Carboxyl terminal domain basic amino acids of mycobacterial topoisomerase I bind DNA to promote strand passage

Bacterial DNA topoisomerase I (topoI) carries out relaxation of negatively supercoiled DNA through a series of orchestrated steps, DNA binding, cleavage, strand passage and religation. The N-terminal domain (NTD) of the type IA topoisomerases harbor DNA cleavage and religation activities, but the carboxyl terminal domain (CTD) is highly diverse. Most of these enzymes contain a varied number of Zn2+ finger motifs in the CTD. The Zn2+ finger motifs were found to be essential in Escherichia coli topoI but dispensable in the Thermotoga maritima enzyme. Although, the CTD of mycobacterial topoI lacks Zn2+ fingers, it is indispensable for the DNA relaxation activity of the enzyme. The divergent CTD harbors three stretches of basic amino acids needed for the strand passage step of the reaction as demonstrated by a new assay. We also show that the basic amino acids constitute an independent DNA-binding site apart from the NTD and assist the simultaneous binding of two molecules of DNA to the enzyme, as required during the catalytic step. Although the NTD binds to DNA in a site-specific fashion to carry out DNA cleavage and religation, the basic residues in CTD bind to non-scissile DNA in a sequence-independent manner to promote the crucial strand passage step during DNA relaxation. The loss of Zn2+ fingers from the mycobacterial topoI could be associated with Zn2+ export and homeostasis.

Role of outer membrane exopolymers of Acidithiobacillus ferrooxidans in adsorption of cells onto pyrite and chalcopyrite

Bacterial surface polymers play a major role in the adhesion of bacterial cells to solid surfaces. Lipopolysaccharides (LPS) are essential constituents of the cell walls of almost all Gram-negative bacteria. This paper reports the results of the investigations on the role of outer membrane exopolymers (LPS) of the chemolithotroph, Acidithiobacillus ferrooxidans, in adsorption of the cells onto pyrite and chalcopyrite. Optimization of EDTA treatment for removal of LPS from cell surface and the surface characterization of EDTA-treated cells are outlined. There was no change in cell morphology or loss in cell motility upon treatment with upto 0.04 mM EDTA for 1 h. Partial removal of LPS by EDTA treatment resulted in reduced adsorption of the cells on both pyrite and chalcopyrite. The protein profile of the EDTA-extractable fraction showed presence of certain outer membrane proteins indicating that EDTA treatment results in temporary gaps in the outer membrane. Also, specificity towards pyrite compared to chalcopyrite that was exhibited by untreated cells was lost when their exopolymer layers were stripped off, which could be attributed to the role of outer membrane proteins in the mineral-specificity exhibited by the bacteria. (C) 2013 Elsevier B.V. All rights reserved.

Understanding the role of domain-domain linkers in the spatial orientation of domains in multi-domain proteins

Inter-domain linkers (IDLs)' bridge flanking domains and support inter-domain communication in multi-domain proteins. Their sequence and conformational preferences enable them to carry out varied functions. They also provide sufficient flexibility to facilitate domain motions and, in conjunction with the interacting interfaces, they also regulate the inter-domain geometry (IDG). In spite of the basic intuitive understanding of the inter-domain orientations with respect to linker conformations and interfaces, we still do not entirely understand the precise relationship among the three. We show that IDG is evolutionarily well conserved and is constrained by the domain-domain interface interactions. The IDLs modulate the interactions by varying their lengths, conformations and local structure, thereby affecting the overall IDG. Results of our analysis provide guidelines in modelling of multi-domain proteins from the tertiary structures of constituent domain components.

Lysis dynamics and membrane oligomerization pathways for Cytolysin A (ClyA) pore-forming toxin

Pore-forming toxins are known for their ability to efficiently form transmembrane pores which eventually leads to cell lysis. The dynamics of lysis and underlying self-assembly or oligomerization pathways leading to pore formation are incompletely understood. In this manuscript the pore-forming kinetics and lysis dynamics of Cytolysin-A (ClyA) toxins on red blood cells (RBCs) are quantified and compared with experimental lysis data. Lysis experiments are carried out on a fixed mass of RBCs, under isotonic conditions in phosphate-buffered saline, for different initial toxin concentrations ranging from 2.94-14.7 nM. Kinetic models which account for monomer binding, conformation and oligomerization to form the dodecameric ClyA pore complex are developed and lysis is assumed to occur when the number of pores per RBC (n(p)) exceeds a critical number, n(pc). By analysing the model in a sublytic regime (n(p) < n(pc)) the number of pores per RBC to initiate lysis is found to lie between 392 and 768 for the sequential oligomerization mechanism and between 5300 and 6300 for the non-sequential mechanism. Rupture rates which are first order in the number of RBCs are seen to provide the best agreement with the lysis experiments. The time constants for pore formation are estimated to lie between 1 and 20 s and monomer conformation time scales were found to be 2-4 times greater than the oligomerization times. Cell rupture takes places in 100s of seconds, and occurs predominantly with a steady number of pores ranging from 515 to 11 000 on the RBC surface for the sequential mechanism. Both the sequential irreversible and non-sequential kinetics provide similar predictions of the hemoglobin release dynamics, however the hemoglobin released as a function of the toxin concentration was accurately captured only with the sequential model. Each mechanism develops a distinct distribution of mers on the surface, providing a unique experimentally observable fingerprint to identify the underlying oligomerization pathways. Our study offers a method to quantify the extent and dynamics of lysis which is an important aspect of developing novel drug and gene delivery strategies based on pore-forming toxins.

STOKES' SYSTEM IN A DOMAIN WITH OSCILLATING BOUNDARY: HOMOGENIZATION AND ERROR ANALYSIS OF AN INTERIOR OPTIMAL CONTROL PROBLEM

Homogenization and error analysis of an optimal interior control problem in the framework of Stokes' system, on a domain with rapidly oscillating boundary, are the subject matters of this article. We consider a three dimensional domain constituted of a parallelepiped with a large number of rectangular cylinders at the top of it. An interior control is applied in a proper subdomain of the parallelepiped, away from the oscillating volume. We consider two types of functionals, namely a functional involving the L-2-norm of the state variable and another one involving its H-1-norm. The asymptotic analysis of optimality systems for both cases, when the cross sectional area of the rectangular cylinders tends to zero, is done here. Our major contribution is to derive error estimates for the state, the co-state and the associated pressures, in appropriate functional spaces.

Investigations of Ramachandran disallowed conformations in protein domain families

In peptide and protein structures, occurrence of (phi,psi.) angles in the disallowed region of the Ramachandran map almost always suggests local regions of error or poor accuracy. However, very rarely genuine disallowed conformations occur as noted in the current study in proteins of known structure available at ultra-high resolution (<= 1.2 (A) over circle). In the current work, extent of conservation of genuine disallowed conformations in homologous proteins of known structures has been analyzed. From a dataset of 124 protein domain families, with structure of at least one constituent member in each family available at a resolution of 1.2 (A) over circle or better, we have analyzed the conservation of 221 disallowed conformations. It is observed that the disallowed conformation is only moderately conservedin protein domain families. In the gross dataset no particular residue type adopting disallowed conformation elicit high conservation of residue type though there are alignment positions in the dataset with complete conservation of both the residue type and the disallowed conformation. Conserved disallowed conformation in protein domain families play biologically significant role in roughly 50% of the cases. The residues with the disallowed conformation or its flanking residues are often located within or around the functional site of the protein. (C) 2013 Elsevier B.V. All rights reserved.

The N-terminal region containing the zinc finger domain of tobacco streak virus coat protein is essential for the formation of virus-like particles

Tobacco streak virus (TSV), a member of the genus Ilarvirus (family Bromoviridae), has a tripartite genome and forms quasi-isometric virions. All three viral capsids, encapsidating RNA 1, RNA 2 or RNA 3 and subgenomic RNA 4, are constituted of a single species of coat protein (CP). Formation of virus-like particles (VLPs) could be observed when the TSV CP gene was cloned and the recombinant CP (rCP) was expressed in E. coli. TSV VLPs were found to be stabilized by Zn2+ ions and could be disassembled in the presence of 500 mM CaCl2. Mutational analysis corroborated previous studies that showed that an N-terminal arginine-rich motif was crucial for RNA binding; however, the results presented here demonstrate that the presence of RNA is not a prerequisite for assembly of TSV VLPs. Instead, the N-terminal region containing the zinc finger domain preceding the arginine-rich motif is essential for assembly of these VLPs.

Using Relationships for Matching Textual Domain Models with Existing Code

We address the task of mapping a given textual domain model (e.g., an industry-standard reference model) for a given domain (e.g., ERP), with the source code of an independently developed application in the same domain. This has applications in improving the understandability of an existing application, migrating it to a more flexible architecture, or integrating it with other related applications. We use the vector-space model to abstractly represent domain model elements as well as source-code artifacts. The key novelty in our approach is to leverage the relationships between source-code artifacts in a principled way to improve the mapping process. We describe experiments wherein we apply our approach to the task of matching two real, open-source applications to corresponding industry-standard domain models. We demonstrate the overall usefulness of our approach, as well as the role of our propagation techniques in improving the precision and recall of the mapping task.

Structural basis for the redox sensitivity of the Mycobacterium tuberculosis SigK-RskA sigma-anti-sigma complex

The host-pathogen interactions in Mycobacterium tuberculosis infection are significantly influenced by redox stimuli and alterations in the levels of secreted antigens. The extracyto-plasmic function (ECF) sigma factor sigma(K) governs the transcription of the serodominant antigens MPT70 and MPT83. The cellular levels of sigma(K) are regulated by the membrane-associated anti-sigma(K) (RskA) that localizes sigma(K) in an inactive complex. The crystal structure of M. tuberculosis sigma(K) in complex with the cytosolic domain of RskA (RskAcyto) revealed a disulfide bridge in the -35 promoter-interaction region of sigma(K). Biochemical experiments reveal that the redox potential of the disulfide-forming cysteines in sigma(K) is consistent with its role as a sensor. The disulfide bond in sigma(K) influences the stability of the sigma(K)-RskA(cyto) complex but does not interfere with sigma(K)-promoter DNA interactions. It is noted that these disulfide-forming cysteines are conserved across homologues, suggesting that this could be a general mechanism for redox-sensitive transcription regulation.

The relationship between classification of multi-domain proteins using an alignment-free approach and their functions: a case study with immunoglobulins

Establishing functional relationships between multi-domain protein sequences is a non-trivial task. Traditionally, delineating functional assignment and relationships of proteins requires domain assignments as a prerequisite. This process is sensitive to alignment quality and domain definitions. In multi-domain proteins due to multiple reasons, the quality of alignments is poor. We report the correspondence between the classification of proteins represented as full-length gene products and their functions. Our approach differs fundamentally from traditional methods in not performing the classification at the level of domains. Our method is based on an alignment free local matching scores (LMS) computation at the amino-acid sequence level followed by hierarchical clustering. As there are no gold standards for full-length protein sequence classification, we resorted to Gene Ontology and domain-architecture based similarity measures to assess our classification. The final clusters obtained using LMS show high functional and domain architectural similarities. Comparison of the current method with alignment based approaches at both domain and full-length protein showed superiority of the LMS scores. Using this method we have recreated objective relationships among different protein kinase sub-families and also classified immunoglobulin containing proteins where sub-family definitions do not exist currently. This method can be applied to any set of protein sequences and hence will be instrumental in analysis of large numbers of full-length protein sequences.

RAPID HUMAN ACTION RECOGNITION IN H.264/AVC COMPRESSED DOMAIN FOR VIDEO SURVEILLANCE

This paper discusses a novel high-speed approach for human action recognition in H. 264/AVC compressed domain. The proposed algorithm utilizes cues from quantization parameters and motion vectors extracted from the compressed video sequence for feature extraction and further classification using Support Vector Machines (SVM). The ultimate goal of our work is to portray a much faster algorithm than pixel domain counterparts, with comparable accuracy, utilizing only the sparse information from compressed video. Partial decoding rules out the complexity of full decoding, and minimizes computational load and memory usage, which can effect in reduced hardware utilization and fast recognition results. The proposed approach can handle illumination changes, scale, and appearance variations, and is robust in outdoor as well as indoor testing scenarios. We have tested our method on two benchmark action datasets and achieved more than 85% accuracy. The proposed algorithm classifies actions with speed (>2000 fps) approximately 100 times more than existing state-of-the-art pixel-domain algorithms.

C. N. R. Rao and the Growth of Solid State and Materials Chemistry as a Central Domain of Research

In celebrating Professor C. N. R. Rao's 80th birthday, this article recalls his singular contributions to solid state and materials chemistry for about sixty years. In so doing, the article also traces the growth of the field as a central domain of research in chemical sciences from its early origins in Europe. Although Rao's major work lies in solid state and materials chemistry - a field which he started and nurtured in India while its importance was being recognized internationally - his contributions to other areas of chemistry (and physics), viz., molecular spectroscopy, phase transitions, fullerenes, graphene, nanomaterials and multiferroics are equally significant. Illustrative examples of his work devoted to rare earth and transition metal oxides, defects and nonstoichiometry, metal-insulator transitions, investigation of crystal and electronic structures of a variety of solids by means of electron microscopies and photoelectron spectroscopy, superconducting cuprates, magnetoresistive manganites, multiferroic metal oxides of various structures and, last but not the least, development of new strategies for chemical synthesis of a wide variety of solids including nanomaterials and framework solids in different dimensionalities, are highlighted. The article also captures his exemplary role as a science teacher, science educationist and institution builder in post-Independence India.

Bi-Domain Protein Tyrosine Phosphatases Reveal an Evolutionary Adaptation to Optimize Signal Transduction

Significance: The bi-domain protein tyrosine phosphatases (PTPs) exemplify functional evolution in signaling proteins for optimal spatiotemporal signal transduction. Bi-domain PTPs are products of gene duplication. The catalytic activity, however, is often localized to one PTP domain. The inactive PTP domain adopts multiple functional roles. These include modulation of catalytic activity, substrate specificity, and stability of the bi-domain enzyme. In some cases, the inactive PTP domain is a receptor for redox stimuli. Since multiple bi-domain PTPs are concurrently active in related cellular pathways, a stringent regulatory mechanism and selective cross-talk is essential to ensure fidelity in signal transduction. Recent Advances: The inactive PTP domain is an activator for the catalytic PTP domain in some cases, whereas it reduces catalytic activity in other bi-domain PTPs. The relative orientation of the two domains provides a conformational rationale for this regulatory mechanism. Recent structural and biochemical data reveal that these PTP domains participate in substrate recruitment. The inactive PTP domain has also been demonstrated to undergo substantial conformational rearrangement and oligomerization under oxidative stress. Critical Issues and Future Directions: The role of the inactive PTP domain in coupling environmental stimuli with catalytic activity needs to be further examined. Another aspect that merits attention is the role of this domain in substrate recruitment. These aspects have been poorly characterized in vivo. These lacunae currently restrict our understanding of neo-functionalization of the inactive PTP domain in the bi-domain enzyme. It appears likely that more data from these research themes could form the basis for understanding the fidelity in intracellular signal transduction.