Protein Structure and Function: Looking through the Network of Side-Chain Interactions

Network theory has become an excellent method of choice through which biological data are smoothly integrated to gain insights into complex biological problems. Understanding protein structure, folding, and function has been an important problem, which is being extensively investigated by the network approach. Since the sequence uniquely determines the structure, this review focuses on the networks of non-covalently connected amino acid side chains in proteins. Questions in structural biology are addressed within the framework of such a formalism. While general applications are mentioned in this review, challenging problems which have demanded the attention of scientific community for a long time, such as allostery and protein folding, are considered in greater detail. Our aim has been to explore these important problems through the eyes of networks. Various methods of constructing protein structure networks (PSN) are consolidated. They include the methods based on geometry, edges weighted by different schemes, and also bipartite network of protein-nucleic acid complexes. A number of network metrics that elegantly capture the general features as well as specific features related to phenomena, such as allostery and protein model validation, are described. Additionally, an integration of network theory with ensembles of equilibrium structures of a single protein or that of a large number of structures from the data bank has been presented to perceive complex phenomena from network perspective. Finally, we discuss briefly the capabilities, limitations, and the scope for further explorations of protein structure networks.

Appraisal of groundwater resource in Holocene soil deposits by resistivity, hydrochemical and granulomerial studies in the Gulf of Mannar Coast from Southern India

This article is aimed to delineate groundwater sources in Holocene deposits area in the Gulf of Mannar Coast from Southern India. For this purpose 2-D electrical resistivity tomography (ERT), hydrochemical and granulomerical studies were carried out and integrated to identify hydrogeological structures and portable groundwater resource in shallow depths which in general appears in the coastal tracts. The 2-D ERT was used to determine the two-dimensional subsurface geological formations by multicore cable with Wenner array. Low resistivity of 1-5 Omega m for saline water appeared due to calcite at the depth of about 5 m below the ground level (bgl). Sea water intrusion was observed around the maximum resistivity as 5 Omega m at the 8 m depth, bgl in the calcite environs, but the calcareous sandstone layer shows around 15-64 Omega m at the 6 m depth, bgl. The hydrochemical variation of TDS, HCO3-, Cl-, Na+, K+, Ca2+, and Mg2+ concentrations was observed for the saline and sea water intrusion in the groundwater system. The granulometic analysis shows that the study area was under the sea between 5400 and 3000 year ago. The events of ice melting an unnatural ice-stone rain/hail among 5000-4000 years ago resulted in the inundation of sea over the area and deposits of late Holocene marine transgression formation up to Puthukottai quartzite region for a stretch of around 17 km.

Error Correcting Functional Source Coding with Decoder Side Information using Row-Latin Rectangles

The functional source coding problem in which the receiver side information (Has-set) and demands (Want-set) include functions of source messages is studied using row-Latin rectangle. The source transmits encoded messages, called the functional source code, in order to satisfy the receiver's demands. We obtain a minimum length using the row-Latin rectangle. Next, we consider the case of transmission errors and provide a necessary and sufficient condition that a functional source code must satisfy so that the receiver can correctly decode the values of the functions in its Want-set.