Optimality of orthogonal sequences with multi-dimensional signaling

The sum capacity on a symbol-synchronous CDMA system having processing gain N and supporting K power constrained users is achieved by employing any set of N orthogonal sequences if a few users are allowed to signal along multiple dimensions. Analogously, the minimum received power (energy-per-chip) on the symbolsynchronous CDMA system supporting K users that demand specified data rates is attained by employing any set of N orthogonal sequences. At most (N - 1) users need to be split and if there are no oversized users, these split users need to signal only in two dimensions each. These results show that sum capacity or minimum sum power can be achieved with minimal downlink signaling.

The PE and PPE proteins of Mycobacterium tuberculosis

India already has earned the dubious distinction of being one of the countries with the highest incidence of tuberculosis (TB). The conventional control measures have had little impact on the relentless march of the TB epidemic. Potential solutions to this problem include the development of new drugs and an effective TB vaccine. In this perspective, identification of the mycobacterial components that have important role(s) in the establishment of the infection assumes crucial importance. Mycobacterium tuberculosis is an intracellular pathogen and it resides inside the macrophage, which is considered to be the most important component of the immune system. M. tuberculosis possesses two highly polymorphic sets of genes called the PE and PPE families. These unique families of proteins account for about 10% of the mycobacterial genome and have drawn considerable interest from different schools of M. tuberculosis researchers across the globe. In this review, we discuss the importance of these proteins in the regulation of dendritic cell and macrophage immune-effector functions, as well as the relevance of these proteins in the clinical manifestation of TB. This information may be helpful to better understand the immunological importance of PE/PPE proteins and their roles in mycobacterial virulence. (C) 2011 Elsevier Ltd. All rights reserved.

Structural biology of Mycobacterium tuberculosis proteins: The Indian efforts

Among the many different objectives of large scale structural genomics projects are expanding the protein fold space, enhancing understanding of a model or disease-related organism, and providing foundations for structure-based drug discovery. Systematic analysis of protein structures of Mycobacterium tuberculosis has been ongoing towards meeting some of these objectives. Indian participation in these efforts has been enthusiastic and substantial. The proteins of M. tuberculosis chosen for structural analysis by the Indian groups span almost all the functional categories. The structures determined by the Indian groups have led to significant improvement in the biochemical knowledge on these proteins and consequently have started providing useful insights into the biology of M. tuberculosis. Moreover, these structures form starting points for inhibitor design studies, early results of which are encouraging. The progress made by Indian structural biologists in determining structures of M. tuberculosis proteins is highlighted in this review. (C) 2011 Elsevier Ltd. All rights reserved.

Stability of domain structures in multi-domain proteins

Multi-domain proteins have many advantages with respect to stability and folding inside cells. Here we attempt to understand the intricate relationship between the domain-domain interactions and the stability of domains in isolation. We provide quantitative treatment and proof for prevailing intuitive ideas on the strategies employed by nature to stabilize otherwise unstable domains. We find that domains incapable of independent stability are stabilized by favourable interactions with tethered domains in the multi-domain context. Stability of such folds to exist independently is optimized by evolution. Specific residue mutations in the sites equivalent to inter-domain interface enhance the overall solvation, thereby stabilizing these domain folds independently. A few naturally occurring variants at these sites alter communication between domains and affect stability leading to disease manifestation. Our analysis provides safe guidelines for mutagenesis which have attractive applications in obtaining stable fragments and domain constructs essential for structural studies by crystallography and NMR.

Pathogen-specific TLR2 Protein Activation Programs Macrophages to Induce Wnt-beta-Catenin Signaling

Innate immunity recognizes and resists various pathogens; however, the mechanisms regulating pathogen versus non-pathogen discrimination are still imprecisely understood. Here, we demonstrate that pathogen-specific activation of TLR2 upon infection with Mycobacterium bovis BCG, in comparison with other pathogenic microbes, including Salmonella typhimurium and Staphylococcus aureus, programs macrophages for robust up-regulation of signaling cohorts of Wnt-beta-catenin signaling. Signaling perturbations or genetic approaches suggest that infection-mediated stimulation of Wnt-beta-catenin is vital for activation of Notch1 signaling. Interestingly, inducible NOS (iNOS) activity is pivotal for TLR2-mediated activation of Wnt-beta-catenin signaling as iNOS(-/-) mice demonstrated compromised ability to trigger activation of Wnt-beta-catenin signaling as well as Notch1-mediated cellular responses. Intriguingly, TLR2-driven integration of iNOS/NO, Wnt-beta-catenin, and Notch1 signaling contributes to its capacity to regulate the battery of genes associated with T(Reg) cell lineage commitment. These findings reveal a role for differential stimulation of TLR2 in deciding the strength of Wnt-beta-catenin signaling, which together with signals from Notch1 contributes toward the modulation of a defined set of effector functions in macrophages and thus establishes a conceptual framework for the development of novel therapeutics.

Investigating Diproline Segments in Proteins: Occurrences, Conformation and Classification

The covalent linkage between the side-chain and the backbone nitrogen atom of proline leads to the formation of the five-membered pyrrolidine ring and hence restriction of the backbone torsional angle phi to values of -60 degrees +/- 30 degrees for the L-proline. Diproline segments constitute a chain fragment with considerably reduced conformational choices. In the current study, the conformational states for the diproline segment ((L)Pro-(L)Pro) found in proteins has been investigated with an emphasis on the cis and trans states for the Pro-Pro peptide bond. The occurrence of diproline segments in turns and other secondary structures has been studied and compared to that of Xaa-Pro-Yaa segments in proteins which gives us a better understanding on the restriction imposed on other residues by the diproline segment and the single proline residue. The study indicates that P(II)-P(II) and P(II)-alpha are the most favorable conformational states for the diproline segment. The analysis on Xaa-Pro-Yaa sequences reveals that the XaaPro peptide bond exists preferably as the trans conformer rather than the cis conformer. The present study may lead to a better understanding of the behavior of proline occurring in diproline segments which can facilitate various designed diproline-based synthetic templates for biological and structural studies. (C) 2011 Wiley Periodicals, Inc. Biopolymers 97: 54-64, 2012.

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.

Auxin-Responsive OsMGH3, a Common Downstream Target of OsMADS1 and OsMADS6, Controls Rice Floret Fertility

GH3 proteins control auxin homeostasis by inactivating excess auxin as conjugates of amino acids and sugars and thereby controlling cellular bioactive auxin. Since auxin regulates many aspects of plant growth and development, regulated expression of these genes offers a mechanism to control various developmental processes. OsMGH3/OsGH3-8 is expressed abundantly in rice florets and is regulated by two related and redundant transcription factors, OsMADS1 and OsMADS6, but its contribution to flower development is not known. We functionally characterize OsMGH3 by overexpression and knock-down analysis and show a partial overlap in these phenotypes with that of mutants in OsMADS1 and OsMADS6. The overexpression of OsMGH3 during the vegetative phase affects the overall plant architecture, whereas its inflorescence-specific overexpression creates short panicles with reduced branching, resembling in part the effects of OsMADS1 overexpression. In contrast, the down-regulation of endogenous OsMGH3 caused phenotypes consistent with auxin overproduction or activated signaling, such as ectopic rooting from aerial nodes. Florets in OsMGH3 knock-down plants were affected in carpel development and pollen viability, both of which reduced fertility. Some of these floret phenotypes are similar to osmads6 mutants. Taken together, we provide evidence for the functional significance of auxin homeostasis and its transcriptional regulation during rice panicle branching and floret organ development.

Chimeras of Escherichia coli and Mycobacterium tuberculosis Single-Stranded DNA Binding Proteins: Characterization and Function in Escherichia coli

Single stranded DNA binding proteins (SSBs) are vital for the survival of organisms. Studies on SSBs from the prototype, Escherichia coli (EcoSSB) and, an important human pathogen, Mycobacterium tuberculosis (MtuSSB) had shown that despite significant variations in their quaternary structures, the DNA binding and oligomerization properties of the two are similar. Here, we used the X-ray crystal structure data of the two SSBs to design a series of chimeric proteins (m beta 1, m beta 1'beta 2, m beta 1-beta 5, m beta 1-beta 6 and m beta 4-beta 5) by transplanting beta 1, beta 1'beta 2, beta 1-beta 5, beta 1-beta 6 and beta 4-beta 5 regions, respectively of the N-terminal (DNA binding) domain of MtuSSB for the corresponding sequences in EcoSSB. In addition, m beta 1'beta 2(ESWR) SSB was generated by mutating the MtuSSB specific `PRIY' sequence in the beta 2 strand of m beta 1'beta 2 SSB to EcoSSB specific `ESWR' sequence. Biochemical characterization revealed that except for m beta 1 SSB, all chimeras and a control construct lacking the C-terminal domain (Delta C SSB) bound DNA in modes corresponding to limited and unlimited modes of binding. However, the DNA on MtuSSB may follow a different path than the EcoSSB. Structural probing by protease digestion revealed that unlike other SSBs used, m beta 1 SSB was also hypersensitive to chymotrypsin treatment. Further, to check for their biological activities, we developed a sensitive assay, and observed that m beta 1-beta 6, MtuSSB, m beta 1'beta 2 and m beta 1-beta 5 SSBs complemented E. coli Delta ssb in a dose dependent manner. Complementation by the m beta 1-beta 5 SSB was poor. In contrast, m beta 1'beta 2(ESWR) SSB complemented E. coli as well as EcoSSB. The inefficiently functioning SSBs resulted in an elongated cell/filamentation phenotype of E. coli. Taken together, our observations suggest that specific interactions within the DNA binding domain of the homotetrameric SSBs are crucial for their biological function.

Gate Drive Card for High Power Three Phase PWM Converters

Gate driver is an integral part of every power converter, drives the power semiconductor devices and also provides protection for the switches against short-circuit events and over-voltages during shut down. Gate drive card for IGBTs and MOSFETs with basic features can be designed easily by making use of discrete electronic components. Gate driver ICs provides attractive features in a single package, which improves reliability and reduces effort of design engineers. Either case needs one or more isolated power supplies to drive each power semiconductor devices and provide isolation to the control circuitry from the power circuit. The primary emphasis is then to provide simplified and compact isolated power supplies to the gate drive card with the requisite isolation strength and which consumes less space, and for providing thermal protection to the power semiconductor modules for 3-� 3 wire or 4 wire inverters.

Functional Analysis of DNA Replication Fork Reversal Catalyzed by Mycobacterium tuberculosis RuvAB Proteins

Initially discovered in Escherichia coli, RuvAB proteins are ubiquitous in bacteria and play a dual role as molecular motor proteins responsible for branch migration of the Holliday junction(s) and reversal of stalled replication forks. Despite mounting genetic evidence for a crucial role of RuvA and RuvB proteins in reversal of stalled replication forks, the mechanistic aspects of this process are still not fully understood. Here, we elucidate the ability of Mycobacterium tuberculosis RuvAB (MtRuvAB) complex to catalyze the reversal of replication forks using a range of DNA replication fork substrates. Our studies show that MtRuvAB, unlike E. coli RuvAB, is able to drive replication fork reversal via the formation of Holliday junction intermediates, suggesting that RuvAB-catalyzed fork reversal involves concerted unwinding and annealing of nascent leading and lagging strands. We also demonstrate the reversal of replication forks carrying hemi-replicated DNA, indicating that MtRuvAB complex-catalyzed fork reversal is independent of symmetry at the fork junction. The fork reversal reaction catalyzed by MtRuvAB is coupled to ATP hydrolysis, is processive, and culminates in the formation of an extended reverse DNA arm. Notably, we found that sequence heterology failed to impede the fork reversal activity of MtRuvAB. We discuss the implications of these results in the context of recognition and processing of varied types of replication fork structures by RuvAB proteins.