Folding Free Energy Determination of an RNA Three-Way Junction Using Fluctuation Theorems

Nonequilibrium work relations and fluctuation theorems permit us to extract equilibrium information from nonequilibrium measurements. They find application in single-molecule pulling experiments where molecular free energies can be determined from irreversible work measurements by using unidirectional (e.g., Jarzynski’s equality) and bidirectional (e.g., Crooks fluctuation theorem and Bennet’s acceptance ratio (BAR)) methods. However, irreversibility and the finite number of pulls limit their applicability: the higher the dissipation, the larger the number of pulls necessary to estimate ΔG within a few kBT. Here, we revisit pulling experiments on an RNA three-way junction (3WJ) that exhibits significant dissipation and work-distribution long tails upon mechanical unfolding. While bidirectional methods are more predictive, unidirectional methods are strongly biased. We also consider a cyclic protocol that combines the forward and reverse work values to increase the statistics of the measurements. For a fixed total experimental time, faster pulling rates permit us to efficiently sample rare events and reduce the bias, compensating for the increased dissipation. This analysis provides a more stringent test of the fluctuation theorem in the large irreversibility regime.     

Effects of Two Natural Bisbenzylisoquinolines,Curine and Guattegaumerine,Extracted from Isolona hexaloba on Rhodamine Efflux by Abcb1b from Rat Glycocholic-Acid-Resistant Hepatocarcinoma Cells

To develop new therapeutic molecules, it is essential to understand the biological effects and targets of clinically relevant compounds. In this article, we describe the extraction and characterization of two alkaloids from the roots of Isolona hexaloba—curine and guattegaumerine. The effect of these alkaloids on the multidrug efflux pump ABCB1 (MDR1/P-Glycoprotein) and their antiproliferative properties were studied. Compared to verapamil, a widely used inhibitor of P-gp, curine and guattegaumerine were found to be weak inhibitors of MDR1/P-Glycoprotein. The highest inhibition of efflux produced by verapamil disappeared in the presence of curine or guattegaumerine as competitors, and the most pronounced effect was achieved with curine. Altogether, this work has provided new insights into the biological effects of these alkaloids on the rat Mdr1b P-gp efflux mechanism and would be beneficial in the design of potent P-gp inhibitors.     

Travelling wave mathematical analysis and efficient numerical resolution for a one-dimensional model of solid propellant combustion

We investigate a model of solid propellant combustion involving surface pyrolysis coupled to finite activation energy gas-phase combustion. Existence and uniqueness of a travelling wave solution are established by extending dynamical system tools classically used for premixed flames, dealing with the additional difficulty arising from the surface regression and pyrolysis. An efficient shooting method allows to solve the problem in phase space without resorting to space discretisation nor fixed-point Newton iterations. The results are compared to solutions from a CFD code developed at ONERA, assessing the efficiency and potential of the method, and the impact of the modelling assumptions is evaluated through parametric studies.     

Erratum to “Unique continuation results for Ricci curvature and applications” [J. Geom. Phys. 58 (2008) 179–207]

Corrections are given to some of the proofs of the paper mentioned in the title.     

Poly(Urethane)-Crosslinked Poly(HEMA) Hydrogels

Abstract

Hydrogels have been prepared from 2-hydroxyethyl methacrylate polymerized in the presence of isocyanate-terminated poly(ethylene glycol) (PEG) crosslinking agents. PEGS of molecular weights 200, 400, and 1000 were investigated. The crosslinked nature of the hydrogels was demonstrated by their insolubility in solvents which normally dissolve poly(HEMA). Hexamethylene diisocyanate (HDI) was mainly used as the isocyanate. The molecular weight of the PEG and the crosslinker content significantly influenced the equilibrium water sorption and mechanical properties of the saturated networks. It was observed that as the molecular weight of the PEG increased, the water sorption increased and the nominal modulus decreased. However, for higher levels of cross-linker, water sorption decreased and modulus increased at low molecular weight PEG; for PEG 1000, water absorption increased as crosslinker content increased. These results are explained by the competing effects of flexibility, crosslink density, and hydrophobicity contributed by the various constituents of the hydrogels.     

Primary Amine‐Initiated Polymerizations of α–Amino Acid N‐Thiocarbonic Acid Anhydrosulfide

The N‐thiocarbonic acid anhydrosulfides NTAs of D,L‐leucine, D,L‐phenylalanine and sarcosine were polymerized in dioxane by addition of n‐hexylamine as initiator. Despite variation of the monomer‐initiator ratio (M/I) only low yields of oligopeptides were obtained from D,L‐Leu‐ and D,L‐Phe‐NTA. Both yields and molecular weights were almost twice as high for polymerizations of Sar‐NTA. MALDI‐TOF mass spectra confirmed that the isolated oligo‐and polypeptides possess the expected structure with one reactive amino end group. Therefore, it is surprising that the polymerizations stopped at low conversions. Two hypotheses explaining this phenomenon are discussed.