POWAINDv1.0: A Program for Protein-Water Interactions Determination

Sahini Banerjee, Department of Biological Sciences, ISI, Kolkata, West Bengal, India, Buddhadev Mondal, Rifat Nawaz Ul Islam, Parth Sarthi Sen Gupta, Debanjan Mitra, Amal Kumar Bandyopadhyay, Department of Zoology, Burdwan Raj Collage, East Burdwan, West Bengal, India, Department of Zoology, The University of Burdwan, East Burdwan, West Bengal, India, Department of Biotechnology, The University of Burdwan, East Burdwan, West Bengal, India, Department of Chemistry, IISER Berhampur, Ganjam, Odisha, India, Department of Chemistry, IISER Berhampur, Ganjam, Odisha, India
2018 Bioinformation  
Protein is the most exposed biomolecule in the aqueous environment of the cell. Its structure maintains a delicate balance between the rigidity and the flexibility that imparts binding specificity to its substrate/ligand, etc. Intramolecular interactions of polar and non-polar groups of amino acid residues and intermolecular weak interactions between these groups and shell-waters may contribute to the overall stability of the tertiary structure. However, the question as to what are the dynamics
more » ... of interactions of shell-water with respect to weak forces and atom-groups of protein (AGP), requires systematic investigations. In this end, we have developed a procedure POWAINDv1.0 that analyzes interactions of crystallographic shell-waters (CSH) in residues and AGP specific manner. The shell-water and AGP specific bridge-interactions are also extracted. Further, the program analyzes favorable and unfavorable nature of each interaction based on the actual and 75% of the sum of van der Waals (vdW) radii of interacting atoms. The EXCEL-outputs are useful in understanding the profile for AGP-CSH interactions and contribution of each component in AGP. Taken together, the program provides intricate details on CSHprotein interactions and finds application in the structural Bioinformatics.
doi:10.6026/97320630014530 pmid:31223212 pmcid:PMC6563665 fatcat:cd4iqhr5erfwvdtfyftq7ltscu