Structural and functional studies of Bacillus stearothermophilus serine hydroxymethyltransferase: the role of Asn(341), Tyr(60) and Phe(351) in tetrahydrofolate binding

SHMT (serine hydoxymethyltransferase), a type I pyridoxal 5'-phosphate-dependent enzyme, catalyses the conversion of L-serine and THF (tetrahydrofolate) into glycine and 5,10-methylene THE SHMT also catalyses several THF-independent side reactions such as cleavage of P-hydroxy amino acids, trans-amination, racemization and decarboxylation. In the present study, the residues Asn(341), Tyr(60) and Phe(351), which are likely to influence THF binding, were mutated to alanine, alanine and glycine respectively, to elucidate the role of these residues in THF-dependent and -independent reactions catalysed by SHMT. The N341A and Y60A bsSHMT (Bacillus stearothermophilus SHMT) mutants were inactive for the THF-dependent activity, while the mutations had no effect on THF-independent activity. However, mutation of Phe(351) to glycine did not have any effect oil either of the activities. The crystal structures of the glycine binary complexes of the mutants showed that N341A bsSHMT forms an external aldimine as in bsSHMT, whereas Y60A and F351G bsSHMTs exist as a Mixture of internal/external aldimine and gem-diamine forms. Crystal structures of all of the three Mutants obtained in the presence of L-allo-threonine were similar to the respective glycine binary complexes. The structure of the ternary complex of F351G bsSHMT with glycine and FTHF (5-formyl THF) showed that the monoglutamate side chain of FTHF is ordered in both the subunits of the asymmetric unit, unlike in the wild-type bsSHMT. The present studies demonstrate that the residues Asn(341) and Tyr(60) are pivotal for the binding of THF/FTHF, whereas Phe(351) is responsible for the asymmetric binding of FTHF in the two subunits of the dimer.

CSSP (Consensus Secondary Structure Prediction): a web-based server for structural biologists

Sequence-structure correlation studies are important in deciphering the relationships between various structural aspects, which may shed light on the protein-folding problem. The first step of this process is the prediction of secondary structure for a protein sequence of unknown three-dimensional structure. To this end, a web server has been created to predict the consensus secondary structure using well known algorithms from the literature. Furthermore, the server allows users to see the occurrence of predicted secondary structural elements in other structure and sequence databases and to visualize predicted helices as a helical wheel plot. The web server is accessible at http://bioserver1.physics.iisc.ernet.in/cssp/.

targetTB: A target identification pipeline for Mycobacterium tuberculosis through an interactome, reactome and genome-scale structural analysis

Background: Tuberculosis still remains one of the largest killer infectious diseases, warranting the identification of newer targets and drugs. Identification and validation of appropriate targets for designing drugs are critical steps in drug discovery, which are at present major bottle-necks. A majority of drugs in current clinical use for many diseases have been designed without the knowledge of the targets, perhaps because standard methodologies to identify such targets in a high-throughput fashion do not really exist. With different kinds of 'omics' data that are now available, computational approaches can be powerful means of obtaining short-lists of possible targets for further experimental validation. Results: We report a comprehensive in silico target identification pipeline, targetTB, for Mycobacterium tuberculosis. The pipeline incorporates a network analysis of the protein-protein interactome, a flux balance analysis of the reactome, experimentally derived phenotype essentiality data, sequence analyses and a structural assessment of targetability, using novel algorithms recently developed by us. Using flux balance analysis and network analysis, proteins critical for survival of M. tuberculosis are first identified, followed by comparative genomics with the host, finally incorporating a novel structural analysis of the binding sites to assess the feasibility of a protein as a target. Further analyses include correlation with expression data and non-similarity to gut flora proteins as well as 'anti-targets' in the host, leading to the identification of 451 high-confidence targets. Through phylogenetic profiling against 228 pathogen genomes, shortlisted targets have been further explored to identify broad-spectrum antibiotic targets, while also identifying those specific to tuberculosis. Targets that address mycobacterial persistence and drug resistance mechanisms are also analysed. Conclusion: The pipeline developed provides rational schema for drug target identification that are likely to have high rates of success, which is expected to save enormous amounts of money, resources and time in the drug discovery process. A thorough comparison with previously suggested targets in the literature demonstrates the usefulness of the integrated approach used in our study, highlighting the importance of systems-level analyses in particular. The method has the potential to be used as a general strategy for target identification and validation and hence significantly impact most drug discovery programmes.

Structural basis for the function of anti-idiotypic antibody in immune memory

We had earlier proposed a hypothesis to explain the mechanism of perpetuation of immunological memory based on the operation of idiotypic network in the complete absence of antigen. Experimental evidences were provided for memory maintenance through anti-idiotypic antibody (Ab2) carrying the internal image of the antigen. In the present work, we describe a structural basis for such memory perpetuation by molecular modeling and structural analysis studies. A three-dimensional model of Ab2 was generated and the structure of the antigenic site on the hemagglutinin protein H of Rinderpest virus was modeled using the structural template of hemagglutinin protein of Measles virus. Our results show that a large portion of heavy chain containing the CDR regions of Ab2 resembles the domain of the hemagglutinin housing the epitope regions. The similarity demonstrates that an internal image of the H antigen is formed in Ab2, which provides a structural basis for functional mimicry demonstrated earlier. This work brings out the importance of the structural similarity between a domain of hemagglutinin protein to that of its corresponding Ab2. It provides evidence that Ab2 is indeed capable of functioning as surrogate antigen and provides support to earlier proposed relay hypothesis which has provided a mechanism for the maintenance of immunological memory.

A do-it-yourself (DIY) switched mode power conversion laboratory

In the education of physical sciences, the role of the laboratory cannot be overemphasised. It is the laboratory exercises which enable the student to assimilate the theoretical basis, verify the same through bench-top experiments, and internalize the subject discipline to acquire mastery of the same. However the resources essential to put together such an environment is substantial. As a result, the students go through a curriculum which is wanting in this respect. This paper presents a low cost alternative to impart such an experience to the student aimed at the subject of switched mode power conversion. The resources are based on an open source circuit simulator (Sequel) developed at IIT Mumbai, and inexpensive construction kits developed at IISc Bangalore. The Sequel programme developed by IIT Mumbai, is a circuit simulation program under linux operating system distributed free of charge. The construction kits developed at IISc Bangalore, is fully documented for anyone to assemble these circuit which minimal equipment such as soldering iron, multimeter, power supply etc. This paper puts together a simple forward dc to dc converter as a vehicle to introduce the programming under sequel to evaluate the transient performance and small signal dynamic model of the same. Bench tests on the assembled construction kit may be done by the student for study of operation, transient performance and closed loop stability margins etc.

Latency, Power and Performance Trade-offs in Network-on-Chips by Link Microarchitecture Exploration

This paper presents a power, latency and throughput trade-off study on NoCs by varying microarchitectural (e.g. pipelining) and circuit level (e.g. frequency and voltage) parameters. We change pipelining depth, operating frequency and supply voltage for 3 example NoCs - 16 node 2D Torus, Tree network and Reduced 2D Torus. We use an in-house NoC exploration framework capable of topology generation and comparison using parameterized models of Routers and links developed in SystemC. The framework utilizes interconnect power and delay models from a low-level modelling tool called Intacte[1]1. We find that increased pipelining can actually reduce latency. We also find that there exists an optimal degree of pipelining which is the most energy efficient in terms of minimizing energy-delay product.

Hybrid structural control using magnetorheological dampers for base isolated structures

In this paper two nonlinear model based control algorithms have been developed to monitor the magnetorheological (MR) damper voltage. The main advantage of the proposed algorithms is that it is possible to directly monitor the voltage required to control the structural vibration considering the effect of the supplied and commanded voltage dynamics of the damper. The efficiency of the proposed techniques has been shown and compared taking an example of a base isolated three-storey building under a set of seismic excitations. Comparison of the performances with a fuzzy based intelligent control algorithm and a widely used clipped optimal strategy has also been shown.

A multiscale study on the structural and mechanical properties of the luffa sponge from Luffa cylindrica plant

Cellular materials that are often observed in biological systems exhibit excellent mechanical properties at remarkably low densities. Luffa sponge is one of such materials with a complex interconnecting porous structure. In this paper, we studied the relationship between its structural and mechanical properties at different levels of its hierarchical organization from a single fiber to a segment of whole sponge. The tensile mechanical behaviors of three single fibers were examined by an Instron testing machine and the ultrastructure of a fractured single fiber was observed in a scanning electronic microscope. Moreover, the compressive mechanical behaviors of the foam-like blocks from different locations of the sponge were examined. The difference of the compressive stress-strain responses of four sets of segmental samples were also compared. The result shows that the single fiber is a porous composite material mainly consisting of cellulose fibrils and lignin/hemicellulose matrix, and its Young's modulus and strength are comparable to wood. The mechanical behavior of the block samples from the hoop wall is superior to that from the core part. Furthermore, it shows that the influence of the inner surface on the mechanical property of the segmental sample is stronger than that of the core part; in particular, the former's Young's modulus, strength and strain energy absorbed are about 1.6 times higher. The present work can improve our understanding of the structure-function relationship of the natural material, which may inspire fabrication of new biomimetic foams with desirable mechanical efficiency for further applications in anti-crushing devices and super-light sandwich panels.

Association between biomechanical structural stresses of atherosclerotic carotid plaques and subsequent ischaemic cerebrovascular events - A longitudinal in vivo magnetic resonance imaging-based finite element study

Background: High-resolution magnetic resonance (MR) imaging has been used for MR imaging-based structural stress analysis of atherosclerotic plaques. The biomechanical stress profile of stable plaques has been observed to differ from that of unstable plaques; however, the role that structural stresses play in determining plaque vulnerability remains speculative. Methods: A total of 61 patients with previous history of symptomatic carotid artery disease underwent carotid plaque MR imaging. Plaque components of the index artery such as fibrous tissue, lipid content and plaque haemorrhage (PH) were delineated and used for finite element analysis-based maximum structural stress (M-C Stress) quantification. These patients were followed up for 2 years. The clinical end point was occurrence of an ischaemic cerebrovascular event. The association of the time to the clinical end point with plaque morphology and M-C Stress was analysed. Results: During a median follow-up duration of 514 days, 20% of patients (n=12) experienced an ischaemic event in the territory of the index carotid artery. Cox regression analysis indicated that M-C Stress (hazard ratio (HR): 12.98 (95% confidence interval (CI): 1.32-26.67, pZ0.02), fibrous cap (FC) disruption (HR: 7.39 (95% CI: 1.61e33.82), p Z 0.009) and PH (HR: 5.85 (95% CI: 1.27e26.77), p Z 0.02) are associated with the development of subsequent cerebrovascular events. Plaques associated with future events had higher M-C Stress than those which had remained asymptomatic (median (interquartile range, IQR): 330 kPa (229e494) vs. 254 kPa (166-290), p Z0.04). Conclusions: High biomechanical structural stresses, in addition to FC rupture and PH, are associated with subsequent cerebrovascular events.

Structural and optical investigations of TiO2 films deposited on transparent substrates by sol-gel technique

An inexpensive and effective simple method for the preparation of nano-crystalline titanium oxide (anatase) thin films at room temperature on different transparent substrates is presented. This method is based on the use of peroxo-titanium complex, i.e. titanium isopropoxide as a single initiating organic precursor. Post-annealing treatment is necessary to convert the deposited amorphous film into titanium oxide (TiO2) crystalline (anatase) phase. These films have been characterized for X-ray diffraction (XRD) studies, atomic force microscopic (AFM) studies and optical measurements. The optical constants such as refractive index and extinction coefficient have been estimated by using envelope technique. Also, the energy gap values have been estimated using Tauc's formula for on glass and quartz substrates are found to be 3.35 eV and 3.39 eV, respectively. (C) 2008 Elsevier B.V. All rights reserved.

Fast Multiple Access Selection through variable power transmissions

Many wireless applications demand a fast mechanism to detect the packet from a node with the highest priority ("best node") only, while packets from nodes with lower priority are irrelevant. In this paper, we introduce an extremely fast contention-based multiple access algorithm that selects the best node and requires only local information of the priorities of the nodes. The algorithm, which we call Variable Power Multiple Access Selection (VP-MAS), uses the local channel state information from the accessing nodes to the receiver, and maps the priorities onto the receive power. It is based on a key result that shows that mapping onto a set of discrete receive power levels is optimal, when the power levels are chosen to exploit packet capture that inherently occurs in a wireless physical layer. The VP-MAS algorithm adjusts the expected number of users that contend in each step and their respective transmission powers, depending on whether previous transmission attempts resulted in capture, idle channel, or collision. We also show how reliable information regarding the total received power at the receiver can be used to improve the algorithm by enhancing the feedback mechanism. The algorithm detects the packet from the best node in 1.5 to 2.1 slots, which is considerably lower than the 2.43 slot average achieved by the best algorithm known to date.

Assessment of carotid plaque vulnerability using structural and geometrical determinants

Background Because many acute cerebral ischemic events are caused by rupture of vulnerable carotid atheroma and subsequent thrombosis, the present study used both idealized and patient-specific carotid atheromatous plaque models to evaluate the effect of structural determinants on stress distributions within plaque. Methods and Results Using a finite element method, structural analysis was performed using models derived from in vivo high-resolution magnetic resonance imaging (MRI) of carotid atheroma in 40 non-consecutive patients (20 symptomatic, 20 asymptomatic). Plaque components were modeled as hyper-elastic materials. The effects of varying fibrous cap thickness, lipid core size and lumen curvature on plaque stress distributions were examined. Lumen curvature and fibrous cap thickness were found to be major determinants of plaque stress. The size of the lipid core did not alter plaque stress significantly when the fibrous cap was relatively thick. The correlation between plaque stress and lumen curvature was significant for both symptomatic (p = 0.01; correlation coefficient: 0.689) and asymptomatic patients (p = 0.01; correlation coefficient: 0.862). Lumen curvature in plaques of symptomatic patients was significantly larger than those of asymptomatic patients (1.50±1.0mm-1 vs 1.25±0.75 mm-1; p = 0.01). Conclusion Specific plaque morphology (large lumen curvature and thin fibrous cap) is closely related to plaque vulnerability. Structural analysis using high-resolution MRI of carotid atheroma may help in detecting vulnerable atheromatous plaque and aid the risk stratification of patients with carotid disease.

On the nature of power flow equations in security analysis

The power system network is assumed to be in steady-state even during low frequency transients. However, depending on generator dynamics, and toad and control characteristics, the system model and the nature of power flow equations can vary The nature of power flow equations describing the system during a contingency is investigated in detail. It is shown that under some mild assumptions on load-voltage characteristics, the power flow equations can be decoupled in an exact manner. When the generator dynamics are considered, the solutions for the load voltages are exact if load nodes are not directly connected to each other

Structural analysis and magnetic resonance imaging predict plaque vulnerability: A study comparing symptomatic and asymptomatic individuals

Background: More than half of all cerebral ischemic events are the result of rupture of extracranial plaques. The clinical determination of carotid plaque vulnerability is currently based solely on luminal stenosis; however, it has been increasingly suggested that plaque morphology and biomechanical stress should also be considered. We used finite element analysis based on in vivo magnetic resonance imaging (MRI) to simulate the stress distributions within plaques of asymptomatic and symptomatic individuals. Methods: Thirty nonconsecutive subjects (15 symptomatic and 15 asymptomatic) underwent high-resolution multisequence in vivo MRI of the carotid bifurcation. Stress analysis was performed based on the geometry derived from in vivo MRI of the carotid artery at the point of maximal stenosis. The finite element analysis model considered plaque components to be hyperelastic. The peak stresses within the plaques of symptomatic and asymptomatic individuals were compared. Results: High stress concentrations were found at the shoulder regions of symptomatic plaques, and the maximal stresses predicted in this group were significantly higher than those in the asymptomatic group (508.2 ± 193.1 vs 269.6 ± 107.9 kPa; P = .004). Conclusions: Maximal predicted plaque stresses in symptomatic patients were higher than those predicted in asymptomatic patients by finite element analysis, suggesting the possibility that plaques with higher stresses may be more prone to be symptomatic and rupture. If further validated by large-scale longitudinal studies, biomechanical stress analysis based on high resolution in vivo MRI could potentially act as a useful tool for risk assessment of carotid atheroma. It may help in the identification of patients with asymptomatic carotid atheroma at greatest risk of developing symptoms or mild-to-moderate symptomatic stenoses, which currently fall outside current clinical guidelines for intervention.

Some aspects of multilevel load-frequency control of a power system

The application of multilevel control strategies for load-frequency control of interconnected power systems is assuming importance. A large multiarea power system may be viewed as an interconnection of several lower-order subsystems, with possible change of interconnection pattern during operation. The solution of the control problem involves the design of a set of local optimal controllers for the individual areas, in a completely decentralised environment, plus a global controller to provide the corrective signal to account for interconnection effects. A global controller, based on the least-square-error principle suggested by Siljak and Sundareshan, has been applied for the LFC problem. A more recent work utilises certain possible beneficial aspects of interconnection to permit more desirable system performances. The paper reports the application of the latter strategy to LFC of a two-area power system. The power-system model studied includes the effects of excitation system and governor controls. A comparison of the two strategies is also made.