Structural biasing elements for in-cell histone deacetylase paralog selectivity

We use the structural dissection of two 1,3-dioxanes with in-cell histone deacetylase (HDAC) paralog selectivity to identify key elements for selective HDAC inhibitors. We demonstrate that o-aminoanilides are inactive toward HDAC6 while apparently inhibiting deacetylases that act upon histone substrates. This finding has important clinical implications for the development of HDAC inhibitor-based treatments that do not interfere with microtubule dynamics associated with HDAC6. We also show that suberoylanilide hydroxamic acid (SAHA) alone is a nonparalog-selective HDAC inhibitor and that the 1,3-dioxane diversity appended to SAHA is essential for HDAC6 paralog selectivity.     

Molecular dynamics simulations of peptide-surface interactions

Proteins, which are bioactive molecules, adsorb on implants placed in the body through complex and poorly understood mechanisms and directly influence biocompatibility. Molecular dynamics modeling using empirical force fields provides one of the most direct methods of theoretically analyzing the behavior of complex molecular systems and is well-suited for the simulation of protein adsorption behavior. To accurately simulate protein adsorption behavior, a force field must correctly represent the thermodynamic driving forces that govern peptide residue-surface interactions. However, since existing force fields were developed without specific consideration of protein-surface interactions, they may not accurately represent this type of molecular behavior. To address this concern, we developed a host-guest peptide adsorption model in the form of a G(4)-X-G(4) peptide (G is glycine, X is a variable residue) to enable determination of the contributions to adsorption free energy of different X residues when adsorbed to functionalized Au-alkanethiol self-assembled monolayers (SAMs). We have previously reported experimental results using surface plasmon resonance (SPR) spectroscopy to measure the free energy of peptide adsorption for this peptide model with X = G and K (lysine) on OH and COOH functionalized SAMs. The objectives of the present research were the development and assessment of methods to calculate adsorption free energy using molecular dynamics simulations with the GROMACS force field for these same peptide adsorption systems, with an oligoethylene oxide (OEG) functionalized SAM surface also being considered. By comparing simulation results to the experimental results, the accuracy of the selected force field to represent the behavior of these molecular systems can be evaluated. From our simulations, the G(4)-G-G(4) and G(4)-K-G(4) peptides showed minimal to no adsorption to the OH SAM surfaces and the G(4)-K-G(4) showed strong adsorption to the COOH SAM surface, which is in agreement with our SPR experiments. Contrary to our experimental results, however, the simulations predicted a relatively strong adsorption of G(4)-G-G(4) peptide to the COOH SAM surface. In addition, both peptides were unexpectedly predicted to adsorb to the OEG surface. These findings demonstrate the need for GROMACS force field parameters to be rebalanced for the simulation of peptide adsorption behavior on SAM surfaces. The developed methods provide a direct means of assessing, modifying, and validating force field performance for the simulation of peptide and protein adsorption to surfaces, without which little confidence can be placed in the simulation results that are generated with these types of systems.     

Evaluation of a hollow cathode atomic emission source designed for continuous solution sample introduction

A hollow cathode discharge capable of continuous operation with solution sample introduction is described. Discharge current densities up to 0.64 are maintained in a helium plasma. Analyte emission intensities are optimized in terms of anode placement in relation to the hollow cathode, carrier gas flow rate, discharge current and sample solution flow rate. Detection limits for selected elements are reported and range from 0.03 for Li to 200 for Zn. Temporal stability of the discharge is examined and a calibration curve for Li is presented.     

Reference material requirements for laboratories and the role of accreditation bodies

It is now over two years since ISO/IEC 17025 General requirements for the competence of testing and calibration laboratories was published. The standard places increased emphasis on the demonstration of traceability of measurements made by laboratories. In the areas of chemical and biological metrology, the introduction of this standard has brought new challenges for laboratories to grapple with. This paper will examine the requirements regarding traceability for chemical and biological measurements, with specific reference to the use of reference materials by laboratories. This will be explored from the perspective of both accreditation bodies and a laboratory which is both a user and producer of certified reference materials. Moreover, the paper will describe mechanisms that are being used to improve the use of reference materials by accredited laboratories and hence the traceability of measurements. Finally the role of accreditation programs for reference material producers in assisting with this aspect will be examined.Electronic Supplementary Material Supplementary material is available for this article if you access the article at . A link in the frame on the left on that page takes you directly to the supplementary material.Presented at BERM-9—Ninth International Symposium on Biological and Environmental Reference Materials, June 15–19, 2003 Berlin, Germany.     

BSA adsorption on bimodal PEO brushes

BSA adsorption onto bimodal PEO brushes at a solid surface was measured using optical reflectometry. Bimodal brushes consist of long (N=770) and short (N=48) PEO chains and were prepared on PS surfaces, applying mixtures of PS(29)-PEO(48) and PS(37)-PEO(770) block copolymers and using the Langmuir-Blodgett technique. Pi-A isotherms of (mixtures of) the block copolymers were measured to establish the brush regime. The isotherms of PS(29)-PEO(48) show hysteresis between compression and expansion cycles, indicating aggregation of the PS(29)-PEO(48) upon compression. Mixtures of PS(29)-PEO(48) and PS(37)-PEO(770) demonstrate a similar hysteresis effect, which eventually vanishes when the ratio of PS(37)-PEO(770) to PS(29)-PEO(48) is increased. The adsorption of BSA was determined at brushes for which the grafting density of the long PEO chains was varied, while the total grafting density was kept constant. BSA adsorption onto monomodal PEO(48) and PEO(770) brushes was determined for comparison. The BSA adsorption behavior of the bimodal brushes is similar to the adsorption of BSA at PEO(770) monomodal brushes. The maximum of BSA adsorption at low grafting density of PEO(770) can be explained by ternary adsorption, implying an attraction between BSA and PEO. The contribution of primary adsorption to the total adsorbed amount is negligible.     

Highly efficient ethylene polymerisation by scandium alkyls supported by neutral fac-kappa3 coordinated N3 donor ligands

Reaction of [M(CH2SiMe3)3(THF)2] (M = Sc or Y) with the neutral fac-kappa3 N3 donor ligands (L) Me3[9]aneN3 or HC(Me2pz)3 gave the corresponding trialkyls [M(L)(CH2SiMe3)3]; activation of the scandium congeners with B(C6F5)3 in the presence of ethylene afforded highly active polymerisation catalysts (Me3[9]aneN3 = 1,4,7-trimethyltriazacyclononane).     

Molecular orbital studies on small molecules using H2+-type elliptical basis orbitals. Application to H2+, H2, He2++ and H3+

H₂⁺-type elliptical orbitals are defined in Section 1. These orbitals, which in elliptical coordinates involve a factor (1 + ξ)^σ, are employed in variational calculations on the ground states of H₂⁺ and H₂ (Sections 2 and 3). Various choices of σ are explored for H₂⁺, while two choices are used for H₂ : the “boundary condition” (Equation 6) and the “cusp condition” (Equation 9) values. Variational energies are calculated and compared to the results of similar calculations. Section 3 concludes by employing the H₂⁺-type orbitals in LCETO-MO-SCF calculations on the ground states of H₂ and He₂⁺⁺. For both molecules a four-function basis set with two (nonlinear) variational parameters yields more than 99% of the Hartree-Fock limit. Section 4 deals with LCETO-MO-SCF calculations on triangular H₃⁺. Three four-function basis sets are used, and the best energy is -1.2306 a.u., which is in reasonable agreement with the Hartree-Fock limit, -1.2999 a.u. Our best basis set is a four-term two-center expansion of the wave function with only one nonlinear variational parameter. Section 5 concludes the paper with a summary of the methods used to evaluate the integrals which arise in SCF calculations in the H₂⁺-type elliptical orbital basis.     

The synthesis of dimethoxy- and trimethoxy[1]benzothieno[2,3-c]quinolines

Three dimethoxy[1]benzothieno[2,3-c]quinolines 24–26 were prepared by photocyclization of the appropriate 3-chloro-N-phenylbenzo[b]thiophene-2-carboxamides 15–17 to [1]benzothieno[2,3-c]quinolin-6(5H)-ones 18–20 followed by chlorination to 6-chloro[1]benzothieno[2,3-c]quinolines 21–23 and then dechlorination resulting in the title compounds. Reaction of 24–26 with methyl iodide furnished the corresponding N-methyl quaternary salts 27–29 . Sodium methoxide readily converted 21–23 to trimethoxy[1]benzothieno[2,3-c]quinolines 30–32 .     

The stereochemistry at silicon of an iron to cyclopentadienyl ligand silyl group migration in (η-C5H5)Fe(CO)2SiR3

The silyl group migration observed upon treating (R)(+)-(η⁵-C₅H₅)Fe(CO)₂-SiMePh(1-Np) with n-BuLi occurs with retention of configuration at silicon. The anion resulting from the migration, (η⁵-C₅H₄SiMePh(1-Np))Fe(CO)₂Li, is alkylated with MeI to give (R)-(−)-(η⁵-C₅H₄SiMePh(1-Np))Fe(CO)₂Me (II). Compound II is independently prepared from (η⁵-C₅H₅)Fe(CO)₂Me. A concerted mechanism for the migration involving frontside nucleophilic attack at silicon is suggested.     

The\overline {MS} and on-shell renormalization schemes in the analysis of neutrino scattering experiments

The relationship between the \(\overline {MS} \) and on-shell renormalization schemes is discussed and the correction, for finite top quark mass, to the formula connecting sin² θ _W =1?M _W ² /M _Z ² and sin² \(\widehat\theta _W (M_W )\) is given. A table is presented to allow easy conversion. The relative sensitivity, to the top quark and Higgs masses, of the two definitions, when extracted from semi-leptonic neutrino scattering experiments is considered.