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Water-mediated ionic interactions in protein structures

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Abstract

It is well known that water molecules play an indispensable role in the structure and function of biological macromolecules. The water-mediated ionic interactions between the charged residues provide stability and plasticity and in turn address the function of the protein structures. Thus, this study specifically addresses the number of possible water-mediated ionic interactions, their occurrence, distribution and nature found in 90% non-redundant protein chains. Further, it provides a statistical report of different charged residue pairs that are mediated by surface or buried water molecules to form the interactions. Also, it discusses its contributions in stabilizing various secondary structural elements of the protein. Thus, the present study shows the ubiquitous nature of the interactions that imparts plasticity and flexibility to a protein molecule.

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Acknowledgements

The corresponding author (KS) thanks the Department of Biotechnology for financial support. The use of the Bioinformatics Centre and the Interactive Graphics Facility is gratefully acknowledged.

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Authors and Affiliations

  1. Bioinformatics Centre, Centre of Excellence in Structural Biology and Bio-computing, Indian Institute of Science, Bangalore, 560 012, India

    R Sabarinathan, K Aishwarya, R Sarani, M Kirti Vaishnavi & K Sekar

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  1. R Sabarinathan
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  2. K Aishwarya
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  3. R Sarani
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  4. M Kirti Vaishnavi
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  5. K Sekar
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Correspondence to K Sekar.

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Corresponding editor: Amit Chattopadhyay

[Sabarinathan R, Aishwarya K, Sarani R, Vaishnavi MK and Sekar K 2011 Water-mediated ionic interactions in protein structures. J. Biosci. 36 253–263] DOI 10.1007/s12038-011-9067-4

Supplementary materials pertaining to this article are available on the Journal of Biosciences Website at http://www.ias.ac.in/jbiosci/Jun2011/pp253–263/suppl.pdf

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Sabarinathan, R., Aishwarya, K., Sarani, R. et al. Water-mediated ionic interactions in protein structures. J Biosci 36, 253–263 (2011). https://doi.org/10.1007/s12038-011-9067-4

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