Protein modeling, molecular network and molecular dynamics study of newly sequenced interleukin-18 (IL-18) gene in Mus musculus.

Interleukin-18 (IL-18) belongs to the superfamily of IL-1 protein and exerts a pleiotropic pro-inflammatory effect on the body. Generally, this protein is significantly involved in immune defense during infection in cells, but sometimes its anomalous activities produce some inflammatory diseases like rheumatoid arthritis and Crohn's disease. In the present study, the IL-18 gene was isolated from mice and was subsequently cloned and sequenced. Further, the network analysis was carried out to explore the functional role of IL-18 protein in animals. The 3D protein structure of the IL-18 protein was generated and docked with appropriate 3-([3-cholamidopropyl]dimethylammonio)-1-propanesulfonate (CPS) ligand. Later the complex structure of the protein was subjected to molecular dynamics simulation (MDS) for 50 ns to determine the effect of ligand on protein. The network analysis explored the correlation of IL-18 protein with others proteins and their involvement in the different significant pathway to defend the cell from various diseases. As confirmed by MDS, the CPS:IL-18 complex was found to be highly stable. Our results further indicated that CPS ligand has the potential to act as a drug molecule, in future, for counteracting IL-18 activity. To date, no structural details were available for animal IL-18. Hence, the finding of this study will be useful in broadening the horizon towards a better understanding of the functional and structural aspects of IL-18 in animals.

Secure wireless communications via cooperative transmitting.

Information-theoretic secrecy is combined with cryptographic secrecy to create a secret-key exchange protocol for wireless networks. A network of transmitters, which already have cryptographically secured channels between them, cooperate to exchange a secret key with a new receiver at a random location, in the presence of passive eavesdroppers at unknown locations. Two spatial point processes, homogeneous Poisson process and independent uniformly distributed points, are used for the spatial distributions of transmitters and eavesdroppers. We analyse the impact of the number of cooperating transmitters and the number of eavesdroppers on the area fraction where secure communication is possible. Upper bounds on the probability of existence of positive secrecy between the cooperating transmitters and the receiver are derived. The closeness of the upper bounds to the real value is then estimated by means of numerical simulations. Simulations also indicate that a deterministic spatial distribution for the transmitters, for example, hexagonal and square lattices, increases the probability of existence of positive secrecy capacity compared to the random spatial distributions. For the same number of friendly nodes, cooperative transmitting provides a dramatically larger secrecy region than cooperative jamming and cooperative relaying.

Understanding Calcium-Dependent Conformational Changes in S100A1 Protein: A Combination of Molecular Dynamics and Gene Expression Study in Skeletal Muscle.

The S100A1 protein, involved in various physiological activities through the binding of calcium ions (Ca2+), participates in several protein-protein interaction (PPI) events after Ca2+-dependent activation. The present work investigates Ca2+-dependent conformational changes in the helix-EF hand-helix using the molecular dynamics (MD) simulation approach that facilitates the understanding of Ca2+-dependent structural and dynamic distinctions between the apo and holo forms of the protein. Furthermore, the process of ion binding by inserting Ca2+ into the bulk of the apo structure was simulated by molecular dynamics. Expectations of the simulation were demonstrated using cluster analysis and a variety of structural metrics, such as interhelical angle estimation, solvent accessible surface area, hydrogen bond analysis, and contact analysis. Ca2+ triggered a rise in the interhelical angles of S100A1 on the binding site and solvent accessible surface area. Significant configurational regulations were observed in the holo protein. The findings would contribute to understanding the molecular basis of the association of Ca2+ with the S100A1 protein, which may be an appropriate study to understand the Ca2+-mediated conformational changes in the protein target. In addition, we investigated the expression profile of S100A1 in myoblast differentiation and muscle regeneration. These data showed that S100A1 is expressed in skeletal muscles. However, the expression decreases with time during the process of myoblast differentiation.

Recent Advances in System Based Study for Anti-Malarial Drug Development Process.

BACKGROUND: Presently, malaria is one of the most prevalent and deadly infectious disease across Africa, Asia, and America that has now started to spread in Europe. Despite large research being carried out in the field, still, there is a lack of efficient anti-malarial therapeutics. In this paper, we highlight the increasing efforts that are urgently needed towards the development and discovery of potential antimalarial drugs, which must be safe and affordable. The new drugs thus mentioned are also able to counter the spread of malaria parasites that have been resistant to the existing agents. OBJECTIVE: The main objective of the review is to highlight the recent development in the use of system biologybased approaches towards the design and discovery of novel anti-malarial inhibitors. METHOD: A huge literature survey was performed to gain advance knowledge about the global persistence of malaria, its available treatment and shortcomings of the available inhibitors. Literature search and depth analysis were also done to gain insight into the use of system biology in drug discovery and how this approach could be utilized towards the development of the novel anti-malarial drug. RESULTS: The system-based analysis has made easy to understand large scale sequencing data, find candidate genes expression during malaria disease progression further design of drug molecules those are complementary of the target proteins in term of shape and configuration. CONCLUSION: The review article focused on the recent computational advances in new generation sequencing, molecular modeling, and docking related to malaria disease and utilization of the modern system and network biology approach to antimalarial potential drug discovery and development.

A New Method for Biostatistical miRNA Pattern Recognition with Topological Properties of Visibility Graphs in 3D Space.

Visibility is a very important topic in computer graphics and especially in calculations of global illumination. Visibility determination, the process of deciding which surface can be seen from a certain point, has also problematic applications in biomedical engineering. The problem of visibility computation with mathematical tools can be presented as a visibility network. Instead of utilizing a 2D visibility network or graphs whose construction is well known, in this paper, a new method for the construction of 3D visibility graphs will be proposed. Drawing graphs as nodes connected by links in a 3D space is visually compelling but computationally difficult. Thus, the construction of 3D visibility graphs is highly complex and requires professional computers or supercomputers. A new method for optimizing the algorithm visibility network in a 3D space and a new method for quantifying the complexity of a network in DNA pattern recognition in biomedical engineering have been developed. Statistical methods have been used to calculate the topological properties of a visibility graph in pattern recognition. A new n-hyper hybrid method is also used for combining an intelligent neural network system for DNA pattern recognition with the topological properties of visibility networks of a 3D space and for evaluating its prospective use in the prediction of cancer.