Allosteric Communication in Cysteinyl tRNA Synthetase A NETWORK OF DIRECT AND INDIRECT READOUT

Protein structure networks are constructed for the identification of long-range signaling pathways in cysteinyl tRNA synthetase (CysRS). Molecular dynamics simulation trajectory of CysRS-ligand complexes were used to determine conformational ensembles in order to gain insight into the allosteric signaling paths. Communication paths between the anticodon binding region and the aminoacylation region have been identified. Extensive interaction between the helix bundle domain and the anticodon binding domain, resulting in structural rigidity in the presence of tRNA, has been detected. Based on the predicted model, six residues along the communication paths have been examined by mutations (single and double) and shown to mediate a coordinated coupling between anticodon recognition and activation of amino acid at the active site. This study on CysRS clearly shows that specific key residues, which are involved in communication between distal sites in allosteric proteins but may be elusive in direct structure analysis, can be identified from dynamics of protein structure networks.

Analysis of a linear one-dimensional active noise control system by means of block diagrams and transfer functions

In arriving at the ideal filter transfer function for an active noise control system in a duct, the effect of the auxiliary sources (generally loudspeakers) on the waves generated by the primary source has invariably been neglected in the existing literature, implying a rigid wall or infinite impedance. The present paper presents a fairly general analysis of a linear one-dimensional noise control system by means of block diagrams and transfer functions. It takes into account the passive as well as active role of a terminal primary source, wall-mounted auxiliary source, open duct radiation impedance, and the effects of mean flow and damping. It is proved that the pressure generated by a source against a load impedance can be looked upon as a sum of two pressure waves, one generated by the source against an anechoic termination and the other by reflecting the rearward wave (incident on the source) off the passive source impedance. Application of this concept is illustrated for both the types of sources. A concise closed-form expression for the ideal filter transfer function is thus derived and discussed. Finally, the dynamics of an adaptive noise control system is discussed briefly, relating its standing-wave variables and transfer functions with those of the progressive-wave model presented here.

A Novel VSI- and CSI-Fed Active-Reactive Induction Motor Drive with Sinusoidal Voltages and Currents

Till date load-commutated inverter (LCI)-fed synchronous motor drive configuration is popular in high power applications (>10 MW). The leading power factor operation of synchronous motor by excitation control offers this simple and rugged drive structure. On the contrary, LCI-fed induction motor drive is absent as it always draws lagging power factor current. Therefore, complicated commutation circuit is required to switch off thyristors for a current source inverter (CSI)-driven induction motor. It poses the major hindrance to scale up the power rating of CSI-fed induction motor drive. Anew power topology for LCI-fed induction motor drive for medium-voltage drive application is proposed. A new induction machine (active-reactive induction machine) with two sets of three-phase winding is introduced as a drive motor. The proposed power configuration ensures sinusoidal voltage and current at the motor terminals. The total drive power is shared among a thyristor-based LCI, an insulated gate bipolar transistor (IGBT)-based two-level voltage source inverter (VSI), and a three-level VSI. The benefits of SCRs and IGBTs are explored in the proposed drive. Experimental results from a prototype drive verify the basic concepts of the drive.

Active current and potential transducers

This paper advocates the use of active current and potential transducers for proper utilisation of fast protective relays. The active current transducer faithfully transforms the primary current containing a slowly decaying d.c. component, thereby providing a good transient response. The active potential transducer helps in fast extinction of ferroresonance oscillations. Results oflaboratory investigations are also presented.

Alkylation of toluene by methanol over alkali exchanged zeolite-X: side chain versus ring alkylation

The ring versus side-chain alkylation of toluene with methanol over alkali-exchanged zeolite-X of differing basicity has been investigated by in situ infrared spectroscopy and TPD measurements. Over the basic Cs-exchanged zeolite the product of alkylation is styrene/ethylbenzene while over the acidic Li-exchanged zeolite ring alkylation occurs to give mainly xylene as the product. FTIR and TPD investigations reveal that, the key difference in the two types of alkylation processes lies in the state of the adsorbed methanol present at higher temperatures in the zeolite. In basic zeolites, methanol decomposes to formaldehyde and formates. The former is the key ‘side-chain’ alkylating species that leads to the formation of styrene. In the acidic zeolites it is shown that methanol bound to the acid sites plays an active role in the ‘ring alkylation’ of toluene to xylene.

Density matrix renormalization group algorithm for Bethe lattices of spin-1/2 or spin-1 sites with Heisenberg antiferromagnetic exchange

A density matrix renormalization group (DMRG) algorithm is presented for the Bethe lattice with connectivity Z = 3 and antiferromagnetic exchange between nearest-neighbor spins s = 1/2 or 1 sites in successive generations g. The algorithm is accurate for s = 1 sites. The ground states are magnetic with spin S(g) = 2(g)s, staggered magnetization that persists for large g > 20, and short-range spin correlation functions that decrease exponentially. A finite energy gap to S > S(g) leads to a magnetization plateau in the extended lattice. Closely similar DMRG results for s = 1/2 and 1 are interpreted in terms of an analytical three-site model.

Dimethyl sulfoxide induced structural transformations and non-monotonic concentration dependence of conformational fluctuation around active site of lysozyme

Experimental studies have observed significant changes in both structure and function of lysozyme (and other proteins) on addition of a small amount of dimethyl sulfoxide (DMSO) in aqueous solution. Our atomistic molecular dynamic simulations of lysozyme in water-DMSO reveal the following sequence of changes on increasing DMSO concentration. (i) At the initial stage (around 5% DMSO concentration) protein's conformational flexibility gets markedly suppressed. From study of radial distribution functions, we attribute this to the preferential solvation of exposed protein hydrophobic residues by the methyl groups of DMSO. (ii) In the next stage (10-15% DMSO concentration range), lysozome partially unfolds accompanied by an increase both in fluctuation and in exposed protein surface area. (iii) Between 15-20% concentration ranges, both conformational fluctuation and solvent accessible protein surface area suddenly decrease again indicating the formation of an intermediate collapse state. These results are in good agreement with near-UV circular dichroism (CD) and fluorescence studies. We explain this apparently surprising behavior in terms of a structural transformation which involves clustering among the methyl groups of DMSO. (iv) Beyond 20% concentration of DMSO, the protein starts its final sojourn towards the unfolding state with further increase in conformational fluctuation and loss in native contacts. Most importantly, analysis of contact map and fluctuation near the active site reveal that both partial unfolding and conformational fluctuations are centered mostly on the hydrophobic core of active site of lysozyme. Our results could offer a general explanation and universal picture of the anomalous behavior of protein structure-function observed in the presence of cosolvents (DMSO, ethanol, tertiary butyl alcohol, dioxane) at their low concentrations. (C) 2012 American Institute of Physics. [http://dx.doi.org/10.1063/1.3694268]

Smart polymer mediated purification and recovery of active proteins from inclusion bodies

Obtaining correctly folded proteins from inclusion bodies of recombinant proteins expressed in bacterial hosts requires solubilization with denaturants and a refolding step. Aggregation competes with the second step. Refolding of eight different proteins was carried out by precipitation with smart polymers. These proteins have different molecular weights, different number of disulfide bridges and some of these are known to be highly prone to aggregation. A high throughput refolding screen based upon fluorescence emission maximum around 340 nm (for correctly folded proteins) was developed to identify the suitable smart polymer. The proteins could be dissociated and recovered after the refolding step. The refolding could be scaled up and high refolding yields in the range of 8 mg L-1 (for CD4D12, the first two domains of human CD4) to 58 mg L-1 (for malETrx, thioredoxin fused with signal peptide of maltose binding protein) were obtained. Dynamic light scattering (DLS) showed that polymer if chosen correctly acted as a pseuclochaperonin and bound to the proteins. It also showed that the time for maximum binding was about 50 min which coincided with the time required for incubation (with the polymer) before precipitation for maximum recovery of folded proteins. The refolded proteins were characterized by fluorescence emission spectra, circular dichroism (CD) spectroscopy, melting temperature (T-m), and surface hydrophobicity measurement by ANS (8-anilinol-naphthalene sulfonic acid) fluorescence. Biological activity assay for thioredoxin and fluorescence based assay in case of maltose binding protein (MBP) were also carried out to confirm correct refolding. (C) 2012 Elsevier B.V. All rights reserved.

Enhancement of circular differential deflection of light in an optically active medium

In this letter, we investigate the circular differential deflection of a light beam refracted at the interface of an optically active medium. We show that the difference between the angles of deviation of the two circularly polarized components of the transmitted beam is enhanced manyfold near total internal reflection, which suggests a simple way of increasing the limit of detection of chiro-optical measurements. (C) 2012 Optical Society of America

Solvent effect on the fluorescence quenching of biologically active carboxamide by aniline and carbon tetrachloride in different solvents using S-V plots

The fluorescence quenching studies of carboxamide namely (E)-N-(3-Chlorophenyl)-2-(3,4,5-trimethoxybenzylideneamino)-4,5,6,7 tetrahydrobenzob]thiophene-3-carboxamide ENCTTTC] by aniline and carbon tetrachloride in six different solvents namely toluene, cyclohexane, n-hexane, n-heptane, n-decane and n-pentane have been carried out at room temperature with a view to understand the quenching mechanisms. The Stern-Volmer (S-V) plots have been found to be nonlinear with a positive deviation for all the solvents studied. In order to interpret these results we have invoked the ground state complex formation and sphere of action static quenching models. Using these models various quenching rate parameters have been determined. The magnitudes of these parameters suggest that sphere of action static quenching model agrees well with the experimental results. Hence the positive deviation is attributed to the static and dynamic quenching. Further, with the use of Finite Sink approximation model, it was possible to check these bimolecular reactions as diffusion-limited and to estimate independently distance parameter R' and mutual diffusion coefficient D. Finally an effort has been made to correlate the values of R' and D with the values of the encounter distance R and the mutual coefficient D determined using the Edward's empirical relation and Stokes Einstein relation. (C) 2011 Elsevier B.V. All rights reserved.