Permeation and gating in proteins: kinetic Monte Carlo reaction path following

We present a new Monte Carlo technique, kinetic Monte Carlo reaction path following (kMCRPF), for the computer simulation of permeation and large-scale gating transitions in protein channels. It combines ideas from Metropolis Monte Carlo (MMC) and kinetic Monte Carlo (kMC) algorithms, and is particularly suitable when a reaction coordinate is well defined. Evolution of transition proceeds on the reaction coordinate by small jumps (kMC technique) toward the nearest lowest-energy uphill or downhill states, with the jumps thermally activated (constrained MMC). This approach permits navigation among potential minima on an energy surface, finding the minimum-energy paths and determining their associated free-energy profiles. The methodological and algorithmic strategies underlying the kMCRPF method are described. We have tested it using an analytical model and applied it to study permeation through the curvilinear ClC chloride and aquaporin pores and to gating in the gramicidin A channel. These studies of permeation and gating in real proteins provide extensive procedural tests of the method.     

Negative dipole potentials of uncharged langmuir monolayers due to fluorination of the hydrophilic heads

The dipole potential, affecting the structure, functions, and interactions of biomembranes, lipid bilayers, and Langmuir monolayers, is positive toward the hydrocarbon moieties. We show that uncharged Langmuir monolayers of docosyl trifluoroethyl ether (DFEE) exhibit large negative dipole potentials, while the nonfluorinated docosyl ethyl ether (DEE) forms films with positive dipole potentials. Comparison of the Delta V values for these ethers with those of the previously studied(37-39) monolayers of trifluoroethyl ester (TFEB) and ethyl ester of behenic acid (EB) shows that the reversal of the sign of Delta V causes the same change Delta(Delta V) = -706 +/- 16 mV due to fluorination of heads. The Delta V values of both TFEB and EB films differ by -122 +/- 16 mV from those of DFEE and DEE monolayers, respectively, with the same density. Such quantitative coincidence points to a common mechanism of reversal of the sign of the dipole potential for the ether and ester films despite the different structure of their heads. The mechanical properties and phase behaviors of these monolayers show that both fluorinated heads are less hydrated, suggesting that the change of the sign of Delta V could, at least partially, be related to different hydration water structure. The same negative contribution of the carbonyl bond in both TFEB and EB films contrasts with the generally accepted positive contribution of the C(delta+)=O(delta-) bond in condensed Langmuir monolayers of fatty acids, their alcohol esters, glycerides, and phospholipids but concurs with the theoretical analysis of Delta V of stearic acid monolayers. Both results question the literature values of the molecular dipole moments of these substances calculated via summation of bonds and atomic group contributions. Mixed monolayers of DFEE and DEE show smooth monotonic variation of Delta V from +450 to -235 mV, indicating a way for adjustment of the sign and magnitude of the dipole potential at the membrane-water boundary and regulation of such membrane behaviors as binding and translocation rate of hydrophobic ions and ion-carriers, adsorption and penetration of amphiphilic peptides, polarization of hydration water, and short-range repulsion. The interaction of the hydrophobic ions tetraphenylboron TPhB- and tetraphenylphosphonium TPhP+ with DFEE and DEE monolayers qualitatively follows the theory of binding of such ions to lipid bilayers, but the shifts Delta(Delta V) from the values obtained on water are much smaller than those for DPPC monolayers. This difference seems to be due to the solid (polycrystalline) character of the DFEE and DEE films that hampers the penetration of TPhB- and TPhP+ in the monolayers and reduces the attractive interaction with the hydrophobic moiety. This conclusion orients the future synthesis of amphiphiles with fluorinated heads to those which could form liquid-expanded Langmuir monolayers.     

Unusual reactivity of tris(pyrazolyl)borate zirconium benzyl complexes

The synthesis and reactivity of [Tp*Zr(CH2Ph)2][B(C6F5)4] (2, Tp* = HB(3,5-Me2pz)3, pz = pyrazolyl) have been explored to probe the possible role of Tp'MR2+ species in group 4 metal Tp'MCl3/MAO olefin polymerization catalysts (Tp' = generic tris(pyrazolyl)borate). The reaction of Tp*Zr(CH2Ph)3 (1) with [Ph3C][B(C6F5)4] in CD2Cl2 at -60 degrees C yields 2. 2 rearranges rapidly to [{(PhCH2)(H)B(mu-Me2pz)2}Zr(eta2-Me2pz)(CH2Ph)][B(C6F5)4] (3) at 0 degrees C. Both 2 and 3 are highly active for ethylene polymerization and alkyne insertion. Reaction of 2 with excess 2-butyne yields the double insertion product [Tp*Zr(CH2Ph)(CMe=CMeCMe=CMeCH2Ph)][B(C6F5)4] (4). Reaction of 3 with excess 2-butyne yields [{(PhCH2)(H)B(mu-Me2pz)2}Zr(Cp*)(eta2-Me2pz)][B(C6F5)4] (6, Cp* = C5Me5) via three successive 2-butyne insertions, intramolecular insertion, chain walking, and beta-Cp* elimination.     

Reaction of copper(II) with ferrocene and 1,1'-dimethylferrocene in aqueous acetonitrile: the copper(II/I) self-exchange rate

The kinetics of the reactions of copper(II) with ferrocene (Fc) and 1,1'-dimethylferrocene (Dmfc) have been studied at 25 degrees C in aqueous acetonitrile (AN) containing 50-97.5 vol % AN. With increasing % AN, the rate constant increases along with the driving-force for the reaction. The results are analyzed in terms of Marcus theory to estimate the Cu(II/I) electron self-exchange rate constant (k11) for the system. Over the solvent range studied, the calculated k11)changes from 1.1 x 10(-9) to 17 x 10(-9) M(-1) s(-1), with an average value of 5 x 10(-9). In addition, the structures of the trifluoromethanesulfonate salts of [Cu(AN)4]+, [Cu(OH2)2(AN)2]2+, and [Cu(AN)4]2+ are reported. It is found that the Cu-NCCH3 bond-length difference between the Cu(I) and Cu(II) oxidation states is only approximately 0.02 A.     

On the contribution of vibrational anharmonicity to the binding energies of water clusters

The second-order vibrational perturbation theory method has been used together with the B3LYP and MP2 electronic structure methods to investigate the effects of anharmonicity on the vibrational zero-point energy (ZPE) contributions to the binding energies of (H2O)n, n = 2-6, clusters. For the low-lying isomers of (H2O)6, the anharmonicity correction to the binding energy is calculated to range from -248 to -355 cm(-1). It is also demonstrated that although high-order electron correlation effects are important for the individual vibrational frequencies, they are relatively unimportant for the net ZPE contributions to the binding energies of water clusters.     

Design and synthesis of an isopenicillin N synthase mimic

Towards the aim of creating a functional mimic of isopenicillin N synthase, a small molecule designed to coordinate around iron(II) and model the enzyme active site has been prepared in nine synthetic steps from 2,6-bis(hydroxymethyl)pyridine, (S)-(+)-mandelic acid and pivaldehyde. One aspartate, two histidines and a water ligand in the natural enzyme are replaced by an α-hydroxy acid, pyridine and aniline in the model compound. Additionally, a free thiol designed to simulate the enzyme substrate, δ-(l-α-aminoadipoyl)-l-cysteinyl-d-valine, is linked to the ligand by a three carbon chain. We postulate that in the presence of molecular oxygen, the complex formed between this synthetic ligand and iron(II) will display oxidative chemistry similar to that observed in the active site of isopenicillin N synthase.     

End-labeled free-solution electrophoresis of DNA

DNA is a free-draining polymer. This subtle but "unfortunate" property of highly charged polyelectrolytes makes it impossible to separate nucleic acids by free-flow electrophoresis. This is why one must typically use a sieving matrix, such as a gel or an entangled polymer solution, in order to obtain some electrophoretic size separation. An alternative approach consists of breaking the charge to friction balance of free-draining DNA molecules. This can be achieved by labeling the DNA with a large, uncharged molecule (essentially a hydrodynamic parachute, which we also call a drag-tag) prior to electrophoresis; the resulting methodology is called end-labeled free-solution electrophoresis (ELFSE). In this article, we review the development of ELFSE over the last decade. In particular, we examine the theoretical concepts used to predict the ultimate performance of ELFSE for single-stranded (ssDNA) sequencing, the experimental results showing that ELFSE can indeed overcome the free-draining issue raised above, and the technological advances that are needed to speed the development of competitive ELFSE-based sequencing and separation technologies. Finally, we also review the reverse process, called free-solution conjugate electrophoresis (FSCE), wherein uncharged polymers of different sizes can be analyzed using a short DNA molecule as an electrophoretic engine.     

Highly regio- and stereoselective intramolecular 1,3-dipolar cycloadditions of norbornadiene-tethered nitrile oxides

[reaction: see text] Intramolecular cycloadditions with high regio- and stereocontrol are important methods for the efficient assembly of complex molecular structures. Efficient routes to the synthesis of norbornadiene-tethered nitrile oxides have been developed, and their intramolecular 1,3-dipolar cycloadditions were studied. The cycloadditions occurred in good yields for a variety of substrates and were found to be highly regio- and stereoselective.     

Catalytic Nitrene Transfer by an FeIV-Imido Complex Generated by a Comproportionation Process

Nitrene transfer reactions have emerged as one of the most powerful and versatile ways to insert an amine function to various kinds of hydrocarbon substrates. However, the mechanisms of nitrene generation have not been studied in depth albeit their formation is taken for granted in most cases without definitive evidence of their occurrence. In the present work, we compare the generation of tosylimido iron species and NTs transfer from Fe^II and Fe^III precursors where the metal is embedded in a tetracarbene macrocycle. Catalytic nitrene transfer to reference substrates (thioanisole, styrene, ethylbenzene and cyclohexane) revealed that the same active species was at play, irrespective of the ferrous versus ferric nature of the precursor. Through combination of spectroscopic (UV-visible, Mössbauer), ESI-MS and DFT studies, an Fe^IV tosylimido species was identified as the catalytically active species and was characterized spectroscopically and computationally. Whereas its formation from the Fe^II precursor was expected by a two-electron oxidative addition, its formation from an Fe^III precursor was unprecedented. Thanks to a combination of spectroscopic (UV-visible, EPR, Hyscore and Mössbauer), ESI-MS and DFT studies, we found that, when starting from the Fe^III precursor, an Fe^III tosyliodinane adduct was formed and decomposed into an Fe^V tosylimido species which generated the catalytically active Fe^IV tosylimide through a comproportionation process with the Fe^III precursor.