The SAMPL6 SAMPLing challenge: assessing the reliability and efficiency of binding free energy calculations

Journal of Computer-Aided Molecular Design - Approaches for computing small molecule binding free energies based on molecular simulations are now regularly being employed by academic and industry...     

Cationic ring-opening polymerization of carbazolyl-containing epoxy monomers by triphenyl carbenium salts as thermal- and photolatent initiators

Abstract  

Photoinitiated cationic polymerizations of various epoxy monomers bearing a carbazole moiety, 9-[3-(allyloxy)-2-(oxiran-2-ylmethoxy)propyl]-9H-carbazole, 9-[3-methoxy-2-(oxiran-2-ylmethoxy)propyl]-9H-carbazole, 9-[2-(oxiran-2-ylmethoxy)ethyl]-9H-carbazole, as well as a composition of 3,6-dibromo-9-(oxiran-2-ylmethyl)-9H-carbazole with 3,4-epoxycyclohexylmethyl 3,4-epoxycyclohexane carboxylate were investigated in bulk using triphenyl carbenium salts having anions such as BF₄ ⁻, SnCl₅ ⁻, and SbCl₆ ⁻. Dark polymerizations of the carbazolyl monomers in the presence of the initiators are studied. These photoinduced polymerization reactions give oligomers of degree of polymerization 4-22. The effect of the anion of the photoinitiator and polymerization time on the polymerization reaction is discussed.     

Determination of critical indices by "slow" spectroscopy: NMR shifts by statistical thermodynamics and density functional theory calculations

The temperature dependencies of NMR shifts in the critical region of two coexisting phases have been simulated using statistical thermodynamics and graph-theory consideration of equilibrium processes of molecular association. Microparameters of magnetic screening of various water and water/pyridine structures used in the statistical averaging have been evaluated by density functional theory calculations (PBE1PBE and B3PW91 functionals in the 6-311++G** basis set). The gauge-including atomic orbital (GIAO) approach has been applied to ensure gauge invariance of the results. Solvent effects were taken into account by a polarized continuum model (PCM). NMR shifts "order parameters" (Deltadelta = |delta+ - delta-|) and "diameters" (phidelta = |(delta+ + delta-)/2 - deltaC|, where delta+, delta-, and deltaC are the chemical shifts of coexisting phases and at the critical point respectively) have been calculated in each case close to the lower critical solution point (TL) and processed using linear regression analysis of Deltadelta approximately |T - TL| and phidelta approximately |T - TL| in the log-log plot. It has been shown that the critical index beta can be evaluated with high precision from the slope of Deltadelta = f(T - TL) at any realistic set of model input parameters. The slope of diameter has been found to depend on both input beta and alpha values. The obtained phidelta slopes (0.58-0.63) are very close to 2beta values. The results are discussed within the concept of complete scaling. Results of simulation are compared and supported by experimental NMR data for water/2,6-lutidine, acetic anhydride/n-heptane, and acetic anhydride/cyclohexane systems.     

Chaperones mainly suppress primary nucleation during formation of functional amyloid required for bacterial biofilm formation

Unlike misfolding in neurodegenerative diseases, aggregation of functional amyloids involved in bacterial biofilm, e.g. CsgA (E. coli) and FapC (Pseudomonas), is carefully regulated. However, it is unclear whether functional aggregation is inhibited by chaperones targeting pathological misfolding and if so by what mechanism. Here we analyze how four entirely different human chaperones or protein modulators (transthyretin, S100A9, Bri2 BRICHOS and DNAJB6) and bacterial CsgC affect CsgA and FapC fibrillation. CsgA is more susceptible to inhibition than FapC and the chaperones vary considerably in the efficiency of their inhibition. However, mechanistic analysis reveals that all predominantly target primary nucleation rather than elongation or secondary nucleation, while stoichiometric considerations suggest that DNAJB6 and CsgC target nuclei rather than monomers. Inhibition efficiency broadly scales with the chaperones'' affinity for monomeric CsgA and FapC. The chaperones tend to target the most aggregation-prone regions of CsgA, but do not display such tendencies towards the more complex FapC sequence. Importantly, the most efficient inhibitors (Bri2 BRICHOS and DNAJB6) significantly reduce bacterial biofilm formation. This commonality of chaperone action may reflect the simplicity of functional amyloid formation, driven largely by primary nucleation, as well as the ability of non-bacterial chaperones to deploy their proteostatic capacities across biological kingdoms.

Unlike misfolding in neurodegenerative diseases, aggregation of functional amyloids involved in bacterial biofilm, e.g. CsgA (E. coli) and FapC (Pseudomonas), is carefully regulated.     

Easily functionalizable carbazole based building blocks with extended conjugated systems for optoelectronic applications

Carbazole based building blocks, possessing diphenylethenyl fragments, have been synthesized. Condensation of the carbazol-2-ol with diphenylacetaldehyde yields 1,3-substituted derivatives. Change of the synthesis sequence, however, (i.e., substitution at the hydroxyl and NH groups, followed by the condensation reaction) results in the 3,6-substituted products. Thermal, optical, electrochemical and photophysical properties of the synthesized derivatives have been investigated. Room temperature hole-drift mobilities, evaluated using xerographic time-of-flight technique, were found to exceed 10⁻⁴ cm² V⁻¹ s⁻¹ at strong electric fields. The obtained results indicate high charge mobility for molecularly doped polymers, especially considering the fact that these measurements were carried out under ambient conditions and not in high vacuum. Commercial availability and relative cheapness of the starting materials, simple synthetic method, number of sites available for easy functionalization and covalent linking to other molecules makes these precursors attractive building blocks for the construction of more complex low-molecular-weight or polymeric materials for optoelectronic applications.     

A class of noninjective circle transformations without periodic points

We construct a class of noninjective aperiodic circle transformations. As a by-product, we establish some new properties of Mersenne numbers.     

Unicity of Types for Supercuspidal Representations of GLN

Let F be a non-Archimedean local field, with the ring of integerso_F. Let G = GL_N(F), K = GL_N (o_F), and be a supercuspidal representationof G. We show that there exists a unique irreducible smoothrepresentation of K, such that the restriction to K of a smoothirreducible representation ' of G contains if and only if 'is isomorphic to ° det, where is an unramified quasicharacterof F^x. Moreover, we show that contains with the multiplicity1. As a corollary we obtain a kind of inertial local Langlandscorrespondence. 2000 Mathematics Subject Classification 22E50.     

Synthesis, chemical properties, and antimicrobial activity of 2- and 2,3-substituted [(tetrahydro-2,4-dioxopyrimidin-1(2H)-yl)phenoxy]naphthalene-1,4-diones

Abstract  

Mono- and disubstituted [(tetrahydro-2,4-dioxopyrimidin-1(2H)-yl)phenoxy]naphthalene-1,4-diones were synthesized by the reaction of dihydro-1-(3-hydroxy- and 4-hydroxyphenyl)pyrimidine-2,4(1H,3H)-diones and their 5- and 6-methyl derivatives with 2,3-dichloro-1,4-naphthoquinone. Their stability in alkaline and acidic media was investigated. Four of the compounds exhibited good antimicrobial activity against Staphylococcus aureus, Mycobacterium luteum, Candida tenuis, and Aspergillus niger.     

Helical Propensity in an Intrinsically Disordered Protein Accelerates Ligand Binding

Many intrinsically disordered proteins fold upon binding to other macromolecules. The secondary structure present in the well‐ordered complex is often formed transiently in the unbound state. The consequence of such transient structure for the binding process is, however, not clear. The activation domain of the activator for thyroid hormone and retinoid receptors (ACTR) is intrinsically disordered and folds upon binding to the nuclear coactivator binding domain (NCBD) of the CREB binding protein. A number of mutants was designed that selectively perturbs the amount of secondary structure in unbound ACTR without interfering with the intermolecular interactions between ACTR and NCBD. Using NMR spectroscopy and fluorescence‐monitored stopped‐flow kinetic measurements we show that the secondary structure content in helix 1 of ACTR indeed influences the binding kinetics. The results thus support the notion of preformed secondary structure as an important determinant for molecular recognition in intrinsically disordered proteins.