Title

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

Authors

Sahini Banerjee¹, Buddhadev Mondal², Rifat Nawaz Ul Islam³, Parth Sarthi Sen Gupta⁴, Debanjan Mitra⁵, Amal Kumar Bandyopadhyay^5,*

Affiliation

¹Department of Biological Sciences, ISI, Kolkata, West Bengal, India; ²Department of Zoology, Burdwan Raj Collage, East Burdwan, West Bengal, India; ³Department of Zoology, The University of Burdwan, East Burdwan, West Bengal, India; 3Department of Biotechnology, The University of Burdwan, East Burdwan, West Bengal, India; ⁴Department of Chemistry, IISER Berhampur, Ganjam, Odisha, India; All authors contributed equally

Email

Amal Kumar Bandyopadhyay - E-mail: akbanerjee@biotech.buruniv.ac.in *Corresponding author

Article Type

Software

Date

Received November 28, 2018; Accepted December 6, 2018; Published December 22, 2018

Protein is the most exposed biomolecules 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, nucleic acids, antigen 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 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 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 CSH-protein interactions and finds application in the structural Bioinformatics.

Keywords

Crystallographic Shell-water, program, water dynamics, bridge interactions, residue-specific interactions, atom specific interactions.

Citation

Banerjee et al. Bioinformation 14(9): 530-539 (2018)

Edited by

P Kangueane

ISSN

0973-2063

Publisher

Biomedical Informatics

License

This is an Open Access article which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly credited. This is distributed under the terms of the Creative Commons Attribution License.