implies “φ is true”, for every φ ∈ C). Our main result is that. (n, k) ≦H (n', k') if n ≦ n' and k ≦ max (k', 2n' + 1).     

Friction tensor for a pair of Brownian particles: Spurious finite-size effects and molecular dynamics estimates

In this work, we show thatin any finite system, the binary friction tensor for two Brownian particlescannot be directly estimated from an evaluation of the microscopic Green-Kubo formula, involving the time integral of force-force autocorrelation functions. This pitfall is associated with a subtle inversion of the thermodynamic and long-time limits and leads to spurious results for the estimates of the friction matrix based on molecular dynamics simulations. Starting from a careful analysis of the coupled Langevin equations for two interacting Brownian particles, we derive a method to circumvent these effects and extract the binary friction tensor from the correlation function matrix of the instantaneous forces exerted by the bath particles on the fixed Brownian particles, and from the relaxation of the total momentum of the bath in afinite system. The general methodology is applied to the case of two hard or soft Brownian spheres in a bath of light particles. Numerical estimates of the relevant correlation functions and of the resulting self and mutual components of the matrix of friction tensors are obtained by molecular dynamics simulations for various spacings between the Brownian particles. This paper is dedicated to B. Jancovici on the occassion of his 65th birthday.     

Glycosylation of organic phosphorus thio- and selenoacids—II: The reaction of organic phosphorus thioselenoacids with glycosyl bromides under kinetically and thermodynamically controlled conditions

Ambident anions derived from phosphorus thioselcnoacids were glycosylated with 2,3,4,6 - tetra - O - acetyl - α - d - glucopyranosyl bromide, 2,3,4,6 - tetra - O - acetyl - α - d - galactopyranosyl bromide and 2,3,4 - tri- O - acetyl - α - d - xylopyranosyl bromide. The products were β-Se-glucosyl- and β-S-glucosylthioselenoates. The Se/S ratio of the glycosylated phosphorothioselenoates depends on the reaction conditions. At higher temperatures an equilibrium was observed. As a result of this equilibrium the Se/S ratio of the linkages formed in the glycosylated products was different from that observed under kinetic control. The structures of the glycosylated phosphorothioselenoates were confirmed by spectroscopy, independent synthesis and selective oxidation.     

VUV photon induced fluorescence study of SF5CF3

The interaction of SF(5)CF(3) with vacuum-UV radiation has been investigated by photon induced fluorescence spectroscopy. Total fluorescence yield and dispersed fluorescence spectra of SF(5)CF(3) were recorded in the 200-1000 nm fluorescence window. In all cases, the fluorescence spectra resemble those of CF(3)X (X = H, F, Cl, and Br) molecules. At photon energies below 20 eV, the emission is attributed to the excited CF(3) and CF(2) fragments. The threshold for the CF(3) emission is 10.2 +/- 0.2 eV, giving an upper limit estimate for the SF(5)-CF(3) bond dissociation energy of 3.9 +/- 0.3 eV. The excitation functions of the CF(3) and CF(2) emissions were measured in the photon energy range 13.6-27.0 eV. The resonant structures observed in SF(5)CF(3) are attributed to electronic transitions from valence to Rydberg orbitals, following similar assignments in CF(3)X molecules. The photoabsorption spectrum of SF(5)CF(3) shows features at the same energies, indicating a strong contribution from Rydberg excitations.     

Heat conduction in transversally graded laminates with non-uniform microstructure

Two-component laminates made of conductors distributed non-periodically as laminas along one direction are considered in this note. The macroscopic properties of these laminates are described by continuous slowly-varying functions across laminas. In order to analyse heat conduction, the approach, called the tolerance modelling, is used. The aim of this note is to use averaged equations of the tolerance model for transversally graded laminates to analyse stationary heat conduction across laminas. (© 2010 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim)     

Partitioning of atmospheric carbon dioxide over Central Europe: insights from combined measurements of CO 2 mixing ratios and their carbon isotope composition

Regular measurements of atmospheric CO ₂ mixing ratios and their carbon isotope composition (¹³C/¹²C and ¹⁴C/¹²C ratios) performed between 2005 and 2009 at two sites of contrasting characteristics (Krakow and the remote mountain site Kasprowy Wierch) located in southern Poland were used to derive fossil fuel-related and biogenic contributions to the total CO ₂ load measured at both sites. Carbon dioxide present in the atmosphere, not coming from fossil fuel and biogenic sources, was considered ‘background’ CO ₂. In Krakow, the average contribution of fossil fuel CO ₂ was approximately 3.4%. The biogenic component was of the same magnitude. Both components revealed a distinct seasonality, with the fossil fuel component reaching maximum values during winter months and the biogenic component shifted in phase by approximately 6 months. The partitioning of the local CO ₂ budget for the Kasprowy Wierch site revealed large differences in the derived components: the fossil fuel component was approximately five times lower than that derived for Krakow, whereas the biogenic component was negative in summer, pointing to the importance of photosynthetic sink associated with extensive forests in the neighbourhood of the station. While the presented study has demonstrated the strength of combined measurements of CO ₂ mixing ratios and their carbon isotope signature as efficient tools for elucidating the partitioning of local atmospheric CO ₂ loads, it also showed the important role of the land cover and the presence of the soil in the footprint of the measurement location, which control the net biogenic surface CO ₂ fluxes.