Application of torsion angle molecular dynamics for efficient sampling of protein conformations

We investigate the application of torsion angle molecular dynamics (TAMD) to augment conformational sampling of peptides and proteins. Interesting conformational changes in proteins mainly involve torsional degrees of freedom. Carrying out molecular dynamics in torsion space does not only explicitly sample the most relevant degrees of freedom, but also allows larger integration time steps with elimination of the bond and angle degrees of freedom. However, the covalent geometry needs to be fixed during internal coordinate dynamics, which can introduce severe distortions to the underlying potential surface in the extensively parameterized modern Cartesian-based protein force fields. A "projection" approach (Katritch et al. J Comput Chem 2003, 24, 254-265) is extended to construct an accurate internal coordinate force field (ICFF) from a source Cartesian force field. Torsion crossterm corrections constructed from local molecular fragments, together with softened van der Waals and electrostatic interactions, are used to recover the potential surface and incorporate implicit bond and angle flexibility. MD simulations of dipeptide models demonstrate that full flexibility in both the backbone phi/psi and side chain chi1 angles are virtually restored. The efficacy of TAMD in enhancing conformational sampling is then further examined by folding simulations of small peptides and refinement experiments of protein NMR structures. The results show that an increase of several fold in conformational sampling efficiency can be reliably achieved. The current study also reveals some complicated intrinsic properties of internal coordinate dynamics, beyond energy conservation, that can limit the maximum size of the integration time step and thus the achievable gain in sampling efficiency.     

Free-radical distributions in emulsion polymerization which employs oil-soluble radical generators

The use of oil-soluble radical generators for emulsion polymerization is considered. When radicals are formed in pairs within particles of a seed latex, the occurrence of radical desorption leads to complex kinetics. Use of radical balances and realistic simplifications produce a method for a relatively simple calculation of radical populations in the particles. Examples are restricted, for illustration purposes, to cases where the average number of radicals per particle, n , is less than one. Very low rates of radical desorption cause a substantial increase in n . As the desorption rate increases, the value of n decreases. n increases slowly with radical generation rate. Large decreases in the chain termination rate coefficient (which may accompany a gel effect) can have a negligible effect on the value of n . Radical distributions obtained from oil-soluble initiators can be slightly broader than those expected from the use of water-soluble initiators. The kinetics of emulsion polymerization will be similar for the two types of radical generator when radicals from oil-soluble generators can desorb from the polymer particles.     

Thermodynamic Parameters for the Association of Fluorinated Benzenesulfonamides with Bovine Carbonic Anhydrase II

This paper describes a calorimetric study of the association of a series of seven fluorinated benzenesulfonamide ligands (C₆H_nF_5?nSO₂NH₂) with bovine carbonic anhydrase II (BCA). Quantitative structure–activity relationships between the free energy, enthalpy, and entropy of binding and pK_a and log P of the ligands allowed the evaluation of the thermodynamic parameters in terms of the two independent effects of fluorination on the ligand: its electrostatic potential and its hydrophobicity. The parameters were partitioned to the three different structural interactions between the ligand and BCA: the Zn^II cofactor–sulfonamide bond (≈65 % of the free energy of binding), the hydrogen bonds between the ligand and BCA (≈10 %), and the contacts between the phenyl ring of the ligand and BCA (≈25 %). Calorimetry revealed that all of the ligands studied bind in a 1:1 stoichiometry with BCA; this result was confirmed by ¹⁹F NMR spectroscopy and X‐ray crystallography (for complexes with human carbonic anhydrase II).     

New spherical-cutoff methods for long-range forces in macromolecular simulation

New atom- and group-based spherical-cutoff methods have been developed for the treatment of nonbonded interactions in molecular dynamics (MD) simulation. A new atom-based method, force switching, leaves short-range forces unaltered by adding a constant to the potential energy, switching forces smoothly to zero over a specified range. A simple improvement to group-based cutoffs is presented: Switched group-shifting shifts the group–group potential energy by a constant before being switched smoothly to zero. Also introduced are generalizations of atom-based force shifting, which adds a constant to the Coulomb force between two charges. These new approaches are compared to existing methods by evaluating the energy of a model hydrogen-bonding system consisting of two N-methyl acetamide molecules and by full MD simulation. Thirty-five 150 ps simulations of carboxymyoglobin (MbCO) hydrated by 350 water molecules indicate that the new methods and atom-based shifting are each able to approximate no-cutoff results when a cutoff at or beyond 12 Å is used. However, atom-based potential-energy switching and truncation unacceptably contaminate group–group electrostatic interactions. Group-based potential truncation should not be used in the presence of explicit water or other mobile electrostatic dipoles because energy is not a state function with this method, resulting in severe heating (about 4 K/ps in the simulations of hydrated MbCO). The distance-dependent dielectric (? ∝? r) is found to alter the temperature dependence of protein dynamics, suppressing anharmonic motion at high temperatures. Force switching and force shifting are the best atom-based spherical cutoffs, whereas switched group-shifting is the preferred group-based method. To achieve realistic simulations, increasing the cutoff distance from 7.5 to 12 Å or beyond is much more important than the differences among the three best cutoff methods. © 1994 by John Wiley & Sons, Inc.

1 This article is a US Government work and, as such, is in the public domain in the United States of America.

     

The microwave spectrum and conformation of bromomethyl cyclopropane

The microwave spectrum of gaseous bromomethyl cyclopropane

is reported in the range 12 to 36 GHz. Lines of the ⁷⁹Br and ⁸¹Br species of cis and gauche forms are assigned and partial r₀-structures derived. The rotational constants in MHz are: gauche C₃H₅CH₂⁷⁹Br, A = 11 469.285, B = 1 374.777, C = 1 295.394; gauche C₃H₅CH₂⁸¹Br, A = 11 400.100, B = 1 364.088, C = 1 283.952; cis C₃H₅CH₂⁷⁹Br, A = 8 759.918, B = 1 597.413, C = 1 522.141; cis C₃H₅CH₂⁸¹Br, A = 8 716.552, B = 1 583.761, C = 1 509.017.     

qNMR for profiling the production of fungal secondary metabolites

Analysis of complex mixtures is a common challenge in natural products research. Quantitative nuclear magnetic resonance spectroscopy offers analysis of complex mixtures at early stages and with benefits that are orthogonal to more common methods of quantitation, including ultraviolet absorption spectroscopy and mass spectrometry. Several experiments were conducted to construct a methodology for use in analysis of extracts of fungal cultures. A broadly applicable method was sought for analysis of both pure and complex samples through use of an externally calibrated method. This method has the benefit of not contaminating valuable samples with the calibrant, and it passed scrutiny for line fitting and reproducibility. The method was implemented to measure the yield of griseofulvin and dechlorogriseofulvin from three fungal isolates. An isolate of Xylaria cubensis (coded MSX48662) was found to biosynthesize griseofulvin in the greatest yield, 149 ± 8 mg per fermentation, and was selected for further supply experiments. Copyright © 2016 John Wiley & Sons, Ltd.     

Solvent‐assisted anionic ring opening polymerization of glycidol: Toward medium and high molecular weight hyperbranched polyglycerols

Hyperbranched polyglycerols (HPGs) are globular structures with a large number of functionalizable hydroxyl groups and have excellent in vitro and in vivo biocompatibility profiles comparable to polyethylene glycol. This work introduces a facile method for the synthesis of medium molecular weights (M_ws) (50–300 kDa) HPGs, which has been difficult to synthesize with low polydispersity, with the assistance of solvents by ring opening polymerization. The influence of different solvents (1,4‐dioxane, tetrahydropyran (THP), ethylene glycol diethyl ether (EGDE) and decane), solvent to glycidol ratio, concentration of glycidol and the time of polymerization on M_w and polydispersity of HPGs has been studied. The M_w and polydispersity of HPGs are significantly affected by the nature of the polymerization phase (homogeneous or heterogeneous) and chemical structure of the solvent. The differences in the solvation of the potassium cations and change in the nucleophilicity of the alkoxide anion in various solvents may be responsible for the changes in M_w and PDI of the HPG. The M_w of the HPG decreases in the order 1,4‐dioxane > THP > EGDE >decane. The microstructure, solution and thermal properties of the HPG do not depend on the nature of solvent. © 2013 Wiley Periodicals, Inc. J. Polym. Sci., Part A: Polym. Chem. 2013, 51, 2614–2621