Role of water molecules and ion pairs in Dps and related ferritin-like structures

A comparative study of water molecules and ion pairs in 11 Dps protein structures has been carried out. The invariant and common water molecules, the conserved residues interacting with them and the conserved ion pairs have been analyzed. Certain water molecules found on the interfaces between subunits are highly conserved and may be implicated in flexibility or continuing association of the subunits of the structure. It is possible that the water molecules, ion pairs and the special case of a water mediated charged network through a single water molecule are involved in maintaining the stability of the protein.

Conformational Angles DataBase (CADB-3.0)

Transitions in amino-acid conformation angles tend to accompany various structural modifications in protein structures. Thus, to benefit the modeling of protein structures, the Conformation Angles DataBase (CADB-3.0) has been updated to visualize the conformational angles in varied regions (fully, generously, additionally and disallowed regions). In addition, options are provided to display the angles in the secondary structural elements (alpha-helix, beta-sheet and 3(10)-helix) of the Ramachandran plot. The database is being updated periodically and can be accessed over the World Wide Web at the following URL: http://cluster.physics.iisc.ernet.in/cadb/.

PSAP: protein structure analysis package

A computing engine, theProtein Structure Analysis Package(PSAP), has been developed to calculate and display various hidden structural and functional features of three-dimensional protein structures. The proposed computing engine has several utilities to enable structural biologists to analyze three-dimensional protein molecules and provides an easy-to-use Web interface to compute and visualize the necessary features dynamically on the client machine. Users need to provide the Protein Data Bank (PDB) identification code or upload three-dimensional atomic coordinates from the client machine. For visualization, the free molecular graphics programsRasMolandJmolare deployed in the computing engine. Furthermore, the computing engine is interfaced with an up-to-date local copy of the PDB. The atomic coordinates are updated every week and hence users can access all the structures available in the PDB. The computing engine is free and is accessible online at http://iris.physics.iisc.ernet.in/psap/.

Ion pairs in non-redundant protein structures

Ion pairs contribute to several functions including the activity of catalytic triads, fusion of viral membranes, stability in thermophilic proteins and solvent-protein interactions. Furthermore, they have the ability to affect the stability of protein structures and are also a part of the forces that act to hold monomers together. This paper deals with the possible ion pair combinations and networks in 25% and 90% non-redundant protein chains. Different types of ion pairs present in various secondary structural elements are analysed. The ion pairs existing between different subunits of multisubunit protein structures are also computed and the results of various analyses are presented in detail. The protein structures used in the analysis are solved using X-ray crystallography, whose resolution is better than or equal to 1.5 A and R-factor better than or equal to 20%. This study can, therefore, be useful for analyses of many protein functions. It also provides insights into the better understanding of the architecture of protein structure.