Crystal structure of a putative aspartic proteinase domain of the Mycobacterium tuberculosis cell surface antigen PE_PGRS16

We report the crystal structure of the first prokaryotic aspartic proteinase-like domain identified in the genome of Mycobacterium tuberculosis. A search in the genomes of Mycobacterium species showed that the C-terminal domains of some of the PE family proteins contain two classic DT/SG motifs of aspartic proteinases with a low overall sequence similarity to HIV proteinase. The three-dimensional structure of one of them, Rv0977 (PE_PGRS16) of M. tuberculosis revealed the characteristic pepsinf-old and catalytic site architecture. However, the active site was completely blocked by the N-terminal His-tag. Surprisingly, the enzyme was found to be inactive even after the removal of the N-terminal His-tag. A comparison of the structure with pepsins showed significant differences in the critical substrate binding residues and in the flap tyrosine conformation that could contribute to the lack of proteolytic activity of Rv0977. (C) 2013 The Authors. Published by Elsevier B.V. on behalf of Federation of European Biochemical Societies. All rights reserved.

Role of the loop L-4,L-5 in allosteric regulation in mtHsp70s: in vivo significance of domain communication and its implications in protein translocation

Mitochondrial Hsp70 (mtHsp70) is essential for a vast repertoire of functions, including protein import, and requires effective interdomain communication for efficient partner-protein interactions. However, the in vivo functional significance of allosteric regulation in eukaryotes is poorly defined. Using integrated biochemical and yeast genetic approaches, we provide compelling evidence that a conserved substrate-binding domain (SBD) loop, L-4,L-5, plays a critical role in allosteric communication governing mtHsp70 chaperone functions across species. In yeast, a temperature-sensitive L-4,L-5 mutation (E467A) disrupts bidirectional domain communication, leading to compromised protein import and mitochondrial function. Loop L-4,L-5 functions synergistically with the linker in modulating the allosteric interface and conformational transitions between SBD and the nucleotide-binding domain (NBD), thus regulating interdomain communication. Second-site intragenic suppressors of E467A isolated within the SBD suppress domain communication defects by conformationally altering the allosteric interface, thereby restoring import and growth phenotypes. Strikingly, the suppressor mutations highlight that restoration of communication from NBD to SBD alone is the minimum essential requirement for effective in vivo function when primed at higher basal ATPase activity, mimicking the J-protein-bound state. Together these findings provide the first mechanistic insights into critical regions within the SBD of mtHsp70s regulating interdomain communication, thus highlighting its importance in protein translocation and mitochondrial biogenesis.

Multimodal therapy for complete regression of malignant melanoma using constrained nonlinear optimal dynamic inversion

Using a realistic nonlinear mathematical model for melanoma dynamics and the technique of optimal dynamic inversion (exact feedback linearization with static optimization), a multimodal automatic drug dosage strategy is proposed in this paper for complete regression of melanoma cancer in humans. The proposed strategy computes different drug dosages and gives a nonlinear state feedback solution for driving the number of cancer cells to zero. However, it is observed that when tumor is regressed to certain value, then there is no need of external drug dosages as immune system and other therapeutic states are able to regress tumor at a sufficiently fast rate which is more than exponential rate. As model has three different drug dosages, after applying dynamic inversion philosophy, drug dosages can be selected in optimized manner without crossing their toxicity limits. The combination of drug dosages is decided by appropriately selecting the control design parameter values based on physical constraints. The process is automated for all possible combinations of the chemotherapy and immunotherapy drug dosages with preferential emphasis of having maximum possible variety of drug inputs at any given point of time. Simulation study with a standard patient model shows that tumor cells are regressed from 2 x 107 to order of 105 cells because of external drug dosages in 36.93 days. After this no external drug dosages are required as immune system and other therapeutic states are able to regress tumor at greater than exponential rate and hence, tumor goes to zero (less than 0.01) in 48.77 days and healthy immune system of the patient is restored. Study with different chemotherapy drug resistance value is also carried out. (C) 2014 Elsevier Ltd. All rights reserved.

Single network adaptive critic aided dynamic inversion for optimal regulation and command tracking with online adaptation for enhanced robustness

To combine the advantages of both stability and optimality-based designs, a single network adaptive critic (SNAC) aided nonlinear dynamic inversion approach is presented in this paper. Here, the gains of a dynamic inversion controller are selected in such a way that the resulting controller behaves very close to a pre-synthesized SNAC controller in the output regulation sense. Because SNAC is based on optimal control theory, it makes the dynamic inversion controller operate nearly optimal. More important, it retains the two major benefits of dynamic inversion, namely (i) a closed-form expression of the controller and (ii) easy scalability to command tracking applications without knowing the reference commands a priori. An extended architecture is also presented in this paper that adapts online to system modeling and inversion errors, as well as reduced control effectiveness, thereby leading to enhanced robustness. The strengths of this hybrid method of applying SNAC to optimize an nonlinear dynamic inversion controller is demonstrated by considering a benchmark problem in robotics, that is, a two-link robotic manipulator system. Copyright (C) 2013 John Wiley & Sons, Ltd.

Frequency-domain stimulated and spontaneous light emission signals at molecular junctions

Using a diagrammatic superoperator formalism we calculate optical signals at molecular junctions where a single molecule is coupled to two metal leads which are held at different chemical potentials. The molecule starts in a nonequilibrium steady state whereby it continuously exchanges electrons with the leads with a constant electron flux. Expressions for frequency domain optical signals measured in response to continuous laser fields are derived by expanding the molecular correlation functions in terms of its many-body states. The nonunitary evolution of molecular states is described by the quantum master equation. (C) 2014 AIP Publishing LLC.

The Non-catalytic ``Cap Domain'' of a Mycobacterial Metallophosphoesterase Regulates Its Expression and Localization in the Cell

Despite highly conserved core catalytic domains, members of the metallophosphoesterase (MPE) superfamily perform diverse and crucial functions ranging from nucleotide and nucleic acid metabolism to phospholipid hydrolysis. Unique structural elements outside of the catalytic core called ``cap domains'' are thought to provide specialization to these enzymes; however, no directed study has been performed to substantiate this. The cap domain of Rv0805, an MPE from Mycobacterium tuberculosis, is located C-terminal to its catalytic domain and is dispensable for the catalytic activity of this enzyme in vitro. We show here that this C-terminal extension (CTE) mediates in vivo localization of the protein to the cell membrane and cell wall as well as modulates expression levels of Rv0805 in mycobacteria. We also demonstrate that Rv0805 interacts with the cell wall of mycobacteria, possibly with the mycolyl-arabinogalactan-peptidoglycan complex, by virtue of its C terminus, a hitherto unknown property of this MPE. Using a panel of mutant proteins, we identify interactions between active site residues of Rv0805 and the CTE that determine its association with the cell wall. Finally, we show that Rv0805 and a truncated mutant devoid of the CTE produce different phenotypic effects when expressed in mycobacteria. Our study thus provides a detailed dissection of the functions of the cap domain of an MPE and suggests that the repertoire of cellular functions of MPEs cannot be understood without exploring the modulatory effects of these subdomains.

Super-Resolution Reconstruction in Frequency-Domain Optical-Coherence Tomography Using the Finite-Rate-of-Innovation Principle

The standard approach to signal reconstruction in frequency-domain optical-coherence tomography (FDOCT) is to apply the inverse Fourier transform to the measurements. This technique offers limited resolution (due to Heisenberg's uncertainty principle). We propose a new super-resolution reconstruction method based on a parametric representation. We consider multilayer specimens, wherein each layer has a constant refractive index and show that the backscattered signal from such a specimen fits accurately in to the framework of finite-rate-of-innovation (FRI) signal model and is represented by a finite number of free parameters. We deploy the high-resolution Prony method and show that high-quality, super-resolved reconstruction is possible with fewer measurements (about one-fourth of the number required for the standard Fourier technique). To further improve robustness to noise in practical scenarios, we take advantage of an iterated singular-value decomposition algorithm (Cadzow denoiser). We present results of Monte Carlo analyses, and assess statistical efficiency of the reconstruction techniques by comparing their performance against the Cramer-Rao bound. Reconstruction results on experimental data obtained from technical as well as biological specimens show a distinct improvement in resolution and signal-to-reconstruction noise offered by the proposed method in comparison with the standard approach.

Time-Domain Approach to Estimate Series Capacitance of an Isolated Phase Winding of a Transformer

Information available in frequency response data is equivalently available in the time domain as a response due to an impulse excitation. The idea to pursue this equivalence to estimate series capacitance is linked to the well-known fact that under impulse excitation, the line/neutral current in a transformer has three distinct components, of which, the initial capacitive component is the first to manifest, followed by the oscillatory and inductive components. Of these, the capacitive component is temporally well separated from the rest-a crucial feature permitting its direct access and analysis. Further, the winding initially behaves as a pure capacitive network, so the initial component must obviously originate from only the (series and shunt) capacitances. With this logic, it should therefore be possible to estimate series capacitance, just by measuring the initial capacitive component of line current and the total shunt capacitance. The principle of the method and details of its implementation on two actual isolated transformerwindings (uniformly wound) are presented. For implementation, a low-voltage recurrent surge generator, a current probe, and a digital oscilloscope are all that is needed. The method is simple and requires no programming and needs least user intervention, thus paving the way for its widespread use.

Structure, interactions and evolutionary implications of a domain-swapped lectin dimer from Mycobacterium smegmatis

Crystal structure determination of the lectin domain of MSMEG_3662 from Mycobacterium smegmatis and its complexes with mannose and methyl-alpha-mannose, the first effort of its kind on a mycobacterial lectin, reveals a structure very similar to beta-prism II fold lectins from plant sources, but with extensive unprecedented domain swapping in dimer formation. The two subunits in a dimer often show small differences in structure, but the two domains, not always related by 2-fold symmetry, have the same structure. Each domain carries three sugar-binding sites, similar to those in plant lectins, one on each Greek key motif. The occurrence of beta-prism II fold lectins in bacteria, with characteristics similar to those from plants, indicates that this family of lectins is of ancient origin and had evolved into a mature system before bacteria and plants diverged. In plants, the number of binding sites per domain varies between one and three, whereas the number is two in the recently reported lectin domains from Pseudomonas putida and Pseudomonas aeruginosa. An analysis of the sequences of the lectins and the lectin domains shows that the level of sequence similarity among the three Greek keys in each domain has a correlation with the number of binding sites in it. Furthermore, sequence conservation among the lectins from different species is the highest for that Greek key which carries a binding site in all of them. Thus, it would appear that carbohydrate binding influences the course of the evolution of the lectin.

Grain and the concomitant ferroelectric domain size dependent physical properties of Ba0.85Ca0.15Zr0.1Ti0.9O3 ceramics fabricated using powders derived from oxalate precursor route

Fine powders comprising nanocrystallites of Ba0.85Ca0.15Zr0.1Ti0.9O3 (BCZT) were synthesized via oxalate precursor method, which facilitated to obtain homogenous and large grain sized ceramics at a lower sintering temperature. The compacted powders were sintered at various temperatures in the range of 1200 degrees C-1500 degrees C for an optimized duration of 10 h. Interestingly the one that was sintered at 1450 degrees C/10 h exhibited well resolved Morphotrophic Phase Boundary. The average grain size associated with this sample was 30 mu m accompanied by higher domain density mostly with 90 degrees twinning. These were believed to have significant contribution towards obtaining large strain of about 0.2% and piezoelectric coefficient as high as 563 pC/N. The maximum force that was generated by BCZT ceramic (having 30 mu m grain size) was found to be 161 MPa, which is much higher than that of known actuator materials such as PZT (40MPa) and NKN-5-LT (7 MPa). (C) 2014 AIP Publishing LLC.

CLAP: A web-server for automatic classification of proteins with special reference to multi-domain proteins

Background: The function of a protein can be deciphered with higher accuracy from its structure than from its amino acid sequence. Due to the huge gap in the available protein sequence and structural space, tools that can generate functionally homogeneous clusters using only the sequence information, hold great importance. For this, traditional alignment-based tools work well in most cases and clustering is performed on the basis of sequence similarity. But, in the case of multi-domain proteins, the alignment quality might be poor due to varied lengths of the proteins, domain shuffling or circular permutations. Multi-domain proteins are ubiquitous in nature, hence alignment-free tools, which overcome the shortcomings of alignment-based protein comparison methods, are required. Further, existing tools classify proteins using only domain-level information and hence miss out on the information encoded in the tethered regions or accessory domains. Our method, on the other hand, takes into account the full-length sequence of a protein, consolidating the complete sequence information to understand a given protein better. Results: Our web-server, CLAP (Classification of Proteins), is one such alignment-free software for automatic classification of protein sequences. It utilizes a pattern-matching algorithm that assigns local matching scores (LMS) to residues that are a part of the matched patterns between two sequences being compared. CLAP works on full-length sequences and does not require prior domain definitions. Pilot studies undertaken previously on protein kinases and immunoglobulins have shown that CLAP yields clusters, which have high functional and domain architectural similarity. Moreover, parsing at a statistically determined cut-off resulted in clusters that corroborated with the sub-family level classification of that particular domain family. Conclusions: CLAP is a useful protein-clustering tool, independent of domain assignment, domain order, sequence length and domain diversity. Our method can be used for any set of protein sequences, yielding functionally relevant clusters with high domain architectural homogeneity. The CLAP web server is freely available for academic use at http://nslab.mbu.iisc.ernet.in/clap/.

A nodal domain theorem for integrable billiards in two dimensions

Eigenfunctions of integrable planar billiards are studied - in particular, the number of nodal domains, nu of the eigenfunctions with Dirichlet boundary conditions are considered. The billiards for which the time-independent Schrodinger equation (Helmholtz equation) is separable admit trivial expressions for the number of domains. Here, we discover that for all separable and nonseparable integrable billiards, nu satisfies certain difference equations. This has been possible because the eigenfunctions can be classified in families labelled by the same value of m mod kn, given a particular k, for a set of quantum numbers, m, n. Further, we observe that the patterns in a family are similar and the algebraic representation of the geometrical nodal patterns is found. Instances of this representation are explained in detail to understand the beauty of the patterns. This paper therefore presents a mathematical connection between integrable systems and difference equations. (C) 2014 Elsevier Inc. All rights reserved.

Interaction of Sesbania mosaic virus (SeMV) RNA-dependent RNA polymerase (RdRp) with the p10 domain of polyprotein 2a and its implications in SeMV replication

Identification of viral encoded proteins that interact with RNA-dependent RNA polymerase (RdRp) is an important step towards unraveling the mechanism of replication. Sesbania mosaic virus (SeMV) RdRp was shown to interact strongly with p10 domain of polyprotein 2a and moderately with the protease domain. Mutational analysis suggested that the C-terminal disordered domain of RdRp is involved in the interaction with p10. Coexpression of full length RdRp and p10 resulted in formation of RdRp-p10 complex which showed significantly higher polymerase activity than RdRp alone. Interestingly, C Delta 43 RdRp also showed a similar increase in activity. Thus, p10 acts as a positive regulator of RdRp by interacting with the C-terminal disordered domain of RdRp. (C) 2014 The Authors. Published by Elsevier B.V.

Quantitative estimation of density variation in high-speed flows through inversion of the measured wavefront distortion

A simple method employing an optical probe is presented to measure density variations in a hypersonic flow obstructed by a test model in a typical shock tunnel. The probe has a plane light wave trans-illuminating the flow and casting a shadow of a random dot pattern. Local slopes of the distorted wavefront are obtained from shifts of the dots in the pattern. Local shifts in the dots are accurately measured by cross-correlating local shifted shadows with the corresponding unshifted originals. The measured slopes are suitably unwrapped by using a discrete cosine transform based phase unwrapping procedure and also through iterative procedures. The unwrapped phase information is used in an iterative scheme for a full quantitative recovery of density distribution in the shock around the model through refraction tomographic inversion. Hypersonic flow field parameters around a missile shaped body at a free-stream Mach number of 5.8 measured using this technique are compared with the numerically estimated values. (C) 2014 Society of Photo-Optical Instrumentation Engineers (SPIE)

Adaptive Flight-Control Design Using Neural-Network-Aided Optimal Nonlinear Dynamic Inversion

A neural-network-aided nonlinear dynamic inversion-based hybrid technique of model reference adaptive control flight-control system design is presented in this paper. Here, the gains of the nonlinear dynamic inversion-based flight-control system are dynamically selected in such a manner that the resulting controller mimics a single network, adaptive control, optimal nonlinear controller for state regulation. Traditional model reference adaptive control methods use a linearized reference model, and the presented control design method employs a nonlinear reference model to compute the nonlinear dynamic inversion gains. This innovation of designing the gain elements after synthesizing the single network adaptive controller maintains the advantages that an optimal controller offers, yet it retains a simple closed-form control expression in state feedback form, which can easily be modified for tracking problems without demanding any a priori knowledge of the reference signals. The strength of the technique is demonstrated by considering the longitudinal motion of a nonlinear aircraft system. An extended single network adaptive control/nonlinear dynamic inversion adaptive control design architecture is also presented, which adapts online to three failure conditions, namely, a thrust failure, an elevator failure, and an inaccuracy in the estimation of C-M alpha. Simulation results demonstrate that the presented adaptive flight controller generates a near-optimal response when compared to a traditional nonlinear dynamic inversion controller.