Improvement of protein structure comparison using a structural alphabet

The three dimensional structure of a protein provides major insights into its function. Protein structure comparison has implications in functional and evolutionary studies. A structural alphabet (SA) is a library of local protein structure prototypes that can abstract every part of protein main chain conformation. Protein Blocks (PBS) is a widely used SA, composed of 16 prototypes, each representing a pentapeptide backbone conformation defined in terms of dihedral angles. Through this description, the 3D structural information can be translated into a 1D sequence of PBs. In a previous study, we have used this approach to compare protein structures encoded in terms of PBs. A classical sequence alignment procedure based on dynamic programming was used, with a dedicated PB Substitution Matrix (SM). PB-based pairwise structural alignment method gave an excellent performance, when compared to other established methods for mining. In this study, we have (i) refined the SMs and (ii) improved the Protein Block Alignment methodology (named as iPBA). The SM was normalized in regards to sequence and structural similarity. Alignment of protein structures often involves similar structural regions separated by dissimilar stretches. A dynamic programming algorithm that weighs these local similar stretches has been designed. Amino acid substitutions scores were also coupled linearly with the PB substitutions. iPBA improves (i) the mining efficiency rate by 6.8% and (ii) more than 82% of the alignments have a better quality. A higher efficiency in aligning multi-domain proteins could be also demonstrated. The quality of alignment is better than DALI and MUSTANG in 81.3% of the cases. Thus our study has resulted in an impressive improvement in the quality of protein structural alignment. (C) 2011 Elsevier Masson SAS. All rights reserved.

A Nonlinear Voltage Regulator With One Tunable Parameter for Multimachine Power Systems

This paper proposes a nonlinear voltage regulator with one tunable parameter for multimachine power systems. Based on output feedback linearization, this regulator can achieve simultaneous voltage regulation and small-signal performance objectives. Conventionally output feedback linearization has been used for voltage regulator design by taking infinite bus voltage as reference. Unfortunately, this controller has poor small-signal performance and cannot be applied to multimachine systems without the estimation of the equivalent external reactance seen from the generator. This paper proposes a voltage regulator design by redefining the rotor angle at each generator with respect to the secondary voltage of the step-up transformer as reference instead of a common synchronously rotating reference frame. Using synchronizing and damping torques analysis, we show that the proposed voltage regulator achieves simultaneous voltage regulation and damping performance over a range of system and operating conditions by controlling the relative angle between the generator internal voltage angle delta and the secondary voltage of the step up transformer. The performance of the proposed voltage regulator is evaluated on a single machine infinite bus system and two widely used multimachine test systems.

The biological and structural characterization of Mycobacterium tuberculosis UvrA provides novel insights into its mechanism of action

Mycobacterium tuberculosis is an extremely well adapted intracellular human pathogen that is exposed to multiple DNA damaging chemical assaults originating from the host defence mechanisms. As a consequence, this bacterium is thought to possess highly efficient DNA repair machineries, the nucleotide excision repair (NER) system amongst these. Although NER is of central importance to DNA repair in M. tuberculosis, our understanding of the processes in this species is limited. The conserved UvrABC endonuclease represents the multi-enzymatic core in bacterial NER, where the UvrA ATPase provides the DNA lesion-sensing function. The herein reported genetic analysis demonstrates that M. tuberculosis UvrA is important for the repair of nitrosative and oxidative DNA damage. Moreover, our biochemical and structural characterization of recombinant M. tuberculosis UvrA contributes new insights into its mechanism of action. In particular, the structural investigation reveals an unprecedented conformation of the UvrB-binding domain that we propose to be of functional relevance. Taken together, our data suggest UvrA as a potential target for the development of novel anti-tubercular agents and provide a biochemical framework for the identification of small-molecule inhibitors interfering with the NER activity in M. tuberculosis.

Lamb wave based identification and parameter estimation of corrosion in metallic plate structure using a circular PWAS array

A circular array of Piezoelectric Wafer Active Sensor (PWAS) has been employed to detect surface damages like corrosion using lamb waves. The array consists of a number of small PWASs of 10 mm diameter and 1 mm thickness. The advantage of a circular array is its compact arrangement and large area of coverage for monitoring with small area of physical access. Growth of corrosion is monitored in a laboratory-scale set-up using the PWAS array and the nature of reflected and transmitted Lamb wave patterns due to corrosion is investigated. The wavelet time-frequency maps of the sensor signals are employed and a damage index is plotted against the damage parameters and varying frequency of the actuation signal (a windowed sine signal). The variation of wavelet coefficient for different growth of corrosion is studied. Wavelet coefficient as function of time gives an insight into the effect of corrosion in time-frequency scale. We present here a method to eliminate the time scale effect which helps in identifying easily the signature of damage in the measured signals. The proposed method becomes useful in determining the approximate location of the corrosion with respect to the location of three neighboring sensors in the circular array. A cumulative damage index is computed for varying damage sizes and the results appear promising.

Viscoelastic phenomenology based structure assignment for closed-loop vibration control of a beam with sensors and actuators

In this paper we incorporate a novel approach to synthesize a class of closed-loop feedback control, based on the variational structure assignment. Properties of a viscoelastic system are used to design an active feedback controller for an undamped structural system with distributed sensor, actuator and controller. Wave dispersion properties of onedimensional beam system have been studied. Efficiency of the chosen viscoelastic model in enhancing damping and stability properties of one-dimensional viscoelastic bar have been analyzed. The variational structure is projected on a solution space of a closed-loop system involving a weakly damped structure with distributed sensor and actuator with controller. These assign the phenomenology based internal strain rate damping parameter of a viscoelastic system to the usual elastic structure but with active control. In the formulation a model of cantilever beam with non-collocated actuator and sensor has been considered. The formulation leads to the matrix identification problem of two dynamic stiffness matrices. The method has been simplified to obtain control system gains for the free vibration control of a cantilever beam system with collocated actuator-sensor, using quadratic optimal control and pole-placement methods.

Accurate Parameter Estimation of Contaminant Transport Inverse Problem using Paartaicle Swarm Optimization

Swarm Intelligence techniques such as particle swarm optimization (PSO) are shown to be incompetent for an accurate estimation of global solutions in several engineering applications. This problem is more severe in case of inverse optimization problems where fitness calculations are computationally expensive. In this work, a novel strategy is introduced to alleviate this problem. The proposed inverse model based on modified particle swarm optimization algorithm is applied for a contaminant transport inverse model. The inverse models based on standard-PSO and proposed-PSO are validated to estimate the accuracy of the models. The proposed model is shown to be out performing the standard one in terms of accuracy in parameter estimation. The preliminary results obtained using the proposed model is presented in this work.

Halogen Bonding and Structural Modularity in 2,3,4-and 3,4,5-Trichlorophenol

The crystal structure of 3,4,5-trichlorophenol contains hydrogen bonded domains that occur respectively in the structures of 4-chlorophenol and 3,5-dichlorophenol. Such modularity is also seen in 2,3,4-trichlorophenol. These structures, and those of the six isomeric dichlorophenols, illustrate the importance of halogen bonding as a structure determining interaction.

Structural Variability in the Monofluoroethynylbenzenes Mediated through Interactions Involving ``Organic'' Fluorine

Competition among weak intermolecular interactions can lead to polymorphism, the appearance of various crystalline forms of a substance with comparable cohesive energies. The crystal structures of 2-fluorophenylacetylene (2FPA) and 3-fluorophenylacetylene (3FPA), both of which are liquids at ambient conditions, have been determined by in situ cryocrystallization. Both compounds exhibit dimorphs, with one of the forms observed in common, P2(1), Z = 2 and the other form being Pna2(1), Z = 4 for 2FPA and P2(1)/c, Z = 12 for 3FPA. Variations in the crystal structures of the dimorphs of each of these compounds arise from subtle differences in the way in which weak intermolecular interactions such as C-H center dot center dot center dot pi and C-H center dot center dot center dot F are manifested. The interactions involving ``organic'' fluorine, are entirely different from those in the known structure of 4-fluorophenylacetylene (4FPA), space group P2(1)/c, Z = 4. The commonalities and differences in these polymorphs of 2FPA and 3FPA have been analyzed in terms of supramolecular synthons and extended long-range synthon aufbau module (LSAM) patterns. These structures are compared with the three polymorphs of phenylacetylene, in terms of the T-shaped C-H center dot center dot center dot pi interaction, a feature common to all these structures.