Intra and Inter-Molecular Communications Through Protein Structure Network

Communication within and across proteins is crucial for the biological functioning of proteins. Experiments such as mutational studies on proteins provide important information on the amino acids, which are crucial for their function. However, the protein structures are complex and it is unlikely that the entire responsibility of the function rests on only a few amino acids. A large fraction of the protein is expected to participate in its function at some level or other. Thus, it is relevant to consider the protein structures as a completely connected network and then deduce the properties, which are related to the global network features. In this direction, our laboratory has been engaged in representing the protein structure as a network of non-covalent connections and we have investigated a variety of problems in structural biology, such as the identification of functional and folding clusters, determinants of quaternary association and characterization of the network properties of protein structures. We have also addressed a few important issues related to protein dynamics, such as the process of oligomerization in multimers, mechanism on protein folding, and ligand induced communications (allosteric effect). In this review we highlight some of the investigations which we have carried out in the recent past. A review on protein structure graphs was presented earlier, in which the focus was on the graphs and graph spectral properties and their implementation in the study of protein structure graphs/networks (PSN). In this article, we briefly summarize the relevant parts of the methodology and the focus is on the advancement brought out in the understanding of protein structure-function relationships through structure networks. The investigations of structural/biological problems are divided into two parts, in which the first part deals with the analysis of PSNs based on static structures obtained from x-ray crystallography. The second part highlights the changes in the network, associated with biological functions, which are deduced from the network analysis on the structures obtained from molecular dynamics simulations.

Integrating voice and data on SALAN: an experimental local area network

This paper is concerned with the integration of voice and data on an experimental local area network used by the School of Automation, of the Indian Institute of Science. SALAN (School of Automation Local Area Network) consists of a number of microprocessor-based communication nodes linked to a shared coaxial cable transmission medium. The communication nodes handle the various low-level functions associated with computer communication, and interface user data equipment to the network. SALAN at present provides a file transfer facility between an Intel Series III microcomputer development system and a Texas Instruments Model 990/4 microcomputer system. Further, a packet voice communication system has also been implemented on SALAN. The various aspects of the design and implementation of the above two utilities are discussed.

Salan: A microprocessor-based medium speed experimental local area network

In this paper the implementation and application of a microprocessor-based medium speed experimental local area network using a coaxial cable transmission medium are dealt with. A separate unidirectional control wire has been used in order to provide a collision-free and fair medium access arbitration. As an application of the network, the design of a packet voice communication system is discussed.

Cholesterol-Esterifying Enzymes in Developing Rat Brain

A cholesterol-esterifying enzyme which incorporates exogenous fatty acids into cholesterol esters in the presence of ATP and coenzyme A was demonstrated in 15-day-old rat brain. This enzyme was maximally active at pH 7.4 and distinct from the cholesterol-esterifying enzyme reported earlier (Eto and Suzuki, 1971), which has a pH optimum at 5.2 and does not require cofactors. Properties of the two enzymes have been compared. Both the enzymes showed negligible esterification with acetate and were maximally active with oleic acid. The pH 5.2 enzyme esterified desmosterol, lanosterol and cholesterol at about the same rate, while the pH 7.4 enzyme was only 50% as active ith lanosterol as it was with cholesterol and desmosterol. Phosphatidyl serine stimulated the pH 5.2 enzyme but not the pH 7.4 enzyme. Phosphatidyl choline and sodium taurocholate showed no effect on either of the enzymes. Both the enzymes were associated with particulate fractions, but the pH 7.4 enzyme was localized more in the microsomes. Purified myelin showed 2.6-fold and 1.5-fold higher specific activities of pH 5.2 and 7.4 enzymes respectively, when compared with homogenate. About 7-10% of total activity of both the enzymes was associated with purified myelin. Brain stem and spinal cord showed higher specific activity of pH 5.2 enzyme than cerebral cortex and cerebellum, while pH 7.4 enzyme specific activity was higher in cerebellum and brain stem than in cerebral cortex and spinal cord. Microsomal pH 7.4 activity showed progressive increase prior to the active period of myelination, reaching a maximum on the 15th day after birth and declined to 20% of the peak activity by 30 days. In contrast, pH 5.2 enzyme reached maximum activity about the 6th day after birth and remained at this level well into adulthood. In 15-day-old rat brain, pH 7.4 enzyme had five to six times higher specific activity than pH 5.2 enzyme, while in adults the activities were equal. The pH 7.4 enzyme showed a threefold higher specific activity than pH 5.2 enzyme in myelin from 15-day-old rats, but in adults the reverse was true. Key Words: Cholesterol esterifying enzymes-Developing rat brain-Myelination. Jagannatha H. M. and Sastry P. S. Cholesterol-esterifying enzymes in developing rat brain. J. Neurochem. 36, 1352- 1360 (1981).

Quasi-2D XY Magnetic Properties and Slow Relaxation in a Body Centered Metal Organic Network of [Co-4] Clusters

Octahedral Co2+ centers have been connected by mu(3)-OH and mu(2)-OH2 units forming [Co-4] clusters which are linked by pyrazine forming a two-dimensional network. The two-dimensional layers are bridged by oxybisbenzoate (OBA) ligands giving rise to a three-dimensional structure. The [Co-4] clusters bond with the pyrazine and the OBA results in a body-centered arrangement of the clusters, which has been observed for the first time. Magnetic studies reveal a noncollinear frustrated spin structure of the bitriangular cluster, resulting in a net magnetic moment of 1.4 mu B per cluster. For T > 32 K, the correlation length of the cluster moments shows a stretched-exponential temperature dependence typical of a Berezinskii-Kosterlitz-Thouless model, which points to a quasi-2D XY behavior. At lower temperature and down to 14 K, the compound behaves as a soft ferromagnet and a slow relaxation is observed, with an energy barrier of ca. 500 K. Then, on further cooling, a hysteretic behavior takes place with a coercive field that reaches 5 Tat 4 K. The slow relaxation is assigned to the creation/annihilation of vortex-antivortex pairs, which are the elementary excitations of a 2D XY spin system.

Ranking of Prospective New Generation Location for a Power Network in a Deregulated System

In developing countries high rate of growth in demand of electric energy is felt, and so the addition of new generating units becomes necessary. In deregulated power systems private generating stations are encouraged to add new generations. Finding the appropriate location of new generator to be installed can be obtained by running repeated power flows, carrying system studies like analyzing the voltage profile, voltage stability, loss analysis etc. In this paper a new methodology is proposed which will mainly consider the existing network topology into account. A concept of T-index is introduced in this paper, which considers the electrical distances between generator and load nodes.This index is used for ranking significant new generation expansion locations and also indicates the amount of permissible generations that can be installed at these new locations. This concept facilitates for the medium and long term planning of power generation expansions within the available transmission corridors. Studies carried out on a sample 7-bus system, EHV equivalent 24-bus system and IEEE 39 bus system are presented for illustration purpose.

Enzymatic acylation of 1-alkyl-, 1-alkenyl-and 1-acyl glycero-3-phosphorylethanolamine in developing rat brain

Rat brain particulate fractions were shown to acylate [32P]1-alkyl-sn-glycero-3-phosphorylethanolamine (GPE). While the main product is 1-alkyl-2-acyl GPE, about 12 per cent of the radioactivity was also found in 1-alkenyl-2-acyl GPE. The acyl transferase activity was completely dependent on added ATP and CoA and it was localized mainly in the microsomal fraction. A comparative study of acyl transferase activities to 1-alkyl-, 1-alkenyl-, and 1-acyl GPE by crude mitochondrial fraction and microsomes of 10, 16 and 22-day-old rat brains showed a progressive increase in activity with development. In the 22-day-old rat brain the order of activity towards the three substrates is as follows: 1-acyl GPE ± 1-alkenyl GPE ± 1-alkyl GPE with a crude mitochondrial fraction and 1-acyl GPE ± 1-alkyl GPE ± 1-alkenyl GPE with microsomes.

Single network adaptive critic design for power system stabilisers

The recently developed single network adaptive critic (SNAC) design has been used in this study to design a power system stabiliser (PSS) for enhancing the small-signal stability of power systems over a wide range of operating conditions. PSS design is formulated as a discrete non-linear quadratic regulator problem. SNAC is then used to solve the resulting discrete-time optimal control problem. SNAC uses only a single critic neural network instead of the action-critic dual network architecture of typical adaptive critic designs. SNAC eliminates the iterative training loops between the action and critic networks and greatly simplifies the training procedure. The performance of the proposed PSS has been tested on a single machine infinite bus test system for various system and loading conditions. The proposed stabiliser, which is relatively easier to synthesise, consistently outperformed stabilisers based on conventional lead-lag and linear quadratic regulator designs.

Relaxation Time of Chemical Reactions from Network Thermodynamics

The relationship for the relaxation time(s) of a chemical reaction in terms of concentrations and rate constants has been derived from the network thermodynamic approach developed by Oster, Perelson, and Katchalsky.Generally, it is necessary to draw the bond graph and the “network analogue” of the reaction scheme, followed by loop or nodal analysis of the network and finally solving of the resulting differential equations. In the case of single-step reactions, however, it is possible to obtain an expression for the relaxation time. This approach is simpler and elegant and has certain advantages over the usual kinetic method. The method has been illustrated by taking different reaction schemes as examples.

Inhibition of the biosynthesis of isoprenoid compounds by phenolic acids in the rat brain

The incorporation of [2-14C]mevalonate into nonsaponifiable lipids by rat brain homogenates is inhibited by phenolic acids derived from tyrosine. The phenyl acids derived from phenylalanine are inhibitory only at very high concentrations compared with phenolic acids. The brain is more sensitive to inhibition by the phenolic acids than the liver. These studies indicate a possible role for phenolic acids in the impairment of cerebral sterol metabolism in phenylketonuria.

Location of concentrators in a computer communication network: a stochastic automation search method

The following problem is considered. Given the locations of the Central Processing Unit (ar;the terminals which have to communicate with it, to determine the number and locations of the concentrators and to assign the terminals to the concentrators in such a way that the total cost is minimized. There is alao a fixed cost associated with each concentrator. There is ail upper limit to the number of terminals which can be connected to a concentrator. The terminals can be connected directly to the CPU also In this paper it is assumed that the concentrators can bo located anywhere in the area A containing the CPU and the terminals. Then this becomes a multimodal optimization problem. In the proposed algorithm a stochastic automaton is used as a search device to locate the minimum of the multimodal cost function . The proposed algorithm involves the following. The area A containing the CPU and the terminals is divided into an arbitrary number of regions (say K). An approximate value for the number of concentrators is assumed (say m). The optimum number is determined by iteration later The m concentrators can be assigned to the K regions in (mk) ways (m > K) or (km) ways (K>m).(All possible assignments are feasible, i.e. a region can contain 0,1,…, to concentrators). Each possible assignment is assumed to represent a state of the stochastic variable structure automaton. To start with, all the states are assigned equal probabilities. At each stage of the search the automaton visits a state according to the current probability distribution. At each visit the automaton selects a 'point' inside that state with uniform probability. The cost associated with that point is calculated and the average cost of that state is updated. Then the probabilities of all the states are updated. The probabilities are taken to bo inversely proportional to the average cost of the states After a certain number of searches the search probabilities become stationary and the automaton visits a particular state again and again. Then the automaton is said to have converged to that state Then by conducting a local gradient search within that state the exact locations of the concentrators are determined This algorithm was applied to a set of test problems and the results were compared with those given by Cooper's (1964, 1967) EAC algorithm and on the average it was found that the proposed algorithm performs better.

Mammalian brain plasma membranes: Isolation, enzymatic, and chemical characterization

Two variants of a simplified procedure for the isolation of plasma membrane fractions from monkey and rat brains, are described. The preparations show marked enrichments in the marker enzymes, (Na+-K+) adenosine triphosphatase, acetylcholinesterase, 5′-nucleotidase and adenylate cyclase. Lipid analysis and a protein electrophoretic pattern are presented. An enzymatic check has been made to assess for contamination by other cellular organelles. The amino acid composition of brain membrane proteins show a resemblance to the reported composition of erythrocyte ghost proteins but differ from myelin proteins.

Oxidation of succinate in heart, brain, and kidney mitochondria in hypobaria and hypoxia

Exposure of rats to hypobaric stress for periods of up to 36 h caused a consistent change in the succinate-NT reductase activity of the heart mitochondria whereas there was no significant change in the activities of either succinate dehydrogenase and succinate-NT reductase of the brain and the kidney. Mitochondrial succinate dehydrogenase of the heart, the brain and the kidney was activated 2- to 7-fold with the substrate and malonate. The activations obtained with oxalate, citrate and dinitrophenol were relatively lower in comparison to succinate and malonate. Benzohydroquinone and 2-nitrophenol had no stimulatory effect on the heart, the brain and the kidney mitochondria. THE ACTIVATIONS OBTAINED WITH THE VARIOUS EFFECTORS PARTIALLY (OR COMPLETELY IN THE CASE OF SUCCINATE) REVERSED ON WASHING THE MITOCHONDRIAL SAMPLES WITH THE SUCROSE HOMOGENIZING MEDIUM. The effect of ubiquinol, which also activated the enzyme, was only partially reversed after the second preincubation with succinate in the brain and the kidney whereas in the heart the activity was fully reversed. The increased activity of succinate dehydrogenase obtained with ATP and ADP was further enhanced by Mg2+ exclusively in the brain mitochondria, suggesting the possibility of Mg2+-AIP complex as the active species. Succinate-NT reductase of the heart, the brain and the kidney mitochondria showed a high activation with ubiquinone whereas its reduced form had no stimulatory effect.