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In interfacing man-made electronic components with specifically folded biomacromolecules, the perturbative effects of junction structure on any signal generated should be considered. We report herein on the electron-transfer characteristics of the blue copper metalloprotein, azurin, as characterized at a refined level by conducting atomic force microscopy (C-AFM). Specifically, the modulation of current-voltage (I-V) behavior with compressional force has been examined. In the absence of assignable resonant electron tunneling within the confined bias region, from -1 to 1 V, the I-V behavior was analyzed with a modified Simmons formula. To interpret the variation of tunneling barrier height and barrier length obtained by fitting with the modified Simmons formula, an atom packing density model associated with protein mechanical deformation was proposed and simulated by molecular dynamics. The barrier heights determined at the minimum forces necessary for stable electrical contact correlate reasonably well with those estimated from bulk biophysical (electroanalytical and photochemical) experiments previously reported. At higher forces, the tunnel barrier decreases to fall within the range observed with saturated organic systems. Molecular dynamics simulations revealed changes in secondary structure and atomic density of the protein with respect to compression. At low compression, where transport measurements are made, secondary structure is retained, and atomic packing density is observed to increase linearly with force. These predictions, and those made at higher compression, are consistent with both experimentally observed modulations of tunneling barrier height with applied force and the applicability of the atom packing density model of electron tunneling in proteins to molecular-level analyses.

We present a study of the structural and electronic properties of Pyrite FeS 2 performed using both localized basis set and plane wave first-principles calculations Calculations performed using either Gaussian or plane wave basis sets yield results consistent with each other. Small differences in the computed geometries are shown to be due to the choice of pseudopotential employed in the plane wave calculations. The computed densities of states are relatively insensitive to the form of basis set and pseudopotential used. We find that density functional and hybrid approaches predict properties such as geometry and densities of states in good agreement with experiment hut that the agreement between the results from Hartree-Fock (HF) calculations and experiment is poor. The reasons for the poor performance of HF theory in this system are examined and are found to be due to the neglect of electronic correlation.

Cyclic peptides are increasingly being shown as powerful inhibitors of fibril formation, and have the potential to be therapeutic agents for combating many debilitating amyloid-related diseases. One such example is a cyclic peptide derivative from the human apolipoprotein C-II, which has the ability to inhibit fibril formation by the fibrillogenic peptide apoC-II(60–70). Using classical molecular dynamics and electronic structure calculations, we were able to provide insight into the interaction between the amyloidogenic peptide apoC-II(60–70) and its cyclic derivative, cyc(60–70). Our results showed that cyc(60–70) induced increased flexibility in apoC-II(60–70), suggesting that one mechanism by which cyc(60–70) inhibits fibrillisation is by destabilising apoC-II(60–70) structure, rendering it incapable of adopting fibril favouring conformations. In contrast, cyc(60–70) shows less flexibility upon binding to apoC-II(60–70), which is predominantly mediated by hydrophobic interactions between the aromatic rings of the peptides. This effectively creates a cap around the fibril-forming region of apoC-II(60–70) and generates an outer hydrophilic shell that discourages further apoC-II(60–70) peptide self-association. We showed that apoC-II(60–70) exhibited stronger binding affinity for the hydrophobic face of cyc(60–70) and weakest binding affinity for the hydrophilic side. This suggests that cyc(60–70) can be an effective fibril inhibitor due to its amphipathic character, like that of the "Janus"-type particles. This property can be exploited in the design of specific inhibitors of amyloid fibril formation.

a-Conotoxin AuIB, a disulfide-bonded peptide of 15 amino acids with a 4/6 intercysteine spacing, inhibits the a3b4 nicotinic acetylcholine receptor (nAChR) subtype, which is a predominant subtype in the peripheral nervous system. The ribbon isomer of AuIB has been shown to be more potent than the native AuIB (globular isomer) and to discriminate between stoichiometries of a3b4 nAChRs expressed in Xenopus oocytes. AuIB also inhibits high voltage-activated N-type calcium channels in rat DRG neurons via the activation of G protein-coupled GABAB receptors. Interestingly, a-conotoxin AuIB possesses analgesic activity in vivo and, therefore, may be a potential drug lead for treating chronic and neuropathic pain. In order to develop improved drugs void of side effects, it is necessary to understand the molecular determinants of AuIB binding to its putative targets: GABAB receptor vs. a3b4 nAChR. The aim of the present study was to determine the critical amino acid residues of AuIB responsible for its interaction with a3b4 nAChRs. Alanine scanning mutagenesis of the native AuIB peptide was carried out to construct AuIB alanine-substituted analogues which were tested in Xenopus oocytes expressing rat a3 and b4 subunits. Two-electrode voltage clamp recording was used to assess the effect of AuIB and its analogues (3 mM) on the ACh-evoked current amplitude. Phenylalanine to alanine mutation at position 9 of AuIB abolished inhibition of a3b4 nAChRs, whereas substitution of glycine at position 1 with alanine significantly reduced inhibition (18.0 p 10.5%, n = 3) compared to native AuIB (48.5 p 6.9%, n = 7) (p l 0.05). Mutation of residues other than cysteine and proline, which are known to disrupt the tertiary structure of a-conotoxins, did not significantly reduce the inhibition of ACh-evoked currents compared to native AuIB. Subsequent homology modelling/docking simulation was performed using a homology model of the rat (a3)2(b4)3 nAChR. The results suggest that interaction of AuIB Phe9 with Lys81 and Trp79 on the b4 nAChR subunit may be essential for AuIB binding/interaction on a3b4 nAChR. In conclusion, we have identified phenylalanine at position 9 as the critical residue for specific interaction of AuIB with the a3b4 nAChR. Future studies using site-directed mutagenesis of the b4 subunit are required to further dissect the mechanism of AuIB binding/interaction on a3b4 nAChR.

To the editor: We read with interest the article by Niesters et al. describing a pilot study to share enterovirus sequence data within the Netherlands for epidemiological investigation [1]. As the authors note, nucleotide sequence data can extend the identification of virus serotype to the tracing of disease transmission patterns through phylogenetic analysis. The article referred to use of a web-based typing tool for enteroviruses and noroviruses based on BLAST analysis followed by a neighbor-joining phylogeny. We believe such analyses can be further enhanced through the inclusion of temporal and geographical discrete variables for the inference of phylogeny (phylogeography). In particular, the application of Bayesian inference to phylogeography offers several advantages, such as the capacity to explicitly account for parameter uncertainty, reducing potential model bias, especially where data are scarce. This approach was referred to in the same issue of Eurosurveillance by Carrico et al. for bacterial molecular epidemiology [2] and has been successfully applied to virological studies for avian influenza A(H5N1) and rabies [3]. Carrico et al. make reference to the computational demands of such methods [2] and indeed, this is an important consideration. From our experience, the use of commodity graphics processing units combined with appropriate parallel threading software extensions can overcome some of the limitations imposed by high computational demand at low cost [4].