Theoretical investigation of infrared spectra and pocket dynamics of photodissociated carbonmonoxy myoglobin

Molecular dynamics simulations of the photodissociated state of carbonmonoxy myoglobin (MbCO) are presented using a fluctuating charge model for CO. A new three-point charge model is fitted to high-level ab initio calculations of the dipole and quadrupole moment functions taken from the literature. The infrared spectrum of the CO molecule in the heme pocket is calculated using the dipole moment time autocorrelation function and shows good agreement with experiment. In particular, the new model reproduces the experimentally observed splitting of the CO absorption spectrum. The splitting of 3–7 cm−1 (compared to the experimental value of 10 cm−1) can be directly attributed to the two possible orientations of CO within the docking site at the edge of the distal heme pocket (the B states), as previously suggested on the basis of experimental femtosecond time-resolved infrared studies. Further information on the time evolution of the position and orientation of the CO molecule is obtained and analyzed. The calculated difference in the free energy between the two possible orientations (Fe···CO and Fe···OC) is 0.3 kcal mol−1 and agrees well with the experimentally estimated value of 0.29 kcal mol−1. A comparison of the new fluctuating charge model with an established fixed charge model reveals some differences that may be critical for the correct prediction of the infrared spectrum and energy barriers. The photodissociation of CO from the myoglobin mutant L29F using the new model shows rapid escape of CO from the distal heme pocket, in good agreement with recent experimental data. The effect of the protein environment on the multipole moments of the CO ligand is investigated and taken into account in a refined model. Molecular dynamics simulations with this refined model are in agreement with the calculations based on the gas-phase model. However, it is demonstrated that even small changes in the electrostatics of CO alter the details of the dynamics.

A new interpretation of the bonding properties and UV–vis spectra of [M3(CO)12] clusters (M = Ru, Os): a TD-DFT study

DFT and TD-DFT calculations (ADF program) were performed in order to analyze the electronic structure of the [M-3(CO)(12)] clusters (M = Ru, Os) and interpret their electronic spectra. The highest occupied molecular orbitals are M-M bonding (sigma) involving different M-M bonds, both for Ru and Os. They participate in low-energy excitation processes and their depopulation should weaken M-M bonds in general. While the LUMO is M-NI and M-CO anti-bonding (sigma*), the next, higher-lying empty orbitals have a main contribution from CO (pi*) and either a small (Ru) or an almost negligible one (Os) from the metal atoms. The main difference between the two clusters comes from the different nature of these low-energy unoccupied orbitals that have a larger metal contribution in the case of ruthenium. The photochemical reactivity of the two clusters is reexamined and compared to earlier interpretations.

Adaptive alarm processor for fault diagnosis on power transmission networks

The authors describe a learning classifier system (LCS) which employs genetic algorithms (GA) for adaptive online diagnosis of power transmission network faults. The system monitors switchgear indications produced by a transmission network, reporting fault diagnoses on any patterns indicative of faulted components. The system evaluates the accuracy of diagnoses via a fault simulator developed by National Grid Co. and adapts to reflect the current network topology by use of genetic algorithms.

Infrared absorption spectra, radiative efficiencies, and global warming potentials of perfluorocarbons: Comparison between experiment and theory

Experimentally and theoretically determined infrared spectra are reported for a series of straight-chain perfluorocarbons: C2F6, C3F8, C4F10, C5F12, C6F14, and C8F18. Theoretical spectra were determined using both density functional (DFT) and ab initio methods. Radiative efficiencies (REs) were determined using the method of Pinnock et al. (1995) and combined with atmospheric lifetimes from the literature to determine global warming potentials (GWPs). Theoretically determined absorption cross sections were within 10% of experimentally determined values. Despite being much less computationally expensive, DFT calculations were generally found to perform better than ab initio methods. There is a strong wavenumber dependence of radiative forcing in the region of the fundamental C-F vibration, and small differences in wavelength between band positions determined by theory and experiment have a significant impact on the REs. We apply an empirical correction to the theoretical spectra and then test this correction on a number of branched chain and cyclic perfluoroalkanes. We then compute absorption cross sections, REs, and GWPs for an additional set of perfluoroalkenes.

Precision of quasi-optical null-balanced bridge techniques for transmission and reflection coefficient measurements

The precision of quasioptical null-balanced bridge instruments for transmission and reflection coefficient measurements at millimeter and submillimeter wavelengths is analyzed. A Jones matrix analysis is used to describe the amount of power reaching the detector as a function of grid angle orientation, sample transmittance/reflectance and phase delay. An analysis is performed of the errors involved in determining the complex transmission and reflection coefficient after taking into account the quantization error in the grid angle and micrometer readings, the transmission or reflection coefficient of the sample, the noise equivalent power of the detector, the source power and the post-detection bandwidth. For a system fitted with a rotating grid with resolution of 0.017 rad and a micrometer quantization error of 1 μm, a 1 mW source, and a detector with a noise equivalent power 5×10−9 W Hz−1/2, the maximum errors at an amplitude transmission or reflection coefficient of 0.5 are below ±0.025.

Tuning the self-assembly of the bioactive dipeptide L-carnosine by incorporation of a bulky aromatic substituent

The dipeptide L-carnosine has a number of important biological properties. Here, we explore the effect of attachment of a bulky hydrophobic aromatic unit, Fmoc [N-(fluorenyl-9-methoxycarbonyl)] on the self-assembly of Fmoc-L-carnosine, i.e., Fmoc-Beta-alanine-histidine (Fmoc-BetaAH). It is shown that Fmoc-BetaAH forms well-defined amyloid fibril containing Beta sheets above a critical aggregation concentration, which is determined from pyrene and ThT fluorescence experiments. Twisted fibrils were imaged by cryogenic transmission electron microscopy. The zinc-binding properties of Fmoc-BetaAH were investigated by FTIR and Raman spectroscopy since the formation of metal ion complexes with the histidine residue in carnosine is well-known, and important to its biological roles. Observed changes in the spectra may reflect differences in the packing of the Fmoc-dipeptides due to electrostatic interactions. Cryo-TEM shows that this leads to changes in the fibril morphology. Hydrogelation is also induced by addition of an appropriate concentration of zinc ions. Our work shows that the Fmoc motif can be employed to drive the self-assembly of carnosine into amyloid fibrils.

Inhibition of synaptic transmission and G protein modulation by synthetic CaV2.2 Ca2+ channel peptides

Abstract: Modulation of presynaptic voltage-dependent Ca+ channels is a major means of controlling neurotransmitter release. The CaV 2.2 Ca2+ channel subunit contains several inhibitory interaction sites for Gβγ subunits, including the amino terminal (NT) and I–II loop. The NT and I–II loop have also been proposed to undergo a G protein-gated inhibitory interaction, whilst the NT itself has also been proposed to suppress CaV 2 channel activity. Here, we investigate the effects of an amino terminal (CaV 2.2[45–55]) ‘NT peptide’ and a I–II loop alpha interaction domain (CaV 2.2[377–393]) ‘AID peptide’ on synaptic transmission, Ca2+ channel activity and G protein modulation in superior cervical ganglion neurones (SCGNs). Presynaptic injection of NT or AID peptide into SCGN synapses inhibited synaptic transmission and also attenuated noradrenaline-induced G protein modulation. In isolated SCGNs, NT and AID peptides reduced whole-cell Ca2+ current amplitude, modified voltage dependence of Ca2+ channel activation and attenuated noradrenaline-induced G protein modulation. Co-application of NT and AID peptide negated inhibitory actions. Together, these data favour direct peptide interaction with presynaptic Ca2+ channels, with effects on current amplitude and gating representing likely mechanisms responsible for inhibition of synaptic transmission. Mutations to residues reported as determinants of Ca2+ channel function within the NT peptide negated inhibitory effects on synaptic transmission, Ca2+ current amplitude and gating and G protein modulation. A mutation within the proposed QXXER motif for G protein modulation did not abolish inhibitory effects of the AID peptide. This study suggests that the CaV 2.2 amino terminal and I–II loop contribute molecular determinants for Ca2+ channel function; the data favour a direct interaction of peptides with Ca2+ channels to inhibit synaptic transmission and attenuate G protein modulation. Non-technical summary: Nerve cells (neurones) in the body communicate with each other by releasing chemicals (neurotransmitters) which act on proteins called receptors. An important group of receptors (called G protein coupled receptors, GPCRs) regulate the release of neurotransmitters by an action on the ion channels that let calcium into the cell. Here, we show for the first time that small peptides based on specific regions of calcium ion channels involved in GPCR signalling can themselves inhibit nerve cell communication. We show that these peptides act directly on calcium channels to make them more difficult to open and thus reduce calcium influx into native neurones. These peptides also reduce GPCR-mediated signalling. This work is important in increasing our knowledge about modulation of the calcium ion channel protein; such knowledge may help in the development of drugs to prevent signalling in pathways such as those involved in pain perception.

Power transmission network simulation for fault diagnosis

The authors discuss an implementation of an object oriented (OO) fault simulator and its use within an adaptive fault diagnostic system. The simulator models the flow of faults around a power network, reporting switchgear indications and protection messages that would be expected in a real fault scenario. The simulator has been used to train an adaptive fault diagnostic system; results and implications are discussed.

Origin of electronic absorption spectra of MLCT-excited and one-electron reduced 2,2′-bipyridine and 1,10-phenanthroline complexes

UV–Vis absorption spectra of one-electron reduction products and 3MLCT excited states of [ReICl(CO)3- (N,N)] (N,N = 2,20-bipyridine, bpy; 1,10-phenanthroline, phen) have been measured by low-temperature spectroelectrochemistry and UV–Vis transient absorption spectroscopy, respectively, and assigned by open-shell TD-DFT calculations. The characters of the electronic transitions are visualized and analyzed using electron density redistribution maps. It follows that reduced and excited states can be approximately formulated as [ReICl(CO)3(N,Nÿ)]ÿ and ⁄[ReIICl(CO)3(N,Nÿ)], respectively. UV–Vis spectra of the reduced complexes are dominated by IL transitions, plus weaker MLCT contributions. Excited-state spectra show an intense band in the UV region of 50% IL origin mixed with LMCT (bpy, 373 nm) or MLCT (phen, 307 nm) excitations. Because of the significant IL contribution, this spectral feature is akin to the principal IL band of the anions. In contrast, the excited-state visible spectral pattern arises from predominantly LMCT transitions, any resemblance with the reduced-state visible spectra being coincidental. The Re complexes studied herein are representatives of a broad class of metal a-diimines, for which similar spectroscopic behavior can be expected.